Merge pull request #2073 from AMICI-dev/release_0.17.0

Release 0.17.0
AMICI-dev · May 9, 2023 · e524930 · e524930
2 parents 1a99308 + 6dbff4f
commit e524930
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diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -1,5 +1,5 @@
 name: Deploy Branch
-on: [push, pull_request, workflow_dispatch]
+on: [push, merge_group, workflow_dispatch]
 
 jobs:
   sdist:
@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/deploy_protected.yml b/.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:
@@ -19,7 +21,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -12,7 +12,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
@@ -4,11 +4,11 @@ on:
     branches:
       - develop
       - master
-
   pull_request:
     branches:
       - master
       - develop
+  merge_group:
   workflow_dispatch:
   schedule:
     - cron:  '48 4 * * *'
@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.8" ]
+        python-version: [ "3.9" ]
         extract_subexpressions: ["true", "false"]
     env:
       AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }}
@@ -51,15 +51,22 @@ jobs:
         pip3 install build && cd python/sdist && python3 -m build --sdist
     - name: Install AMICI sdist
       run: |
+        pip3 install --user petab[vis] && \
         AMICI_PARALLEL_COMPILE=2 pip3 install -v --user \
-            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test]
+            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis]
 
     # retrieve test models
     - name: Download and test 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/" \
           && AMICI_PARALLEL_COMPILE=2 tests/benchmark-models/test_benchmark_collection.sh
+          
+    # run gradient checks
+    - name: Run Gradient Checks
+      run: |
+        pip install git+https://github.com/ICB-DCM/fiddy.git \
+          && cd tests/benchmark-models && pytest ./test_petab_benchmark.py
 
     # upload results
     - uses: actions/upload-artifact@v3

diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
@@ -8,6 +8,7 @@ on:
     branches:
       - develop
       - master
+  merge_group:
   workflow_dispatch:
   schedule:
     - cron:  '48 4 * * *'
@@ -20,7 +21,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -55,7 +56,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ 3.8 ]
+        python-version: [ "3.10" ]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
@@ -67,7 +68,7 @@ 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: |

diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
@@ -1,5 +1,5 @@
 name: Installation
-on: [push, pull_request, workflow_dispatch]
+on: [push, merge_group, workflow_dispatch]
 
 jobs:
   archive:
@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -57,7 +57,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/test_matlab.yml b/.github/workflows/test_matlab.yml
@@ -1,5 +1,5 @@
 name: Matlab
-on: [push, pull_request, workflow_dispatch]
+on: [push, merge_group, workflow_dispatch]
 
 jobs:
   matlab:

diff --git a/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
@@ -23,7 +23,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
@@ -4,12 +4,11 @@ on:
     branches:
       - develop
       - master
-
   pull_request:
     branches:
       - master
       - develop
-
+  merge_group:
   workflow_dispatch:
 
 jobs:
@@ -23,7 +22,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
@@ -63,7 +62,7 @@ jobs:
       # retrieve test models
       - name: Download and install PEtab test suite
         run: |
-          git clone --depth 1 --branch develop \
+          git clone --depth 1 --branch main \
             https://github.com/PEtab-dev/petab_test_suite \
             && source ./build/venv/bin/activate \
             && cd petab_test_suite && pip3 install -e .
@@ -76,7 +75,6 @@ jobs:
 
       # run test models
       - name: Run PEtab test suite
-        # git clone --depth 1 https://github.com/petab-dev/petab_test_suite
         run: |
           source ./build/venv/bin/activate \
           && AMICI_PARALLEL_COMPILE=2 pytest -v \

diff --git a/.github/workflows/test_pypi.yml b/.github/workflows/test_pypi.yml
@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, '3.10']
+        python-version: [3.9, 3.9, '3.10']
         os: [ubuntu-22.04, macos-latest]
 
     runs-on: ${{ matrix.os }}

diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
@@ -1,5 +1,5 @@
 name: C++/Python Tests
-on: [push, pull_request, workflow_dispatch]
+on: [push, merge_group, workflow_dispatch]
 
 jobs:
   build:
@@ -9,12 +9,13 @@ jobs:
     runs-on: ubuntu-22.04
 
     env:
+      AMICI_PARALLEL_COMPILE: ""
       ENABLE_GCOV_COVERAGE: "TRUE"
       CI_SONARCLOUD: "TRUE"
 
     strategy:
       matrix:
-        python-version: [ 3.8 ]
+        python-version: [ 3.9 ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -55,6 +56,7 @@ jobs:
             g++ \
             libatlas-base-dev \
             libboost-serialization-dev \
+            libboost-chrono-dev \
             libhdf5-serial-dev \
             python3-venv \
             swig \
@@ -94,6 +96,11 @@ jobs:
           --cov-append \
           ${AMICI_DIR}/python/tests
 
+    - name: Install notebook dependencies
+      run: |
+        source build/venv/bin/activate \
+        && pip install jax[cpu]
+
     - name: example notebooks
       run: |
         scripts/runNotebook.sh python/examples/example_*/
@@ -117,7 +124,7 @@ 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
 
@@ -146,7 +153,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
 
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow

diff --git a/.github/workflows/test_python_ver_matrix.yml b/.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: ['3.9', '3.10', '3.11']
         experimental: [false]
 
     steps:

diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -8,7 +8,8 @@ on:
   pull_request:
     paths:
       - .github/workflows/test_sbml_semantic_test_suite.yml
-      - python/sdist/amici/ode_export.py
+      - python/sdist/amici/de_export.py
+      - python/sdist/amici/de_model.py
       - python/sdist/amici/sbml_import.py
       - python/sdist/amici/import_utils.py
       - scripts/run-SBMLTestsuite.sh
@@ -28,7 +29,7 @@ jobs:
       matrix:
         cases: ["1-250", "251-500", "501-750", "751-1000",
                 "1000-1250", "1251-"]
-        python-version: [ 3.8 ]
+        python-version: [ "3.9" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/test_windows.yml b/.github/workflows/test_windows.yml
@@ -1,7 +1,7 @@
 name: Windows Tests
 on:
   push:
-  pull_request:
+  merge_group:
   workflow_dispatch:
   schedule:
     - cron:  '48 4 * * *'
@@ -23,7 +23,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.8" ]
+        python-version: [ "3.9" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.gitignore b/.gitignore
@@ -154,6 +154,7 @@ python/examples/example_presimulation/model_presimulation/*
 python/examples/example_presimulation/model_presimulation_re/*
 python/examples/example_constant_species/model_constant_species_reduced/*
 python/examples/example_constant_species/model_constant_species/*
+python/examples/example_jax/amici_models/*
 python/tests/sbml_test_models/*
 python/tests/piecewise_test/*
 
@@ -163,7 +164,9 @@ 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 +180,7 @@ 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
@@ -195,3 +199,6 @@ Benchmark-Models-PEtab/
 /test_bmc/
 
 CS_Signalling_ERBB_RAS_AKT/
+cache_fiddy/*
+debug/*
+tests/benchmark-models/cache_fiddy/*
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -19,12 +19,9 @@ python:
     - requirements: documentation/rtd_requirements.txt
     - requirements: documentation/rtd_requirements2.txt
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-22.04"
   apt_packages:
-    # for custom doxygen
-    - libclang-cpp9
-    - libclang1-9
     - libatlas-base-dev
     - swig
   tools:
-    python: "3.8"
+    python: "3.9"