Merge branch 'develop' into adjoint_event

.github/actions/install-macos-dependencies/action.yml

@@ -0,0 +1,31 @@
+name: Install AMICI dependencies for MacOS
+description: Install AMICI dependencies for MacOS
+
+runs:
+  using: "composite"
+  steps:
+    # use all available cores
+    - run: echo "AMICI_PARALLEL_COMPILE=" >> $GITHUB_ENV
+      shell: bash
+
+    # AMICI repository root
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+      shell: bash
+
+    # BioNetGen path
+    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
+      shell: bash
+
+    # CMake hints
+    # Ensure CMake is using the python version that we will use for the python tests later on
+    - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
+      shell: bash
+
+    # install amici dependencies
+    - name: homebrew
+      run: brew install hdf5 swig gcc libomp boost
+      shell: bash

.github/workflows/deploy_release.yml

@@ -29,6 +29,11 @@ jobs:
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
 
+    - 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
+
     - name: sdist
       run: scripts/buildSdist.sh
 

.github/workflows/test_doc.yml

@@ -43,7 +43,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: [ "3.10" ]
+        python-version: [ "3.11" ]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}

.github/workflows/test_matlab.yml

@@ -1,5 +1,12 @@
 name: Matlab
-on: [push, merge_group, workflow_dispatch]
+on:
+  push:
+  merge_group:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - master
+
 
 jobs:
   matlab:

.github/workflows/test_petab_test_suite.yml

@@ -72,7 +72,7 @@ jobs:
         run: |
           source ./build/venv/bin/activate \
             && pytest --cov-report=xml:coverage.xml \
-              --cov=./ python/tests/test_*petab*.py
+              --cov=./ python/tests/test_*petab*.py python/tests/petab/
 
       # run test models
       - name: Run PEtab test suite

.github/workflows/test_pypi.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         os: [ubuntu-22.04, macos-latest]
 
     runs-on: ${{ matrix.os }}

.github/workflows/test_python_cplusplus.yml

@@ -218,8 +218,8 @@ jobs:
 
     # TODO: Include notebooks in coverage report
 
-  osx:
-    name: Tests OSX
+  macos_cpp_py:
+    name: Tests MacOS C++/Python
     runs-on: macos-latest
 
     steps:
@@ -231,16 +231,11 @@ jobs:
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
-    # Ensure CMake is using the python version that we will use for the python tests later on
-    - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
-    - run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
-    - run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
+    - name: Install dependencies
+      uses: ./.github/actions/install-macos-dependencies
 
-    # install amici dependencies
     - name: homebrew
-      run: brew install hdf5 swig gcc cppcheck libomp boost
+      run: brew install cppcheck
 
     - name: Build AMICI
       run: scripts/buildAll.sh
@@ -254,8 +249,47 @@ jobs:
     - name: cppcheck
       run: scripts/run-cppcheck.sh
 
-    - name: Python tests
-      run: scripts/run-python-tests.sh
-
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
+
+    - name: Python tests
+      run: |
+        scripts/run-python-tests.sh \
+          test_pregenerated_models.py \
+          test_splines_short.py \
+          test_misc.py
+
+
+  macos_python:
+    name: Tests MacOS Python
+    runs-on: macos-latest
+
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - uses: actions/checkout@v3
+    - run: git fetch --prune --unshallow
+
+    - name: Install dependencies
+      uses: ./.github/actions/install-macos-dependencies
+
+    - name: Install python package
+      run: |
+        pip show numpy > /dev/null || python3 -m pip install numpy
+        scripts/installAmiciSource.sh
+
+    - name: Check OpenMP support
+      run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+
+    - name: Get BioNetGen
+      run: scripts/buildBNGL.sh
+
+    - name: Python tests
+      run: |
+        scripts/run-python-tests.sh \
+          --ignore=test_pregenerated_models.py \
+          --ignore=test_splines_short.py \
+          --ignore=test_misc.py

.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']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
         experimental: [false]
 
     steps:
@@ -44,15 +44,27 @@ jobs:
     - name: Install apt dependencies
       uses: ./.github/actions/install-apt-dependencies
 
-    # install AMICI
     - name: Build BNGL
       run: scripts/buildBNGL.sh
+
     - name: Install python package
       run: scripts/installAmiciSource.sh
 
+    # until https://github.com/dateutil/dateutil >2.8.2 is released https://github.com/dateutil/dateutil/issues/1314
+    - run: source build/venv/bin/activate && pip3 install git+https://github.com/dateutil/dateutil.git@296d419fe6bf3b22897f8f210735ac9c4e1cb796
+      if: matrix.python-version == '3.12'
+
+    # install pysb before sympy to allow for sympy>=1.12 (https://github.com/pysb/pysb/commit/e83937cb8c74afc9b2fa96595b68464946745f33)
+    - run: source build/venv/bin/activate && pip3 install git+https://github.com/pysb/pysb
+
+    # until sympy>1.12 is released
+    - run: source build/venv/bin/activate && pip3 install git+https://github.com/sympy/sympy.git@master
+      if: matrix.python-version == '3.12'
+
     - name: Python tests
       run: |
         source build/venv/bin/activate \
-          && pip3 install git+https://github.com/pysb/pysb \
-          && python3 -m pytest --ignore-glob=*petab* \
+          && python3 -m pytest \
+            --durations=10 \
+            --ignore-glob=*petab* \
             --ignore-glob=*test_splines.py ${AMICI_DIR}/python/tests

.pre-commit-config.yaml

@@ -1,12 +1,6 @@
 # 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", "--line-length", "79"]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
@@ -16,15 +10,28 @@ repos:
     args: [--allow-multiple-documents]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/psf/black
-  rev: 23.7.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.11
   hooks:
-    - id: black-jupyter
-      # 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
-      args: ["--line-length", "79"]
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+        - --config
+        - python/sdist/pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - python/sdist/pyproject.toml
+
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+    -   id: pyupgrade
+        args: ["--py39-plus"]
+        additional_dependencies: [pyupgrade==3.15.0]
 
 exclude: '^(ThirdParty|models)/'

.readthedocs.yml

@@ -24,4 +24,4 @@ build:
     - libatlas-base-dev
     - swig
   tools:
-    python: "3.9"
+    python: "3.11"

CHANGELOG.md

@@ -2,11 +2,97 @@
 
 ## v0.X Series
 
+### v0.21.1 (2024-01-17)
+
+Fixed package configuration for PyPI upload. No further changes.
+
+### v0.21.0 (2024-01-16)
+
+**Deprecations**
+
+* Moved PEtab-related functionality from `amici.petab_*` to the
+  petab-subpackage `amici.petab.*`. The old public functions are still
+  available but will be removed in a future release.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2205,
+  https://github.com/AMICI-dev/AMICI/pull/2211,
+  https://github.com/AMICI-dev/AMICI/pull/2252
+
+**Features**
+
+* Handle events occurring at fixed timepoints without root-finding.
+  This avoids event-after-reinitialization errors in many cases a brings a
+  slight performance improvement.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2227
+* Added `PetabProblem` class for handling PEtab-defined simulation conditions,
+  making it easier to perform customized operations based on PEtab-defined
+  simulation conditions.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2255
+* code-gen: Simplified `switch` statements, leading to reduced file sizes and
+  faster compilation for certain models.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2240
+* Made `Model` and `ModelPtr` deepcopyable
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2247
+* Made `Solver` and `SolverPtr` deepcopyable
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2245
+* Added a debugging helper `get_model_for_preeq` for debugging simulation
+  issues during pre-equilibration.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2250
+* Added `SwigPtrView` fields to `dir()` outputs
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2244
+* Use proper labels for in plotting functions if IDs are available in
+  `ReturnData`.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2249
+* Added `ExpData::clear_observations` to set all measurements/sigmas to NaN
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2258
+
+**Fixes**
+
+* Fixed AMICI hiding all warnings. Previously, importing `amici` resulted
+  in all warnings being hidden in the rest of the program.
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2243
+* CMake: Fixed model debug builds
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2222
+* Fixed CMake potentially using incorrect Python library for building model
+  extension
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2220
+* CMake: fixed cxx flag check
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2225
+* Fixed potential out-of-bounds read in `Model::checkFinite` for
+  matlab-imported models
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2232
+* Fixed piecewise/Heaviside handling
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2234
+* Deterministic order of event assignments
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2242
+* Proper error message in case of unsupported state-dependent sigmas
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2239
+* Fixed swig shadow warning + other linting issues
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2261
+* Fixed `SwigPtrView.__getattr__`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2259
+* `simulate_petab`: Avoid warning when simulating with default parameters
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2265
+
+**Documentation**
+
+* Updated Python package installation instructions for Arch Linux
+  by @willov in https://github.com/AMICI-dev/AMICI/pull/2212
+* Updated `ExpData` documentation
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2254
+* Documented simulation starting time `t0`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2263
+* Updated PEtab example
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2255
+
+...
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.20.0...v0.21.0
+
 ### v0.20.0 (2023-11-23)
 
 **Fixes**
 
-* Fixed CMake cmake_minimum_required deprecation warning
+* Fixed CMake `cmake_minimum_required` deprecation warning
   by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2183
 * Fixed misleading preequilibration failure messages
   by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2181