Specify visualization dependencies (#2070)

* Specify visualization dependencies

So far, matplotlib was implicitly required through petab. In petab==0.2.0, matplotlib became an optional dependency.

* ..

Author: dweindl

.github/workflows/test_benchmark_collection_models.yml

@@ -51,8 +51,9 @@ jobs:
         pip3 install build && cd python/sdist && python3 -m build --sdist
     - name: Install AMICI sdist
       run: |
+        pip3 install --user petab[vis] && \
         AMICI_PARALLEL_COMPILE=2 pip3 install -v --user \
-            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test]
+            $(ls -t python/sdist/dist/amici-*.tar.gz | head -1)[petab,test,vis]
 
     # retrieve test models
     - name: Download and test benchmark collection

documentation/rtd_requirements.txt

@@ -9,7 +9,7 @@ nbsphinx>=0.8.9
 nbformat==5.4.0
 recommonmark>=0.6.0
 sphinx_rtd_theme>=1.0.0
-petab>=0.1.20
+petab[vis]>=0.1.20
 sphinx-autodoc-typehints==1.19.2
 git+https://github.com/readthedocs/sphinx-hoverxref@main
 ipython==8.10.0

python/sdist/setup.cfg

@@ -52,6 +52,7 @@ test =
     pytest-rerunfailures
     coverage
     shyaml
+vis = matplotlib
 
 [options.package_data]
 amici =