Release 0.14.0 (#1898)

* Fix pandas groupby deprecation warning (#1873) Fixes #1872 * Update reference list (#1874) * Code printing: Use SymPy C99 math optimizations (#1377) for SBML import. Does not currently work with PySB import. Also fixes some argument type issues. Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> * PEtab import: Add option for treating fixed parameters as constants (#1877) Makes the changes from #1810 optional, as sometimes users prefer more flexible models. The default remains to treat non-estimated parameters in PEtab as constants in AMICI. Also adds a basic check for loading existing models during PEtab, to see if they are compatible to what was supposed to be imported. Only checks non-constant parameter IDs so far. * Make sympy code optimizations optional (#1878) Turns out that applying sympy optimizations as introduced in #1377 is potentially very costly. Therefore, they are disabled by default. They can be enabled by setting `AmiciCxxCodePrinter.optimizations` as shown in the test case. * Update reference list (#1884) * GHA: update actions (#1885) Fixes some GHA warnings. * Add macos hdf5 header/library paths (#1894) * Doxygen 1.9.5 on RTD (#1889) Older binaries are no longer available. * Code-gen: Fix missing `return` in non-void-returning functions (#1892) ... and set `-Werror` for compiling models in debug mode. * Add operator== for ExpData (#1881) Adds `operator==` for `amici::ExpData` and fixes issues for other `operator==` in case of NaNs in arrays. Closes #1880 * Fix SetuptoolsDeprecationWarning (#1893) Setuptools meanwhile requires listing data directories as subpackages. Fixes #1888. * Dockerfile: Update base image to Ubuntu 22.04 (#1896) * GHA: Pin python version for osx tests (#1891) Fixes #1890. Also: * use homebrew boost version * fix CMake logic for selecting a specific Python version. * Fix `petab_import.import_model(..., compile=False)` failure (#1897) Fixes a bug where amici would fail importing an extension that was never built. * bump version, update changelog * fix changelog * -Wno-error=deprecated-declarations Co-authored-by: Daniel Weindl <dweindl@users.noreply.github.com> Co-authored-by: Lorenzo Contento <lcontento@users.noreply.github.com> Co-authored-by: Daniel Weindl <daniel.weindl@helmholtz-muenchen.de> Co-authored-by: Doresic <85789271+Doresic@users.noreply.github.com>
AMICI-dev · Nov 23, 2022 · b5177d9 · b5177d9
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diff --git a/.github/workflows/deploy_branch.yml b/.github/workflows/deploy_branch.yml
@@ -13,11 +13,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 20
 

diff --git a/.github/workflows/deploy_protected.yml b/.github/workflows/deploy_protected.yml
@@ -22,10 +22,10 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
     - run: git archive -o docker/amici.tar.gz --format=tar.gz HEAD
     - name: Publish to Registry
       uses: elgohr/Publish-Docker-Github-Action@v4

diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
@@ -16,11 +16,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 20
 

diff --git a/.github/workflows/test_benchmark_collection_models.yml b/.github/workflows/test_benchmark_collection_models.yml
@@ -29,11 +29,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 20
 

diff --git a/.github/workflows/test_doc.yml b/.github/workflows/test_doc.yml
@@ -24,11 +24,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
     - name: apt
@@ -59,11 +59,11 @@ jobs:
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v3
       - run: git fetch --prune --unshallow
 
       - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

diff --git a/.github/workflows/test_install.yml b/.github/workflows/test_install.yml
@@ -13,11 +13,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -61,11 +61,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

diff --git a/.github/workflows/test_matlab.yml b/.github/workflows/test_matlab.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV

diff --git a/.github/workflows/test_performance.yml b/.github/workflows/test_performance.yml
@@ -27,11 +27,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 20
 

diff --git a/.github/workflows/test_petab_test_suite.yml b/.github/workflows/test_petab_test_suite.yml
@@ -27,11 +27,11 @@ jobs:
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 20
 

diff --git a/.github/workflows/test_pypi.yml b/.github/workflows/test_pypi.yml
@@ -36,7 +36,7 @@ jobs:
           fi
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 

diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
@@ -18,11 +18,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -143,20 +143,27 @@ jobs:
     runs-on: macos-latest
 
     steps:
-    - uses: actions/checkout@master
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.8
+
+    - 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
 
     # install amici dependencies
     - name: homebrew
       run: |
         brew install hdf5 swig gcc cppcheck libomp boost \
           && brew ls -v boost \
           && brew ls -v libomp \
-          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.78.0_1/lib/" >> $GITHUB_ENV \
-          && echo CPPFLAGS="-I/usr/local/Cellar/boost/1.78.0_1/include/" >> $GITHUB_ENV
+          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.80.0/lib/" >> $GITHUB_ENV \
+          && echo CPPFLAGS="-I/usr/local/Cellar/boost/1.80.0/include/" >> $GITHUB_ENV
 
     - name: Build AMICI
       run: |

diff --git a/.github/workflows/test_python_ver_matrix.yml b/.github/workflows/test_python_ver_matrix.yml
@@ -32,11 +32,11 @@ jobs:
     - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 20
 

diff --git a/.github/workflows/test_sbml_semantic_test_suite.yml b/.github/workflows/test_sbml_semantic_test_suite.yml
@@ -32,11 +32,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 1
     - name: apt

diff --git a/.github/workflows/test_valgrind.yml b/.github/workflows/test_valgrind.yml
@@ -27,11 +27,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
     # install amici dependencies
@@ -71,11 +71,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
     # install amici dependencies

diff --git a/.github/workflows/test_windows.yml b/.github/workflows/test_windows.yml
@@ -23,11 +23,11 @@ jobs:
 
     steps:
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
     - shell: bash

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,54 @@
 
 ## v0.X Series
 
+### v0.14.0 (2022-11-23)
+
+#### Features:
+
+* Added optional functionality to apply C99 math optimization to generated C++ code
+  by @dweindl and @lcontento in https://github.com/AMICI-dev/AMICI/pull/1377, https://github.com/AMICI-dev/AMICI/pull/1878
+
+* Added option to treat fixed parameters as constants in PEtab import
+
+  by @dweindl in  https://github.com/AMICI-dev/AMICI/pull/1877
+
+* Added equality operator for ExpData
+
+  by @dweindl in  https://github.com/AMICI-dev/AMICI/pull/1881
+
+* Updated base image for Dockerfile to Ubuntu 22.04/Python 3.10
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1896
+
+
+#### Fixes:
+
+* Fixed deprecation warnings
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1873, https://github.com/AMICI-dev/AMICI/pull/1893
+
+* Fixes/updates to GitHub actions
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1885, https://github.com/AMICI-dev/AMICI/pull/1893, https://github.com/AMICI-dev/AMICI/pull/1889, https://github.com/AMICI-dev/AMICI/pull/1891
+
+* Added hdf5 search directories for arm64 architecture (M1/M2 macs)
+
+  by @Doresic in https://github.com/AMICI-dev/AMICI/pull/1894
+
+* Fixed missing return in generated non-void functions
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1892
+
+* Fixed import failure for pre-compiled models
+
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1897
+
+#### Documentation:
+
+* Update reference list 
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1874, https://github.com/AMICI-dev/AMICI/pull/1884
+
+**Full Changelog**:
+https://github.com/AMICI-dev/AMICI/compare/v0.13.0...v0.14.0
+
 ### v0.13.0 (2022-10-04)
 
 * Fixed extraction of common subexpressions
@@ -314,7 +362,7 @@ Fixes:
   @PaulJonasJost in https://github.com/AMICI-dev/AMICI/pull/1620
 * Fixed wrong array size in warnings by @dweindl in
   https://github.com/AMICI-dev/AMICI/pull/1624
- 
+
 NOTE: AMICI 0.11.23 requires numpy<1.22.0 
 
 **Full Changelog**:
@@ -918,7 +966,7 @@ Misc:
 
 * Simplify/fix AMICI installation
    * If available use environment modules to detect dependencies
- 
+
   * Add SWIG installation script
 
 * Update list of publication
@@ -949,7 +997,7 @@ Detaills:
     * Improve finding swig executable and allow user override via SWIG environment variable
     * Provide installation hints if no SWIG found (Closes #724)
     * Allow overriding cmake executable with environment variables in build scripts (Closes #738)
- 
+
 
 ### v0.10.9 (2019-07-24)
 

diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
 RUN apt update \
     && apt-get install -y \

diff --git a/documentation/amici_refs.bib b/documentation/amici_refs.bib
@@ -1052,6 +1052,29 @@ @Article{LakrisenkoSta2022
   url          = {https://www.biorxiv.org/content/early/2022/08/11/2022.08.08.503176},
 }
 
+@Article{VillaverdeRai2022,
+  author  = {Villaverde, Alejandro F. and Raimúndez, Elba and Hasenauer, Jan and Banga, Julio R.},
+  journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
+  title   = {Assessment of Prediction Uncertainty Quantification Methods in Systems Biology},
+  year    = {2022},
+  pages   = {1-12},
+  doi     = {10.1109/TCBB.2022.3213914},
+}
+
+@Article{MishraWan2023,
+  author   = {Shekhar Mishra and Ziyu Wang and Michael J. Volk and Huimin Zhao},
+  journal  = {Metabolic Engineering},
+  title    = {Design and application of a kinetic model of lipid metabolism in Saccharomyces cerevisiae},
+  year     = {2023},
+  issn     = {1096-7176},
+  pages    = {12-18},
+  volume   = {75},
+  abstract = {Lipid biosynthesis plays a vital role in living cells and has been increasingly engineered to overproduce various lipid-based chemicals. However, owing to the tightly constrained and interconnected nature of lipid biosynthesis, both understanding and engineering of lipid metabolism remain challenging, even with the help of mathematical models. Here we report the development of a kinetic metabolic model of lipid metabolism in Saccharomyces cerevisiae that integrates fatty acid biosynthesis, glycerophospholipid metabolism, sphingolipid metabolism, storage lipids, lumped sterol synthesis, and the synthesis and transport of relevant target-chemicals, such as fatty acids and fatty alcohols. The model was trained on lipidomic data of a reference S. cerevisiae strain, single knockout mutants, and lipid overproduction strains reported in literature. The model was used to design mutants for fatty alcohol overproduction and the lipidomic analysis of the resultant mutant strains coupled with model-guided hypothesis led to discovery of a futile cycle in the triacylglycerol biosynthesis pathway. In addition, the model was used to explain successful and unsuccessful mutant designs in metabolic engineering literature. Thus, this kinetic model of lipid metabolism can not only enable the discovery of new phenomenon in lipid metabolism but also the engineering of mutant strains for overproduction of lipids.},
+  doi      = {https://doi.org/10.1016/j.ymben.2022.11.003},
+  keywords = {Lipid metabolism, Kinetic model, Free fatty acid, Fatty alcohol},
+  url      = {https://www.sciencedirect.com/science/article/pii/S1096717622001380},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}
 
 @Comment{jabref-meta: grouping:

diff --git a/documentation/conf.py b/documentation/conf.py
@@ -123,7 +123,7 @@ def install_amici_deps_rtd():
 
 def install_doxygen():
     """Get a more recent doxygen"""
-    version = '1.9.3'
+    version = '1.9.5'
     doxygen_exe = os.path.join(amici_dir, 'ThirdParty',
                                f'doxygen-{version}', 'bin', 'doxygen')
     # to create a symlink to doxygen in a location that is already on PATH