Update amici to v0.26.3-20-g8253a97d (#388)

* Update amici to [8253a97d413cbbcfec335fb50fd1355107804e9e](AMICI-dev/AMICI@8253a97) * GHA: disable ceres due to #391 * Address amici deprecations Mysterious amici errors on GHA, specifically for Weber_BMC2015, not locally reproducible, remain AMICI-dev/AMICI#2491. They already occurred (at least) with amici v0.26.1. --- git subrepo clone --branch=8253a97d413cbbcfec335fb50fd1355107804e9e --force [email protected]:dweindl/AMICI.git deps/AMICI subrepo: subdir: "deps/AMICI" merged: "8253a97d" upstream: origin: "[email protected]:dweindl/AMICI.git" branch: "8253a97d413cbbcfec335fb50fd1355107804e9e" commit: "8253a97d" git-subrepo: version: "0.4.6" origin: "https://github.com/ingydotnet/git-subrepo" commit: "110b9eb"
ICB-DCM · Oct 19, 2024 · c76c7d3 · c76c7d3
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diff --git a/.github/workflows/benchmark_models.yml b/.github/workflows/benchmark_models.yml
@@ -33,13 +33,15 @@ jobs:
             -DCMAKE_BUILD_TYPE=Debug \
             -DENABLE_PYTHON=ON \
             -DBUILD_TESTS=OFF \
+            -DCMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH};${AMICI_PATH}/ThirdParty/SuiteSparse/install" \
           && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
 
     - name: Configure parpe
       run: |
         cmake \
           -S"${PARPE_BASE}" \
           -B"${PARPE_BUILD}" \
+          -DPARPE_ENABLE_CERES=OFF \
           -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
           -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
           -DGCOVR_REPORT=TRUE \

diff --git a/.github/workflows/parpe_tests.yml b/.github/workflows/parpe_tests.yml
@@ -55,6 +55,7 @@ jobs:
           -DCMAKE_BUILD_TYPE=Debug \
           -DENABLE_PYTHON=ON \
           -DBUILD_TESTS=OFF \
+          -DCMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH};${AMICI_PATH}/ThirdParty/SuiteSparse/install" \
           && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
 
     - name: Install parPE deps
@@ -75,7 +76,8 @@ jobs:
           -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
           -DGCOV_REPORT=TRUE \
           -DBUILD_TESTING=TRUE \
-          -DPARPE_ENABLE_FIDES=TRUE
+          -DPARPE_ENABLE_FIDES=TRUE \
+          -DPARPE_ENABLE_CERES=FALSE
 
     - name: Build parPE
       # with sonar build wrapper

diff --git a/.github/workflows/petab_testsuite.yml b/.github/workflows/petab_testsuite.yml
@@ -34,13 +34,15 @@ jobs:
             -DCMAKE_BUILD_TYPE=Debug \
             -DENABLE_PYTHON=ON \
             -DBUILD_TESTS=OFF \
+            -DCMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH};${AMICI_PATH}/ThirdParty/SuiteSparse/install" \
           && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
 
     - name: Configure parpe
       run: |
         cmake \
           -S"${PARPE_BASE}" \
           -B"${PARPE_BUILD}" \
+          -DPARPE_ENABLE_CERES=OFF \
           -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
           -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
           -DGCOVR_REPORT=TRUE \

diff --git a/README.md b/README.md
@@ -48,7 +48,7 @@ described in [doc/petab_model_import.md](doc/petab_model_import.md).
 
 For full functionality, parPE requires the following libraries:
 
-* CMAKE (>=3.15)
+* CMAKE (>=3.22)
 * MPI ([OpenMPI](https://www.open-mpi.org/),
   [MPICH](https://www.mpich.org/), ...)
 * IPOPT (>= 1.2.7) (requires coinhsl)
@@ -60,7 +60,7 @@ For full functionality, parPE requires the following libraries:
 * [AMICI](https://github.com/AMICI-dev/AMICI) (included in this repository)
   (uses SuiteSparse, Sundials)
 * C++17 compiler
-* Python >= 3.9, including header files
+* Python >= 3.10, including header files
 
 On Debian-based systems, dependencies can be installed via:
 ```shell
@@ -109,10 +109,10 @@ Other sample build scripts are provided as `/build*.sh`.
 
 ## Recently tested compilers
 
-* GCC 10.2.0
-* Intel icpc (ICC) 17.0.6
+* GCC 13.2.0
+* Clang 18.1.3
 
-## Docker
+## Containers
 
 There is a Dockerfile available in `container/charliecloud/` and images
 can be found on [dockerhub](https://hub.docker.com/r/dweindl/parpe/).
@@ -153,7 +153,7 @@ parPE is being used or has been used in the following projects:
 
 parPE has been developed within research projects receiving external funding:
 
-* Through  the  European  Union's  Horizon  2020  research  and innovation
+* Through the European Union's Horizon 2020 research and innovation
   programme under grant agreement no. 686282
   ([CanPathPro](http://canpathpro.eu/)).
 

diff --git a/benchmark_collection/import_and_run.sh b/benchmark_collection/import_and_run.sh
@@ -47,12 +47,12 @@ amici_root="${AMICI_ROOT:-${parpe_dir}/deps/AMICI/}"
 cd "${petab_model_dir}"
 
 echo "Running petablint on ${petab_yaml}..."
-petablint -v -y "${model_name}".yaml
+petablint -v "${model_name}".yaml
 
 # import AMICI model
 if [[ ! -d ${amici_model_dir} ]]; then
   echo "Importing model..."
-  cmd="amici_import_petab.py --verbose -y ${model_name}.yaml -n ${model_name} -o ${amici_model_dir}"
+  cmd="amici_import_petab.py --verbose ${model_name}.yaml -n ${model_name} -o ${amici_model_dir}"
   echo "${cmd}"
   ${cmd}
 fi

diff --git a/container/charliecloud/parpe_base/install_parpe.sh b/container/charliecloud/parpe_base/install_parpe.sh
@@ -4,6 +4,7 @@ set -euo pipefail
 set -x
 
 export PARPE_BASE="${PARPE_DIR:-/parPE}"
+export CMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH:-""}
 
 # unpack git archive
 mkdir "$PARPE_BASE" && cd "$PARPE_BASE"
@@ -21,7 +22,8 @@ cmake \
   -DCMAKE_BUILD_TYPE=RelWithDebInfo \
   -DENABLE_PYTHON=ON \
   -DBUILD_TESTS=OFF \
-  .. && make -j
+  -DCMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH};${AMICI_PATH}/ThirdParty/SuiteSparse/install" \
+  .. && cmake --build . --parallel
 
 # install fides optimizer
 cd "$PARPE_BASE/ThirdParty" && ./installFides.sh
@@ -45,6 +47,7 @@ mpi_cmd="$mpi_cmd;--mca;orte_base_help_aggregate;0"
 cmake \
       -DPARPE_BUILD_OPTIMIZED=OFF \
       -DPARPE_ENABLE_FIDES=ON \
+      -DPARPE_ENABLE_CERES=OFF \
       -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
       -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
       -DMPI_INCLUDE_DIRS=/usr/include/openmpi-x86_64/ \

diff --git a/deps/AMICI/.github/workflows/deploy_release.yml b/deps/AMICI/.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/deps/AMICI/.github/workflows/test_benchmark_collection_models.yml b/deps/AMICI/.github/workflows/test_benchmark_collection_models.yml
@@ -61,13 +61,14 @@ jobs:
       run: |
         git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
           && export BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
+          && pip3 install -e $BENCHMARK_COLLECTION/../src/python \
           && AMICI_PARALLEL_COMPILE="" 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
+          && cd tests/benchmark-models && pytest --durations=10 ./test_petab_benchmark.py
 
     # upload results
     - uses: actions/upload-artifact@v4

diff --git a/deps/AMICI/.github/workflows/test_petab_test_suite.yml b/deps/AMICI/.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
@@ -68,12 +68,18 @@ 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 \
             && python3 -m pip uninstall -y petab \
             && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@develop \
-            && python3 -m pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching \
+            && python3 -m pip install git+https://github.com/pysb/pysb@master \
             && python3 -m pip install sympy>=1.12.1
 
 

diff --git a/deps/AMICI/.github/workflows/test_python_cplusplus.yml b/deps/AMICI/.github/workflows/test_python_cplusplus.yml
@@ -38,6 +38,11 @@ jobs:
     - name: Set up AMICI C++ libraries
       uses: ./.github/actions/setup-amici-cpp
 
+    - name: Install libsuitesparse-dev
+      # We don't need libsuitesparse-dev, but let's have it installed,
+      # to ensure that its presence does not break the build
+      run: sudo apt-get install -y libsuitesparse-dev
+
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
 
@@ -125,6 +130,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Cache
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
@@ -201,6 +213,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Cache
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/pooch
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
 
@@ -259,6 +278,17 @@ jobs:
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
 
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Python tests
       run: |
         scripts/run-python-tests.sh \
@@ -301,6 +331,24 @@ jobs:
     - name: Get BioNetGen
       run: scripts/buildBNGL.sh
 
+
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        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/deps/AMICI/.github/workflows/test_python_ver_matrix.yml b/deps/AMICI/.github/workflows/test_python_ver_matrix.yml
@@ -60,6 +60,17 @@ jobs:
     - run: source venv/bin/activate && pip3 install "sympy>=1.12.1"
       if: matrix.python-version != '3.12'
 
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(source venv/bin/activate && python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Python tests
       run: |
         source venv/bin/activate \

diff --git a/deps/AMICI/.github/workflows/test_windows.yml b/deps/AMICI/.github/workflows/test_windows.yml
@@ -77,6 +77,18 @@ jobs:
 
     - run: python -m amici
 
+    - name: Get Pooch Cache Directory
+      id: get-pooch-cache
+      run: |
+        echo "pooch-cache=$(python -c 'import pooch; print(pooch.os_cache("pooch"))')" >> $GITHUB_ENV
+      shell: bash
+
+    - name: Cache Pooch Directory
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.pooch-cache }}
+        key: ${{ runner.os }}-py${{ matrix.python-version }}-${{ github.job }}
+
     - name: Run Python tests
       shell: bash
       run: |

diff --git a/deps/AMICI/.gitignore b/deps/AMICI/.gitignore
@@ -182,6 +182,7 @@ ThirdParty/sundials/build/*
 ThirdParty/SuiteSparse/lib/*
 ThirdParty/SuiteSparse/include/
 ThirdParty/SuiteSparse/share/*
+ThirdParty/SuiteSparse/install/*
 ThirdParty/SuperLU_MT_3.1/
 ThirdParty/superlu_mt_3.1.tar.gz
 ThirdParty/swig-*
@@ -203,3 +204,4 @@ cache_fiddy/*
 debug/*
 tests/benchmark-models/cache_fiddy/*
 venv/*
+.coverage
diff --git a/deps/AMICI/.gitrepo b/deps/AMICI/.gitrepo
@@ -5,8 +5,8 @@
 ;
 [subrepo]
 	remote = [email protected]:ICB-DCM/AMICI.git
-	branch = v0.26.1
-	commit = b0d79fffd3ab6e39296353d906e27033bc13dd4c
-	parent = 157fd81f04bd866127bc75f46887c4ce7c43566d
+	branch = 8253a97d413cbbcfec335fb50fd1355107804e9e
+	commit = 8253a97d413cbbcfec335fb50fd1355107804e9e
+	parent = 4b6205d1b4661c227beee7039416c516d47e91f9
 	cmdver = 0.4.6
 	method = merge
diff --git a/deps/AMICI/.pre-commit-config.yaml b/deps/AMICI/.pre-commit-config.yaml
@@ -12,7 +12,7 @@ repos:
   - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.4.1
+  rev: v0.6.7
   hooks:
     # Run the linter.
     - id: ruff
@@ -28,7 +28,7 @@ repos:
         - python/sdist/pyproject.toml
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
+    rev: v3.17.0
     hooks:
     -   id: pyupgrade
         args: ["--py310-plus"]