Amici workshop notebook (#1026)

* Added notebook for workshop

* Removed unnecessary import

* updated workshop nb

* updated nb

* print to display

* small changes

* removed amici_import.ipynb

* small fix

* removed amici_import notebook and replaced it with Amici_workshop_2023 notebook.

* changed name of the yaml file.

* changed number of starts

* ran notebook

* less sampling

* increase time for notebook.

* Update Amici_workshop_2023.ipynb

* Update Amici_workshop_2023.ipynb

* small text changes

* small text changes

* renamed file

* tidy up names in refs

* add link to nb

* faster profiles in amici notebook.

* fewer number of starts in amici notebook

* boehm model typo for loading

* boehm model typo

* speed up store nb

* update to codecov action v3 due to deprecation

* fix sphinx, rtd theme deps; add timings to amici.ipynb

---------

Co-authored-by: Polina Lakrisenko <p.lakrisenko@gmail.com>
Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
Co-authored-by: Yannik Schaelte <yannik.schaelte@gmail.com>

.github/workflows/ci.yml

@@ -118,7 +118,7 @@ jobs:
       run: tox -e julia
 
     - name: Coverage
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -187,7 +187,7 @@ jobs:
       run: tox -e hierarchical
 
     - name: Coverage
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml

README.md

@@ -21,7 +21,7 @@ pyPESTO features include:
 * Interface to [AMICI](https://github.com/AMICI-dev/AMICI/) for efficient
   simulation and sensitivity analysis of ordinary differential equation (ODE)
   models
-  ([example](https://github.com/ICB-DCM/pyPESTO/blob/main/doc/example/amici_import.ipynb))
+  ([example](https://github.com/ICB-DCM/pyPESTO/blob/main/doc/example/amici.ipynb))
 * Parameter estimation pipeline for systems biology problems specified in
   [SBML](http://sbml.org/) and [PEtab](https://github.com/PEtab-dev/PEtab)
   ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/petab_import.ipynb))

doc/conf.py

@@ -54,6 +54,8 @@
     'myst_parser',
     # bibtex references
     'sphinxcontrib.bibtex',
+    # ensure that jQuery is installed
+    'sphinxcontrib.jquery',
 ]
 
 # default autodoc options

doc/example.rst

@@ -34,7 +34,7 @@ PEtab and AMICI
 .. toctree::
    :maxdepth: 2
 
-   example/amici_import.ipynb
+   example/amici.ipynb
    example/petab_import.ipynb
 
 Algorithms and features