Load git config flags from pyproject.toml when verifying installation

Make include paths absolute Disable R & pytorch installation for python 3.7 job Only activate test environment, not base
cropsinsilico · Feb 12, 2024 · 7e89a60 · 7e89a60
1 parent bf5403d
commit 7e89a60
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Showing 4 changed files with 127 additions and 15 deletions.
diff --git a/.github/workflows/test-install.yml b/.github/workflows/test-install.yml
@@ -325,6 +325,14 @@ jobs:
       name: Set SBML installation based on matrix value
       run: echo "INSTALLSBML=1" >> $GITHUB_ENV
       shell: bash -l {0}
+    - if: matrix.install-r != true
+      name: Set R installation based on matrix value
+      run: echo "INSTALLR=0" >> $GITHUB_ENV
+      shell: bash -l {0}
+    - if: matrix.install-pytorch != true
+      name: Set Pytorch installation based on matrix value
+      run: echo "INSTALLPYTORCH=0" >> $GITHUB_ENV
+      shell: bash -l {0}
     - name: Store an ID string for the job
       run: echo "YGG_GHA_JOB_ID=${{ runner.os }}-${{ matrix.install-method }}-py${{
         matrix.python-version }}-C${{ env.INSTALLC }}-RMQ${{ env.INSTALLRMQ }}${{
@@ -504,8 +512,8 @@ jobs:
     - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method
         == 'mamba')
       name: Run cmake test in command prompt (CONDA)
-      run: CALL "%CONDA_BAT%" activate base && CALL "%CONDA_BAT%" activate test &&
-        pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
+      run: CALL "%CONDA_BAT%" activate test && pytest --ci --cov-append --nocapture
+        tests/drivers/test_CMakeModelDriver.py
       shell: cmd /C CALL {0}
       timeout-minutes: 180
     - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method
@@ -600,6 +608,8 @@ jobs:
         - install-c: true
           install-method: conda
           install-mpi: false
+          install-pytorch: false
+          install-r: false
           install-sbml: false
           os-base: ubuntu
           python-version: 3.7
@@ -608,6 +618,8 @@ jobs:
         - install-c: true
           install-method: conda
           install-mpi: false
+          install-pytorch: true
+          install-r: true
           install-sbml: true
           os-base: ubuntu
           python-version: 3.9
@@ -616,6 +628,8 @@ jobs:
         - install-c: true
           install-method: conda
           install-mpi: false
+          install-pytorch: true
+          install-r: true
           install-sbml: false
           os-base: ubuntu
           python-version: '3.10'
@@ -624,6 +638,8 @@ jobs:
         - install-c: true
           install-method: conda
           install-mpi: false
+          install-pytorch: true
+          install-r: true
           install-sbml: false
           os-base: ubuntu
           python-version: '3.11'
@@ -632,6 +648,8 @@ jobs:
         - install-c: true
           install-method: conda
           install-mpi: false
+          install-pytorch: true
+          install-r: true
           install-sbml: false
           os-base: macos
           python-version: 3.8
@@ -643,6 +661,10 @@ jobs:
         - conda
         install-mpi:
         - true
+        install-pytorch:
+        - true
+        install-r:
+        - true
         install-sbml:
         - false
         os-base:
@@ -696,6 +718,14 @@ jobs:
       name: Set SBML installation based on matrix value
       run: echo "INSTALLSBML=1" >> $GITHUB_ENV
       shell: bash -l {0}
+    - if: matrix.install-r != true
+      name: Set R installation based on matrix value
+      run: echo "INSTALLR=0" >> $GITHUB_ENV
+      shell: bash -l {0}
+    - if: matrix.install-pytorch != true
+      name: Set Pytorch installation based on matrix value
+      run: echo "INSTALLPYTORCH=0" >> $GITHUB_ENV
+      shell: bash -l {0}
     - name: Store an ID string for the job
       run: echo "YGG_GHA_JOB_ID=${{ runner.os }}-${{ matrix.install-method }}-py${{
         matrix.python-version }}-C${{ env.INSTALLC }}-RMQ${{ env.INSTALLRMQ }}${{
@@ -875,8 +905,8 @@ jobs:
     - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method
         == 'mamba')
       name: Run cmake test in command prompt (CONDA)
-      run: CALL "%CONDA_BAT%" activate base && CALL "%CONDA_BAT%" activate test &&
-        pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
+      run: CALL "%CONDA_BAT%" activate test && pytest --ci --cov-append --nocapture
+        tests/drivers/test_CMakeModelDriver.py
       shell: cmd /C CALL {0}
       timeout-minutes: 180
     - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method
@@ -971,6 +1001,8 @@ jobs:
         - install-c: false
           install-method: pip
           install-mpi: false
+          install-pytorch: true
+          install-r: false
           install-sbml: false
           os-base: windows
           python-version: 3.8
@@ -982,6 +1014,10 @@ jobs:
         - pip
         install-mpi:
         - true
+        install-pytorch:
+        - true
+        install-r:
+        - true
         install-sbml:
         - false
         os-base:
@@ -1051,6 +1087,14 @@ jobs:
       name: Set SBML installation based on matrix value
       run: echo "INSTALLSBML=1" >> $GITHUB_ENV
       shell: bash -l {0}
+    - if: matrix.install-r != true
+      name: Set R installation based on matrix value
+      run: echo "INSTALLR=0" >> $GITHUB_ENV
+      shell: bash -l {0}
+    - if: matrix.install-pytorch != true
+      name: Set Pytorch installation based on matrix value
+      run: echo "INSTALLPYTORCH=0" >> $GITHUB_ENV
+      shell: bash -l {0}
     - name: Store an ID string for the job
       run: echo "YGG_GHA_JOB_ID=${{ runner.os }}-${{ matrix.install-method }}-py${{
         matrix.python-version }}-C${{ env.INSTALLC }}-RMQ${{ env.INSTALLRMQ }}${{
@@ -1230,8 +1274,8 @@ jobs:
     - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method
         == 'mamba')
       name: Run cmake test in command prompt (CONDA)
-      run: CALL "%CONDA_BAT%" activate base && CALL "%CONDA_BAT%" activate test &&
-        pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
+      run: CALL "%CONDA_BAT%" activate test && pytest --ci --cov-append --nocapture
+        tests/drivers/test_CMakeModelDriver.py
       shell: cmd /C CALL {0}
       timeout-minutes: 180
     - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method
@@ -1328,6 +1372,10 @@ jobs:
         - conda
         install-mpi:
         - false
+        install-pytorch:
+        - true
+        install-r:
+        - true
         install-sbml:
         - false
         os-base:
@@ -1389,6 +1437,14 @@ jobs:
       name: Set SBML installation based on matrix value
       run: echo "INSTALLSBML=1" >> $GITHUB_ENV
       shell: bash -l {0}
+    - if: matrix.install-r != true
+      name: Set R installation based on matrix value
+      run: echo "INSTALLR=0" >> $GITHUB_ENV
+      shell: bash -l {0}
+    - if: matrix.install-pytorch != true
+      name: Set Pytorch installation based on matrix value
+      run: echo "INSTALLPYTORCH=0" >> $GITHUB_ENV
+      shell: bash -l {0}
     - name: Store an ID string for the job
       run: echo "YGG_GHA_JOB_ID=${{ runner.os }}-${{ matrix.install-method }}-py${{
         matrix.python-version }}-C${{ env.INSTALLC }}-RMQ${{ env.INSTALLRMQ }}${{
@@ -1568,8 +1624,8 @@ jobs:
     - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method
         == 'mamba')
       name: Run cmake test in command prompt (CONDA)
-      run: CALL "%CONDA_BAT%" activate base && CALL "%CONDA_BAT%" activate test &&
-        pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
+      run: CALL "%CONDA_BAT%" activate test && pytest --ci --cov-append --nocapture
+        tests/drivers/test_CMakeModelDriver.py
       shell: cmd /C CALL {0}
       timeout-minutes: 180
     - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method
@@ -1666,6 +1722,10 @@ jobs:
         - pip
         install-mpi:
         - false
+        install-pytorch:
+        - true
+        install-r:
+        - true
         install-sbml:
         - false
         os-base:
@@ -1726,6 +1786,14 @@ jobs:
       name: Set SBML installation based on matrix value
       run: echo "INSTALLSBML=1" >> $GITHUB_ENV
       shell: bash -l {0}
+    - if: matrix.install-r != true
+      name: Set R installation based on matrix value
+      run: echo "INSTALLR=0" >> $GITHUB_ENV
+      shell: bash -l {0}
+    - if: matrix.install-pytorch != true
+      name: Set Pytorch installation based on matrix value
+      run: echo "INSTALLPYTORCH=0" >> $GITHUB_ENV
+      shell: bash -l {0}
     - name: Store an ID string for the job
       run: echo "YGG_GHA_JOB_ID=${{ runner.os }}-${{ matrix.install-method }}-py${{
         matrix.python-version }}-C${{ env.INSTALLC }}-RMQ${{ env.INSTALLRMQ }}${{
@@ -1905,8 +1973,8 @@ jobs:
     - if: runner.os == 'Windows' && (matrix.install-method == 'conda' || matrix.install-method
         == 'mamba')
       name: Run cmake test in command prompt (CONDA)
-      run: CALL "%CONDA_BAT%" activate base && CALL "%CONDA_BAT%" activate test &&
-        pytest --ci --cov-append --nocapture tests/drivers/test_CMakeModelDriver.py
+      run: CALL "%CONDA_BAT%" activate test && pytest --ci --cov-append --nocapture
+        tests/drivers/test_CMakeModelDriver.py
       shell: cmd /C CALL {0}
       timeout-minutes: 180
     - if: runner.os == 'Windows' && matrix.install-method != 'conda' && matrix.install-method
@@ -2003,6 +2071,10 @@ jobs:
         - pip
         install-mpi:
         - false
+        install-pytorch:
+        - true
+        install-r:
+        - true
         install-sbml:
         - false
         os-base:

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -139,9 +139,19 @@ def setup_ci(opts, disable_extra=False):
     if not os.path.isfile('pyproject.toml'):
         raise RuntimeError("The CI tests must be run from the root "
                            "directory of the yggdrasil git repository.")
-    src_cmd = ('python -c \"import setuptools_scm; '
-               'print(setuptools_scm.get_version('
-               'git_describe_command = \\\"git describe --tags --long\\\"))\"')
+    try:
+        import tomllib
+        with open('pyproject.toml', "rb") as f:
+            pyproject_data = tomllib.load(f)
+    except ImportError:
+        import toml as toml
+        with open('pyproject.toml', "r") as f:
+            pyproject_data = toml.load(f)
+    git_version = pyproject_data['tool']['setuptools_scm']['git_describe_command']
+    src_cmd = (
+        f'python -c \"import setuptools_scm; '
+        f'print(setuptools_scm.get_version('
+        f'git_describe_command = \\\"{git_version}\\\"))\"')
     dst_cmd = ('python -c \"import yggdrasil; '
                'print(yggdrasil.__version__)\"')
     dir_cmd = ('python -c \"import yggdrasil; '