Merge pull request #2433 from dweindl/release_0.25.0

Release 0.25.0
AMICI-dev · May 8, 2024 · 7487607 · 7487607
2 parents 29b7ee8 + 52996d3
commit 7487607
Show file tree

Hide file tree

Showing 97 changed files with 999 additions and 586 deletions.
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1 @@
+f59fed72eb4d0cedf6abf2a96fe95087ce61478a
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,10 @@
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    ignore:
+      - dependency-name: "*"
+        update-types: ["version-update:semver-patch", "version-update:semver-minor"]
diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/deploy_protected.yml b/.github/workflows/deploy_protected.yml
@@ -29,14 +29,14 @@ jobs:
           fi
 
   dockerhub:
-    name: Deploy Dockerhub
+    name: Deploy Docker Hub
     needs: [check-secret]
     if: needs.check-secret.outputs.secrets-defined == 'true'
     runs-on: ubuntu-22.04
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -50,7 +50,7 @@ jobs:
     - name: Set up Docker Buildx
       uses: docker/setup-buildx-action@v3
     - name: Publish to Registry
-      uses: elgohr/Publish-Docker-Github-Action@v4
+      uses: elgohr/Publish-Docker-Github-Action@v5
       with:
         name: dweindl/amici
         username: ${{ secrets.DOCKER_USERNAME }}

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -12,7 +12,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     environment:
       name: pypi
@@ -39,7 +39,7 @@ jobs:
     - 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/setup.cfg
+      run: sed -i '/git+https/d' python/sdist/pyproject.toml
 
     - name: sdist
       run: scripts/buildSdist.sh
@@ -74,3 +74,29 @@ jobs:
             -H "Accept: application/vnd.github.v3+json" \
               https://api.github.com/repos/${DOWNSTREAM_REPOSITORY}/actions/workflows/${WORKFLOW_FILE}/dispatches \
             -d "{\"ref\": \"dev\", \"inputs\": {\"simulatorVersion\": \"${PACKAGE_VERSION}\", \"simulatorVersionLatest\": \"true\"}}"
+
+  dockerhub:
+    name: Release to Docker Hub
+    runs-on: ubuntu-22.04
+
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+    - uses: actions/checkout@v4
+    - run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@v3
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+    - name: Publish to Registry
+      uses: elgohr/Publish-Docker-Github-Action@v5
+      with:
+        name: dweindl/amici
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+        workdir: container/
+        dockerfile: Dockerfile
+        tag_semver: true
+        platforms: linux/amd64,linux/arm64
diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
         extract_subexpressions: ["true", "false"]
     env:
       AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }}

diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
@@ -20,7 +20,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
@@ -9,7 +9,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -50,7 +50,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -83,7 +83,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
@@ -23,7 +23,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     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
@@ -22,7 +22,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ["3.11"]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}

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: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
         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
@@ -15,7 +15,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     steps:
     - name: Cache
@@ -117,7 +117,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.10" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -193,7 +193,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
@@ -233,7 +233,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.11"
 
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow
@@ -282,7 +282,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: "3.11"
 
     - uses: actions/checkout@v4
     - run: git fetch --prune --unshallow

diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml
@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
         experimental: [false]
 
     steps:

diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -29,7 +29,7 @@ jobs:
       matrix:
         cases: ["1-250", "251-500", "501-750", "751-1000",
                 "1000-1250", "1251-"]
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml
@@ -18,7 +18,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     env:
       ENABLE_AMICI_DEBUGGING: "TRUE"
@@ -57,7 +57,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     env:
       ENABLE_AMICI_DEBUGGING: "TRUE"

diff --git a/.github/workflows/test_windows.yml b/.github/workflows/test_windows.yml
@@ -27,7 +27,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.9" ]
+        python-version: [ "3.11" ]
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
   - id: check-added-large-files
   - id: check-merge-conflict
@@ -12,7 +12,7 @@ repos:
   - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.1.11
+  rev: v0.4.1
   hooks:
     # Run the linter.
     - id: ruff
@@ -28,10 +28,9 @@ repos:
         - python/sdist/pyproject.toml
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.2
     hooks:
     -   id: pyupgrade
-        args: ["--py39-plus"]
-        additional_dependencies: [pyupgrade==3.15.0]
+        args: ["--py310-plus"]
 
 exclude: '^(ThirdParty|models)/'
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,10 +2,42 @@
 
 ## v0.X Series
 
+### v0.25.0 (2024-05-TBD)
+
+This release requires Python >= 3.10.
+
+**Fixes**
+* Fixed a bug in event handling that could lead to incorrect simulation
+  results for models with events that assign to compartments *and* have
+  additional event assignments
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2428
+* SBML import: handle `useValuesFromTriggerTime` attribute on events.
+  This attribute was previously ignored. It is possible that now AMICI fails
+  to import models that it previously imported successfully. For cases where
+  `useValuesFromTriggerTime=True` made a difference, AMICI might have produced
+  incorrect results before.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2429
+* Faster code generation for models with events if they don't have
+  state-dependent triggers
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2417
+* Most warnings now come with a more informative code location
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2421
+* `amici.ExpData` was changed so that `isinstance(edata, amici.ExpData)` works
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2396
+
+**Features**
+* Event-assignments to compartments are now supported. Previously, this only
+  worked for compartments that were rate rule targets.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2425
+* Releases are now deployed to Docker Hub
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2413
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.24.0...v0.25.0
+
 ### v0.24.0 (2024-04-22)
 
 This will be the last release supporting Python 3.9.
-Future releases will require Python 3.10.
+Future releases will require Python>=3.10.
 
 **Fixes**
 
@@ -27,7 +59,7 @@ Future releases will require Python 3.10.
   the correct SUNDIALS installation
   by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2397
 
-* **Features**
+**Features**
 
 * Optionally include measurements in `plot_observable_trajectories`
   by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2381

diff --git a/documentation/conf.py b/documentation/conf.py
@@ -558,15 +558,15 @@ def fix_typehints(sig: str) -> str:
     sig = sig.replace("sunindextype", "int")
     sig = sig.replace("H5::H5File", "object")
 
-    # remove const
-    sig = sig.replace(" const ", r" ")
-    sig = re.sub(r" const$", r"", sig)
+    # remove const / const&
+    sig = sig.replace(" const&? ", r" ")
+    sig = re.sub(r" const&?$", r"", sig)
 
     # remove pass by reference
     sig = re.sub(r" &(,|\))", r"\1", sig)
     sig = re.sub(r" &$", r"", sig)
 
-    # turn gsl_spans and pointers int Iterables
+    # turn gsl_spans and pointers into Iterables
     sig = re.sub(r"([\w.]+) \*", r"Iterable[\1]", sig)
     sig = re.sub(r"gsl::span< ([\w.]+) >", r"Iterable[\1]", sig)
 

diff --git a/documentation/gfx/amici_workflow.png b/documentation/gfx/amici_workflow.png