Development

.github/workflows/non-omv-local.yml

@@ -1,49 +1,45 @@
-
 name: Testing non OMV scripts (locally using docker)
 
 on:
   push:
-    branches: [ master, development, experimental, test*, feature/* ]
+    branches: [master, development, experimental, test*, feature/*]
   pull_request:
-    branches: [ master, development, experimental, test*, feature/* ]
+    branches: [master, development, experimental, test*, feature/*]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9, "3.10" ]
+        python-version: [3.9, "3.10"]
 
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-    - name: Set up Python  ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version:  ${{ matrix.python-version }}
+      - name: Set up Python  ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
 
-    - name: Install dependencies
-      run: |
+      - 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
+          sudo apt-get install libncurses6 --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: Final version info
+        run: |
+          omv list -V # list installed engines
+          pip list
+          env
 
-    - name: Test local biosimulators compatibility table creation
-      run: |
+      - name: Test local biosimulators compatibility table creation
+        run: |
           cd SBML/tests
           sudo rm -rf output
           python ./test_biosimulators_local.py --output-dir=tmp_plots
-
-

.github/workflows/non-omv-remote.yml

@@ -1,55 +1,50 @@
-
 name: Testing non OMV scripts (remotely via URLs)
 
 on:
   push:
-    branches: [ master, development, experimental, test*, feature/* ]
+    branches: [master, development, experimental, test*, feature/*]
   pull_request:
-    branches: [ master, development, experimental, test*, feature/* ]
+    branches: [master, development, experimental, test*, feature/*]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.9, "3.10" ]
+        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: Check health status of biosimulations API
-      run: |
-        cd SBML/tests
-        python ./test_biosimulators_api.py
-
-    - name: Test remote biosimulators compatibility table creation
-      run: |
-        cd SBML/tests
-        sudo rm -rf output
-        python ./test_biosimulators_remote.py --output-dir=tmp_plots
-
-
+      - 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 libncurses6 --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: Check health status of biosimulations API
+        run: |
+          cd SBML/tests
+          python ./test_biosimulators_api.py
+
+      - name: Test remote biosimulators compatibility table creation
+        run: |
+          cd SBML/tests
+          sudo rm -rf output
+          python ./test_biosimulators_remote.py --output-dir=tmp_plots

.github/workflows/non-omv.yml

@@ -1,72 +1,70 @@
-
 name: Testing non OMV scripts
 
 on:
   push:
-    branches: [ master, development, experimental, test*, feature/* ]
+    branches: [master, development, experimental, test*, feature/*]
   pull_request:
-    branches: [ master, development, experimental, test*, feature/* ]
-      
+    branches: [master, development, experimental, test*, feature/*]
+
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.10", "3.11" ]
+        python-version: ["3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
+
+      - name: Set up Python  ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
 
-    - 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: Install OMV
-      run: |
-        pip install git+https://github.com/OpenSourceBrain/osb-model-validation
+      - name: Install dependencies
+        run: |
+          pip install .
 
-    - name: Run tests
-      run: |
-        omv install jneuroml
 
-    - name: Test tellurium
-      run: |
-        pip install tellurium
-        sudo apt-get install libncurses5 --fix-missing
-        cd tellurium
-        python simple.py -nogui
+      - name: Test tellurium
+        run: |
+          sudo apt-get install libncurses6 --fix-missing
+          cd tellurium
+          python simple.py -nogui
 
-        cd ../SBML/tests
-        pip install python-libsedml
-        python ./test_tellurium.py 
+          cd ../SBML/tests
+          
+          python ./test_tellurium.py
 
-    - name: Test validity of files
-      run: |
-        pip install pyNeuroML pyNeuroML[annotations]
-        cd SBML/tests
-        ./validateAll.sh
+      - name: Test validity of files
+        run: |
+          pip install pyNeuroML pyNeuroML[annotations]
+          cd SBML/tests
+          ./validateAll.sh
 
-    - name: Test omex file creation
-      run: |
-        pip install "pymetadata>=0.4.2" docker "requests<2.32.0"
-        cd SBML/tests    
-        python ./test_biosimulators_docker.py
+      - name: Test omex file creation
+        run: |
+          pip install "pymetadata>=0.4.2" docker "requests<2.32.0"
+          cd SBML/tests
+          python ./test_biosimulators_docker.py
 
-    - name: Test test_suite output regeneration
-      run: |
-        cd test_suite        
-        ./test_results_regeneration.sh
+      - 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: Final version info
+        run: |
+          omv list -V # list installed engines
+          pip list
+          env
 
-    - name: Create results table
-      run: |
-        cd SBML/tests
-        python ./test_creation_combined_results_table.py
+      - name: Create results table
+        run: |
+          cd SBML/tests
+          python ./test_creation_combined_results_table.py

.github/workflows/omv-ci.yml

@@ -2,38 +2,48 @@ name: Continuous build using OMV
 
 on:
   push:
-    branches: [ master, development, experimental, test*, feature/* ]
+    branches: [master, development, experimental, test*, feature/*]
   pull_request:
-    branches: [ master, development, experimental, test*, feature/* ]
+    branches: [master, development, experimental, test*, feature/*]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.10", "3.11" ]
-        engine: [ jLEMS, jNeuroML, jNeuroML_NEURON, jNeuroML_validate, PyLEMS, PyLEMS_NeuroML2, jNeuroML_Brian2, Brian2, pyNeuroML_validate_sbml ]
+        python-version: ["3.10", "3.11"]
+        engine:
+          [
+            jLEMS,
+            jNeuroML,
+            jNeuroML_NEURON,
+            jNeuroML_validate,
+            PyLEMS,
+            PyLEMS_NeuroML2,
+            jNeuroML_Brian2,
+            Brian2,
+            pyNeuroML_validate_sbml,
+          ]
 
     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
-        pip install scipy sympy matplotlib cython pandas tables
-
-    - name: Run OMV tests on engine ${{ matrix.engine }}
-      run: |
-        omv all -V --engine=${{ matrix.engine }}
-
-    - name: OMV final version info
-      run: |
-        omv list -V # list installed engines
-        env
+      - 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
+          pip install scipy sympy matplotlib cython pandas tables
+
+      - name: Run OMV tests on engine ${{ matrix.engine }}
+        run: |
+          omv all -V --engine=${{ matrix.engine }}
+
+      - name: OMV final version info
+        run: |
+          omv list -V # list installed engines
+          env

.gitignore

@@ -36,6 +36,7 @@ arm64
 /SBML/ex9.csv
 /SBML/hr.csv
 /test_suite/semantic/
+/test_suite/SBML_test_suite/
 /test_suite/semantic_tests_with_sedml_and_graphs.v*.zip*
 .vscode
 /BioModels/cache
@@ -45,3 +46,4 @@ venv
 /SBML/.DS_Store
 /SBML/LEMS_NML2_Ex9_FN_missing_xmlns.omex
 /SBML/output
+*.egg-info