Copy files from other working repository, rf-shimming-7t-neurolibre

.github/workflows/main.yml

@@ -0,0 +1,48 @@
+name: deploy-book
+
+# Only run this when the v2 branch changes
+on:
+  push:
+    branches:
+    - main
+    # If your git repository has the Jupyter Book within some-subfolder next to
+    # unrelated files, you can make this run only if a file within that specific
+    # folder has been modified.
+    # paths:
+    # - source/**
+
+# This job installs dependencies, build the book, and pushes it to `gh-pages`
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    # Install dependencies
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        pip install -r binder/requirements.txt
+    - name: Download data
+      run: |
+        cd content
+        repo2data -r ../binder/data_requirement.json
+        cd ..
+    - name: Postbuild
+      run: |
+        chmod +xxx binder/postBuild
+        binder/postBuild
+    # Build the book
+    - name: Build the book
+      run: |
+        jupyter-book build content/index.ipynb --builder singlehtml
+    # Push the book's HTML to github-pages
+    - name: GitHub Pages action
+      uses: peaceiris/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./content/_build/_page/index/singlehtml

.gitignore

@@ -1,12 +1,3 @@
-# Dataset
-ds004906
-
-# Apple files
-.DS_Store
-
-# Visual Studio
-.vscode
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -23,12 +14,12 @@ dist/
 downloads/
 eggs/
 .eggs/
-lib/
 lib64/
 parts/
 sdist/
 var/
 wheels/
+pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -58,7 +49,6 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
-cover/
 
 # Translations
 *.mo
@@ -81,7 +71,6 @@ instance/
 docs/_build/
 
 # PyBuilder
-.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -92,9 +81,7 @@ profile_default/
 ipython_config.py
 
 # pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
+.python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -103,22 +90,7 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.lock
 
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/#use-with-ide
-.pdm.toml
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
 __pypackages__/
 
 # Celery stuff
@@ -155,15 +127,19 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-# pytype static type analyzer
-.pytype/
+_build/
+
+# macos garbage
+.DS_Store
+
+# builds
+*.html
 
-# Cython debug symbols
-cython_debug/
+# data
+*.zip
+content/data/
+content/neuromod-anat-brain-qmri/
+content/spinalcord_results/
 
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+# Cloned repos
+content/analysis*

binder/colab_output.json

@@ -0,0 +1,5 @@
+{ 
+    "src": "https://drive.google.com/uc?id=1-8-EsLKDpV2LqcQmhzPguiyUb1xJyM4j",
+    "dst": "../data",
+    "projectName": "rf-shimming-7t-colab"
+}

binder/data_requirement.json

@@ -0,0 +1,5 @@
+{ 
+    "src": "https://drive.google.com/uc?id=1OY-lEDIqcSJY_Mymo6Fd8vfhY5L7phXr",
+    "dst": "../data",
+    "projectName": "rf-shimming-7t"
+}

binder/environment_archive.yml

@@ -0,0 +1,26 @@
+name: notebook
+
+channels:
+  - default
+  - conda-forge
+
+dependencies:
+ - pip
+ - matplotlib
+ - nibabel
+ - numpy
+ - pandas
+ - scipy
+ - statsmodels
+ - plotly
+ - pandas
+ - markdown
+ - wget
+ - jupyterlab-mathjax3
+ - osfclient
+ - pip:
+   - jupyter-book==0.13.0
+   - repo2data
+   - datalad-installer
+   - pybids
+   - yes

binder/postBuild

@@ -0,0 +1,22 @@
+#!/bin/bash
+set -e 
+
+touch ~/.bashrc
+cd content
+repo2data -r ../binder/data_requirement.json
+cd ..
+git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox ~/content/sct
+cd ~/content/sct
+yes | ./install_sct
+echo 'export PATH=~/content/sct/bin:$PATH' >> ~/.bashrc
+echo 'export MPLBACKEND='Agg'' >> ~/.bashrc
+
+echo 'export PATH=~/content/sct/bin:$PATH' >> ~/.bash_profile
+echo 'export MPLBACKEND='Agg'' >> ~/.bash_profile
+
+echo 'export PATH=~/content/sct/bin:$PATH' >> ~/.bash_login
+echo 'export MPLBACKEND='Agg'' >> ~/.bash_login
+
+echo 'export PATH=~/content/sct/bin:$PATH' >> ~/.profile
+echo 'export MPLBACKEND='Agg'' >> ~/.profile
+cd ~/

binder/runtime.txt

@@ -0,0 +1 @@
+python-3.8

content/_config.yml

@@ -0,0 +1,37 @@
+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: RF Shimming 7T
+logo: logo.png
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: force
+
+launch_buttons:
+  notebook_interface: "jupyterlab"
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/shimming-toolbox/rf-shimming-7t-neurolibre  # Online location of your book
+  path_to_book: content  # Optional path to your book, relative to the repository root
+  branch: main  # Which branch of the repository should be used when creating links (optional)
+
+only_build_toc_files: true
+
+execute:
+  timeout: 600
+
+sphinx:
+  local_extensions          :   # A list of local extensions to load by sphinx specified by "name: path" items
+  recursive_update          : false # A boolean indicating whether to overwrite the Sphinx config (true) or recursively update
+  config                    :   # key-value pairs to directly over-ride the Sphinx configuration
+    bibtex_reference_style: author_year
+    bibtex_default_style: plain
+    bibtex_tooltips: true
+    html_static_path: ['_static']
+    html_css_files: ['custom.css']
+
+bibtex_bibfiles:
+  - ../paper.bib

content/_neurolibre.yml

@@ -0,0 +1,2 @@
+book_layout: traditional
+single_page: index.ipynb

content/_static/custom.css

@@ -0,0 +1,52 @@
+p {
+  text-align: justify;
+}
+a {
+  color: #870000!important;
+}
+a:hover {
+  color: brick!important;
+}
+a:visited {
+  color: #6f42c1!important;
+}
+body, h1, h2, h3, h4, h5 {
+    font-family: 'STIX Two Text';
+}
+h1 {
+    color: #342727!important;
+}
+.caption {
+    text-align:justify;
+    line-height:1.25;
+    font-size:80%
+}
+
+#site-navigation {
+    display: none;
+}
+
+#main-content{
+    margin: 0 auto;
+}
+
+
+.fa, .far, .fas {
+    color: red;
+}
+
+.header-article::after{
+  content: url('https://neurolibre.org/assets/joss2-b7ea8dd1f24ce2b0825db17e3495576253ba4c64df3384a66354713d76c40a75.svg');
+  width: 150px; 
+  height: 80px;
+  position: relative;
+  right: 10px;
+}
+
+.header-article::before{
+  content: url('https://raw.githubusercontent.com/neurolibre/brand/b5e10e051a0059824ca2f4204e1288927e551d49/svg/neurolibre_logo.svg');
+  width: 33px; 
+  height: 33px;
+  position: absolute;
+  left: 10px;
+}

content/_toc.yml

@@ -0,0 +1,5 @@
+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-article
+root: paper