Merge branch 'main-educational:main' into main

.github/workflows/deploy-book.yml

@@ -19,6 +19,10 @@ jobs:
  with:
  python-version: 3.8
 
+ - name: Install pytorch
+ run: |
+ pip install torch==1.13.0
+
  - name: Install dependencies
  run: |
  pip install -r binder/requirements.txt

README.md

@@ -1,6 +1,15 @@
 # brain_encoding_decoding
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/main-educational/brain_decoding/main?labpath=notebooks%2Fmultiple_decoders_haxby_tutorial.ipynb)
+[![Jupyter Book Badge](https://jupyterbook.org/badge.svg)](https://main-educational.github.io/brain_encoding_decoding/intro.html) 
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/main-educational/brain_encoding_decoding/HEAD)
+[![Docker Hub](https://img.shields.io/docker/pulls/user/repo)]() 
+[![GitHub size](https://img.shields.io/github/repo-size/main-educational/brain_encoding_decoding)](https:/main-educational/brain_encoding_decoding/archive/master.zip)
+[![GitHub issues](https://img.shields.io/github/issues/main-educational/brain_encoding_decoding?style=plastic)](https:/main-educational/brain_encoding_decoding)
+[![GitHub PR](https://img.shields.io/github/issues-pr/main-educational/brain_encoding_decoding)](https:/main-educational/brain_encoding_decoding/pulls)
+[![License](https://img.shields.io/github/license/main-educational/brain_encoding_decoding)](https:/main-educational/brain_encoding_decoding)
+[![CONP](https://img.shields.io/badge/Supported%20by-%20CONP%2FPCNO-red)](https://conp.ca/)
+
+
 
 This is a jupyter book presenting an introduction to brain encoding and decoding using python. It is rendered on [main-educational.github.io/brain_encoding_decoding](https://main-educational.github.io/brain_encoding_decoding/intro.html). See the introduction of the jupyter book for more details, and acknowledgements.
 

binder/requirements.txt

@@ -1,22 +1,21 @@
 nilearn==0.8.1
-pandas==1.1.5
-numpy==1.19.5
-keras==2.6.0
-tensorflow==2.6.2
-scikit-learn==0.24.2
-pandas==1.1.5
+numpy==1.22
+keras==2.8.0
+tensorflow==2.8.2
+scikit-learn==1.0.2
+joblib==1.1.0
+pandas==1.2.0
 matplotlib==3.3.4
 seaborn==0.11.1
 jupyter-book==0.12.1
 sphinx-design
-torch==1.11.0
+torch==1.13.0
 psutil==5.8.0
 torchvision
-torch-cluster
---find-links https://data.pyg.org/whl/torch-1.11.0+cpu.html
-torch-scatter
---find-links https://data.pyg.org/whl/torch-1.11.0+cpu.html
-torch-sparse
---find-links https://data.pyg.org/whl/torch-1.11.0+cpu.html
+tensorboard==2.8.0
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.1
+tensorflow-estimator==2.8.0
 torch-geometric
---find-links https://data.pyg.org/whl/torch-1.11.0+cpu.html
+torch-scatter==2.0.8
+torch-sparse==0.6.11

content/_config.yml

@@ -5,8 +5,8 @@
 
 #######################################################################################
 # Book settings
-title : "Introduction to brain decoding in fMRI" # The title of the book. Will be placed in the left navbar.
-author : # The author of the book
+title : "Introduction to brain decoding & encoding in fMRI" # The title of the book. Will be placed in the left navbar.
+author : "Peer Herholz, Pierre Bellec, Shima Rastegarnia, Hao-Ting Wang, Loic Tetrel, Bertrand Thirion, Alexis Thual, Isil Bilgin, Alexandre Pasquiou, Pravish Sainath" # The author of the book
 copyright : "2022" # Copyright year to be placed in the footer
 logo : "../images/neurolibre-logo.png" # A path to the book logo
 exclude_patterns : [] # Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb")
@@ -60,7 +60,7 @@ sphinx:
  .Rmd:
  - jupytext.reads
  - fmt: Rmd
- mathjax_config:
+ mathjax3_config:
  TeX:
  Macros:
  "N": "\\mathbb{N}"

content/_toc.yml

@@ -7,4 +7,5 @@ chapters:
 - file: haxby_data
 - file: svm_decoding
 - file: mlp_decoding
-- file: gcn_decoding
+- file: gcn_decoding
+- file: encoding