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Merge pull request #2433 from dweindl/release_0.25.0
Release 0.25.0
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‎.git-blame-ignore-revs

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f59fed72eb4d0cedf6abf2a96fe95087ce61478a

‎.github/dependabot.yml

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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"
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ignore:
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- dependency-name: "*"
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update-types: ["version-update:semver-patch", "version-update:semver-minor"]

‎.github/workflows/deploy_branch.yml

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strategy:
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matrix:
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python-version: ["3.11"]
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steps:
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- name: Set up Python ${{ matrix.python-version }}

‎.github/workflows/deploy_protected.yml

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

‎.github/workflows/deploy_release.yml

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strategy:
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matrix:
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environment:
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name: pypi
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- name: Remove direct dependencies from setup.cfg
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# Remove any "git+https"-based dependencies that are not supported
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# by PyPI and are only required for testing.
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run: sed -i '/git+https/d' python/sdist/setup.cfg
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run: sed -i '/git+https/d' python/sdist/pyproject.toml
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- name: sdist
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run: scripts/buildSdist.sh
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-H "Accept: application/vnd.github.v3+json" \
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https://api.github.com/repos/${DOWNSTREAM_REPOSITORY}/actions/workflows/${WORKFLOW_FILE}/dispatches \
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-d "{\"ref\": \"dev\", \"inputs\": {\"simulatorVersion\": \"${PACKAGE_VERSION}\", \"simulatorVersionLatest\": \"true\"}}"
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dockerhub:
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name: Release to Docker Hub
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runs-on: ubuntu-22.04
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steps:
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- uses: actions/checkout@v4
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- run: git archive -o container/amici.tar.gz --format=tar.gz HEAD
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v3
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Publish to Registry
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uses: elgohr/Publish-Docker-Github-Action@v5
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with:
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name: dweindl/amici
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username: ${{ secrets.DOCKER_USERNAME }}
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password: ${{ secrets.DOCKER_PASSWORD }}
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workdir: container/
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dockerfile: Dockerfile
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tag_semver: true
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platforms: linux/amd64,linux/arm64

‎.github/workflows/test_benchmark_collection_models.yml

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fail-fast: false
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matrix:
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python-version: [ "3.9" ]
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python-version: [ "3.11" ]
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extract_subexpressions: ["true", "false"]
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env:
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AMICI_EXTRACT_CSE: ${{ matrix.extract_subexpressions }}

‎.github/workflows/test_doc.yml

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- name: Set up Python ${{ matrix.python-version }}

‎.github/workflows/test_install.yml

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‎.github/workflows/test_performance.yml

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‎.github/workflows/test_petab_test_suite.yml

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‎.github/workflows/test_pypi.yml

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python-version: ["3.9", "3.10", "3.11", "3.12"]
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python-version: ["3.10", "3.11", "3.12"]
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‎.github/workflows/test_python_cplusplus.yml

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‎.github/workflows/test_python_ver_matrix.yml

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python-version: ['3.10', '3.11', '3.12']
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‎.github/workflows/test_sbml_semantic_test_suite.yml

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‎.github/workflows/test_valgrind.yml

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‎.github/workflows/test_windows.yml

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‎.pre-commit-config.yaml

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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.6.0
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- id: check-added-large-files
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- id: check-merge-conflict
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- id: trailing-whitespace
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.4.1
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- python/sdist/pyproject.toml
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rev: v3.15.2
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‎CHANGELOG.md

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## v0.X Series
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### v0.25.0 (2024-05-TBD)
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This release requires Python >= 3.10.
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**Fixes**
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* Fixed a bug in event handling that could lead to incorrect simulation
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results for models with events that assign to compartments *and* have
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additional event assignments
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2428
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* SBML import: handle `useValuesFromTriggerTime` attribute on events.
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This attribute was previously ignored. It is possible that now AMICI fails
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to import models that it previously imported successfully. For cases where
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`useValuesFromTriggerTime=True` made a difference, AMICI might have produced
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incorrect results before.
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2429
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* Faster code generation for models with events if they don't have
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state-dependent triggers
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2417
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* Most warnings now come with a more informative code location
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2421
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* `amici.ExpData` was changed so that `isinstance(edata, amici.ExpData)` works
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2396
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**Features**
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* Event-assignments to compartments are now supported. Previously, this only
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worked for compartments that were rate rule targets.
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2425
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* Releases are now deployed to Docker Hub
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by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2413
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**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.24.0...v0.25.0
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### v0.24.0 (2024-04-22)
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This will be the last release supporting Python 3.9.
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Future releases will require Python 3.10.
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Future releases will require Python>=3.10.
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* **Features**
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**Features**
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* Optionally include measurements in `plot_observable_trajectories`
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‎documentation/conf.py

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sig = sig.replace(" const ", r" ")
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sig = re.sub(r" const$", r"", sig)
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# remove const / const&
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sig = sig.replace(" const&? ", r" ")
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sig = re.sub(r" const&?$", r"", sig)
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sig = re.sub(r" &(,|\))", r"\1", sig)
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sig = re.sub(r" &$", r"", sig)
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# turn gsl_spans and pointers into Iterables
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sig = re.sub(r"([\w.]+) \*", r"Iterable[\1]", sig)
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sig = re.sub(r"gsl::span< ([\w.]+) >", r"Iterable[\1]", sig)
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‎documentation/gfx/amici_workflow.png

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