From ab94d5f502e918bfad0e502ad22220e53ce47c60 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 27 Aug 2024 11:04:40 +0100 Subject: [PATCH 01/21] update README to use sbml-level_version instead of suite-glob in process_test_suite.py --- test_suite/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test_suite/README.md b/test_suite/README.md index 6f5d9e7..e4ae43d 100644 --- a/test_suite/README.md +++ b/test_suite/README.md @@ -35,7 +35,7 @@ pip install docker Navigate to the directory containing the `process_test_suite.py` script and execute it, specifying the path to the extracted test files. For example if the extraction folder is `C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic` and the `process_test_suite.py` script is in the current directory. ``` - python process_test_suite.py --suite-path C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic --suite-glob '*/*-sbml-l3v2.xml' --output-file ./results_test.md --limit 5 + python process_test_suite.py --suite-path C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic --sbml-level_version 'l3v2' --output-file ./results_test.md --limit 5 ``` ## Command Line Options From fac0715591687c6edfa482ccdb44b71f33b4045e Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 27 Aug 2024 12:08:16 +0100 Subject: [PATCH 02/21] Adjust README to use sbml-level_version instead of suite-glob and allow level_version to be set to 'highest' or to a specific level --- test_suite/README.md | 10 +++++----- test_suite/process_test_suite.py | 26 +++++++++++++------------- 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/test_suite/README.md b/test_suite/README.md index e4ae43d..2c26a5e 100644 --- a/test_suite/README.md +++ b/test_suite/README.md @@ -35,7 +35,7 @@ pip install docker Navigate to the directory containing the `process_test_suite.py` script and execute it, specifying the path to the extracted test files. For example if the extraction folder is `C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic` and the `process_test_suite.py` script is in the current directory. ``` - python process_test_suite.py --suite-path C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic --sbml-level_version 'l3v2' --output-file ./results_test.md --limit 5 + python process_test_suite.py --suite-path C:\Users\Username\Documents\compbiolibs\SBML_test_suite\semantic --sbml-level_version 'sbml-l3v2' --output-file ./results_test.md --limit 5 ``` ## Command Line Options @@ -52,10 +52,10 @@ The `process_test_suite.py` script provides various command-line options to cust **Usage:** `--suite-path ` **Default:** `.` (current directory) -- `--suite-glob` - **Description:** Shell-style glob pattern to match SBML files within the specified suite path. - **Usage:** `--suite-glob ` - **Default:** `000*/*-sbml-l3v2.xml` +- `--sbml-level_version' + **Description:** String that specifies level and version of files to select for processing (e.g. 'l3v2') + **Usage:** `--sbml-level_version ` + **Default:** `highest` - `--suite-url-base` **Description:** Base URL for the online test case files to include as links in the results. Set to an empty string to disable links. diff --git a/test_suite/process_test_suite.py b/test_suite/process_test_suite.py index 73d8b83..1a2862c 100755 --- a/test_suite/process_test_suite.py +++ b/test_suite/process_test_suite.py @@ -57,8 +57,8 @@ def parse_arguments(): "--sbml-level_version", action="store", type=str, - default="sbml-l3v2", - help="SBML level and version to test, default is 'sbml-l3v2'", + default="highest", + help="SBML level and version to test (e.g. 'l3v2'), default is '' which will try to find the highest level and version in the folder", ) parser.add_argument( @@ -119,21 +119,21 @@ def process_cases(args): subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit] for subfolder in subfolders: - # find relevant files in the subfolder - sbml_file_name = f"*-{args.sbml_level_version}.xml" - sedml_file_name = f"*-{args.sbml_level_version}-sedml.xml" - sbml_file_path = glob.glob(os.path.join(subfolder, sbml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sbml_file_name))) > 0 else [] - sedml_file_path = glob.glob(os.path.join(subfolder, sedml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sedml_file_name))) > 0 else [] - - # if no files found with the specified sbml_level_version, try to find any sbml or sedml files - if sbml_file_path == [] or sedml_file_path == []: - print(f"Folder {subfolder} has no {args.sbml_level_version} SBML or SED-ML files") + # if sbml_level_version is empty string (default), find the highest level and version in the folder + if args.sbml_level_version == "highest": sedml_file_paths = glob.glob(os.path.join(subfolder, "*-sbml-*sedml.xml")) # get last entry in list of sedml_file_paths (because it has the highest level and version number considering the alphabetical order and naming convention) sedml_file_path = sedml_file_paths[-1] if sedml_file_paths != [] else [] sbml_file_path = sedml_file_path.replace("-sedml.xml",".xml") if sedml_file_path != [] else [] - if sbml_file_path == [] or sedml_file_path == []: - print(f"Folder {subfolder} has no SBML or SED-ML files") + else: + # find relevant files in the subfolder + sbml_file_name = f"*-sbml-{args.sbml_level_version}.xml" + sedml_file_name = f"*-sbml-{args.sbml_level_version}-sedml.xml" + sbml_file_path = glob.glob(os.path.join(subfolder, sbml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sbml_file_name))) > 0 else [] + sedml_file_path = glob.glob(os.path.join(subfolder, sedml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sedml_file_name))) > 0 else [] + + if sbml_file_path == [] or sedml_file_path == []: + print(f"Folder {subfolder} has no SBML or SED-ML files {args.sbml_level_version}") continue print(f"Processing {sbml_file_path} and {sedml_file_path}") From a0b7cff5368f621991d344c9091df149a6f4f292 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 28 Aug 2024 08:46:39 +0100 Subject: [PATCH 03/21] Create test_compatibility_biosimulators results table for first three examples in SBML test suite. Change check_file_compatibility_test and dependencies so that it deals with .xml extensions as well. --- .../results_compatibility_biosimulators.md | 46 +++--- .../test_00001/00001-sbml-l3v2-sedml.omex | Bin 0 -> 1989 bytes .../test_00001/00001-sbml-l3v2-sedml.xml | 66 ++++++++ test_suite/test_00001/00001-sbml-l3v2.xml | 52 +++++++ .../tests/d1_plots_local/amici_plot_1.pdf | Bin 0 -> 9578 bytes .../tests/d1_plots_local/bionetgen_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/boolnet_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/cbmpy_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/cobrapy_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/copasi_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/gillespy2_plot_1.pdf | Bin 0 -> 9592 bytes .../tests/d1_plots_local/ginsim_plot_1.pdf | Bin 0 -> 5948 bytes .../d1_plots_local/libsbmlsim_plot_1.pdf | Bin 0 -> 9597 bytes .../tests/d1_plots_local/masspy_plot_1.pdf | Bin 0 -> 5948 bytes 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.../d1_plots_remote/tellurium_plot_1.pdf | Bin 0 -> 9586 bytes .../results_compatibility_biosimulators.md | 23 +++ .../test_00002/00002-sbml-l3v2-sedml.omex | Bin 0 -> 2029 bytes .../test_00002/00002-sbml-l3v2-sedml.xml | 66 ++++++++ test_suite/test_00002/00002-sbml-l3v2.xml | 71 +++++++++ .../tests/d1_plots_local/amici_plot_1.pdf | Bin 0 -> 9601 bytes .../tests/d1_plots_local/bionetgen_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/boolnet_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/cbmpy_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/cobrapy_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/copasi_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/gillespy2_plot_1.pdf | Bin 0 -> 9585 bytes .../tests/d1_plots_local/ginsim_plot_1.pdf | Bin 0 -> 5948 bytes .../d1_plots_local/libsbmlsim_plot_1.pdf | Bin 0 -> 9591 bytes .../tests/d1_plots_local/masspy_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/pysces_plot_1.pdf | Bin 0 -> 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.../results_compatibility_biosimulators.md | 23 +++ .../test_00003/00003-sbml-l3v2-sedml.omex | Bin 0 -> 1993 bytes .../test_00003/00003-sbml-l3v2-sedml.xml | 66 ++++++++ test_suite/test_00003/00003-sbml-l3v2.xml | 52 +++++++ .../tests/d1_plots_local/amici_plot_1.pdf | Bin 0 -> 8638 bytes .../tests/d1_plots_local/bionetgen_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/boolnet_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/cbmpy_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/cobrapy_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/copasi_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/gillespy2_plot_1.pdf | Bin 0 -> 8640 bytes .../tests/d1_plots_local/ginsim_plot_1.pdf | Bin 0 -> 5948 bytes .../d1_plots_local/libsbmlsim_plot_1.pdf | Bin 0 -> 8638 bytes .../tests/d1_plots_local/masspy_plot_1.pdf | Bin 0 -> 5948 bytes .../tests/d1_plots_local/pysces_plot_1.pdf | Bin 0 -> 8628 bytes .../tests/d1_plots_local/rbapy_plot_1.pdf | Bin 0 -> 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..._test_suite_compatibility_biosimulators.py | 144 ++++++++++++++++++ utils/__init__.py | 87 ++++++----- 93 files changed, 658 insertions(+), 61 deletions(-) create mode 100644 test_suite/test_00001/00001-sbml-l3v2-sedml.omex create mode 100644 test_suite/test_00001/00001-sbml-l3v2-sedml.xml create mode 100644 test_suite/test_00001/00001-sbml-l3v2.xml create mode 100644 test_suite/test_00001/tests/d1_plots_local/amici_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/bionetgen_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/boolnet_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/cbmpy_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/cobrapy_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/copasi_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/gillespy2_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/ginsim_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/libsbmlsim_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/masspy_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/pysces_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/rbapy_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_local/tellurium_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/amici_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/bionetgen_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/boolnet_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/cbmpy_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/cobrapy_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/copasi_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/gillespy2_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/ginsim_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/libsbmlsim_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/masspy_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/pysces_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/rbapy_plot_1.pdf create mode 100644 test_suite/test_00001/tests/d1_plots_remote/tellurium_plot_1.pdf create mode 100644 test_suite/test_00001/tests/results_compatibility_biosimulators.md create mode 100644 test_suite/test_00002/00002-sbml-l3v2-sedml.omex create mode 100644 test_suite/test_00002/00002-sbml-l3v2-sedml.xml create mode 100644 test_suite/test_00002/00002-sbml-l3v2.xml create mode 100644 test_suite/test_00002/tests/d1_plots_local/amici_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/bionetgen_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/boolnet_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/cbmpy_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/cobrapy_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/copasi_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/gillespy2_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/ginsim_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/libsbmlsim_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/masspy_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/pysces_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/rbapy_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_local/tellurium_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/amici_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/bionetgen_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/boolnet_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/cbmpy_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/cobrapy_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/copasi_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/gillespy2_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/ginsim_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/libsbmlsim_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/masspy_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/pysces_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/rbapy_plot_1.pdf create mode 100644 test_suite/test_00002/tests/d1_plots_remote/tellurium_plot_1.pdf create mode 100644 test_suite/test_00002/tests/results_compatibility_biosimulators.md create mode 100644 test_suite/test_00003/00003-sbml-l3v2-sedml.omex create mode 100644 test_suite/test_00003/00003-sbml-l3v2-sedml.xml create mode 100644 test_suite/test_00003/00003-sbml-l3v2.xml create mode 100644 test_suite/test_00003/tests/d1_plots_local/amici_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/bionetgen_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/boolnet_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/cbmpy_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/cobrapy_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/copasi_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/gillespy2_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/ginsim_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/libsbmlsim_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/masspy_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/pysces_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/rbapy_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_local/tellurium_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/amici_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/bionetgen_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/boolnet_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/cbmpy_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/cobrapy_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/copasi_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/gillespy2_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/ginsim_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/libsbmlsim_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/masspy_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/pysces_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/rbapy_plot_1.pdf create mode 100644 test_suite/test_00003/tests/d1_plots_remote/tellurium_plot_1.pdf create mode 100644 test_suite/test_00003/tests/results_compatibility_biosimulators.md create mode 100644 test_suite/test_test_suite_compatibility_biosimulators.py diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index 995762c..f13856d 100644 --- a/SBML/tests/results_compatibility_biosimulators.md +++ b/SBML/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|:----------------------------------------------------------| -| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
| pass | pass |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with amici
| | | | plot | plot | -| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
| FAIL | FAIL |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']
 |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with bionetgen. The following file types will be compatible ['BNGL', 'SED-ML']
 |
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
| plot | plot | -| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
| FAIL | FAIL |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']
 |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with boolnet. The following file types will be compatible ['SBML-qual', 'SED-ML']
 |
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
| plot | plot | -| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with brian2
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
| | | -| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
| FAIL | FAIL |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cbmpy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
| plot | plot | -| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
| FAIL | FAIL |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with cobrapy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
| plot | plot | -| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
| FAIL | FAIL |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with copasi
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

could not convert string to float: 'Values[V]'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```
| plot | plot | -| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
| pass | pass |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with gillespy2
| | | | plot | plot | -| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
| FAIL | FAIL |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']
 |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with ginsim. The following file types will be compatible ['SBML-qual', 'SED-ML']
 |
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
| plot | plot | -| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
| pass | pass |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with libsbmlsim
| | | | plot | plot | -| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
| FAIL | FAIL |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with masspy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
| plot | plot | -| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with netpyne
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
| | | -| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']
 |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with neuron. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']
 |
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
| | | -| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
| FAIL | FAIL |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']
 |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with opencor. The following file types will be compatible ['CellML', 'SED-ML']
 |
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
| | | -| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']
 |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with pyneuroml. The following file types will be compatible ['NeuroML', 'SED-ML', 'LEMS']
 |
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
| | | -| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
| FAIL | FAIL |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with pysces
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Model at /tmp/tmp36492nwm/./LEMS_NML2_Ex9_FN.sbml could not be imported:

File /tmp/tmp36492nwm/./LEMS_NML2_Ex9_FN.sbml.xml does not exist
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```
| plot | plot | -| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
| FAIL | FAIL |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']
 |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with rbapy. The following file types will be compatible ['RBApy', 'SED-ML']
 |
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
| plot | plot | -| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
| FAIL | FAIL |
FAILsmoldyn compatible file types unknown.
 |
FAILsmoldyn compatible file types unknown.
 |
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
| | | -| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
| pass | pass |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with tellurium
| | | | plot | plot | -| 19 |
vcellhttps://github.com/virtualcell/vcell
| pass | FAIL |
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell
|
passThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are compatible with vcell
| | |
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
| | | -| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
| FAIL | FAIL |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']
 |
FAILThe file extensions suggest the input file types are '['SED-ML', 'SBML']'. These are not compatible with xpp. The following file types will be compatible ['XPP', 'SED-ML']
 |
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
| | | \ No newline at end of file +| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|:----------------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
| pass | pass |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
| | | | plot | plot | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
| FAIL | FAIL |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
 |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
 |
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
| plot | plot | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
| FAIL | FAIL |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
 |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
 |
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
| plot | plot | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
| FAIL | FAIL |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
| plot | plot | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
| FAIL | FAIL |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `sim1` is not supported.
- Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
| plot | plot | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
| FAIL | FAIL |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

could not convert string to float: 'Values[V]'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```
| plot | plot | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
| pass | pass |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
| | | | plot | plot | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
| FAIL | FAIL |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
 |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
 |
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `sim1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
Output start time: 0.0
Output end time: 200.0
Number of steps: 20000
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
| plot | plot | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
| pass | pass |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
| | | | plot | plot | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
| FAIL | FAIL |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
| plot | plot | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
 |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
 |
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
| FAIL | FAIL |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
 |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
 |
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
 |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
 |
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
| FAIL | FAIL |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Model at /tmp/tmpquunm0rr/./LEMS_NML2_Ex9_FN.sbml could not be imported:

File /tmp/tmpquunm0rr/./LEMS_NML2_Ex9_FN.sbml.xml does not exist
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```
| plot | plot | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
| FAIL | FAIL |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
 |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
 |
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `net1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
| plot | plot | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
| FAIL | FAIL |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn
 |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn
 |
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
| pass | pass |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
| | | | plot | plot | +| 19 |
vcellhttps://github.com/virtualcell/vcell
| pass | FAIL |
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
| | |
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
| FAIL | FAIL |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
 |
FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
 |
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
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zJjIZH=L<00zwrP|06ucbx>z#sT}#?tTvF^W!LU*P|4mrx4Q2!vj8G jOf#iNbq00{K447KM58-+)0rwwBH@S#X=!a^9mM|t5s~}c literal 0 HcmV?d00001 diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md new file mode 100644 index 0000000..e35c5d1 --- /dev/null +++ b/test_suite/test_00001/tests/results_compatibility_biosimulators.md @@ -0,0 +1,23 @@ +| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------| +| 0 |
amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
| pass | pass |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
| | | | plot | plot | +| 1 |
bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
| plot | plot | +| 2 |
boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
| plot | plot | +| 3 |
brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
| | | +| 4 |
cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
| plot | plot | +| 5 |
cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
Only allows steady state simulations
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

UniformTimeCourseSimulation `simulation_1` is not supported.
- Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
- SteadyStateSimulation
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
| plot | plot | +| 6 |
copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

could not convert string to float: 'Compartments[compartment].Volume'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```
| plot | plot | +| 7 |
gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
| pass | pass |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
| | | | plot | plot | +| 8 |
ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Simulation `simulation_1` is invalid.
- The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
Output start time: 0.0
Output end time: 5.0
Number of steps: 50
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
| plot | plot | +| 9 |
libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
| pass | pass |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
| | | | plot | plot | +| 10 |
masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
`(model, errors) = validate_sbml_model(filename)`
If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
| plot | plot | +| 11 |
netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
| | | +| 12 |
neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
| | | +| 13 |
opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
| | | +| 14 |
pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
| | | +| 15 |
pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
| pass | pass |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
| | | | plot | plot | +| 16 |
rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
|
CAEECombineArchiveExecutionError
|
DetailsThe COMBINE/OMEX did not execute successfully:

The SED document did not execute successfully:

Language for model `model_1` is not supported.
- Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
| plot | plot | +| 17 |
smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
| | | +| 18 |
telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
| pass | pass |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
| | | | plot | plot | +| 19 |
vcellhttps://github.com/virtualcell/vcell
| pass | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
| | |
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
| | | +| 20 |
xpphttps://docs.biosimulators.org/Biosimulators_XPP/
| FAIL | FAIL |
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
|
MNFEModuleNotFoundError
|
DetailsNo module named 'libsbml'
|
Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
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    Cx3TenvXw(UZ}X3 z?{lQlD?0ERz+3JldxN@&=JKiM$7{~lLX^-b3>s3x5wH-N2y##~2KZS}5P_F4BGdfc z=>-#I6bjZc`1_}4k3hoAnSeSDsFTpEItZi=6_h>TD$nog(jp3h)OL4qp@13t>PCa$ zbj2J}At8{~piBc21PW+?&AEdHJfV9-XuuSb2HpUHA`Ei3yEDxV@Ht<*`d!?ji*7O7 z_^p~H!lg^%e@GID$&2h70AVqIB~y(6C%8gI!T|o@72pdc3>L7dMfTl3zbzC3X|>n| z^)FDFb9d69x_VJyD=?=~ye;955jlvyBd{SHW@&M3F=e-f2q@J54?z6C&Vxm(KscZm zP-p|XQh^9q0)m7`K|~c4gdyS~ED1#iJm3?)57T1_==l~)gz5ipfLOeb1+*~0b1VWL ziw0Hz3qS=208B(ufrvzKjm1ECus9J0JO;v$@CX190oWBD4<-S}fC$Wyr~(*3fj->A z_pty#<&g-+!*h~UNT8j^!7Y6=SRw*$VJ6^B!9V~82am;rjnB^kXu-PlJ{AWAp+W~d zc-aN_NkqUez!T6Iu)+CtabR6MIHOn+JPrrpL8}6U1-Ep-z;pz<5a1SGpRP1mfPe=e zSOmN#9*m(2Wsy0!rP~j@5)QsV!6Jg$hPMW{0O)#wmzxI!9&C|55|;1p4q$M83JlmW zdFmRH@Gn;3J<*K`7!*9}pIKn0P$&fb-ogYV z0ts3K*bwGz0JejF16|g@E?}Ej0(5(TZDJAVwz6OoustjVm@oP@m;<(rMSyosK;eN7 z0k5zPtNdd-><-zK3SOq zcMm*?83emedWoFwK^My3^S+4w@(xhY-7iouot*BGG4z@@0ytZsZaUf$5FI48|T|ID$^dYeKrzd4#VR}#iDui$R_SuU*4vsOpz)``F&Ttq7h6YQA{t3fA5Krj)StyPGgZ!O$Xo1fV z;ABA#M0H;;ADWlDBNT{LCMshTAvYS$H()ao>HW_wWgmZ6c?1$fcjtXh;H!qEqkNrR zAV;#3Cs<`+20%%l-ra|)4SxY5r@a}2!r)LU7!?#2LqrpmP&io>N>+Y}T!Q>5E(qXW zun6Et7Jk4FK>y(2!~*_7)I}U{(ZEuc;czIh)#W&F9+uzFiU3r(39OHw#(>{n|2|3Xu46 z90m)U2mJdjKMWB*oXc=3f64`m2EK6_9hN}&Lw;D2${%z%H2x2{;4pvAha)T$B|Hf=m?JmyIMvE-02_u;YsK})*xVTz=`~OT@?ap2_4O!?CwSJr++17?jAw` sb_yZQe0<;oMt4*CR2Sf<-~&c?O#w8rKaFnEDk^vaLRwnKSQqhs0D_MJC;$Ke literal 0 HcmV?d00001 diff --git a/test_suite/test_00002/tests/results_compatibility_biosimulators.md b/test_suite/test_00002/tests/results_compatibility_biosimulators.md new file mode 100644 index 0000000..332ba2b --- /dev/null +++ b/test_suite/test_00002/tests/results_compatibility_biosimulators.md @@ -0,0 +1,23 @@ +| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------| +| 0 |

    amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    | | | | plot | plot | +| 1 |
    bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
    | plot | plot | +| 2 |
    boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
    | plot | plot | +| 3 |
    brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
    | | | +| 4 |
    cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
    | plot | plot | +| 5 |
    cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
    Only allows steady state simulations
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
    | plot | plot | +| 6 |
    copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    could not convert string to float: 'Compartments[compartment].Volume'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```
    | plot | plot | +| 7 |
    gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    | | | | plot | plot | +| 8 |
    ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
    Output start time: 0.0
    Output end time: 5.0
    Number of steps: 50
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
    | plot | plot | +| 9 |
    libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    | | | | plot | plot | +| 10 |
    masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
    `(model, errors) = validate_sbml_model(filename)`
    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
    | plot | plot | +| 11 |
    netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
    | | | +| 12 |
    neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
    | | | +| 13 |
    opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
    | | | +| 14 |
    pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
    | | | +| 15 |
    pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    | | | | plot | plot | +| 16 |
    rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
    | plot | plot | +| 17 |
    smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
    | | | +| 18 |
    telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    | | | | plot | plot | +| 19 |
    vcellhttps://github.com/virtualcell/vcell
    | pass | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    | | |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
    | | | +| 20 |
    xpphttps://docs.biosimulators.org/Biosimulators_XPP/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
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b/test_suite/test_00003/tests/results_compatibility_biosimulators.md @@ -0,0 +1,23 @@ +| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------| +| 0 |

    amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    | | | | plot | plot | +| 1 |
    bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
    | plot | plot | +| 2 |
    boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
    | plot | plot | +| 3 |
    brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
    | | | +| 4 |
    cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
    | plot | plot | +| 5 |
    cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
    Only allows steady state simulations
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
    | plot | plot | +| 6 |
    copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    could not convert string to float: 'Compartments[compartment].Volume'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```
    | plot | plot | +| 7 |
    gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    | | | | plot | plot | +| 8 |
    ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
    Output start time: 0.0
    Output end time: 5.0
    Number of steps: 50
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
    | plot | plot | +| 9 |
    libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    | | | | plot | plot | +| 10 |
    masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
    `(model, errors) = validate_sbml_model(filename)`
    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
    | plot | plot | +| 11 |
    netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
    | | | +| 12 |
    neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
    | | | +| 13 |
    opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
    | | | +| 14 |
    pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
    | | | +| 15 |
    pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    | | | | plot | plot | +| 16 |
    rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
    | plot | plot | +| 17 |
    smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
    | | | +| 18 |
    telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    | | | | plot | plot | +| 19 |
    vcellhttps://github.com/virtualcell/vcell
    | pass | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    | | |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
    | | | +| 20 |
    xpphttps://docs.biosimulators.org/Biosimulators_XPP/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
    | | | \ No newline at end of file diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py new file mode 100644 index 0000000..1a1a590 --- /dev/null +++ b/test_suite/test_test_suite_compatibility_biosimulators.py @@ -0,0 +1,144 @@ +#!/usr/bin/env python3 + +""" +produce a markdown table of the results of running various tests on the SBML Test Suite + +get this version of the test suite that includes sedml versions or the sedml validation will fail: +https://github.com/sbmlteam/sbml-test-suite/releases/download/3.4.0/semantic_tests_with_sedml_and_graphs.v3.4.0.zip +""" + +import os +import glob +from pyneuroml.sbml import validate_sbml_files +from pyneuroml.sedml import validate_sedml_files +import sys +import shutil +sys.path.append("..") +import utils +engines = utils.engines + + +md_description = \ +''' +Markdown file description goes here. +''' + + +#suppress stdout output from validation functions to make progress counter readable +suppress_stdout = True + +def parse_arguments(): + "Parse command line arguments" + + import argparse + + parser = argparse.ArgumentParser( + description="Run various tests on the SBML Test Suite (or any similar set of SBML/SEDML files)" + ) + + parser.add_argument( + "--limit", + action="store", + type=int, + default=0, + help="Limit to the first n test cases, 0 means no limit", + ) + + parser.add_argument( + "--suite-path", + action="store", + type=str, + default=".", + help="Path to test suite directory, eg '~/repos/sbml-test-suite/cases/semantic'", + ) + + parser.add_argument( + "--sbml-level_version", + action="store", + type=str, + default="highest", + help="SBML level and version to test (e.g. 'l3v2'), default is '' which will try to find the highest level and version in the folder", + ) + + parser.add_argument( + "--suite-url-base", + action="store", + type=str, + default="https://github.com/sbmlteam/sbml-test-suite/blob/release/cases/semantic", + help="Base of the URL-to-suite-test-cases link to embed in results, use '' empty string to disable links", + ) + + return parser.parse_args() + +def process_cases(args): + """ + process the test cases and write results out as a markdown table + with links to the test case files online (as noted above the sedml files are actually in a zip file) + with a summary of how many cases were tested and how many tests failed + + examples of command line instructions + + To test all the cases in the test suite: + python test_test_suite_compatibility_biosimulators.py --limit 0 --suite-path /path/to/sbml-test-suite/cases/semantic --sbml-level_version l3v2 + + To test the first 10 cases in the test suite: + python test_test_suite_compatibility_biosimulators.py --limit 10 --suite-path /path/to/sbml-test-suite/cases/semantic --sbml-level_version l3v2 + + To test the highest level and version of SBML of the first 5 cases in the test suite: + python test_test_suite_compatibility_biosimulators.py --limit 5 --suite-path /path/to/sbml-test-suite/cases/semantic --sbml-level_version highest + """ + + starting_dir = os.getcwd() # where results will be written + + os.chdir(args.suite_path) # change to test suite directory + suite_path_abs = os.getcwd() # absolute path to test suite + + subfolders = os.listdir(suite_path_abs) if args.limit == 0 else os.listdir(suite_path_abs)[:args.limit] + print(f"Processing {len(subfolders)} subfolders in {args.suite_path}") + test_folder = 'tests' + + for subfolder in subfolders: + # create an equivalently named folder in the starting directory + os.chdir(args.suite_path) + print(f"Processing {subfolder}") + + # if sbml_level_version is empty string (default), find the highest level and version in the folder + if args.sbml_level_version == "highest": + sedml_file_paths = glob.glob(os.path.join(subfolder, "*-sbml-*sedml.xml")) + # get last entry in list of sedml_file_paths (because it has the highest level and version number considering the alphabetical order and naming convention) + sedml_file_path = sedml_file_paths[-1] if sedml_file_paths != [] else [] + sbml_file_path = sedml_file_path.replace("-sedml.xml",".xml") if sedml_file_path != [] else [] + else: + sbml_file_name = f"*-sbml-{args.sbml_level_version}.xml" + sedml_file_name = f"*-sbml-{args.sbml_level_version}-sedml.xml" + sbml_file_path = glob.glob(os.path.join(subfolder, sbml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sbml_file_name))) > 0 else [] + sedml_file_path = glob.glob(os.path.join(subfolder, sedml_file_name))[0] if len(glob.glob(os.path.join(subfolder, sedml_file_name))) > 0 else [] + + if sbml_file_path == [] or sedml_file_path == []: + print(f"Folder {subfolder} has no SBML or SED-ML files {args.sbml_level_version}") + continue + + new_subfolder = "test_" + subfolder + new_directory = os.path.join(starting_dir, new_subfolder) + os.makedirs(new_directory, exist_ok=True) + print (f"Copying {sbml_file_path} and {sedml_file_path} to {starting_dir}/{subfolder}") + new_sbml_file_path = os.path.join(new_directory, os.path.basename(sbml_file_path)) + new_sedml_file_path = os.path.join(new_directory, os.path.basename(sedml_file_path)) + shutil.copy(sbml_file_path, new_sbml_file_path) + shutil.copy(sedml_file_path, new_sedml_file_path) + + os.chdir(new_directory) + print(f"Changed to {new_directory}") + + utils.run_biosimulators_remotely_and_locally(os.path.basename(sedml_file_path), + os.path.basename(sbml_file_path), + os.path.join(test_folder,'d1_plots_remote'), + os.path.join(test_folder,'d1_plots_local'), + engines=engines, test_folder=test_folder) + + +if __name__ == "__main__": + args = parse_arguments() + + process_cases(args) + diff --git a/utils/__init__.py b/utils/__init__.py index af152b1..79bf4bb 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -23,7 +23,7 @@ engines = { 'amici': { - 'formats': ('sbml', 'sedml'), + 'formats': [('sbml', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_AMICI/', 'status': "" }, @@ -33,52 +33,52 @@ 'status': "" }, 'bionetgen': { - 'formats': ('bngl', 'sedml'), + 'formats': [('bngl', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_BioNetGen/', 'status': "" }, 'boolnet': { - 'formats': ('sbmlqual', 'sedml'), + 'formats': [('sbmlqual', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_BoolNet/', 'status': "" }, 'cbmpy': { - 'formats': ('sbml', 'sedml'), + 'formats': [('sbml', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_CBMPy/', 'status': "" }, 'cobrapy': { - 'formats': ('sbml', 'sedml'), + 'formats': [('sbml', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_COBRApy/', 'status': "Only allows steady state simulations" }, 'copasi': { - 'formats': ('sbml', 'sedml'), + 'formats': [('sbml', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_COPASI/', 'status': "" }, 'gillespy2': { - 'formats': ('sbml', 'sedml'), + 'formats': [('sbml', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_GillesPy2/', 'status': "" }, 'ginsim': { - 'formats': ('sbmlqual', 'sedml'), + 'formats': [('sbmlqual', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_GINsim/', 'status': "" }, 'libsbmlsim': { - 'formats': ('sbml', 'sedml'), + 'formats': [('sbml', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_LibSBMLSim/', 'status': "" }, 'masspy': { - 'formats': ('sbml', 'sedml'), + 'formats': [('sbml', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_MASSpy/', 'status': "" }, 'netpyne': { - 'formats': ('sbml', 'sedml'), + 'formats': [('sbml', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_pyNeuroML/', 'status': "" }, @@ -88,7 +88,7 @@ 'status': "" }, 'opencor': { - 'formats': ('cellml', 'sedml'), + 'formats': [('cellml', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_OpenCOR/', 'status': "" }, @@ -98,22 +98,22 @@ 'status': "" }, 'pysces': { - 'formats': ('sbml', 'sedml'), + 'formats': [('sbml', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_PySCeS/', 'status': "" }, 'rbapy': { - 'formats': ('rbapy', 'sedml'), + 'formats': [('rbapy', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_RBApy/', 'status': "" }, 'smoldyn': { - 'formats': None, + 'formats': ['unclear'], 'url': 'https://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api', 'status': "" }, 'tellurium': { - 'formats': ('sbml', 'sedml'), + 'formats': [('sbml', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_tellurium/', 'status': "" }, @@ -123,7 +123,7 @@ 'status': "" }, 'xpp': { - 'formats': ('xpp', 'sedml'), + 'formats': [('xpp', 'sedml')], 'url': 'https://docs.biosimulators.org/Biosimulators_XPP/', 'status': "" } @@ -140,7 +140,8 @@ 'rbapy':'RBApy',\ 'xpp':'XPP',\ 'smoldyn':'Smoldyn',\ - 'cellml':'CellML'\ + 'cellml':'CellML',\ + 'xml':'XML'\ } @@ -430,25 +431,28 @@ def display_error_message(error_message): def check_file_compatibility_test(engine, types_dict, model_filepath, experiment_filepath): ''' - Check if the file extensions suggest the file types are compatible with the engine + Check if the file extensions suggest the file types are compatible with the engine. + This is done by comparing the file extensions of the model and experiment files with the file types supported by the engine. + For SED-ML files, the expected file extension is '.sedml'. For SBML files, the expected file extension is '.sbml'. ''' - input_filetypes = set(get_filetypes(model_filepath, experiment_filepath)) - input_file_types_text = [types_dict[i] for i in input_filetypes] - - - engine_filetypes = engines[engine]['formats'] - if engine_filetypes is not None: - # Flatten the list if the engine_filetypes is a list of tuples - if all(isinstance(i, tuple) for i in engine_filetypes): - engine_filetypes = {item for sublist in engine_filetypes for item in sublist} - engine_file_types_text = [types_dict[i] for i in engine_filetypes if i in types_dict] - if input_filetypes.issubset(engine_filetypes): - return 'pass', (f"The file extensions suggest the input file types are '{input_file_types_text}'. These are compatible with {engine}") - else: - return 'FAIL', (f"The file extensions suggest the input file types are '{input_file_types_text}'. These are not compatible with {engine}. The following file types will be compatible {engine_file_types_text}") + input_filetypes_tuple = get_filetypes(model_filepath, experiment_filepath) + print('input filetypes:', input_filetypes_tuple) + engine_filetypes_tuple_list = engines[engine]['formats'] + print('engine filetypes:', engine_filetypes_tuple_list) + flat_engine_filetypes_tuple_list = [item for sublist in engine_filetypes_tuple_list for item in sublist] if \ + engine_filetypes_tuple_list != 'unclear' else engine_filetypes_tuple_list + print('flat list:', flat_engine_filetypes_tuple_list) + compatible_filetypes = [types_dict[i] for i in flat_engine_filetypes_tuple_list if i in list(types_dict.keys())] + print('compatible filetypes:', compatible_filetypes) + + if input_filetypes_tuple in engine_filetypes_tuple_list: + file_types = [types_dict[i] for i in input_filetypes_tuple] + return 'pass', (f"The file extensions {input_filetypes_tuple} suggest the input file types are '{file_types}'. {compatible_filetypes} are compatible with {engine}") + if 'xml' in input_filetypes_tuple: + return 'unsure', (f"The file extensions of the input files are '{input_filetypes_tuple}'. These may be compatible with {engine}. {compatible_filetypes} are compatible with {engine}") else: - return 'FAIL', (f"{engine} compatible file types unknown.") - + return 'FAIL', (f"The file extensions {input_filetypes_tuple} suggest the input file types are not compatibe with {engine}. {compatible_filetypes} are compatible with {engine}") + def collapsible_content(content, title='Details'): """ @@ -470,6 +474,12 @@ def get_filetypes(model_filepath, simulation_filepath): """ if model_filepath.endswith(".sbml") and simulation_filepath.endswith(".sedml"): filetypes = ('sbml', 'sedml') + elif model_filepath.endswith(".xml") and simulation_filepath.endswith(".xml"): + filetypes = ('xml', 'xml') + elif model_filepath.endswith(".xml") and simulation_filepath.endswith(".sedml"): + filetypes = ('xml', 'sedml') + elif model_filepath.endswith(".sbml") and simulation_filepath.endswith(".xml"): + filetypes = ('sbml', 'xml') else: filetypes = "other" return filetypes @@ -1095,9 +1105,10 @@ def create_results_table(results, types_dict, sbml_filepath, sedml_filepath, eng # compatibility_message results_table['Compat'] = results_table['Engine'].apply(lambda x: check_file_compatibility_test(x, types_dict, sbml_filepath, sedml_filepath)) results_table['Compat'] = results_table['Compat'].apply(lambda x: collapsible_content(x[1], title=x[0])) - results_table['Compat'] = results_table['Compat'].apply(lambda x: f' {x}'\ - if 'FAIL' in x else f'{x}') - + results_table['Compat'] = results_table['Compat'].apply(lambda x: + f' {x}' if 'FAIL' in x else + f'{x}' if 'xml' in x or 'unsure' in x else + f' {x}' if 'pass' in x else x) # pass / FAIL results_table['pass / FAIL'] = results_table['pass / FAIL'].apply(lambda x: f'\ {x}' if x == 'FAIL' \ From 85ab845936c9c2e704a5387f8371026d336e2660 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 23 Sep 2024 14:10:12 +0100 Subject: [PATCH 04/21] fix broken d1 plot links results_table SBML folder Co-authored-by: Robert Vickerstaff --- .../results_compatibility_biosimulators.md | 46 +++++++++---------- .../tests/test_compatibility_biosimulators.py | 4 +- utils/__init__.py | 3 +- 3 files changed, 26 insertions(+), 27 deletions(-) diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index f13856d..689549c 100644 --- a/SBML/tests/results_compatibility_biosimulators.md +++ b/SBML/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------|:----------------------------------------------------------| -| 0 |
    amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
    | pass | pass |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
    | | | | plot | plot | -| 1 |
    bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
     |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `net1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
    | plot | plot | -| 2 |
    boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
     |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `sim1` is invalid.
    - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
    | plot | plot | -| 3 |
    brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
    | | | -| 4 |
    cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `sim1` is not supported.
    - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
    | plot | plot | -| 5 |
    cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
    Only allows steady state simulations
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `sim1` is not supported.
    - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
    | plot | plot | -| 6 |
    copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    could not convert string to float: 'Values[V]'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```
    | plot | plot | -| 7 |
    gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
    | pass | pass |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
    | | | | plot | plot | -| 8 |
    ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
     |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `sim1` is invalid.
    - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
    Output start time: 0.0
    Output end time: 200.0
    Number of steps: 20000
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
    | plot | plot | -| 9 |
    libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
    | pass | pass |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    | | | | plot | plot | -| 10 |
    masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
    `(model, errors) = validate_sbml_model(filename)`
    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
    | plot | plot | -| 11 |
    netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
    | | | -| 12 |
    neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
    | | | -| 13 |
    opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
    | | | -| 14 |
    pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
    | | | -| 15 |
    pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Model at /tmp/tmpquunm0rr/./LEMS_NML2_Ex9_FN.sbml could not be imported:

    File /tmp/tmpquunm0rr/./LEMS_NML2_Ex9_FN.sbml.xml does not exist
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```
    | plot | plot | -| 16 |
    rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
     |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `net1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
    | plot | plot | -| 17 |
    smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
    | | | -| 18 |
    telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
    | pass | pass |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
    | | | | plot | plot | -| 19 |
    vcellhttps://github.com/virtualcell/vcell
    | pass | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    | | |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
    | | | -| 20 |
    xpphttps://docs.biosimulators.org/Biosimulators_XPP/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
    | | | \ No newline at end of file +| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:----------------------------------------------------| +| 0 |
    amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
    | pass | pass |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with amici
    | | | | plot | plot | +| 1 |
    bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
     |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `net1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
    | plot | plot | +| 2 |
    boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
     |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `sim1` is invalid.
    - Number of points (20000) must be equal to the difference between the output end (200.0) and start times (0.0).
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
    | plot | plot | +| 3 |
    brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
    | | | +| 4 |
    cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `sim1` is not supported.
    - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
    | plot | plot | +| 5 |
    cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
    Only allows steady state simulations
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `sim1` is not supported.
    - Simulation sim1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
    | plot | plot | +| 6 |
    copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
    | pass | pass |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with copasi
    | | | | plot | plot | +| 7 |
    gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
    | pass | pass |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with gillespy2
    | | | | plot | plot | +| 8 |
    ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
     |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `sim1` is invalid.
    - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.01`:
    Output start time: 0.0
    Output end time: 200.0
    Number of steps: 20000
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
    | plot | plot | +| 9 |
    libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
    | pass | pass |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    | | | | plot | plot | +| 10 |
    masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with masspy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
    `(model, errors) = validate_sbml_model(filename)`
    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
    | plot | plot | +| 11 |
    netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
    | | | +| 12 |
    neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
    | | | +| 13 |
    opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
    | | | +| 14 |
    pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
    | | | +| 15 |
    pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Model at /tmp/tmpv03zz6ui/./LEMS_NML2_Ex9_FN.sbml could not be imported:

    File /tmp/tmpv03zz6ui/./LEMS_NML2_Ex9_FN.sbml.xml does not exist
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```
    | plot | plot | +| 16 |
    rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
     |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `net1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
    | plot | plot | +| 17 |
    smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
    | | | +| 18 |
    telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
    | pass | pass |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
    | | | | plot | plot | +| 19 |
    vcellhttps://github.com/virtualcell/vcell
    | None | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    | | |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
    | | | +| 20 |
    xpphttps://docs.biosimulators.org/Biosimulators_XPP/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```(109, 'GetOverlappedResult', 'The pipe has been ended.')```
    | | | \ No newline at end of file diff --git a/SBML/tests/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py index c801471..40b7710 100644 --- a/SBML/tests/test_compatibility_biosimulators.py +++ b/SBML/tests/test_compatibility_biosimulators.py @@ -37,8 +37,8 @@ test_folder = 'tests' -d1_plots_remote_dir = os.path.join(test_folder, args.output_dir + '_remote') -d1_plots_local_dir = os.path.join(test_folder, args.output_dir + '_local') +d1_plots_remote_dir = os.path.join(args.output_dir + '_remote') +d1_plots_local_dir = os.path.join(args.output_dir + '_local') print('d1 plots will be saved in:', d1_plots_remote_dir, 'and', d1_plots_local_dir) diff --git a/utils/__init__.py b/utils/__init__.py index 79bf4bb..ca146c3 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -439,8 +439,7 @@ def check_file_compatibility_test(engine, types_dict, model_filepath, experiment print('input filetypes:', input_filetypes_tuple) engine_filetypes_tuple_list = engines[engine]['formats'] print('engine filetypes:', engine_filetypes_tuple_list) - flat_engine_filetypes_tuple_list = [item for sublist in engine_filetypes_tuple_list for item in sublist] if \ - engine_filetypes_tuple_list != 'unclear' else engine_filetypes_tuple_list + flat_engine_filetypes_tuple_list = [item for sublist in engine_filetypes_tuple_list for item in sublist if sublist != 'unclear'] print('flat list:', flat_engine_filetypes_tuple_list) compatible_filetypes = [types_dict[i] for i in flat_engine_filetypes_tuple_list if i in list(types_dict.keys())] print('compatible filetypes:', compatible_filetypes) From 6c2a07c2ffbd5afec8d7af254fa8e4577a3f2f64 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 23 Sep 2024 15:48:41 +0100 Subject: [PATCH 05/21] fix broken d1_plots_path in a different way to avoid problems with folder structure --- SBML/tests/results_compatibility_biosimulators.md | 4 ++-- SBML/tests/test_compatibility_biosimulators.py | 6 +++--- utils/__init__.py | 7 +++---- 3 files changed, 8 insertions(+), 9 deletions(-) diff --git a/SBML/tests/results_compatibility_biosimulators.md b/SBML/tests/results_compatibility_biosimulators.md index 689549c..c558ced 100644 --- a/SBML/tests/results_compatibility_biosimulators.md +++ b/SBML/tests/results_compatibility_biosimulators.md @@ -15,9 +15,9 @@ | 12 |
    neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
    | | | | 13 |
    opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with opencor. ['CellML', 'SED-ML'] are compatible with opencor
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
    | | | | 14 |
    pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
    | | | -| 15 |
    pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Model at /tmp/tmpv03zz6ui/./LEMS_NML2_Ex9_FN.sbml could not be imported:

    File /tmp/tmpv03zz6ui/./LEMS_NML2_Ex9_FN.sbml.xml does not exist
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```
    | plot | plot | +| 15 |
    pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
    | FAIL | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with pysces
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Model at /tmp/tmpod71_ka_/./LEMS_NML2_Ex9_FN.sbml could not be imported:

    File /tmp/tmpod71_ka_/./LEMS_NML2_Ex9_FN.sbml.xml does not exist
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/pysces' returned non-zero exit status 1```
    | plot | plot | | 16 |
    rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
     |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `net1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
    | plot | plot | | 17 |
    smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with smoldyn. [] are compatible with smoldyn
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
    | | | | 18 |
    telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
    | pass | pass |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML'] are compatible with tellurium
    | | | | plot | plot | | 19 |
    vcellhttps://github.com/virtualcell/vcell
    | None | FAIL |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    |
    passThe file extensions ('sbml', 'sedml') suggest the input file types are '['SBML', 'SED-ML']'. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    | | |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
    | | | -| 20 |
    xpphttps://docs.biosimulators.org/Biosimulators_XPP/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```(109, 'GetOverlappedResult', 'The pipe has been ended.')```
    | | | \ No newline at end of file +| 20 |
    xpphttps://docs.biosimulators.org/Biosimulators_XPP/
    | FAIL | FAIL |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
     |
    FAILThe file extensions ('sbml', 'sedml') suggest the input file types are not compatibe with xpp. ['XPP', 'SED-ML'] are compatible with xpp
     |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/LEMS_NML2_Ex9_FN_missing_xmlns.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
    | | | \ No newline at end of file diff --git a/SBML/tests/test_compatibility_biosimulators.py b/SBML/tests/test_compatibility_biosimulators.py index 40b7710..83ce930 100644 --- a/SBML/tests/test_compatibility_biosimulators.py +++ b/SBML/tests/test_compatibility_biosimulators.py @@ -37,8 +37,8 @@ test_folder = 'tests' -d1_plots_remote_dir = os.path.join(args.output_dir + '_remote') -d1_plots_local_dir = os.path.join(args.output_dir + '_local') +d1_plots_remote_dir = os.path.join(test_folder, args.output_dir + '_remote') +d1_plots_local_dir = os.path.join(test_folder, args.output_dir + '_local') print('d1 plots will be saved in:', d1_plots_remote_dir, 'and', d1_plots_local_dir) @@ -46,4 +46,4 @@ sbml_file_name, d1_plots_remote_dir, d1_plots_local_dir, - engines=engines, test_folder='tests') \ No newline at end of file + engines=engines, test_folder=test_folder) \ No newline at end of file diff --git a/utils/__init__.py b/utils/__init__.py index ca146c3..12bd767 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -365,7 +365,10 @@ def d1_plots_dict(engines=engines, d1_plots_path='d1_plots'): Create a dictionary with engine names as keys and d1 plot paths as values. """ d1_plots = find_files(d1_plots_path, '.pdf') + # to fix broken links in output table after changing the file structure, remove the first two parts of the path + d1_plots = [os.path.join(*Path(d1_plot).parts[1:]) for d1_plot in d1_plots] d1_plots_dict = {e: d1_plot for e in engines.keys() for d1_plot in d1_plots if e in d1_plot} + return d1_plots_dict @@ -436,13 +439,9 @@ def check_file_compatibility_test(engine, types_dict, model_filepath, experiment For SED-ML files, the expected file extension is '.sedml'. For SBML files, the expected file extension is '.sbml'. ''' input_filetypes_tuple = get_filetypes(model_filepath, experiment_filepath) - print('input filetypes:', input_filetypes_tuple) engine_filetypes_tuple_list = engines[engine]['formats'] - print('engine filetypes:', engine_filetypes_tuple_list) flat_engine_filetypes_tuple_list = [item for sublist in engine_filetypes_tuple_list for item in sublist if sublist != 'unclear'] - print('flat list:', flat_engine_filetypes_tuple_list) compatible_filetypes = [types_dict[i] for i in flat_engine_filetypes_tuple_list if i in list(types_dict.keys())] - print('compatible filetypes:', compatible_filetypes) if input_filetypes_tuple in engine_filetypes_tuple_list: file_types = [types_dict[i] for i in input_filetypes_tuple] From ab238ee01b38a0a7ff8c65171957de89da783377 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 23 Sep 2024 17:40:06 +0100 Subject: [PATCH 06/21] update results table with correct plot links --- .../results_compatibility_biosimulators.md | 46 +++++++++---------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md index e35c5d1..1fd797f 100644 --- a/test_suite/test_00001/tests/results_compatibility_biosimulators.md +++ b/test_suite/test_00001/tests/results_compatibility_biosimulators.md @@ -1,23 +1,23 @@ -| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------| -| 0 |
    amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    | | | | plot | plot | -| 1 |
    bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
    | plot | plot | -| 2 |
    boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
    | plot | plot | -| 3 |
    brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
    | | | -| 4 |
    cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
    | plot | plot | -| 5 |
    cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
    Only allows steady state simulations
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
    | plot | plot | -| 6 |
    copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    could not convert string to float: 'Compartments[compartment].Volume'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```
    | plot | plot | -| 7 |
    gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    | | | | plot | plot | -| 8 |
    ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
    Output start time: 0.0
    Output end time: 5.0
    Number of steps: 50
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
    | plot | plot | -| 9 |
    libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    | | | | plot | plot | -| 10 |
    masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
    `(model, errors) = validate_sbml_model(filename)`
    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
    | plot | plot | -| 11 |
    netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
    | | | -| 12 |
    neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
    | | | -| 13 |
    opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
    | | | -| 14 |
    pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
    | | | -| 15 |
    pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    | | | | plot | plot | -| 16 |
    rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
    | plot | plot | -| 17 |
    smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
    | | | -| 18 |
    telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    | | | | plot | plot | -| 19 |
    vcellhttps://github.com/virtualcell/vcell
    | pass | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    | | |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
    | | | -| 20 |
    xpphttps://docs.biosimulators.org/Biosimulators_XPP/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
    | | | \ No newline at end of file +| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | +|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------|:--------------------------------------------------------| +| 0 |
    amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    | | | | plot | plot | +| 1 |
    bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
    | plot | plot | +| 2 |
    boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
    | plot | plot | +| 3 |
    brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
    | | | +| 4 |
    cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
    | plot | plot | +| 5 |
    cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
    Only allows steady state simulations
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
    | plot | plot | +| 6 |
    copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    | | | | plot | plot | +| 7 |
    gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    | | | | plot | plot | +| 8 |
    ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
    Output start time: 0.0
    Output end time: 5.0
    Number of steps: 50
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
    | plot | plot | +| 9 |
    libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    | | | | plot | plot | +| 10 |
    masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
    `(model, errors) = validate_sbml_model(filename)`
    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
    | plot | plot | +| 11 |
    netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
    | | | +| 12 |
    neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
    | | | +| 13 |
    opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
    | | | +| 14 |
    pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
    | | | +| 15 |
    pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    | | | | plot | plot | +| 16 |
    rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
    | plot | plot | +| 17 |
    smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
    | | | +| 18 |
    telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    | | | | plot | plot | +| 19 |
    vcellhttps://github.com/virtualcell/vcell
    | None | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    | | |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
    | | | +| 20 |
    xpphttps://docs.biosimulators.org/Biosimulators_XPP/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00001-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
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    Cx3TenvXw(UZ}X3 z?{lQlD?0ERz+3JldxN@&=JKiM$7{~lLX^-b3>s3x5wH-N2y##~2KZS}5P_F4BGdfc z=>-#I6bjZc`1_}4k3hoAnSeSDsFTpEItZi=6_h>TD$nog(jp3h)OL4qp@13t>PCa$ zbj2J}At8{~piBc21PW+?&AEdHJfV9-XuuSb2HpUHA`Ei3yEDxV@Ht<*`d!?ji*7O7 z_^p~H!lg^%e@GID$&2h70AVqIB~y(6C%8gI!T|o@72pdc3>L7dMfTl3zbzC3X|>n| z^)FDFb9d69x_VJyD=?=~ye;955jlvyBd{SHW@&M3F=e-f2q@J54?z6C&Vxm(KscZm zP-p|XQh^9q0)m7`K|~c4gdyS~ED1#iJm3?)57T1_==l~)gz5ipfLOeb1+*~0b1VWL ziw0Hz3qS=208B(ufrvzKjm1ECus9J0JO;v$@CX190oWBD4<-S}fC$Wyr~(*3fj->A z_pty#<&g-+!*h~UNT8j^!7Y6=SRw*$VJ6^B!9V~82am;rjnB^kXu-PlJ{AWAp+W~d zc-aN_NkqUez!T6Iu)+CtabR6MIHOn+JPrrpL8}6U1-Ep-z;pz<5a1SGpRP1mfPe=e zSOmN#9*m(2Wsy0!rP~j@5)QsV!6Jg$hPMW{0O)#wmzxI!9&C|55|;1p4q$M83JlmW zdFmRH@Gn;3J<*K`7!*9}pIKn0P$&fb-ogYV z0ts3K*bwGz0JejF16|g@E?}Ej0(5(TZDJAVwz6OoustjVm@oP@m;<(rMSyosK;eN7 z0k5zPtNdd-><-zK3SOq zcMm*?83emedWoFwK^My3^S+4w@(xhY-7iouot*BGG4z@@0ytZsZaUf$5FI48|T|ID$^dYeKrzd4#VR}#iDui$R_SuU*4vsOpz)``F&Ttq7h6YQA{t3fA5Krj)StyPGgZ!O$Xo1fV z;ABA#M0H;;ADWlDBNT{LCMshTAvYS$H()ao>HW_wWgmZ6c?1$fcjtXh;H!qEqkNrR zAV;#3Cs<`+20%%l-ra|)4SxY5r@a}2!r)LU7!?#2LqrpmP&io>N>+Y}T!Q>5E(qXW zun6Et7Jk4FK>y(2!~*_7)I}U{(ZEuc;czIh)#W&F9+uzFiU3r(39OHw#(>{n|2|3Xu46 z90m)U2mJdjKMWB*oXc=3f64`m2EK6_9hN}&Lw;D2${%z%H2x2{;4pvAha)T$B|Hf=m?JmyIMvE-02_u;YsK})*xVTz=`~OT@?ap2_4O!?CwSJr++17?jAw` sb_yZQe0<;oMt4*CR2Sf<-~&c?O#w8rKaFnEDk^vaLRwnKSQqhs0D_MJC;$Ke diff --git a/test_suite/test_00002/tests/results_compatibility_biosimulators.md b/test_suite/test_00002/tests/results_compatibility_biosimulators.md deleted file mode 100644 index 332ba2b..0000000 --- a/test_suite/test_00002/tests/results_compatibility_biosimulators.md +++ /dev/null @@ -1,23 +0,0 @@ -| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------| -| 0 |

    amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    | | | | plot | plot | -| 1 |
    bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
    | plot | plot | -| 2 |
    boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
    | plot | plot | -| 3 |
    brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
    | | | -| 4 |
    cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
    | plot | plot | -| 5 |
    cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
    Only allows steady state simulations
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
    | plot | plot | -| 6 |
    copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    could not convert string to float: 'Compartments[compartment].Volume'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```
    | plot | plot | -| 7 |
    gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    | | | | plot | plot | -| 8 |
    ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
    Output start time: 0.0
    Output end time: 5.0
    Number of steps: 50
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
    | plot | plot | -| 9 |
    libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    | | | | plot | plot | -| 10 |
    masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
    `(model, errors) = validate_sbml_model(filename)`
    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
    | plot | plot | -| 11 |
    netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
    | | | -| 12 |
    neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
    | | | -| 13 |
    opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
    | | | -| 14 |
    pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
    | | | -| 15 |
    pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    | | | | plot | plot | -| 16 |
    rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
    | plot | plot | -| 17 |
    smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
    | | | -| 18 |
    telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    | | | | plot | plot | -| 19 |
    vcellhttps://github.com/virtualcell/vcell
    | pass | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    | | |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
    | | | -| 20 |
    xpphttps://docs.biosimulators.org/Biosimulators_XPP/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00002-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
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@@ -1,23 +0,0 @@ -| | Engine | pass / FAIL (R) | pass / FAIL (L) | Compat (R) | Compat (L) | Type (R) | Error (R) | Error (L) | d1 (R) | d1 (L) | -|---:|:-------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------|:--------------------------------------------------------------| -| 0 |

    amicihttps://docs.biosimulators.org/Biosimulators_AMICI/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with amici. ['SBML', 'SED-ML'] are compatible with amici
    | | | | plot | plot | -| 1 |
    bionetgenhttps://docs.biosimulators.org/Biosimulators_BioNetGen/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with bionetgen. ['BNGL', 'SED-ML'] are compatible with bionetgen
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in BNGL format (e.g., `sed:model/@language` must match `^urn:sedml:language:bngl(\.$)` such as `urn:sedml:language:bngl`).
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/bionetgen' returned non-zero exit status 1```
    | plot | plot | -| 2 |
    boolnethttps://docs.biosimulators.org/Biosimulators_BoolNet/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with boolnet. ['SBML-qual', 'SED-ML'] are compatible with boolnet
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - Number of points (50) must be equal to the difference between the output end (5.0) and start times (0.0).
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/boolnet' returned non-zero exit status 1```
    | plot | plot | -| 3 |
    brian2https://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with brian2. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML', 'SBML', 'SED-ML'] are compatible with brian2
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/brian2' returned non-zero exit status 1```
    | | | -| 4 |
    cbmpyhttps://docs.biosimulators.org/Biosimulators_CBMPy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cbmpy. ['SBML', 'SED-ML'] are compatible with cbmpy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cbmpy' returned non-zero exit status 1```
    | plot | plot | -| 5 |
    cobrapyhttps://docs.biosimulators.org/Biosimulators_COBRApy/
    Only allows steady state simulations
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with cobrapy. ['SBML', 'SED-ML'] are compatible with cobrapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    UniformTimeCourseSimulation `simulation_1` is not supported.
    - Simulation simulation_1 of type `UniformTimeCourseSimulation` is not supported. Simulation must be an instance of one of the following:
    - SteadyStateSimulation
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/cobrapy' returned non-zero exit status 1```
    | plot | plot | -| 6 |
    copasihttps://docs.biosimulators.org/Biosimulators_COPASI/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with copasi. ['SBML', 'SED-ML'] are compatible with copasi
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    could not convert string to float: 'Compartments[compartment].Volume'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/copasi' returned non-zero exit status 1```
    | plot | plot | -| 7 |
    gillespy2https://docs.biosimulators.org/Biosimulators_GillesPy2/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with gillespy2. ['SBML', 'SED-ML'] are compatible with gillespy2
    | | | | plot | plot | -| 8 |
    ginsimhttps://docs.biosimulators.org/Biosimulators_GINsim/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with ginsim. ['SBML-qual', 'SED-ML'] are compatible with ginsim
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Simulation `simulation_1` is invalid.
    - The interval between the output start and time time must be an integer multiple of the number of steps, not `0.1`:
    Output start time: 0.0
    Output end time: 5.0
    Number of steps: 50
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/ginsim' returned non-zero exit status 1```
    | plot | plot | -| 9 |
    libsbmlsimhttps://docs.biosimulators.org/Biosimulators_LibSBMLSim/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with libsbmlsim. ['SBML', 'SED-ML'] are compatible with libsbmlsim
    | | | | plot | plot | -| 10 |
    masspyhttps://docs.biosimulators.org/Biosimulators_MASSpy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with masspy. ['SBML', 'SED-ML'] are compatible with masspy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .
    `(model, errors) = validate_sbml_model(filename)`
    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/masspy' returned non-zero exit status 1```
    | plot | plot | -| 11 |
    netpynehttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with netpyne. ['SBML', 'SED-ML'] are compatible with netpyne
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/netpyne' returned non-zero exit status 1```
    | | | -| 12 |
    neuronhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with neuron. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with neuron
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/neuron' returned non-zero exit status 1```
    | | | -| 13 |
    opencorhttps://docs.biosimulators.org/Biosimulators_OpenCOR/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with opencor. ['CellML', 'SED-ML'] are compatible with opencor
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/opencor' returned non-zero exit status 1```
    | | | -| 14 |
    pyneuromlhttps://docs.biosimulators.org/Biosimulators_pyNeuroML/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pyneuroml. ['NeuroML', 'SED-ML', 'LEMS', 'SED-ML'] are compatible with pyneuroml
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/pyneuroml' returned non-zero exit status 1```
    | | | -| 15 |
    pysceshttps://docs.biosimulators.org/Biosimulators_PySCeS/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with pysces. ['SBML', 'SED-ML'] are compatible with pysces
    | | | | plot | plot | -| 16 |
    rbapyhttps://docs.biosimulators.org/Biosimulators_RBApy/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with rbapy. ['RBApy', 'SED-ML'] are compatible with rbapy
    |
    CAEECombineArchiveExecutionError
    |
    DetailsThe COMBINE/OMEX did not execute successfully:

    The SED document did not execute successfully:

    Language for model `model_1` is not supported.
    - Model language `urn:sedml:language:sbml` is not supported. Models must be in RBA format (e.g., `sed:model/@language` must match `^urn:sedml:language:rba(\.$)` such as `urn:sedml:language:rba`).
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/rbapy' returned non-zero exit status 1```
    | plot | plot | -| 17 |
    smoldynhttps://smoldyn.readthedocs.io/en/latest/python/api.html#sed-ml-combine-biosimulators-api
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with smoldyn. [] are compatible with smoldyn
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/smoldyn' returned non-zero exit status 1```
    | | | -| 18 |
    telluriumhttps://docs.biosimulators.org/Biosimulators_tellurium/
    | pass | pass |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with tellurium. ['SBML', 'SED-ML'] are compatible with tellurium
    | | | | plot | plot | -| 19 |
    vcellhttps://github.com/virtualcell/vcell
    | pass | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with vcell. ['SBML', 'SED-ML', 'BNGL', 'SED-ML'] are compatible with vcell
    | | |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/vcell' returned non-zero exit status 1```
    | | | -| 20 |
    xpphttps://docs.biosimulators.org/Biosimulators_XPP/
    | FAIL | FAIL |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    unsureThe file extensions of the input files are '('xml', 'xml')'. These may be compatible with xpp. ['XPP', 'SED-ML'] are compatible with xpp
    |
    MNFEModuleNotFoundError
    |
    DetailsNo module named 'libsbml'
    |
    Details```Command '-i /root/in/00003-sbml-l3v2-sedml.omex -o /root/out' in image 'ghcr.io/biosimulators/xpp' returned non-zero exit status 1```
    | | | \ No newline at end of file From 86052129376a4650ae54c9a8d1a16888b0113fe4 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Mon, 23 Sep 2024 18:12:00 +0100 Subject: [PATCH 08/21] add non-omv-remote.yml and non-omv-local.yml --- .github/workflows/non-omv-local.yml | 40 +++++++++++++++++++++ .github/workflows/non-omv-remote.yml | 40 +++++++++++++++++++++ SBML/tests/test_biosimulators_local.py | 48 +++++++++++++++++++++++++ SBML/tests/test_biosimulators_remote.py | 48 +++++++++++++++++++++++++ 4 files changed, 176 insertions(+) create mode 100644 .github/workflows/non-omv-local.yml create mode 100644 .github/workflows/non-omv-remote.yml create mode 100644 SBML/tests/test_biosimulators_local.py create mode 100644 SBML/tests/test_biosimulators_remote.py diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml new file mode 100644 index 0000000..9742918 --- /dev/null +++ b/.github/workflows/non-omv-local.yml @@ -0,0 +1,40 @@ + +name: Testing non OMV scripts for remote biosimulators testing + +on: + push: + branches: [ master, development, experimental, test*, feature/* ] + pull_request: + branches: [ master, development, experimental, test*, feature/* ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: [ 3.9, "3.10" ] + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + # - name: Install OMV + # run: | + # pip install git+https://github.com/OpenSourceBrain/osb-model-validation + + # - name: Run tests + # run: | + # omv install jneuroml + + - name: Test remote biosimulators compatibility table creation + run: | + cd SBML/tests + sudo rm -rf output + python ./test_biosimulators_remote.py --output-dir=tmp_plots + diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml new file mode 100644 index 0000000..9742918 --- /dev/null +++ b/.github/workflows/non-omv-remote.yml @@ -0,0 +1,40 @@ + +name: Testing non OMV scripts for remote biosimulators testing + +on: + push: + branches: [ master, development, experimental, test*, feature/* ] + pull_request: + branches: [ master, development, experimental, test*, feature/* ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: [ 3.9, "3.10" ] + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + # - name: Install OMV + # run: | + # pip install git+https://github.com/OpenSourceBrain/osb-model-validation + + # - name: Run tests + # run: | + # omv install jneuroml + + - name: Test remote biosimulators compatibility table creation + run: | + cd SBML/tests + sudo rm -rf output + python ./test_biosimulators_remote.py --output-dir=tmp_plots + diff --git a/SBML/tests/test_biosimulators_local.py b/SBML/tests/test_biosimulators_local.py new file mode 100644 index 0000000..982efd5 --- /dev/null +++ b/SBML/tests/test_biosimulators_local.py @@ -0,0 +1,48 @@ +#!/usr/bin/env python + +""" +This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file. +It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation. +The results are then displayed in a table and saved to a markdown file. +""" + +import sys +import os +sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))) # to import utils +import utils +import argparse + +engines = utils.engines +types_dict = utils.types_dict + +# Save the current working directory +cwd = os.getcwd() +print('Current working directory:', cwd) + +# SBML folder is one folder up relative to cwd +path_to_sbml_folder = os.path.abspath(os.path.join(cwd, os.pardir)) +print('Path to SBML folder:', path_to_sbml_folder) + +# change the working directory to the SBML folder (because here the SBML and SED-ML files are located) +os.chdir(path_to_sbml_folder) +print('Changed working directory to:', os.getcwd()) + +sbml_file_name = 'LEMS_NML2_Ex9_FN.sbml' +sedml_file_name = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing + +# output_dir is set to 'd1_plots' by default but can be changed using the --output-dir argument (required to deal with GitHub Actions permission issues) +parser = argparse.ArgumentParser(description='Test compatibility of different biosimulation engines') +parser.add_argument('--output-dir',action='store',default='d1_plots',help='prefix of the output directory where the d1 plots will be saved') +args = parser.parse_args() + +test_folder = 'tests' + +d1_plots_local_dir = os.path.join(test_folder, args.output_dir + '_local') + +print('d1 plots will be saved in:', d1_plots_local_dir) + +results_remote = utils.run_biosimulators_locally(sedml_file_name=sedml_file_name, + sbml_file_name=sbml_file_name, + d1_plots_remote_dir=d1_plots_local_dir, + engines=engines, test_folder=test_folder) + \ No newline at end of file diff --git a/SBML/tests/test_biosimulators_remote.py b/SBML/tests/test_biosimulators_remote.py new file mode 100644 index 0000000..75b2b3b --- /dev/null +++ b/SBML/tests/test_biosimulators_remote.py @@ -0,0 +1,48 @@ +#!/usr/bin/env python + +""" +This script tests the compatibility of different biosimulation engines with a given SBML and SED-ML file. +It runs each engine and records the result (pass/fail) and any error messages encountered during the simulation. +The results are then displayed in a table and saved to a markdown file. +""" + +import sys +import os +sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))) # to import utils +import utils +import argparse + +engines = utils.engines +types_dict = utils.types_dict + +# Save the current working directory +cwd = os.getcwd() +print('Current working directory:', cwd) + +# SBML folder is one folder up relative to cwd +path_to_sbml_folder = os.path.abspath(os.path.join(cwd, os.pardir)) +print('Path to SBML folder:', path_to_sbml_folder) + +# change the working directory to the SBML folder (because here the SBML and SED-ML files are located) +os.chdir(path_to_sbml_folder) +print('Changed working directory to:', os.getcwd()) + +sbml_file_name = 'LEMS_NML2_Ex9_FN.sbml' +sedml_file_name = 'LEMS_NML2_Ex9_FN_missing_xmlns.sedml' #xmlns:sbml missing + +# output_dir is set to 'd1_plots' by default but can be changed using the --output-dir argument (required to deal with GitHub Actions permission issues) +parser = argparse.ArgumentParser(description='Test compatibility of different biosimulation engines') +parser.add_argument('--output-dir',action='store',default='d1_plots',help='prefix of the output directory where the d1 plots will be saved') +args = parser.parse_args() + +test_folder = 'tests' + +d1_plots_remote_dir = os.path.join(test_folder, args.output_dir + '_remote') + +print('d1 plots will be saved in:', d1_plots_remote_dir) + +results_remote = utils.run_biosimulators_remotely(sedml_file_name=sedml_file_name, + sbml_file_name=sbml_file_name, + d1_plots_remote_dir=d1_plots_remote_dir, + engines=engines, test_folder=test_folder) + \ No newline at end of file From 7cd27107a18e5f465d32d163285f3d94e7baf325 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 24 Sep 2024 10:43:32 +0100 Subject: [PATCH 09/21] add installation command for jneuroml in non-omv-local.yml and non-omv-remote.yml --- .github/workflows/non-omv-local.yml | 6 +++--- .github/workflows/non-omv-remote.yml | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml index 9742918..be18dcf 100644 --- a/.github/workflows/non-omv-local.yml +++ b/.github/workflows/non-omv-local.yml @@ -28,9 +28,9 @@ jobs: # run: | # pip install git+https://github.com/OpenSourceBrain/osb-model-validation - # - name: Run tests - # run: | - # omv install jneuroml + - name: Run tests + run: | + omv install jneuroml - name: Test remote biosimulators compatibility table creation run: | diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml index 9742918..be18dcf 100644 --- a/.github/workflows/non-omv-remote.yml +++ b/.github/workflows/non-omv-remote.yml @@ -28,9 +28,9 @@ jobs: # run: | # pip install git+https://github.com/OpenSourceBrain/osb-model-validation - # - name: Run tests - # run: | - # omv install jneuroml + - name: Run tests + run: | + omv install jneuroml - name: Test remote biosimulators compatibility table creation run: | From 0612b6d4eb8419aa0d661bbd89e297328b7b5075 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 24 Sep 2024 10:44:50 +0100 Subject: [PATCH 10/21] add installation command for OMV in non-omv-local.yml and non-omv-remote.yml --- .github/workflows/non-omv-local.yml | 6 +++--- .github/workflows/non-omv-remote.yml | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml index be18dcf..75b74c1 100644 --- a/.github/workflows/non-omv-local.yml +++ b/.github/workflows/non-omv-local.yml @@ -24,9 +24,9 @@ jobs: with: python-version: ${{ matrix.python-version }} - # - name: Install OMV - # run: | - # pip install git+https://github.com/OpenSourceBrain/osb-model-validation + - name: Install OMV + run: | + pip install git+https://github.com/OpenSourceBrain/osb-model-validation - name: Run tests run: | diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml index be18dcf..75b74c1 100644 --- a/.github/workflows/non-omv-remote.yml +++ b/.github/workflows/non-omv-remote.yml @@ -24,9 +24,9 @@ jobs: with: python-version: ${{ matrix.python-version }} - # - name: Install OMV - # run: | - # pip install git+https://github.com/OpenSourceBrain/osb-model-validation + - name: Install OMV + run: | + pip install git+https://github.com/OpenSourceBrain/osb-model-validation - name: Run tests run: | From c4d0073c74210fc88c8cdb404f32a8806d802f9d Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 24 Sep 2024 10:52:35 +0100 Subject: [PATCH 11/21] remove non-omv-local.yml and non-omv-remote.yml and add workflows to non-omv.yml --- .github/workflows/non-omv-local.yml | 40 ---------------------------- .github/workflows/non-omv-remote.yml | 40 ---------------------------- .github/workflows/non-omv.yml | 15 +++++++++++ 3 files changed, 15 insertions(+), 80 deletions(-) delete mode 100644 .github/workflows/non-omv-local.yml delete mode 100644 .github/workflows/non-omv-remote.yml diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml deleted file mode 100644 index 75b74c1..0000000 --- a/.github/workflows/non-omv-local.yml +++ /dev/null @@ -1,40 +0,0 @@ - -name: Testing non OMV scripts for remote biosimulators testing - -on: - push: - branches: [ master, development, experimental, test*, feature/* ] - pull_request: - branches: [ master, development, experimental, test*, feature/* ] - -jobs: - build: - - runs-on: ubuntu-latest - strategy: - fail-fast: false - matrix: - python-version: [ 3.9, "3.10" ] - - steps: - - uses: actions/checkout@v4 - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Install OMV - run: | - pip install git+https://github.com/OpenSourceBrain/osb-model-validation - - - name: Run tests - run: | - omv install jneuroml - - - name: Test remote biosimulators compatibility table creation - run: | - cd SBML/tests - sudo rm -rf output - python ./test_biosimulators_remote.py --output-dir=tmp_plots - diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml deleted file mode 100644 index 75b74c1..0000000 --- a/.github/workflows/non-omv-remote.yml +++ /dev/null @@ -1,40 +0,0 @@ - -name: Testing non OMV scripts for remote biosimulators testing - -on: - push: - branches: [ master, development, experimental, test*, feature/* ] - pull_request: - branches: [ master, development, experimental, test*, feature/* ] - -jobs: - build: - - runs-on: ubuntu-latest - strategy: - fail-fast: false - matrix: - python-version: [ 3.9, "3.10" ] - - steps: - - uses: actions/checkout@v4 - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Install OMV - run: | - pip install git+https://github.com/OpenSourceBrain/osb-model-validation - - - name: Run tests - run: | - omv install jneuroml - - - name: Test remote biosimulators compatibility table creation - run: | - cd SBML/tests - sudo rm -rf output - python ./test_biosimulators_remote.py --output-dir=tmp_plots - diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index de3a9b4..97922da 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -73,3 +73,18 @@ jobs: omv list -V # list installed engines pip list env + + - name: Test remote biosimulators compatibility table creation + run: | + cd SBML/tests + sudo rm -rf output + python ./test_biosimulators_remote.py --output-dir=tmp_plots + + + - name: Test local biosimulators compatibility table creation + run: | + cd SBML/tests + sudo rm -rf output + python ./test_biosimulators_local.py --output-dir=tmp_plots + + \ No newline at end of file From 6a8a02567e1c7d62d2923a781e4bf3f1afcc1d6c Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 24 Sep 2024 11:07:46 +0100 Subject: [PATCH 12/21] add non-omv-local.yml and non-omv-remote.yml --- .github/workflows/non-omv-local.yml | 47 ++++++++++++++++++++++++++++ .github/workflows/non-omv-remote.yml | 47 ++++++++++++++++++++++++++++ .github/workflows/non-omv.yml | 2 +- 3 files changed, 95 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/non-omv-local.yml create mode 100644 .github/workflows/non-omv-remote.yml diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml new file mode 100644 index 0000000..a34eda0 --- /dev/null +++ b/.github/workflows/non-omv-local.yml @@ -0,0 +1,47 @@ + +name: Testing non OMV scripts + +on: + push: + branches: [ master, development, experimental, test*, feature/* ] + pull_request: + branches: [ master, development, experimental, test*, feature/* ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: [ 3.9, "3.10" ] + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install OMV + run: | + pip install git+https://github.com/OpenSourceBrain/osb-model-validation + + - name: Run tests + run: | + omv install jneuroml + + - name: Final version info + run: | + omv list -V # list installed engines + pip list + env + + - name: Test local biosimulators compatibility table creation + run: | + cd SBML/tests + sudo rm -rf output + python ./test_biosimulators_local.py --output-dir=tmp_plots + + \ No newline at end of file diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml new file mode 100644 index 0000000..3d8ba21 --- /dev/null +++ b/.github/workflows/non-omv-remote.yml @@ -0,0 +1,47 @@ + +name: Testing non OMV scripts + +on: + push: + branches: [ master, development, experimental, test*, feature/* ] + pull_request: + branches: [ master, development, experimental, test*, feature/* ] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: [ 3.9, "3.10" ] + + steps: + - uses: actions/checkout@v4 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install OMV + run: | + pip install git+https://github.com/OpenSourceBrain/osb-model-validation + + - name: Run tests + run: | + omv install jneuroml + + - name: Final version info + run: | + omv list -V # list installed engines + pip list + env + + - name: Test remote biosimulators compatibility table creation + run: | + cd SBML/tests + sudo rm -rf output + python ./test_biosimulators_remote.py --output-dir=tmp_plots + + \ No newline at end of file diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index 97922da..c5fea53 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -82,7 +82,7 @@ jobs: - name: Test local biosimulators compatibility table creation - run: | + run: | cd SBML/tests sudo rm -rf output python ./test_biosimulators_local.py --output-dir=tmp_plots From 9a4710d67b9a5fca63dc738c9da6f1b64dd7125f Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 24 Sep 2024 11:31:19 +0100 Subject: [PATCH 13/21] add pyneuroml installation to non-omv local and remote ymls --- .github/workflows/non-omv-local.yml | 4 ++++ .github/workflows/non-omv-remote.yml | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml index a34eda0..235ae71 100644 --- a/.github/workflows/non-omv-local.yml +++ b/.github/workflows/non-omv-local.yml @@ -28,6 +28,10 @@ jobs: run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation + - name: Install pyNeuroML + run: | + pip install pyNeuroML pyNeuroML[annotations] + - name: Run tests run: | omv install jneuroml diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml index 3d8ba21..ef3d879 100644 --- a/.github/workflows/non-omv-remote.yml +++ b/.github/workflows/non-omv-remote.yml @@ -27,6 +27,10 @@ jobs: - name: Install OMV run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation + + - name: Install pyNeuroML + run: | + pip install pyNeuroML pyNeuroML[annotations] - name: Run tests run: | From d4681fca1520f8d93400ed4eb2b61238845703ec Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 24 Sep 2024 11:34:24 +0100 Subject: [PATCH 14/21] add libsedml installation to non-omv local and remote ymls --- .github/workflows/non-omv-local.yml | 4 ++++ .github/workflows/non-omv-remote.yml | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml index 235ae71..79fc4d6 100644 --- a/.github/workflows/non-omv-local.yml +++ b/.github/workflows/non-omv-local.yml @@ -32,6 +32,10 @@ jobs: run: | pip install pyNeuroML pyNeuroML[annotations] + - name: Install libsedml + run: | + pip install python-libsedml + - name: Run tests run: | omv install jneuroml diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml index ef3d879..4877102 100644 --- a/.github/workflows/non-omv-remote.yml +++ b/.github/workflows/non-omv-remote.yml @@ -32,6 +32,10 @@ jobs: run: | pip install pyNeuroML pyNeuroML[annotations] + - name: Install libsedml + run: | + pip install python-libsedml + - name: Run tests run: | omv install jneuroml From bc2fc7c4e6f4f7fd248c7acd96331f5300ec9a3e Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 24 Sep 2024 11:41:55 +0100 Subject: [PATCH 15/21] add tellurium and sudo libncurses5 installation to non-omv local and remote ymls --- .github/workflows/non-omv-local.yml | 5 +++++ .github/workflows/non-omv-remote.yml | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml index 79fc4d6..ee15fc5 100644 --- a/.github/workflows/non-omv-local.yml +++ b/.github/workflows/non-omv-local.yml @@ -36,6 +36,11 @@ jobs: run: | pip install python-libsedml + - name: Install Tellurium + run: | + pip install tellurium + sudo apt-get install libncurses5 --fix-missing + - name: Run tests run: | omv install jneuroml diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml index 4877102..34f0ae6 100644 --- a/.github/workflows/non-omv-remote.yml +++ b/.github/workflows/non-omv-remote.yml @@ -36,6 +36,11 @@ jobs: run: | pip install python-libsedml + - name: Install Tellurium and libncurses5 + run: | + pip install tellurium + sudo apt-get install libncurses5 --fix-missing + - name: Run tests run: | omv install jneuroml From 650ab28ba7bb544e624e8618e49846f7bd0c5014 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 24 Sep 2024 11:46:57 +0100 Subject: [PATCH 16/21] add pymetadata installation to non-omv local and remote ymls and add all required modules to "Install dependencies" --- .github/workflows/non-omv-local.yml | 21 +++++---------------- .github/workflows/non-omv-remote.yml | 19 ++++--------------- 2 files changed, 9 insertions(+), 31 deletions(-) diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml index ee15fc5..135b829 100644 --- a/.github/workflows/non-omv-local.yml +++ b/.github/workflows/non-omv-local.yml @@ -24,26 +24,15 @@ jobs: with: python-version: ${{ matrix.python-version }} - - name: Install OMV - run: | - pip install git+https://github.com/OpenSourceBrain/osb-model-validation - - - name: Install pyNeuroML - run: | - pip install pyNeuroML pyNeuroML[annotations] - - - name: Install libsedml + - name: Install dependencies run: | + pip install git+https://github.com/OpenSourceBrain/osb-model-validation + pip install pyNeuroML pyNeuroML[annotations] pip install python-libsedml - - - name: Install Tellurium - run: | pip install tellurium sudo apt-get install libncurses5 --fix-missing - - - name: Run tests - run: | - omv install jneuroml + omv install jneuroml + pip install "pymetadata>=0.4.2" docker "requests<2.32.0" - name: Final version info run: | diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml index 34f0ae6..fc92b2e 100644 --- a/.github/workflows/non-omv-remote.yml +++ b/.github/workflows/non-omv-remote.yml @@ -24,26 +24,15 @@ jobs: with: python-version: ${{ matrix.python-version }} - - name: Install OMV + - name: Install dependencies run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation - - - name: Install pyNeuroML - run: | pip install pyNeuroML pyNeuroML[annotations] - - - name: Install libsedml - run: | pip install python-libsedml - - - name: Install Tellurium and libncurses5 - run: | - pip install tellurium - sudo apt-get install libncurses5 --fix-missing - - - name: Run tests - run: | + pip install tellurium + sudo apt-get install libncurses5 --fix-missing omv install jneuroml + pip install "pymetadata>=0.4.2" docker "requests<2.32.0" - name: Final version info run: | From 8480395b2ee8e8c52305cec95a4ace3fe0fa4c74 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 24 Sep 2024 12:11:02 +0100 Subject: [PATCH 17/21] fix indentation test_biosimulators_local.py script in non-omv.yml --- .github/workflows/non-omv.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index c5fea53..de8ff58 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -83,8 +83,8 @@ jobs: - name: Test local biosimulators compatibility table creation run: | - cd SBML/tests - sudo rm -rf output - python ./test_biosimulators_local.py --output-dir=tmp_plots + cd SBML/tests + sudo rm -rf output + python ./test_biosimulators_local.py --output-dir=tmp_plots \ No newline at end of file From 2138f9145bbf6b1b322ef8af29d7848a587d4aec Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 24 Sep 2024 12:15:59 +0100 Subject: [PATCH 18/21] fix typos (remote --> local) --- SBML/tests/test_biosimulators_local.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/SBML/tests/test_biosimulators_local.py b/SBML/tests/test_biosimulators_local.py index 982efd5..d3ddf1e 100644 --- a/SBML/tests/test_biosimulators_local.py +++ b/SBML/tests/test_biosimulators_local.py @@ -41,8 +41,8 @@ print('d1 plots will be saved in:', d1_plots_local_dir) -results_remote = utils.run_biosimulators_locally(sedml_file_name=sedml_file_name, +results_local = utils.run_biosimulators_locally(sedml_file_name=sedml_file_name, sbml_file_name=sbml_file_name, - d1_plots_remote_dir=d1_plots_local_dir, + d1_plots_local_dir=d1_plots_local_dir, engines=engines, test_folder=test_folder) \ No newline at end of file From f75db3a238ccd0d581d7c8b41e06ed608e876811 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 24 Sep 2024 16:25:39 +0100 Subject: [PATCH 19/21] remove remote and local (docker) related tests from non-omv.yml --- .github/workflows/non-omv.yml | 25 +------------------------ 1 file changed, 1 insertion(+), 24 deletions(-) diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml index de8ff58..94f51e2 100644 --- a/.github/workflows/non-omv.yml +++ b/.github/workflows/non-omv.yml @@ -55,36 +55,13 @@ jobs: cd SBML/tests python ./test_biosimulators_docker.py - - name: Test biosimulators compatibility table creation - run: | - cd SBML/tests - sudo rm -rf output - python ./test_compatibility_biosimulators.py --output-dir=tmp_plots - - - name: Test test_suite output regeneration run: | cd test_suite ./test_results_regeneration.sh - - name: Final version info run: | omv list -V # list installed engines pip list - env - - - name: Test remote biosimulators compatibility table creation - run: | - cd SBML/tests - sudo rm -rf output - python ./test_biosimulators_remote.py --output-dir=tmp_plots - - - - name: Test local biosimulators compatibility table creation - run: | - cd SBML/tests - sudo rm -rf output - python ./test_biosimulators_local.py --output-dir=tmp_plots - - \ No newline at end of file + env \ No newline at end of file From 0f8917fe09a4310d2f7745b28743bfc71e70d875 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Wed, 25 Sep 2024 10:40:57 +0100 Subject: [PATCH 20/21] add description to local and remote non omv github action workflows --- .github/workflows/non-omv-local.yml | 2 +- .github/workflows/non-omv-remote.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml index 135b829..8f3ab6c 100644 --- a/.github/workflows/non-omv-local.yml +++ b/.github/workflows/non-omv-local.yml @@ -1,5 +1,5 @@ -name: Testing non OMV scripts +name: Testing non OMV scripts (locally using docker) on: push: diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml index fc92b2e..602fbf2 100644 --- a/.github/workflows/non-omv-remote.yml +++ b/.github/workflows/non-omv-remote.yml @@ -1,5 +1,5 @@ -name: Testing non OMV scripts +name: Testing non OMV scripts (remotely via URLs) on: push: From bbdc6227ab494e13df5b99ba18b86ab17828bce5 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Thu, 26 Sep 2024 07:58:50 +0100 Subject: [PATCH 21/21] Raise HTTPError when downloading of engine results via URL fails and fix pyneuroml import to correct branch (for accessing correct version of biosimulations.submit_simulation_archive) Co-authored-by: Robert Vickerstaff --- .github/workflows/non-omv-local.yml | 2 +- .github/workflows/non-omv-remote.yml | 2 +- utils/__init__.py | 11 ++++++++--- 3 files changed, 10 insertions(+), 5 deletions(-) diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml index 8f3ab6c..fb60d8b 100644 --- a/.github/workflows/non-omv-local.yml +++ b/.github/workflows/non-omv-local.yml @@ -27,7 +27,7 @@ jobs: - name: Install dependencies run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation - pip install pyNeuroML pyNeuroML[annotations] + pip install pyNeuroML[annotations] pip install python-libsedml pip install tellurium sudo apt-get install libncurses5 --fix-missing diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml index 602fbf2..2a3541b 100644 --- a/.github/workflows/non-omv-remote.yml +++ b/.github/workflows/non-omv-remote.yml @@ -27,7 +27,7 @@ jobs: - name: Install dependencies run: | pip install git+https://github.com/OpenSourceBrain/osb-model-validation - pip install pyNeuroML pyNeuroML[annotations] + pip install pyNeuroML[annotations] pip install python-libsedml pip install tellurium sudo apt-get install libncurses5 --fix-missing diff --git a/utils/__init__.py b/utils/__init__.py index 12bd767..ec35c6d 100644 --- a/utils/__init__.py +++ b/utils/__init__.py @@ -20,6 +20,7 @@ import glob from pyneuroml import biosimulations import pandas as pd +from requests.exceptions import HTTPError engines = { 'amici': { @@ -1033,7 +1034,7 @@ def download_file_from_link(engine, download_link, output_file='results.zip', ma return filepath else: print(f'Failed to download {engine} results.') - return False + raise HTTPError(f'Failed to download {engine} results.') # unzip the file in file_path if it is a zip file and remove the zip file, replace with the unzipped folder def unzip_file(file_path, output_dir=None): @@ -1144,11 +1145,15 @@ def run_biosimulators_remotely(sedml_file_name, download_links_dict[e] = download_link extract_dir_dict = dict() + results_remote = dict() for e, link in download_links_dict.items(): - extract_dir = get_remote_results(e, link, remote_output_dir) + try: + extract_dir = get_remote_results(e, link, remote_output_dir) + except HTTPError as emessage: + results_remote[e] = ["FAIL", str(emessage), type(emessage).__name__] + continue extract_dir_dict[e] = extract_dir - results_remote = dict() for e, extract_dir in extract_dir_dict.items(): status = "" error_message = ""