REF,ENH Use jupyter-book for the rendered website (#40)

* ENH start setting up jupyter-book

* Continue with conversion

* Update tutorials

* Update all notebooks

* Remove scripts

* Rename static assets

* Update readme

* Test tutorials using jupyter-book

* FIX codespell

* Update

* Add makefile to push pages

* Organize book files

* Update makefile

* FIX avoid warning with nans

* Clean up repository and add readme

* Add preview to makefile and fix readme

* update readme

* Add merged notebooks

* Fix 3d flatmap

* FIX reference [skip ci]

Author: mvdoc

.github/workflows/run_tutorials.yml

@@ -40,7 +40,7 @@ jobs:
         pip install -U wheel
         # install himalaya from source to get early testing
         pip install git+https://github.com/gallantlab/himalaya.git
-        pip install -e ."[github]"
+        pip install -e ."[docs,github]"
         # use neurodebian installer for travis
         bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
         sudo apt-get update -qq
@@ -55,10 +55,4 @@ jobs:
     - name: Run some tutorials
       run: |
         # run tutorials with a shortcut option to skip model fitting
-        HIMALAYA_SKIP_FIT=True python tutorials/shortclips/00_download_shortclips.py
-        HIMALAYA_SKIP_FIT=True python tutorials/shortclips/01_plot_explainable_variance.py
-        HIMALAYA_SKIP_FIT=True python tutorials/shortclips/02_plot_ridge_regression.py
-        HIMALAYA_SKIP_FIT=True python tutorials/shortclips/03_plot_wordnet_model.py
-        HIMALAYA_SKIP_FIT=True python tutorials/shortclips/04_plot_hemodynamic_response.py
-        HIMALAYA_SKIP_FIT=True python tutorials/shortclips/05_plot_motion_energy_model.py
-        HIMALAYA_SKIP_FIT=True python tutorials/shortclips/06_plot_banded_ridge_model.py
+        HIMALAYA_SKIP_FIT=True jupyter-book build tutorials

.gitignore

@@ -12,3 +12,4 @@ dist/
 # Documentation build
 doc/_build/
 doc/_auto_examples/
+tutorials/_build

README.rst

@@ -29,14 +29,19 @@ To explore these tutorials, one can:
 
 - read the rendered examples in the tutorials
   `website <https://gallantlab.github.io/voxelwise_tutorials/>`_ (recommended)
-- run the Python scripts (`tutorials <tutorials>`_ directory)
-- run the Jupyter notebooks (`tutorials/notebooks <tutorials/notebooks>`_ directory)
 - run the merged notebook in
   `Colab <https://colab.research.google.com/github/gallantlab/voxelwise_tutorials/blob/main/tutorials/notebooks/shortclips/merged_for_colab.ipynb>`_.
+- run the Jupyter notebooks (`tutorials/notebooks <tutorials/notebooks>`_ directory) locally
 
 The tutorials are best explored in order, starting with the "Shortclips"
 tutorial.
 
+Dockerfiles
+===========
+This repository contains Dockerfiles to run the tutorials locally. Please see the
+instructions in the `docker <docker>`_ directory.
+
+
 Helper Python package
 =====================