CMake-based Python extension builds

.github/workflows/deploy_protected.yml

@@ -8,6 +8,8 @@ on:
   pull_request:
     paths:
       - container/Dockerfile
+      # ensure all relevant files are still included in sdist
+      - python/sdist/MANIFEST.in
   workflow_dispatch:
 
 jobs:

.github/workflows/test_doc.yml

@@ -67,7 +67,7 @@ jobs:
       - run: git fetch --prune --unshallow
 
       - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-      - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.0.2/install/bin/swig" >> $GITHUB_ENV
+      - run: echo "SWIG=${AMICI_DIR}/ThirdParty/swig-4.1.1/install/bin/swig" >> $GITHUB_ENV
 
       - name: Build doxygen
         run: |

.github/workflows/test_python_cplusplus.yml

@@ -9,6 +9,7 @@ jobs:
     runs-on: ubuntu-22.04
 
     env:
+      AMICI_PARALLEL_COMPILE: ""
       ENABLE_GCOV_COVERAGE: "TRUE"
       CI_SONARCLOUD: "TRUE"
 
@@ -117,7 +118,7 @@ jobs:
         -d ${AMICI_DIR}/build/CMakeFiles/amici.dir/src \
         -b ${AMICI_DIR} -c -o coverage_cpp.info \
         && lcov --compat-libtool --no-external \
-        -d ${AMICI_DIR}/python/sdist/build/temp.linux-x86_64-$(python -c "import sys; print(sys.implementation.cache_tag)")/amici/src \
+        -d ${AMICI_DIR}/python/sdist/build/$(python -c "import sys, sysconfig; print(f'temp.{sysconfig.get_platform()}-{sys.implementation.cache_tag}_amici')")/CMakeFiles/amici.dir/src \
         -b ${AMICI_DIR}/python/sdist -c -o coverage_py.info \
         && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
 

.github/workflows/test_python_ver_matrix.yml

@@ -20,11 +20,12 @@ jobs:
     continue-on-error: ${{ matrix.experimental }}
     env:
       AMICI_SKIP_CMAKE_TESTS: "TRUE"
+      AMICI_PARALLEL_COMPILE: ""
 
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
         experimental: [false]
 
     steps:

.gitignore

@@ -163,7 +163,9 @@ python/sdist/amici/amici.py
 python/sdist/amici/amici_wrap.cxx
 python/sdist/amici/amici_without_hdf5.py
 python/sdist/amici/amici_wrap_without_hdf5.cxx
-
+python/sdist/amici/include/
+python/sdist/amici/lib/
+python/sdist/amici/share/
 python/sdist/build/*
 python/sdist/amici/git_version.txt
 
@@ -177,6 +179,7 @@ ThirdParty/doxygen/*
 ThirdParty/mtocpp-master*
 ThirdParty/sundials/build/*
 ThirdParty/SuiteSparse/lib/*
+ThirdParty/SuiteSparse/include/
 ThirdParty/SuiteSparse/share/*
 ThirdParty/SuperLU_MT_3.1/
 ThirdParty/superlu_mt_3.1.tar.gz