Merge pull request #2115 from AMICI-dev/release_0.18.0

Release 0.18.0

Author: dweindl

.coveragerc

@@ -16,4 +16,3 @@ exclude_lines =
     raise
     except:
     import
-

.github/CODEOWNERS

@@ -2,4 +2,3 @@
 
 # default owners
 * @AMICI-dev/amici-maintainers
-

.github/workflows/test_benchmark_collection_models.yml

@@ -61,7 +61,7 @@ jobs:
         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: |

.github/workflows/test_petab_test_suite.yml

@@ -43,8 +43,6 @@ jobs:
             libatlas-base-dev \
             python3-venv
 
-      - run: pip3 install pysb petab
-
       - name: Build BNGL
         run: |
           scripts/buildBNGL.sh
@@ -59,6 +57,11 @@ jobs:
         run: |
           scripts/installAmiciSource.sh
 
+      - name: Install petab
+        run: |
+          source ./build/venv/bin/activate \
+            && pip3 install wheel pytest shyaml pytest-cov pysb
+
       # retrieve test models
       - name: Download and install PEtab test suite
         run: |

.github/workflows/test_python_cplusplus.yml

@@ -1,5 +1,11 @@
 name: C++/Python Tests
-on: [push, merge_group, workflow_dispatch]
+on:
+  push:
+  merge_group:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - master
 
 jobs:
   build:
@@ -91,11 +97,23 @@ jobs:
         source build/venv/bin/activate \
         && pytest \
           --ignore-glob=*petab* \
+          --ignore-glob=*test_splines.py \
           --cov=amici \
           --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
           --cov-append \
           ${AMICI_DIR}/python/tests
 
+
+    - name: Python tests splines
+      if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}}
+      run: |
+        source build/venv/bin/activate \
+        && pytest \
+          --cov=amici \
+          --cov-report=xml:"${AMICI_DIR}/build/coverage_py.xml" \
+          --cov-append \
+          ${AMICI_DIR}/python/tests/test_splines.py
+
     - name: Install notebook dependencies
       run: |
         source build/venv/bin/activate \

.github/workflows/test_python_ver_matrix.yml

@@ -63,4 +63,5 @@ jobs:
       run: |
         source build/venv/bin/activate \
           && pip3 install git+https://github.com/pysb/pysb \
-          && python3 -m pytest --ignore-glob=*petab* ${AMICI_DIR}/python/tests
+          && python3 -m pytest --ignore-glob=*petab* \
+            --ignore-glob=*test_splines.py ${AMICI_DIR}/python/tests

.github/workflows/test_windows.yml

@@ -5,12 +5,15 @@ on:
   workflow_dispatch:
   schedule:
     - cron:  '48 4 * * *'
+  pull_request:
+    branches:
+      - master
 
 jobs:
   build:
     name: Tests Windows
 
-    runs-on: windows-2019
+    runs-on: windows-latest
 
     env:
       AMICI_SKIP_CMAKE_TESTS: "TRUE"
@@ -74,4 +77,14 @@ jobs:
     - run: python -m amici
 
     - name: Run Python tests
-      run: python -m pytest --ignore-glob=*petab* --ignore-glob=*special* python/tests
+      shell: bash
+      run: |
+        python -m pytest \
+          --ignore-glob=*petab* \
+          --ignore-glob=*special* \
+          --ignore-glob=*test_splines.py \
+          python/tests
+
+    - name: Python tests splines
+      if: ${{ github.base_ref == 'master' || github.event.merge_group.base_ref == 'master'}}
+      run: python -m pytest python/tests/test_splines.py

.gitignore

@@ -42,7 +42,7 @@ models/model_robertson/build/*
 !models/model_calvetti
 models/model_calvetti/build/*
 
-amici_models/*
+amici_models/
 
 simulate_model_*_hdf.m
 simulate_model_*.m

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pycqa/isort
+  rev: 5.12.0
+  hooks:
+    - id: isort
+      name: isort (python)
+      args: ["--profile", "black", "--filter-files"]
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: check-added-large-files
+  - id: check-merge-conflict
+  - id: check-yaml
+    args: [--allow-multiple-documents]
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+- repo: https://github.com/psf/black
+  rev: 23.3.0
+  hooks:
+    - id: black
+      # It is recommended to specify the latest version of Python
+      # supported by your project here, or alternatively use
+      # pre-commit's default_language_version, see
+      # https://pre-commit.com/#top_level-default_language_version
+      language_version: python3.11
+exclude: '^(ThirdParty|models)/'