Minor release Check Version Warning

bioexcel · Sep 30, 2023 · cc84485 · cc84485
1 parent 0e1d2ff
commit cc84485
Show file tree

Hide file tree

Showing 9 changed files with 31 additions and 24 deletions.
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_gromacs?label=Conda)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_gromacs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_gromacs?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:4.1.0--pyhdfd78af_1)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:4.1.1--pyhdfd78af_1)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_gromacs)
 [![](https://img.shields.io/pypi/pyversions/biobb-gromacs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-gromacs/)
@@ -34,7 +34,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-gromacs.readthedocs.io/en/latest/).
 
 ### Version
-v4.1.0 2023.3
+v4.1.1 2023.3
 
 ### Installation
 Using PIP:
@@ -44,7 +44,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_gromacs>=4.1.0"
+        pip install "biobb_gromacs>=4.1.1"
 
 
 * Usage: [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html)
@@ -54,7 +54,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_gromacs>=4.1.0"
+        conda install -c bioconda "biobb_gromacs>=4.1.1"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-gromacs.readthedocs.io/en/latest/command_line.html)
@@ -64,13 +64,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_gromacs:4.1.0--pyhdfd78af_1
+        docker pull quay.io/biocontainers/biobb_gromacs:4.1.1--pyhdfd78af_1
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_gromacs:4.1.0--pyhdfd78af_1 <command>
+        docker run quay.io/biocontainers/biobb_gromacs:4.1.1--pyhdfd78af_1 <command>
 
 
 Using SINGULARITY:
@@ -80,7 +80,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:4.1.0--pyhdfd78af_1
+        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:4.1.1--pyhdfd78af_1
 
 
 * Usage:

diff --git a/biobb_gromacs/__init__.py b/biobb_gromacs/__init__.py
@@ -1,3 +1,3 @@
 name = "biobb_gromacs"
 __all__ = ["gromacs", "gromacs_extra"]
-__version__ = "4.1.0"
+__version__ = "4.1.1"
diff --git a/biobb_gromacs/docs/source/change_log.md b/biobb_gromacs/docs/source/change_log.md
@@ -1,5 +1,11 @@
 # Biobb GROMACS changelog
 
+## What's new in version [4.1.1](https://github.com/bioexcel/biobb_gromacs/releases/tag/v4.1.1)?
+
+### New features
+
+* Check for GROMACS version now raises a warning instead of an Exception.
+
 ## What's new in version [4.1.0](https://github.com/bioexcel/biobb_gromacs/releases/tag/v4.1.0)?
 
 ### New features

diff --git a/biobb_gromacs/docs/source/command_line.md b/biobb_gromacs/docs/source/command_line.md
@@ -766,7 +766,7 @@ Command:
 ```python
 append_ligand -h
 ```
-    /bin/sh: /Users/pau/anaconda3/envs/dev/bin/append_ligand: Permission denied
+    /bin/sh: /Users/pau/mambaforge/envs/dev38/bin/append_ligand: Permission denied
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 
@@ -1149,7 +1149,7 @@ Command:
 ```python
 grompp_mdrun -h
 ```
-    usage: grompp_mdrun [-h] [-c CONFIG] --input_gro_path INPUT_GRO_PATH --input_top_zip_path INPUT_TOP_ZIP_PATH --output_trr_path OUTPUT_TRR_PATH --output_gro_path OUTPUT_GRO_PATH --output_edr_path OUTPUT_EDR_PATH --output_log_path OUTPUT_LOG_PATH [--input_cpt_path INPUT_CPT_PATH] [--input_ndx_path INPUT_NDX_PATH] [--input_mdp_path INPUT_MDP_PATH] [--output_xtc_path OUTPUT_XTC_PATH] [--output_cpt_path OUTPUT_CPT_PATH] [--output_dhdl_path OUTPUT_DHDL_PATH]
+    usage: grompp_mdrun [-h] [-c CONFIG] --input_gro_path INPUT_GRO_PATH --input_top_zip_path INPUT_TOP_ZIP_PATH --output_trr_path OUTPUT_TRR_PATH --output_gro_path OUTPUT_GRO_PATH --output_edr_path OUTPUT_EDR_PATH --output_log_path OUTPUT_LOG_PATH [--input_cpt_path INPUT_CPT_PATH] [--input_ndx_path INPUT_NDX_PATH] [--input_mdp_path INPUT_MDP_PATH] [--output_xtc_path OUTPUT_XTC_PATH] [--output_cpt_path OUTPUT_CPT_PATH] [--output_dhdl_path OUTPUT_DHDL_PATH] [--output_tpr_path OUTPUT_TPR_PATH]
 
     Wrapper for the GROMACS grompp_mdrun module.
 
@@ -1163,6 +1163,7 @@ grompp_mdrun -h
       --output_xtc_path OUTPUT_XTC_PATH
       --output_cpt_path OUTPUT_CPT_PATH
       --output_dhdl_path OUTPUT_DHDL_PATH
+      --output_tpr_path OUTPUT_TPR_PATH
 
     required arguments:
       --input_gro_path INPUT_GRO_PATH

diff --git a/biobb_gromacs/docs/source/conf.py b/biobb_gromacs/docs/source/conf.py
@@ -77,9 +77,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'4.1.0'
+version = u'4.1.1'
 # The full version, including alpha/beta/rc tags.
-release = u'4.1.0'
+release = u'4.1.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/biobb_gromacs/docs/source/readme.md b/biobb_gromacs/docs/source/readme.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_gromacs?label=Conda)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_gromacs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_gromacs?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:4.1.0--pyhdfd78af_1)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:4.1.1--pyhdfd78af_1)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_gromacs)
 [![](https://img.shields.io/pypi/pyversions/biobb-gromacs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-gromacs/)
@@ -34,7 +34,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-gromacs.readthedocs.io/en/latest/).
 
 ### Version
-v4.1.0 2023.3
+v4.1.1 2023.3
 
 ### Installation
 Using PIP:
@@ -44,7 +44,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_gromacs>=4.1.0"
+        pip install "biobb_gromacs>=4.1.1"
 
 
 * Usage: [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html)
@@ -54,7 +54,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_gromacs>=4.1.0"
+        conda install -c bioconda "biobb_gromacs>=4.1.1"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-gromacs.readthedocs.io/en/latest/command_line.html)
@@ -64,13 +64,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_gromacs:4.1.0--pyhdfd78af_1
+        docker pull quay.io/biocontainers/biobb_gromacs:4.1.1--pyhdfd78af_1
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_gromacs:4.1.0--pyhdfd78af_1 <command>
+        docker run quay.io/biocontainers/biobb_gromacs:4.1.1--pyhdfd78af_1 <command>
 
 
 Using SINGULARITY:
@@ -80,7 +80,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:4.1.0--pyhdfd78af_1
+        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:4.1.1--pyhdfd78af_1
 
 
 * Usage:

diff --git a/biobb_gromacs/docs/source/schema.html b/biobb_gromacs/docs/source/schema.html
@@ -10,7 +10,7 @@
   "applicationSubCategory": "http://www.edamontology.org/topic_3892",
   "citation": "https://www.nature.com/articles/s41597-019-0177-4",
   "license": "https://www.apache.org/licenses/LICENSE-2.0",
-  "softwareVersion": "4.1.0",
+  "softwareVersion": "4.1.1",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_gromacs",
   "isAccessibleForFree": "True",

diff --git a/biobb_gromacs/json_schemas/biobb_gromacs.json b/biobb_gromacs/json_schemas/biobb_gromacs.json
@@ -4,9 +4,9 @@
     "github": "https://github.com/bioexcel/biobb_gromacs",
     "readthedocs": "https://biobb-gromacs.readthedocs.io/en/latest/",
     "conda": "https://anaconda.org/bioconda/biobb_gromacs",
-    "docker": "https://quay.io/biocontainers/biobb_gromacs:4.1.0--pyhdfd78af_1",
-    "singularity": "https://depot.galaxyproject.org/singularity/biobb_gromacs:4.1.0--pyhdfd78af_1",
-    "version": "4.1.0",
+    "docker": "https://quay.io/biocontainers/biobb_gromacs:4.1.1--pyhdfd78af_1",
+    "singularity": "https://depot.galaxyproject.org/singularity/biobb_gromacs:4.1.1--pyhdfd78af_1",
+    "version": "4.1.1",
     "rest": false,
     "tools": [
         {

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_gromacs",
-    version="4.1.0",
+    version="4.1.1",
     author="Biobb developers",
     author_email="[email protected]",
     description="biobb_gromacs is the Biobb module collection to perform molecular dynamics simulations.",