Release 0.11.24

Merge pull request #1644 from AMICI-dev/release_0.11.24

.github/workflows/deploy_branch.yml

@@ -7,7 +7,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    strategy:
+      matrix:
+        python-version: [3.8]
+
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
       with:
         fetch-depth: 20

.github/workflows/deploy_protected.yml

@@ -16,7 +16,15 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    strategy:
+      matrix:
+        python-version: [3.8]
+
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
     - uses: actions/checkout@master
     - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
     - name: Publish to Registry

.github/workflows/deploy_release.yml

@@ -10,7 +10,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    strategy:
+      matrix:
+        python-version: [3.8]
+
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
       with:
         fetch-depth: 20

.github/workflows/test_benchmark_collection_models.yml

@@ -19,7 +19,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    strategy:
+      matrix:
+        python-version: [ 3.8 ]
+
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
       with:
         fetch-depth: 20

.github/workflows/test_doc.yml

@@ -18,7 +18,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    strategy:
+      matrix:
+        python-version: [3.8]
+
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
     - run: git fetch --prune --unshallow
 
@@ -44,7 +53,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    strategy:
+      matrix:
+        python-version: [ 3.8 ]
+
     steps:
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
       - uses: actions/checkout@master
       - run: git fetch --prune --unshallow
 
@@ -55,12 +73,6 @@ jobs:
         run: |
           sudo scripts/downloadAndBuildDoxygen.sh
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          # Semantic version range syntax or exact version of a Python version
-          python-version: '3.8'
-
       # install amici dependencies
       - name: apt
         run: |

.github/workflows/test_install.yml

@@ -7,7 +7,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    strategy:
+      matrix:
+        python-version: [3.8]
+
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
     - run: git fetch --prune --unshallow
 
@@ -46,7 +55,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    strategy:
+      matrix:
+        python-version: [3.8]
+
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
     - run: git fetch --prune --unshallow
 

.github/workflows/test_performance.yml

@@ -21,7 +21,16 @@ jobs:
 
     runs-on: ubuntu-20.04
 
+    strategy:
+      matrix:
+        python-version: [3.8]
+
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
       with:
         fetch-depth: 20
@@ -31,7 +40,7 @@ jobs:
       run: |
         sudo apt-get update \
           && sudo apt-get install -y swig libatlas-base-dev
-    - run: pip3 install petab shyaml
+    - run: pip3 install petab shyaml build
 
     - run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH
     - run: echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH
@@ -40,7 +49,8 @@ jobs:
     - name: Create AMICI sdist
       run: |
         cd python/sdist \
-          && check_time.sh create_sdist /usr/bin/python3 setup.py sdist
+          && check_time.sh create_sdist python3 -m build --sdist
+
     - name: Install AMICI sdist
       run: |
         AMICI_PARALLEL_COMPILE=2 check_time.sh \

.github/workflows/test_petab_test_suite.yml

@@ -21,7 +21,16 @@ jobs:
     env:
       ENABLE_GCOV_COVERAGE: TRUE
 
+    strategy:
+      matrix:
+        python-version: [3.8]
+
     steps:
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
       - uses: actions/checkout@master
         with:
           fetch-depth: 20

.github/workflows/test_pypi.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9, '3.10']
         os: [ubuntu-20.04, macos-latest]
 
     runs-on: ${{ matrix.os }}

.github/workflows/test_python_cplusplus.yml

@@ -12,7 +12,16 @@ jobs:
       ENABLE_GCOV_COVERAGE: "TRUE"
       CI_SONARCLOUD: "TRUE"
 
+    strategy:
+      matrix:
+        python-version: [ 3.8 ]
+
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
     - run: git fetch --prune --unshallow
 

.github/workflows/test_python_ver_matrix.yml

@@ -22,12 +22,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10']
+        python-version: [3.8, 3.9, '3.10']
         experimental: [false]
-# Temporarily disabled because the respective jobs somehow runs infinitely
-#        include:
-#          - python-version:  3.10.0-alpha.5
-#            experimental: true
 
     steps:
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -27,8 +27,14 @@ jobs:
       matrix:
         cases: ["1 - 250", "251 - 500", "501 - 750", "751 - 1000",
                 "1000-1250", "1251-1780"]
+        python-version: [ 3.8 ]
 
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
       with:
         fetch-depth: 1

.github/workflows/test_valgrind.yml

@@ -16,7 +16,16 @@ jobs:
     # TODO: prepare image with more deps preinstalled
     runs-on: ubuntu-20.04
 
+    strategy:
+      matrix:
+        python-version: [ 3.8 ]
+
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
     - run: git fetch --prune --unshallow
 

.github/workflows/test_windows.yml

@@ -9,9 +9,19 @@ jobs:
 
     env:
       AMICI_SKIP_CMAKE_TESTS: "TRUE"
-      openBLAS_version: "0.3.12"
+      openBLAS_version: "0.3.19"
+      AMICI_DLL_DIRS: "C:\\BLAS\\bin"
+
+    strategy:
+      matrix:
+        python-version: [ "3.8" ]
 
     steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
     - uses: actions/checkout@master
     - run: git fetch --prune --unshallow
 
@@ -48,5 +58,7 @@ jobs:
       shell: bash
       run: pip install -v $(ls -t dist/amici-*.tar.gz | head -1)
 
+    - run: python -m amici
+
     - name: Run Python tests
       run: python -m pytest --ignore-glob=*petab* --ignore-glob=*special* python/tests

CHANGELOG.md

@@ -2,6 +2,29 @@
 
 ## v0.X Series
 
+### v0.11.24 (2022-02-01)
+
+Features:
+* Introduced environment variable `AMICI_DLL_DIRS` to control DLL directories
+  on Windows (useful for setting BLAS library directory, as required by
+  Python>=3.8) by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1637
+* Dropped Python3.7 support by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1635
+* Include header files in CMake targets for better IDE integration by @dweindl
+  in https://github.com/AMICI-dev/AMICI/pull/1639
+
+Fixes:
+* Fixed an issue in PEtab import where all-integer parameters would previously
+  result in a TypeError by @stephanmg in
+  https://github.com/AMICI-dev/AMICI/pull/1634
+* Fixed tempdir deletion issues for test suite on Windows by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1636
+* Added functions to provide state IDs/names for x_solver by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1638
+* Fixed docs on RTD by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1643
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.11.23...v0.11.24
+
 ### v0.11.23 (2022-01-11)
 
 Features:

CMakeLists.txt

@@ -144,6 +144,36 @@ set(AMICI_SRC_LIST
     ${CMAKE_SOURCE_DIR}/src/sundials_linsol_wrapper.cpp
     ${CMAKE_SOURCE_DIR}/src/abstract_model.cpp
     ${CMAKE_SOURCE_DIR}/src/vector.cpp
+    ${CMAKE_SOURCE_DIR}/include/amici/abstract_model.h
+    ${CMAKE_SOURCE_DIR}/include/amici/amici.h
+    ${CMAKE_SOURCE_DIR}/include/amici/backwardproblem.h
+    ${CMAKE_SOURCE_DIR}/include/amici/cblas.h
+    ${CMAKE_SOURCE_DIR}/include/amici/defines.h
+    ${CMAKE_SOURCE_DIR}/include/amici/edata.h
+    ${CMAKE_SOURCE_DIR}/include/amici/exception.h
+    ${CMAKE_SOURCE_DIR}/include/amici/forwardproblem.h
+    ${CMAKE_SOURCE_DIR}/include/amici/hdf5.h
+    ${CMAKE_SOURCE_DIR}/include/amici/interface_matlab.h
+    ${CMAKE_SOURCE_DIR}/include/amici/misc.h
+    ${CMAKE_SOURCE_DIR}/include/amici/model_dae.h
+    ${CMAKE_SOURCE_DIR}/include/amici/model_dimensions.h
+    ${CMAKE_SOURCE_DIR}/include/amici/model.h
+    ${CMAKE_SOURCE_DIR}/include/amici/model_ode.h
+    ${CMAKE_SOURCE_DIR}/include/amici/model_state.h
+    ${CMAKE_SOURCE_DIR}/include/amici/newton_solver.h
+    ${CMAKE_SOURCE_DIR}/include/amici/rdata.h
+    ${CMAKE_SOURCE_DIR}/include/amici/returndata_matlab.h
+    ${CMAKE_SOURCE_DIR}/include/amici/serialization.h
+    ${CMAKE_SOURCE_DIR}/include/amici/simulation_parameters.h
+    ${CMAKE_SOURCE_DIR}/include/amici/solver_cvodes.h
+    ${CMAKE_SOURCE_DIR}/include/amici/solver.h
+    ${CMAKE_SOURCE_DIR}/include/amici/solver_idas.h
+    ${CMAKE_SOURCE_DIR}/include/amici/spline.h
+    ${CMAKE_SOURCE_DIR}/include/amici/steadystateproblem.h
+    ${CMAKE_SOURCE_DIR}/include/amici/sundials_linsol_wrapper.h
+    ${CMAKE_SOURCE_DIR}/include/amici/sundials_matrix_wrapper.h
+    ${CMAKE_SOURCE_DIR}/include/amici/symbolic_functions.h
+    ${CMAKE_SOURCE_DIR}/include/amici/vector.h
     )
 if(ENABLE_HDF5)
     list(APPEND AMICI_SRC_LIST ${CMAKE_SOURCE_DIR}/src/hdf5.cpp)

documentation/README.md

@@ -67,7 +67,7 @@ Graphics for documentation are kept in `documentation/gfx/`.
 
 ### When using Markdown
 
-* Note that there are some incompatibilities of Github Markdown and Doxygen
+* Note that there are some incompatibilities of GitHub Markdown and Doxygen
   Markdown. Ideally documentation should be written in a format compatible with
   both.
   This affects for example images links which currently cause trouble in

documentation/conf.py

@@ -129,10 +129,10 @@ def install_doxygen():
     some_dir_on_path = os.environ['PATH'].split(os.pathsep)[0]
     cmd = (
         f"cd '{os.path.join(amici_dir, 'ThirdParty')}' "
-        f"&& wget 'https://doxygen.nl/files/"
+        f"&& wget 'https://www.doxygen.nl/files/"
         f"doxygen-{version}.linux.bin.tar.gz' "
         f"&& tar -xzf doxygen-{version}.linux.bin.tar.gz "
-        f"&& ln -s '{doxygen_exe}' '{some_dir_on_path}'"
+        f"&& ln -sf '{doxygen_exe}' '{some_dir_on_path}'"
     )
     subprocess.run(cmd, shell=True, check=True)
     assert os.path.islink(os.path.join(some_dir_on_path, 'doxygen'))