Merge branch 'develop' into update_sundials

AMICI-dev · Oct 1, 2024 · f5f462a · f5f462a
2 parents 7619ca8 + 7f27bb3
commit f5f462a
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Showing 8 changed files with 27 additions and 10 deletions.
diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -36,11 +36,6 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
-    - name: Remove direct dependencies from setup.cfg
-      # Remove any "git+https"-based dependencies that are not supported
-      #  by PyPI and are only required for testing.
-      run: sed -i '/git+https/d' python/sdist/pyproject.toml
-
     - name: sdist
       run: scripts/buildSdist.sh
 

diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
@@ -15,7 +15,7 @@ jobs:
   build:
     name: PEtab Testsuite
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
 
     env:
       ENABLE_GCOV_COVERAGE: TRUE
@@ -68,6 +68,12 @@ jobs:
             && source ./venv/bin/activate \
             && cd petab_test_suite && pip3 install -e .
 
+      - name: Install PEtab benchmark collection
+        run: |
+          git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
+            && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+            && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python
+
       - name: Install petab
         run: |
           source ./venv/bin/activate \

diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
@@ -338,6 +338,12 @@ jobs:
         path: ${{ env.pooch-cache }}
         key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
 
+    - name: Install PEtab benchmark collection
+      run: |
+        git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
+          && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+          && source venv/bin/activate && python -m pip install -e $BENCHMARK_COLLECTION/../src/python
+
     - name: Python tests
       run: |
         scripts/run-python-tests.sh \

diff --git a/python/sdist/pyproject.toml b/python/sdist/pyproject.toml
@@ -61,7 +61,6 @@ classifiers = [
 petab = ["petab>=0.4.0"]
 pysb = ["pysb>=1.13.1"]
 test = [
-    "benchmark_models_petab @ git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python",
     "h5py",
     "pytest",
     "pytest-cov",

diff --git a/python/sdist/setup.py b/python/sdist/setup.py
@@ -55,7 +55,7 @@ def get_extensions():
     suitesparse = CMakeExtension(
         name="SuiteSparse",
         install_prefix="amici",
-        source_dir="amici/ThirdParty/SuiteSparse/",
+        source_dir="amici/ThirdParty/SuiteSparse",
         cmake_build_type=build_type,
         cmake_configure_options=[
             *global_cmake_configure_options,

diff --git a/scripts/buildSuiteSparse.sh b/scripts/buildSuiteSparse.sh
@@ -10,7 +10,17 @@ amici_path=$(cd "$script_path/.." && pwd)
 suitesparse_root="${amici_path}/ThirdParty/SuiteSparse"
 
 cd "${suitesparse_root}/build"
+
+if [[ "${GITHUB_REPOSITORY:-}" = *"/AMICI" ]] ||
+  [ "${ENABLE_AMICI_DEBUGGING:-}" = TRUE ]; then
+  # Running on CI server
+  build_type="Debug"
+else
+  build_type="RelWithDebInfo"
+fi
+
 cmake -DSUITESPARSE_ENABLE_PROJECTS="amd;btf;colamd;klu" \
+  -DCMAKE_BUILD_TYPE="$build_type" \
   -DCMAKE_INSTALL_PREFIX="${suitesparse_root}/install" \
   -DCHOLMOD_CAMD=OFF \
   -DKLU_USE_CHOLMOD=OFF \

diff --git a/scripts/buildSundials.sh b/scripts/buildSundials.sh
@@ -14,7 +14,8 @@ sundials_build_path="${amici_path}/ThirdParty/sundials/build/"
 cmake=${CMAKE:-cmake}
 make=${MAKE:-make}
 
-if [[ $GITHUB_ACTIONS = true ]]; then
+if [[ "${GITHUB_REPOSITORY:-}" = *"/AMICI" ]] ||
+  [ "${ENABLE_AMICI_DEBUGGING:-}" = TRUE ]; then
   # Running on CI server
   build_type="Debug"
 else

diff --git a/scripts/installAmiciSource.sh b/scripts/installAmiciSource.sh
@@ -33,7 +33,7 @@ fi
 export PYTHON_EXECUTABLE="${AMICI_PATH}/venv/bin/python"
 
 python -m pip install --upgrade pip wheel
-python -m pip install --upgrade pip setuptools cmake_build_extension==0.6.0 numpy
+python -m pip install --upgrade pip setuptools cmake_build_extension==0.6.0 numpy petab
 python -m pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching # pin to PR for SPM with compartments
 AMICI_BUILD_TEMP="${AMICI_PATH}/python/sdist/build/temp" \
   python -m pip install --verbose -e "${AMICI_PATH}/python/sdist[petab,test,vis]" --no-build-isolation