Merge pull request #1823 from AMICI-dev/release_0.11.30

Release 0.11.30

.coveragerc

@@ -6,6 +6,7 @@ omit =
     */amici_without_hdf5.py
     */ThirdParty/*
     *.template.*
+    /tmp/*
 parallel = true
 
 [report]

.github/workflows/deploy_branch.yml

@@ -5,7 +5,7 @@ jobs:
   sdist:
     name: Deploy Python Source Distribution
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
@@ -33,7 +33,7 @@ jobs:
         scripts/buildSdist.sh
 
     - name: "Upload artifact: sdist"
-      uses: actions/upload-artifact@v1
+      uses: actions/upload-artifact@v3
       with:
         name: sdist
-        path: python/sdist/dist
+        path: python/sdist/dist/amici-*.gz

.github/workflows/deploy_protected.yml

@@ -14,7 +14,7 @@ jobs:
     # https://github.com/marketplace/actions/publish-docker
     name: Deploy Dockerhub
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
@@ -28,7 +28,7 @@ jobs:
     - uses: actions/checkout@master
     - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
     - name: Publish to Registry
-      uses: elgohr/Publish-Docker-Github-Action@2.8
+      uses: elgohr/Publish-Docker-Github-Action@v4
       with:
         name: dweindl/amici
         username: ${{ secrets.DOCKER_USERNAME }}

.github/workflows/deploy_release.yml

@@ -8,7 +8,7 @@ jobs:
   pypi:
     name: Deploy PyPI
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
@@ -45,7 +45,7 @@ jobs:
   bioSimulatorsUpdateCliAndDockerImage:
     name: Release to BioSimulators
     needs: pypi
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     env:
       # Owner/repository-id for the GitHub repository for the downstream command-line interface and Docker image
       DOWNSTREAM_REPOSITORY: biosimulators/Biosimulators_AMICI

.github/workflows/test_benchmark_collection_models.yml

@@ -17,7 +17,7 @@ jobs:
   build:
     name: Benchmark Collection
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:

.github/workflows/test_doc.yml

@@ -16,7 +16,7 @@ jobs:
   doxygen:
     name: Test Doxygen
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
@@ -51,7 +51,7 @@ jobs:
   sphinx:
     name: Test Sphinx
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:

.github/workflows/test_install.yml

@@ -5,7 +5,7 @@ jobs:
   archive:
     name: Archive Install
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
@@ -53,7 +53,7 @@ jobs:
   sdist:
     name: sdist Install
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:

.github/workflows/test_performance.yml

@@ -19,7 +19,7 @@ jobs:
   build:
     name: Performance Test
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
@@ -66,7 +66,7 @@ jobs:
         AMICI_IMPORT_NPROCS=2 check_time.sh petab_import python tests/performance/test.py import
 
     - name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
-      uses: actions/upload-artifact@v1
+      uses: actions/upload-artifact@v3
       with:
         name: CS_Signalling_ERBB_RAS_AKT
         path: CS_Signalling_ERBB_RAS_AKT/CS_Signalling_ERBB_RAS_AKT_petab

.github/workflows/test_petab_test_suite.yml

@@ -16,7 +16,7 @@ jobs:
   build:
     name: PEtab Testsuite
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     env:
       ENABLE_GCOV_COVERAGE: TRUE

.github/workflows/test_pypi.yml

@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [3.8, 3.9, '3.10']
-        os: [ubuntu-20.04, macos-latest]
+        os: [ubuntu-22.04, macos-latest]
 
     runs-on: ${{ matrix.os }}
 

.github/workflows/test_python_cplusplus.yml

@@ -6,7 +6,7 @@ jobs:
     name: Tests Ubuntu
 
     # TODO: prepare image with more deps preinstalled
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     env:
       ENABLE_GCOV_COVERAGE: "TRUE"
@@ -87,7 +87,7 @@ jobs:
     - name: Python tests
       run: |
         source build/venv/bin/activate \
-        && pip3 install coverage pytest pytest-cov \
+        && pip3 install coverage pytest pytest-cov pytest-rerunfailures \
         && pytest \
           --ignore-glob=*petab* \
           --cov=amici \

.github/workflows/test_python_ver_matrix.yml

@@ -14,7 +14,7 @@ jobs:
   build:
     name: Python Version Matrix
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     continue-on-error: ${{ matrix.experimental }}
     env:
       AMICI_SKIP_CMAKE_TESTS: "TRUE"

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -21,7 +21,7 @@ on:
 jobs:
   build:
     name: SBML Semantic Test Suite
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       fail-fast: false
@@ -47,7 +47,7 @@ jobs:
     - run: AMICI_PARALLEL_COMPILE=2 ./scripts/run-SBMLTestsuite.sh ${{ matrix.cases }}
 
     - name: "Upload artifact: SBML semantic test suite results"
-      uses: actions/upload-artifact@v1
+      uses: actions/upload-artifact@v3
       with:
         name: amici-semantic-results
         path: tests/amici-semantic-results

.github/workflows/test_valgrind.yml

@@ -14,7 +14,7 @@ jobs:
     name: Tests Valgrind
 
     # TODO: prepare image with more deps preinstalled
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:

CHANGELOG.md

@@ -2,6 +2,44 @@
 
 ## v0.X Series
 
+### v0.11.30 (2022-07-07)
+
+Features:
+* Allow overriding model name during PySB import by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1801
+* Added __repr__ for parameter mapping classes by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1799
+* More informative warning messages for NaNs/Infs by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1798
+* Moved `sim_steps` increment by @plakrisenko in
+  https://github.com/AMICI-dev/AMICI/pull/1806
+* Re-arranged application of parameters from `ExpData` to avoid initial
+  sensitivities error by @dilpath in
+  https://github.com/AMICI-dev/AMICI/pull/1805
+* Checking for unused parameters in `simulate_petab` by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1816
+* Add `create_parameter_mapping` kwarg forwarding by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1820
+
+Other
+* Remove `constant_species_to_parameters` by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1809
+
+Fixes
+* Fixed handling of SBML models given as `pathlib.Path` in
+  `petab_import.import_model_sbml by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1808
+* Fixed missing CPU time reset by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1814
+* Raise in `simulate_petab` with `scaled_parameters=True`
+  `problem_parameters=None` by @dweindl in
+  https://github.com/AMICI-dev/AMICI/pull/1819
+
+...
+
+**Full Changelog**:
+https://github.com/AMICI-dev/AMICI/compare/v0.11.29...v0.11.30
+
 ### v0.11.29 (2022-05-06)
 
 ## What's Changed

documentation/amici_refs.bib

@@ -1025,6 +1025,20 @@ @article {Froehlich2022.02.17.480899
 	journal = {bioRxiv}
 }
 
+@Article{SluijsMaa2022,
+  author   = {van Sluijs, Bob and Maas, Roel J. M. and van der Linden, Ardjan J. and de Greef, Tom F. A. and Huck, Wilhelm T. S.},
+  journal  = {Nature Communications},
+  title    = {A microfluidic optimal experimental design platform for forward design of cell-free genetic networks},
+  year     = {2022},
+  issn     = {2041-1723},
+  number   = {1},
+  pages    = {3626},
+  volume   = {13},
+  abstract = {Cell-free protein synthesis has been widely used as a “breadboard” for design of synthetic genetic networks. However, due to a severe lack of modularity, forward engineering of genetic networks remains challenging. Here, we demonstrate how a combination of optimal experimental design and microfluidics allows us to devise dynamic cell-free gene expression experiments providing maximum information content for subsequent non-linear model identification. Importantly, we reveal that applying this methodology to a library of genetic circuits, that share common elements, further increases the information content of the data resulting in higher accuracy of model parameters. To show modularity of model parameters, we design a pulse decoder and bistable switch, and predict their behaviour both qualitatively and quantitatively. Finally, we update the parameter database and indicate that network topology affects parameter estimation accuracy. Utilizing our methodology provides us with more accurate model parameters, a necessity for forward engineering of complex genetic networks.},
+  doi      = {10.1038/s41467-022-31306-3},
+  refid    = {van Sluijs2022},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}
 
 @Comment{jabref-meta: grouping:

documentation/conf.py

@@ -236,7 +236,10 @@ def install_doxygen():
 
 intersphinx_mapping = {
     'pysb': ('https://pysb.readthedocs.io/en/stable/', None),
-    'petab': ('https://petab.readthedocs.io/en/stable/', None),
+    'petab': (
+        'https://petab.readthedocs.io/projects/libpetab-python/en/latest/',
+        None
+    ),
     'pandas': ('https://pandas.pydata.org/docs/', None),
     'numpy': ('https://numpy.org/devdocs/', None),
     'sympy': ('https://docs.sympy.org/latest/', None),

documentation/references.md

@@ -1,6 +1,6 @@
 # References
 
-List of publications using AMICI. Total number is 66.
+List of publications using AMICI. Total number is 67.
 
 If you applied AMICI in your work and your publication is missing, please let us know via a new Github issue.
 
@@ -12,6 +12,9 @@ If you applied AMICI in your work and your publication is missing, please let us
 <div id="ref-SchmuckerFar2022">
 <p>Schmucker, Robin, Gabriele Farina, James Faeder, Fabian Fröhlich, Ali Sinan Saglam, and Tuomas Sandholm. 2022. “Combination Treatment Optimization Using a Pan-Cancer Pathway Model.” <em>PLOS Computational Biology</em> 17 (12): 1–22. <a href="https://doi.org/10.1371/journal.pcbi.1009689">https://doi.org/10.1371/journal.pcbi.1009689</a>.</p>
 </div>
+<div id="ref-SluijsMaa2022">
+<p>Sluijs, Bob van, Roel J. M. Maas, Ardjan J. van der Linden, Tom F. A. de Greef, and Wilhelm T. S. Huck. 2022. “A Microfluidic Optimal Experimental Design Platform for Forward Design of Cell-Free Genetic Networks.” <em>Nature Communications</em> 13 (1): 3626. <a href="https://doi.org/10.1038/s41467-022-31306-3">https://doi.org/10.1038/s41467-022-31306-3</a>.</p>
+</div>
 <div id="ref-StaporSch2022">
 <p>Stapor, Paul, Leonard Schmiester, Christoph Wierling, Simon Merkt, Dilan Pathirana, Bodo M. H. Lange, Daniel Weindl, and Jan Hasenauer. 2022. “Mini-batch optimization enables training of ODE models on large-scale datasets.” <em>Nature Communications</em> 13 (1): 34. <a href="https://doi.org/10.1038/s41467-021-27374-6">https://doi.org/10.1038/s41467-021-27374-6</a>.</p>
 </div>

include/amici/amici.h

@@ -96,16 +96,6 @@ class AmiciApplication {
      * @param ... arguments to be formatted
      */
     void errorF(const char *identifier, const char *format, ...) const;
-
-    /**
-     * @brief Checks the values in an array for NaNs and Infs
-     *
-     * @param array array
-     * @param fun name of calling function
-     * @return AMICI_RECOVERABLE_ERROR if a NaN/Inf value was found,
-     * AMICI_SUCCESS otherwise
-     */
-    int checkFinite(gsl::span<const realtype> array, const char *fun);
 };
 
 /**

include/amici/model.h

@@ -65,6 +65,28 @@ enum class ModelQuantity {
     qBdot_ss,
     xBdot_ss,
     JSparseB_ss,
+    deltax,
+    deltasx,
+    deltaxB,
+    k,
+    p,
+    ts,
+    dJydy,
+    dJydy_matlab,
+    deltaqB,
+    dsigmaydp,
+    dsigmaydy,
+    dJydsigma,
+    dJydx,
+    dzdx,
+    dzdp,
+    dJrzdsigma,
+    dJrzdz,
+    dJzdsigma,
+    dJzdz,
+    drzdp,
+    drzdx,
+    dsigmazdp,
 };
 
 extern const std::map<ModelQuantity, std::string> model_quantity_to_str;
@@ -1869,7 +1891,7 @@ class Model : public AbstractModel, public ModelDimensions {
     /** vector of bools indicating whether state variables are to be assumed to
      * be positive */
     std::vector<bool> state_is_non_negative_;
-    
+
     /** Vector of booleans indicating the initial boolean value for every event trigger function. Events at t0
      * can only trigger if the initial value is set to `false`. Must be specified during model compilation by
      * setting the `initialValue` attribute of an event trigger. */