PEtab v2 import (#2974)

Experimental import of SBML- and PySB-based PEtab v2 problems.
Not particularly performant or feature-complete yet - to be extended.

Closes #2662.

Author: dweindl

.github/workflows/test_benchmark_collection_models.yml

@@ -54,7 +54,7 @@ jobs:
       run: |
         python3 -m pip uninstall -y petab && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@main \
         &&  python3 -m pip install -U sympy \
-        &&  python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git@amici100
+        &&  python3 -m pip install git+https://github.com/ICB-DCM/fiddy.git@main
 
     - name: Download benchmark collection
       run: |

.github/workflows/test_petab_test_suite.yml

@@ -11,7 +11,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
+  petab_v1:
     name: PEtab Testsuite
 
     runs-on: ubuntu-latest
@@ -87,7 +87,7 @@ jobs:
         run: |
           source ./venv/bin/activate \
             && python3 -m pip uninstall -y petab \
-            && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@main \
+            && python3 -m pip install git+https://github.com/petab-dev/libpetab-python.git@8dc6c1c4b801fba5acc35fcd25308a659d01050e \
             && python3 -m pip install git+https://github.com/pysb/pysb@master \
             && python3 -m pip install sympy>=1.12.1
 
@@ -102,11 +102,103 @@ jobs:
       - name: Run PEtab test suite
         run: |
           source ./venv/bin/activate \
-          && AMICI_PARALLEL_COMPILE="" pytest -v \
+          && AMICI_PARALLEL_COMPILE="" pytest -rxXs -v \
             --cov-report=xml:coverage.xml \
             --cov-append \
             --cov=amici \
-            tests/petab_test_suite/
+            tests/petab_test_suite/test_petab_suite.py
+
+      - name: Codecov
+        if: github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev'
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.xml
+          flags: petab
+          fail_ci_if_error: true
+
+
+  petab_v2:
+    name: PEtab v2 Testsuite
+
+    runs-on: ubuntu-latest
+
+    env:
+      ENABLE_GCOV_COVERAGE: TRUE
+
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 20
+
+      - name: Install apt dependencies
+        uses: ./.github/actions/install-apt-dependencies
+
+      # install dependencies
+      - name: apt
+        run: |
+          sudo apt-get update \
+            && sudo apt-get install -y python3-venv
+
+      - name: Build BNGL
+        run: scripts/buildBNGL.sh
+
+      - run: |
+          echo "${HOME}/.local/bin/" >> $GITHUB_PATH
+          echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH
+          echo "BNGPATH=${GITHUB_WORKSPACE}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
+
+      # install AMICI
+      - name: Install python package
+        run: scripts/installAmiciSource.sh
+
+      - name: Install petab
+        run: |
+          source ./venv/bin/activate \
+            && pip3 install wheel pytest shyaml pytest-cov pysb>=1.16
+
+      # retrieve test models
+      - name: Download and install PEtab test suite
+        run: |
+          git clone https://github.com/PEtab-dev/petab_test_suite \
+            && source ./venv/bin/activate \
+            && cd petab_test_suite \
+            && git checkout c12b9dc4e4c5585b1b83a1d6e89fd22447c46d03 \
+            && pip3 install -e .
+
+# TODO: once there is a PEtab v2 benchmark collection
+#      - name: Install PEtab benchmark collection
+#        run: |
+#          git clone --depth 1 https://github.com/benchmarking-initiative/Benchmark-Models-PEtab.git \
+#            && export BENCHMARK_COLLECTION="$(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@8dc6c1c4b801fba5acc35fcd25308a659d01050e \
+            && python3 -m pip install git+https://github.com/pysb/pysb@master \
+            && python3 -m pip install sympy>=1.12.1
+
+      # run test models
+      - name: Run PEtab test suite
+        run: |
+          source ./venv/bin/activate \
+          && AMICI_PARALLEL_COMPILE="" pytest -rxXs -v \
+            --cov-report=xml:coverage.xml \
+            --cov-append \
+            --cov=amici \
+            tests/petab_test_suite/test_petab_v2_suite.py
 
       - name: Codecov
         if: (github.event_name == 'pull_request' || github.repository_owner == 'AMICI-dev') && github.actor != 'dependabot[bot]'

.gitignore

@@ -141,8 +141,6 @@ tests/sbml/sbml-test-suite/
 */sbml-semantic-test-cases/*
 tests/sbml/SBMLTestModels/
 tests/benchmark_models/test_bmc
-tests/petab_test_suite
-petab_test_suite
 */tests/BIOMD0000000529/*
 
 python/examples/example_steadystate/model_steadystate_scaled/*
@@ -200,3 +198,4 @@ tests/benchmark_models/cache_fiddy/*
 venv/*
 .coverage
 tests/sciml/models/*
+amici_models

CHANGELOG.md

@@ -51,6 +51,14 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
 
 **Features**
 
+* Experimental support for the PEtab data format v2.0.0 (draft, see
+  https://petab.readthedocs.io/en/latest/v2/documentation_data_format.html)
+  for SBML- and PySB-based problems (see `amici.petab.petab_importer`). The API is subject to change.
+
+  * Current limitations for PySB-based PEtab problems:
+    * Only species and `pysb.Expression` are supported as condition table
+      targets.
+
 * Many relevant `ReturnData` fields are now available as `xarray.DataArray`
   via `ReturnData.xr.{x,y,w,x0,sx,...}`.
   `DataArray`s include the identifiers and are often more convenient than the
@@ -83,6 +91,7 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni
   can now be specified via the `AMICI_MODELS_ROOT` environment variable.
   See `amici.get_model_dir` for details.
 
+
 ## v0.X Series
 
 ### v0.34.2 (2025-11-03)