add .ipynb notebooks to document sympy & related routines

CMakeLists.txt

@@ -45,6 +45,23 @@ set(NMODL_ClangFormat_DEPENDENCIES pyastgen parser-gen
     FORCE)
 add_subdirectory(cmake/hpc-coding-conventions/cpp)
 
+# =============================================================================
+# Format & execute ipynb notebooks in place (pip install nbconvert clean-ipynb)
+# =============================================================================
+add_custom_target(nb-format
+                  jupyter
+                  nbconvert
+                  --to
+                  notebook
+                  --execute
+                  --inplace
+                  --ExecutePreprocessor.timeout=360
+                  "${CMAKE_SOURCE_DIR}/docs/notebooks/*.ipynb"
+                  &&
+                  clean_ipynb
+                  --keep-output
+                  "${CMAKE_SOURCE_DIR}/docs/notebooks/*.ipynb")
+
 # =============================================================================
 # Include cmake modules
 # =============================================================================

docs/index.rst

@@ -22,9 +22,13 @@ Welcome to nmodl's documentation!
    :maxdepth: 3
    :caption: Jupyter Notebooks:
 
-   notebooks/nmodl-python-sympy-examples
-   notebooks/nmodl-python-tutorial
-   notebooks/kinetic-schemes
+   notebooks/nmodl-python-tutorial.ipynb
+   notebooks/nmodl-odes-overview.ipynb
+   notebooks/nmodl-kinetic-schemes.ipynb
+   notebooks/nmodl-sympy-solver.ipynb
+   notebooks/nmodl-linear-solver.ipynb
+   notebooks/nmodl-nonlinear-solver.ipynb
+   notebooks/nmodl-sympy-conductance.ipynb
 
 .. toctree::
    :maxdepth: 2

docs/notebooks/README.md

@@ -0,0 +1,14 @@
+## NMODL jupyter notebooks
+
+To get started with the NMODL python interface:
+  - [nmodl-python-tutorial.ipynb](nmodl-python-tutorial.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/BlueBrain/nmodl/blob/add_sympy_documentation/docs/notebooks/nmodl-python-tutorial.ipynb)
+
+For an overview of ODEs in NODL:
+  - [nmodl-odes-overview.ipynb](nmodl-odes-overview.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/BlueBrain/nmodl/blob/add_sympy_documentation/docs/notebooks/nmodl-odes-overview.ipynb)
+
+For more specific implementation details:
+  - [nmodl-kinetic-schemes.ipynb](nmodl-kinetic-schemes.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/BlueBrain/nmodl/blob/add_sympy_documentation/docs/notebooks/nmodl-kinetic-schemes.ipynb)
+  - [nmodl-sympy-solver.ipynb](nmodl-sympy-solver.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/BlueBrain/nmodl/blob/add_sympy_documentation/docs/notebooks/nmodl-sympy-solver.ipynb)
+  - [nmodl-linear-solver.ipynb](nmodl-linear-solver.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/BlueBrain/nmodl/blob/add_sympy_documentation/docs/notebooks/nmodl-linear-solver.ipynb)
+  - [nmodl-nonlinear-solver.ipynb](nmodl-nonlinear-solver.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/BlueBrain/nmodl/blob/add_sympy_documentation/docs/notebooks/nmodl-nonlinear-solver.ipynb)
+  - [nmodl-sympy-conductance.ipynb](nmodl-sympy-conductance.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/BlueBrain/nmodl/blob/add_sympy_documentation/docs/notebooks/nmodl-sympy-conductance.ipynb)