Merge pull request #59 from OpenSourceBrain/development

Add remote results to tables and restructure folder hiearchy
OpenSourceBrain · Sep 27, 2024 · 70beeb8 · 70beeb8
2 parents a989aa3 + 34c6a77
commit 70beeb8
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diff --git a/.github/workflows/non-omv-local.yml b/.github/workflows/non-omv-local.yml
@@ -0,0 +1,49 @@
+
+name: Testing non OMV scripts (locally using docker)
+
+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 dependencies
+      run: |
+          pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+          pip install pyNeuroML[annotations]
+          pip install python-libsedml
+          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: |
+        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
+  
+
diff --git a/.github/workflows/non-omv-remote.yml b/.github/workflows/non-omv-remote.yml
@@ -0,0 +1,49 @@
+
+name: Testing non OMV scripts (remotely via URLs)
+
+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 dependencies
+      run: |
+        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+        pip install pyNeuroML[annotations]
+        pip install python-libsedml
+        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: |
+        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
+  
+
diff --git a/.github/workflows/non-omv.yml b/.github/workflows/non-omv.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9, "3.10" ]
+        python-version: [ "3.10", "3.11" ]
 
     steps:
     - uses: actions/checkout@v4
@@ -39,37 +39,29 @@ jobs:
         cd tellurium
         python simple.py -nogui
 
-        cd ../SBML
+        cd ../SBML/tests
         pip install python-libsedml
-        python test_tellurium.py 
+        python ./test_tellurium.py 
 
     - name: Test validity of files
       run: |
-        pip install pyNeuroML
-        cd SBML
+        pip install pyNeuroML pyNeuroML[annotations]
+        cd SBML/tests
         ./validateAll.sh
 
-    - name: test omex file creation
+    - name: Test omex file creation
       run: |
         pip install "pymetadata>=0.4.2" docker "requests<2.32.0"
-        cd SBML        
-        ./test_biosimulators_docker.py
-
-    - name: test biosimulators compatibility table creation
-      run: |
-        cd SBML
-        sudo rm -rf output
-        python ./test_compatibility_biosimulators.py --output-dir=tmp_plots
-
+        cd SBML/tests    
+        python ./test_biosimulators_docker.py
 
     - 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
+        env
diff --git a/.github/workflows/omv-ci.yml b/.github/workflows/omv-ci.yml
@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9, "3.10" ]
+        python-version: [ "3.10", "3.11" ]
         engine: [ jLEMS, jNeuroML, jNeuroML_NEURON, jNeuroML_validate, PyLEMS, PyLEMS_NeuroML2, jNeuroML_Brian2, Brian2, pyNeuroML_validate_sbml ]
 
     steps:

diff --git a/.gitignore b/.gitignore
@@ -43,3 +43,5 @@ arm64
 __pycache__
 venv
 /SBML/.DS_Store
+/SBML/LEMS_NML2_Ex9_FN_missing_xmlns.omex
+/SBML/output
diff --git a/LEMS/BIOMD0000000127_url_LEMS.xml b/LEMS/BIOMD0000000127_url_LEMS.xml
@@ -1,9 +1,9 @@
 <Lems>
 <!--
     This LEMS file has been generated by org.neuroml.importer.sbml.SBMLImporter (see https://github.com/NeuroML/org.neuroml.import)
-         org.neuroml.import  v1.10.0
-         org.neuroml.model   v1.10.0
-         jLEMS               v0.11.0
+         org.neuroml.import  v1.10.1
+         org.neuroml.model   v1.10.1
+         jLEMS               v0.11.1
 -->
 
     <Dimension name="time" m="0" l="0" t="1" i="0" k="0" n="0" j="0"/>
@@ -197,7 +197,7 @@
             <TimeDerivative variable="i" value="tscale * 0"/>
             <TimeDerivative variable="v" value="tscale * ((((((0.04 * (v ^ 2.0)) + (5.0 * v)) + 140.0) - U) + i))"/>
             <TimeDerivative variable="U" value="tscale * ((a * ((b * v) - U)))"/>
-            <TimeDerivative variable="time" value="1"/>
+            <TimeDerivative variable="time" value="tscale* 1"/>
             <OnStart>
                 <StateAssignment variable="i" value="0.0"/>
                 <StateAssignment variable="v" value="-70.0"/>

diff --git a/LEMS/BIOMD0000000184_LEMS.xml b/LEMS/BIOMD0000000184_LEMS.xml
@@ -1,9 +1,9 @@
 <Lems>
 <!--
     This LEMS file has been generated by org.neuroml.importer.sbml.SBMLImporter (see https://github.com/NeuroML/org.neuroml.import)
-         org.neuroml.import  v1.10.0
-         org.neuroml.model   v1.10.0
-         jLEMS               v0.11.0
+         org.neuroml.import  v1.10.1
+         org.neuroml.model   v1.10.1
+         jLEMS               v0.11.1
 -->
 
     <Dimension name="time" m="0" l="0" t="1" i="0" k="0" n="0" j="0"/>

diff --git a/SBML/.test.validate.sbml.omt b/SBML/.test.validate.sbml.omt
@@ -1,5 +1,5 @@
 # Script for running automated tests on OSB using github actions, see https://github.com/OpenSourceBrain/osb-model-validation 
 
-# This test will validate the SBML files in the current directory using: pyneuroml -validate-sbml *.xml *.sbml
+# This test will validate the SBML files in the current directory using: pynml -validate-sbml *.xml *.sbml
 target: "*.xml *.sbml"
 engine: pyNeuroML_validate_sbml