chore: set up GH pages for reports (#2)

.github/workflows/deploy.yml

@@ -0,0 +1,45 @@
+name: deploy
+
+on:
+  # Trigger the workflow on push to main branch
+  push:
+    branches:
+      - main
+
+# This job installs dependencies, build the book, and pushes it to `gh-pages`
+jobs:
+  build-and-deploy-book:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.8]
+    steps:
+    - uses: actions/checkout@v2
+
+    # Install dependencies
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        pip install -r requirements.txt
+    # Copy README into build folder to include it as intro
+    - name: Copy README
+      run: |
+        cp README.md notebooks/
+    # Build the book
+    - name: Build the book
+      run: |
+        jupyter-book build reports
+    - name: Clean notebook outputs for nicer HTML render
+      run: curl -s -S https://gist.githubusercontent.com/AlFontal/896e180f9f7772c4825067591f34c94b/raw > clean_notebook.py; 
+              python clean_notebook.py --path reports
+
+    # Deploy the book's HTML to gh-pages branch
+    - name: GitHub Pages action
+      uses: peaceiris/actions-gh-pages@v3.6.1
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: reports/_build/html

.gitignore

@@ -137,6 +137,17 @@ data/air_pollution/stations/doc/TM20140000.txt
 data/air_pollution/stations/doc/TM20130000.txt
 data/air_pollution/stations/doc/TM20120000.txt
 data/air_pollution/stations/doc/TM20110000.txt
+data/doc/images/*
 
 # Japanese e-Stat site API key
 .appID
+data/shapefiles/administrative_boundaries/municipality_shapes.cpg
+data/shapefiles/administrative_boundaries/municipality_shapes.dbf
+data/shapefiles/administrative_boundaries/municipality_shapes.prj
+data/shapefiles/administrative_boundaries/municipality_shapes.shp
+data/shapefiles/administrative_boundaries/municipality_shapes.shx
+data/shapefiles/administrative_boundaries/prefecture_shapes.cpg
+data/shapefiles/administrative_boundaries/prefecture_shapes.dbf
+data/shapefiles/administrative_boundaries/prefecture_shapes.prj
+data/shapefiles/administrative_boundaries/prefecture_shapes.shp
+data/shapefiles/administrative_boundaries/prefecture_shapes.shx

reports/_config.yml

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+# yaml-language-server: $schema=./_config.yaml
+#######################################################################################
+# A default configuration that will be loaded for all jupyter books
+# See the documentation for help and more options: 
+# https://jupyterbook.org/customize/config.html
+
+#######################################################################################
+# Book settings
+title                       : KD and Tokyo's air sources  # The title of the book. Will be placed in the left navbar.
+author                      : Alejandro Fontal  # The author of the book
+copyright                   : "2022"  # Copyright year to be placed in the footer
+logo                        : images/logo.png # A path to the book logo
+
+execute:
+  execute_notebooks: "off"
+
+repository:
+  url: https://github.com/AlFontal/vasculitis2022-conference
+  branch: main
+html:
+  use_repository_button: true
+  use_issues_button: true
+  favicon: images/favicon.ico
+  baseurl: 'https://alfontal.github.io/vasculitis2022-conference'
+  comments:
+    utterances: 
+      repo: 'AlFontal/vasculitis2022-conference'
+  extra_navbar: |
+            <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">
+            <div>           
+            <hr>
+            <a href="https://helical-itn.eu/">
+            <img src="https://helical-itn.eu/wp-content/uploads/2020/01/cropped-HELICAL_logo-3.png" width=200px>
+            </a>
+            <p></p>
+            <a href="https://www.isglobal.org/en/-/clima-y-salud">
+            <img src="https://www.isglobal.org/isglobal-new-theme/assets/images/isglobal/logo-isglobal-en.png" width=200px>
+            </a>
+            <hr>
+            <a href="https://www.linkedin.com/in/alfontal/">
+            <img class="profile" src="https://avatars.githubusercontent.com/u/10958332?s=400&amp;u=51edd1406d2af0c2f1723a0bf8f111d48a1b7fe7&amp;v=4" alt="Alejandro Fontal">
+            <p style="text-align: center; font-size:16px"><b>Alejandro Fontal</b></p>
+            </a>
+            <a href="https://github.com/AlFontal" class="fa fa-github" style="font-size: 25px;"></a>
+            <a href="https://www.linkedin.com/in/alfontal/" class="fa fa-linkedin" style="font-size: 25px;"></a></a>
+            <a href="https://twitter.com/alefontal" class="fa fa-twitter" style="font-size: 25px;"></a></a>
+            <a href="mailto:alejandro.fontal.92@gmail.com" class="fa fa-envelope" style="font-size: 25px;"></a></a>
+            </div>
+  google_analytics_id: G-TC2X861BC8
+
+bibtex_bibfiles: references.bib
+
+sphinx:
+  config:
+    html_js_files:
+      - https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js
+    bibtex_reference_style: author_year
+
+    html_baseurl: 'https://alfontal.github.io/vasculitis2022-conference/'
+
+  extra_extensions:
+   - sphinx_sitemap
+

reports/_toc.yml

@@ -0,0 +1,7 @@
+format: jb-article
+root: README
+sections:
+- file: prefecture_weighted_averages
+  title: From station to prefectural data
+
+

requirements.txt

@@ -0,0 +1,8 @@
+bs4
+html5lib
+jupyter-book==v0.12.3
+matplotlib
+numpy
+ghp-import
+sphinxcontrib-bibtex==2.2.0
+sphinx-sitemap