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 reports/index.md
+    # 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

README.md

@@ -1,16 +1,24 @@
 # Japan's environmental Data
 
+![License Badge](https://img.shields.io/github/license/AlFontal/environmental-data-japan?color=blue)
+![Pages Badge](https://github.com/AlFontal/environmental-data-japan/actions/workflows/deploy.yml/badge.svg)
+[![Pages site badge](https://img.shields.io/badge/Pages%20Site-Online-green)](https://alfontal.github.io/environmental-data-japan)
+
+[![Stations data](https://img.shields.io/badge/Stations-Download-orange)](https://github.com/AlFontal/environmental-data-japan/tree/main/data/air_pollution/stations/clean)
+[![Municipal data](https://img.shields.io/badge/Municipalities-Download-orange)](https://github.com/AlFontal/environmental-data-japan/tree/main/data/air_pollution/municipalities)
+[![Prefectures data](https://img.shields.io/badge/Prefectures-Download-orange)](https://github.com/AlFontal/environmental-data-japan/tree/main/data/air_pollution/prefectures)
+
 Repository collecting and organizing environmental data sources for Japan.
 
 Here, we have downloaded and processed the data available through the site made available by the Japanese National Institute for Environmental Studies (NIES) (<https://tenbou.nies.go.jp/download/>).
 
 More specifically, we have downloaded the Air Pollution Monitoring data for a total of 2039 stations located around the whole country (represented as red dots in the map below):
 
-<img src="https://github.com/AlFontal/environmental-data-japan/raw/main/data/air_pollution/stations/doc/stations_map.png" alt="Japanese Monitoring Stations Map" title="Japanese Monitoring Stations Map">
+<img src="https://github.com/AlFontal/environmental-data-japan/raw/main/data/air_pollution/stations/doc/stations_map.png" alt="Japanese Monitoring Stations Map" title="Japanese Monitoring Stations Map" width=400px>
 
 ## The stations
 
-Information for the exact location of each station (latitude, longitude and altitude) and the environmental variables available can be found in the table in [`/data/air_pollution/stations/doc/stations_info.csv`](data/air_pollution/stations/doc/stations_info.csv)
+Information for the exact location of each station (latitude, longitude and altitude) and the environmental variables available can be found in the table in [`/data/air_pollution/stations/doc/stations_info.csv`](https://github.com/AlFontal/environmental-data-japan/data/air_pollution/stations/doc/stations_info.csv)
 
 ## Variables measured
 
@@ -39,20 +47,20 @@ Since the repository includes data for over 2000 stations, the measured variable
 
 ### (1) Station data
 
-Daily data for each station and its measured variables from 2011-01-01 to 2018-12-31 can be accessed in the [`data/air_pollution/stations/clean`](data/air_pollution/stations/clean) folder, classified in subfolders according to the prefecture where they are located.
+Daily data for each station and its measured variables from 2011-01-01 to 2018-12-31 can be accessed in the [`data/air_pollution/stations/clean`](https://github.com/AlFontal/environmental-data-japan/data/air_pollution/stations/clean) folder, classified in subfolders according to the prefecture where they are located.
 
 ### (2) Municipalities
 
-Averaged daily data for all stations within each municipality in Japan during the same period can be found in the [`data/air_pollution/municipalities`](data/air_pollution/municipalities/) folder, with the first 2 digits of each CSV file indicating the prefecture code and the last 3 digits indicating the municipal code.
+Averaged daily data for all stations within each municipality in Japan during the same period can be found in the [`data/air_pollution/municipalities`](https://github.com/AlFontal/environmental-data-japan/data/air_pollution/municipalities/) folder, with the first 2 digits of each CSV file indicating the prefecture code and the last 3 digits indicating the municipal code.
 
 ### (3) Prefectures
 
 Estimates of the daily data for each prefecture have been estimated by averaging over the municipal averages in each prefecture.
 
 At this point, three different methods have been used to compute the averages, weighing the municipalities differently according to diverse criteria:
 
-+ **Area-based weighted averages**: These averages are completely population-naïve and try to better estimate the overall values for each variable across the whole area of the prefecture, wheighing high and low population density areas exactly the same. The time-series for these can be found in [`data/air_pollution/prefectures/area_weighted`](data/air_pollution/prefectures/area_weighted).
++ **Area-based weighted averages**: These averages are completely population-naïve and try to better estimate the overall values for each variable across the whole area of the prefecture, wheighing high and low population density areas exactly the same. The time-series for these can be found in [`data/air_pollution/prefectures/area_weighted`](https://github.com/AlFontal/environmental-data-japan/data/air_pollution/prefectures/area_weighted).
 
-+ **Population-weighted averages**: These averages are computed trying to estimate the values of each variable that represent the most accurate exposure of the population of each prefecture to each pollutant/meteorological variable. For these purpose, the values for each variable have been averaged weighing every municipal term according to their population share in the prefecture. The time-series for these can be found in [`data/air_pollution/prefectures/population_weighted`](data/air_pollution/prefectures/population_weighted).
++ **Population-weighted averages**: These averages are computed trying to estimate the values of each variable that represent the most accurate exposure of the population of each prefecture to each pollutant/meteorological variable. For these purpose, the values for each variable have been averaged weighing every municipal term according to their population share in the prefecture. The time-series for these can be found in [`data/air_pollution/prefectures/population_weighted`](https://github.com/AlFontal/environmental-data-japan/data/air_pollution/prefectures/population_weighted).
 
-+ **Infant population-weighted averages**: Following the same principal as the previous averages, these include the daily prefecture-level estimates of each measured variable based on the share of *children under 5 years old* in each municipal term. The time-series for these can be found in [`data/air_pollution/prefectures/under_5_weighted`](data/air_pollution/prefectures/under_5_weighted).
++ **Infant population-weighted averages**: Following the same principal as the previous averages, these include the daily prefecture-level estimates of each measured variable based on the share of *children under 5 years old* in each municipal term. The time-series for these can be found in [`data/air_pollution/prefectures/under_5_weighted`](https://github.com/AlFontal/environmental-data-japan/data/air_pollution/prefectures/under_5_weighted).

reports/_config.yml

@@ -0,0 +1,62 @@
+# 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                       : Japan's Environmental Data  # 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/environmental-data-japan
+  branch: main
+html:
+  use_repository_button: true
+  use_issues_button: true
+  favicon: images/favicon.ico
+  baseurl: 'https://alfontal.github.io/environmental-data-japan'
+  comments:
+    utterances: 
+      repo: 'AlFontal/environmental-data-japan'
+  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>
+
+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/environmental-data-japan/'
+
+  extra_extensions:
+   - sphinx_sitemap
+

reports/_static/custom.css

@@ -0,0 +1,40 @@
+@import url('https://fonts.googleapis.com/css2?family=Crimson+Pro&family=Noto+Serif&display=swap');
+
+div.cell div.cell_input {
+    padding-left: 0em;
+    padding-right: 0em;
+    border: 1px #ccc solid;
+    background-color: #f7f7f7;
+    /* I am overriding the default green left sidebar for code cells */
+    /*! border-left-color: green; */
+    /*! border-left-width: medium; */
+  }
+
+ :root {
+    --pst-font-family-base-system: 'Noto serif', serif;
+  }
+
+  p {
+    text-align: justify;
+  }
+
+  .fa {
+      margin: 0 10px 0 0;
+      color: #083466;
+      text-decoration: none;
+  }
+
+
+
+
+  .fa:hover {
+    opacity: 0.7;
+  }
+
+  img.profile {
+      display: block;
+      border-radius: 50%;
+      margin: 0 auto;
+      width: 120px;
+      height: 120px;
+  }

reports/_toc.yml

@@ -0,0 +1,7 @@
+format: jb-article
+root: index
+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