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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Lorenzo Contento <[email protected]>
Co-authored-by: Daniel Weindl <[email protected]>
Co-authored-by: Doresic <[email protected]>

Author: 4 people

.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
 

.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

.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
 

.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
 

.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

.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

.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

.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
 

.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
 

.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 }}