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

Release 0.17.0

Author: dweindl

.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 }}

.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 }}

.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 }}

.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

.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: |

.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 }}

.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:

.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 }}

.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 \

.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 }}