Merge branch 'develop' into test_numpy2

.git-blame-ignore-revs

@@ -0,0 +1 @@
+f59fed72eb4d0cedf6abf2a96fe95087ce61478a

.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 }}

.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 }}

.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

.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 }}

.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 }}

.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 }}

.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 }}

.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 }}

.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 }}

.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

.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:

.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 }}

.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"

.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 }}

.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)/'

CHANGELOG.md

@@ -2,6 +2,48 @@
 
 ## v0.X Series
 
+### v0.24.0 (2024-04-22)
+
+This will be the last release supporting Python 3.9.
+Future releases will require Python 3.10.
+
+**Fixes**
+
+* Fix cmake error `cannot create directory: /cmake/Amici`
+  during model import in cases where BLAS was not found via `FindBLAS`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2389
+* Added status code `AMICI_CONSTR_FAIL`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2379
+* Fixed certain initial state issues with PEtab
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2382
+* Fixed Solver `operator==` and copyctor
+  (constraints were not copied correctly)
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2388
+* Avoid confusing warnings about non-finite timepoints
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2395
+* Fixed incorrect exception types / messages for `IDASolver`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2398
+* cmake: set SUNDIALS path hint for python package to help CMake find
+  the correct SUNDIALS installation
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2397
+
+* **Features**
+
+* Optionally include measurements in `plot_observable_trajectories`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2381
+* Improved type annotations in swig-wrappers
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2401
+* Additional attributes are accessible directly via `ReturnDataView` and
+  `ExpDataView`, e.g. `ReturnDataView.ny`, `ReturnDataView.nx`
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2405
+* Allow subselection of state variables for convergence check during
+  steady-state simulations via `Model.set_steadystate_mask([1, 0, ..., 1])`
+  (positive value: check; non-positive: don't check).
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2387
+
+**Full Changelog**: https://github.com/AMICI-dev/AMICI/compare/v0.23.1...v0.24.0
+
+
 ### v0.23.1 (2024-03-11)
 
 * Fixes installation issues related to building SuiteSparse on some systems

documentation/amici_refs.bib

@@ -1275,6 +1275,37 @@ @Article{SluijsZho2024
   publisher        = {Springer Science and Business Media LLC},
 }
 
+@Article{KissVen2024,
+  author           = {Kiss, Anna E and Venkatasubramani, Anuroop V and Pathirana, Dilan and Krause, Silke and Sparr, Aline Campos and Hasenauer, Jan and Imhof, Axel and Müller, Marisa and Becker, Peter B},
+  journal          = {Nucleic Acids Research},
+  title            = {{Processivity and specificity of histone acetylation by the male-specific lethal complex}},
+  year             = {2024},
+  issn             = {0305-1048},
+  month            = {02},
+  pages            = {gkae123},
+  abstract         = {{Acetylation of lysine 16 of histone H4 (H4K16ac) stands out among the histone modifications, because it decompacts the chromatin fiber. The metazoan acetyltransferase MOF (KAT8) regulates transcription through H4K16 acetylation. Antibody-based studies had yielded inconclusive results about the selectivity of MOF to acetylate the H4 N-terminus. We used targeted mass spectrometry to examine the activity of MOF in the male-specific lethal core (4-MSL) complex on nucleosome array substrates. This complex is part of the Dosage Compensation Complex (DCC) that activates X-chromosomal genes in male Drosophila. During short reaction times, MOF acetylated H4K16 efficiently and with excellent selectivity. Upon longer incubation, the enzyme progressively acetylated lysines 12, 8 and 5, leading to a mixture of oligo-acetylated H4. Mathematical modeling suggests that MOF recognizes and acetylates H4K16 with high selectivity, but remains substrate-bound and continues to acetylate more N-terminal H4 lysines in a processive manner. The 4-MSL complex lacks non-coding roX RNA, a critical component of the DCC. Remarkably, addition of RNA to the reaction non-specifically suppressed H4 oligo-acetylation in favor of specific H4K16 acetylation. Because RNA destabilizes the MSL-nucleosome interaction in vitro we speculate that RNA accelerates enzyme-substrate turn-over in vivo, thus limiting the processivity of MOF, thereby increasing specific H4K16 acetylation.}},
+  creationdate     = {2024-02-28T18:25:06},
+  doi              = {10.1093/nar/gkae123},
+  eprint           = {https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkae123/56756494/gkae123.pdf},
+  modificationdate = {2024-02-28T18:25:06},
+  url              = {https://doi.org/10.1093/nar/gkae123},
+}
+
+@Article{DoresicGre2024,
+  author           = {Domagoj Dore{\v s}i{\'c} and Stephan Grein and Jan Hasenauer},
+  journal          = {bioRxiv},
+  title            = {Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data},
+  year             = {2024},
+  abstract         = {Quantitative dynamical models facilitate the understanding of biological processes and the prediction of their dynamics. The parameters of these models are commonly estimated from experimental data. Yet, experimental data generated from different techniques do not provide direct information about the state of the system but a non-linear (monotonic) transformation of it. For such semi-quantitative data, when this transformation is unknown, it is not apparent how the model simulations and the experimental data can be compared. Here, we propose a versatile spline-based approach for the integration of a broad spectrum of semi-quantitative data into parameter estimation. We derive analytical formulas for the gradients of the hierarchical objective function and show that this substantially increases the estimation efficiency. Subsequently, we demonstrate that the method allows for the reliable discovery of unknown measurement transformations. Furthermore, we show that this approach can significantly improve the parameter inference based on semi-quantitative data in comparison to available methods. Modelers can easily apply our method by using our implementation in the open-source Python Parameter EStimation TOolbox (pyPESTO).Competing Interest StatementThe authors have declared no competing interest.},
+  creationdate     = {2024-04-20T13:05:06},
+  doi              = {10.1101/2024.01.26.577371},
+  elocation-id     = {2024.01.26.577371},
+  eprint           = {https://www.biorxiv.org/content/early/2024/01/30/2024.01.26.577371.full.pdf},
+  modificationdate = {2024-04-20T13:05:06},
+  publisher        = {Cold Spring Harbor Laboratory},
+  url              = {https://www.biorxiv.org/content/early/2024/01/30/2024.01.26.577371},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}
 
 @Comment{jabref-meta: grouping:

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)