Lint the repo (#31)

* Lint the repo * Lint code in comment (tut01) * Apply suggestions from code review Co-authored-by: Yvonne Fröhlich <94163266+yvonnefroehlich@users.noreply.github.com> * Lint again --------- Co-authored-by: yvonnefroelich <yvonne.froehlich@kit.edu> Co-authored-by: Yvonne Fröhlich <94163266+yvonnefroehlich@users.noreply.github.com>
GenericMappingTools · Dec 5, 2024 · 68b9c78 · 68b9c78
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diff --git a/.github/workflows/deploy-book.yml b/.github/workflows/deploy-book.yml
@@ -13,8 +13,8 @@ on:
     # unrelated files, you can make this run only if a file within that specific
     # folder has been modified.
     paths:
-      - '.github/workflows/deploy-book.yml'
-      - 'book/**'
+      - ".github/workflows/deploy-book.yml"
+      - "book/**"
 
 # This job installs dependencies, builds the book, and pushes it to `gh-pages`
 jobs:
@@ -29,30 +29,30 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    # Checkout current git repository
-    - name: Checkout
-      uses: actions/checkout@v4.1.7
+      # Checkout current git repository
+      - name: Checkout
+        uses: actions/checkout@v4.1.7
 
-    # Install Mambaforge with conda-forge dependencies
-    - name: Setup Mambaforge
-      uses: mamba-org/setup-micromamba@v1.9.0
-      with:
-        environment-name: agu24workshop
-        environment-file: conda-lock.yml
-        create-args: >-
-          python=${{ matrix.python-version }}
-        condarc: |
-          channels:
-            - conda-forge
-            - nodefaults
+      # Install Mambaforge with conda-forge dependencies
+      - name: Setup Mambaforge
+        uses: mamba-org/setup-micromamba@v1.9.0
+        with:
+          environment-name: agu24workshop
+          environment-file: conda-lock.yml
+          create-args: >-
+            python=${{ matrix.python-version }}
+          condarc: |
+            channels:
+              - conda-forge
+              - nodefaults
 
-    # Build the book
-    - name: Build the book
-      run: jupyter-book build book/
+      # Build the book
+      - name: Build the book
+        run: jupyter-book build book/
 
-    # Push the book's HTML to github-pages
-    - name: GitHub Pages action
-      uses: peaceiris/actions-gh-pages@v4.0.0
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: book/_build/html
+      # Push the book's HTML to github-pages
+      - name: GitHub Pages action
+        uses: peaceiris/actions-gh-pages@v4.0.0
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: book/_build/html
diff --git a/README.md b/README.md
@@ -9,6 +9,7 @@ pre-conference workshop (PREWS9) at the
 [AGU24 Annual Meeting](https://www.agu.org/annual-meeting).
 
 **Presenters**
+
 - [Wei Ji Leong](https://github.com/weiji14)
 - [Yvonne Fröhlich](https://github.com/yvonnefroehlich)
 - [Jing-Hui Tong](https://github.com/jhtong33)
@@ -17,6 +18,7 @@ pre-conference workshop (PREWS9) at the
 - [Andre Luiz Belem](https://github.com/andrebelem)
 
 **When**
+
 - Sunday 8 December 2024, 8:30-17:00 (EST) / 13:10-22:00 (UTC)
 - [Event Time Zone Converter](https://www.timeanddate.com/worldclock/fixedtime.html?msg=AGU24+workshop%3A+Mastering+Geospatial+Visualizations+with+GMT%2FPyGMT&iso=20241208T0830&p1=263&ah=8&am=30)
 
@@ -27,21 +29,20 @@ Washington, DC 20001, United States
 
 ## Schedule
 
-|  Time (EST) | Topic                                                   |
-|:-----------:|:-------------------------------------------------------:|
-| 08:30-08:40 | Introduction to GMT / PyGMT                             |
-| 08:40-08:55 | Installation                                            |
-| 08:55-09:45 | Tutorial 1 - First figure + Subplots / layout           |
-| 09:45-10:15 | **Break**                                               |
-| 10:15-11:00 | Tutorial 2 - Integration with scientific Python ecosystem: pandas / GeoPandas |
-| 11:00-11:45 | Tutorial 3 - Integration with scientific Python ecosystem: Xarray (grids)     |
-| 11:45-12:45 | **Lunch**                                               |
-| 12:45-13:30 | Tutorial 4 - Geophysics (Seismology)                    |
-| 13:30-14:15 | Tutorial 5 - 3-D Topography (Planetary / Antarctic maps) |
-| 14:15-14:45 | **Break**                                               |
-| 14:45-15:30 | Tutorial 6 - Animations with GMT                        |
-| 15:30-17:00 | Final exercises / mini-project                          |
-
+| Time (EST)  |                                            Topic                                             |
+| :---------: | :------------------------------------------------------------------------------------------: |
+| 08:30-08:40 |                                 Introduction to GMT / PyGMT                                  |
+| 08:40-08:55 |                                         Installation                                         |
+| 08:55-09:45 |                       Tutorial 1 - First figure and Subplots / layout                        |
+| 09:45-10:15 |                                          **Break**                                           |
+| 10:15-11:00 | Tutorial 2 - Integration with scientific Python ecosystem: pandas / GeoPandas (tabular data) |
+| 11:00-11:45 |       Tutorial 3 - Integration with scientific Python ecosystem: Xarray (gridded data)       |
+| 11:45-12:45 |                                          **Lunch**                                           |
+| 12:45-13:30 |                             Tutorial 4 - Geophysics (Seismology)                             |
+| 13:30-14:15 |                   Tutorial 5 - 3-D Topography (Planetary / Antarctic maps)                   |
+| 14:15-14:45 |                                          **Break**                                           |
+| 14:45-15:30 |                               Tutorial 6 - Animations with GMT                               |
+| 15:30-17:00 |                                Final exercises / mini-project                                |
 
 ## Getting started
 
@@ -51,7 +52,6 @@ Launch on regular [Binder](https://mybinder.readthedocs.io/en/latest/index.html)
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/GenericMappingTools/agu24workshop/main)
 
-
 ## Code of Conduct
 
 All involved individuals must follow the

diff --git a/book/_config.yml b/book/_config.yml
@@ -9,7 +9,7 @@ logo: logo.webp
 # See https://jupyterbook.org/content/execute.html
 execute:
   execute_notebooks: cache
-  timeout: 270  # https://jupyterbook.org/en/stable/content/execute.html#setting-execution-timeout
+  timeout: 270 # https://jupyterbook.org/en/stable/content/execute.html#setting-execution-timeout
 
 # Define the name of the latex output file for PDF builds
 latex:
@@ -27,9 +27,9 @@ launch_buttons:
 
 # Information about where the book exists on the web
 repository:
-  url: https://github.com/GenericMappingTools/agu24workshop  # Online location of your book
-  path_to_book: book  # Optional path to your book, relative to the repository root
-  branch: main  # Which branch of the repository should be used when creating links (optional)
+  url: https://github.com/GenericMappingTools/agu24workshop # Online location of your book
+  path_to_book: book # Optional path to your book, relative to the repository root
+  branch: main # Which branch of the repository should be used when creating links (optional)
 
 # Add GitHub buttons to your book
 # See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository

diff --git a/book/_toc.yml b/book/_toc.yml
@@ -4,19 +4,19 @@
 format: jb-book
 root: intro
 parts:
-- caption: 🔗 Details
-  chapters:
-    - title: AGU24 Homepage
-      url: https://www.agu.org/annual-meeting
-    - title: Course materials on GitHub
-      url: https://github.com/GenericMappingTools/agu24workshop
-- caption: 🧑‍🏫 Tutorials
-  chapters:
-  - file: tut01_firstfigure
-  - file: tut02_spe_pd_gpd
-  - file: tut03_spe_xarray
-  - file: tut04_geophysics
-  - file: tut05_topography
-  - file: tut06_animation
-    sections:
-      - file: tut06_animation_extended
+  - caption: 🔗 Details
+    chapters:
+      - title: AGU24 Homepage
+        url: https://www.agu.org/annual-meeting
+      - title: Course materials on GitHub
+        url: https://github.com/GenericMappingTools/agu24workshop
+  - caption: 🧑‍🏫 Tutorials
+    chapters:
+      - file: tut01_firstfigure
+      - file: tut02_spe_pd_gpd
+      - file: tut03_spe_xarray
+      - file: tut04_geophysics
+      - file: tut05_topography
+      - file: tut06_animation
+        sections:
+          - file: tut06_animation_extended
diff --git a/book/intro.md b/book/intro.md
@@ -8,13 +8,12 @@ tutorials for making maps 🗺️ and animations 🎦
 :gutter: 1
 :padding: 1
 
-
 :::::{grid-item}
 ::::{grid} 1 1 1 1
 :gutter: 1
 
 :::{grid-item-card} Tutorial 1 - First figure 🚀 and Subplots / layout
-:img-top: _images/fd70248f75b8b37ee54b3135f77705f98c6d8489eb18b6910184b447d0f0638d.png
+:img-top: \_images/fd70248f75b8b37ee54b3135f77705f98c6d8489eb18b6910184b447d0f0638d.png
 :link: ./tut01_firstfigure.html
 by [Jing-Hui Tong](https://orcid.org/0009-0002-7195-3071)
 +++
@@ -29,7 +28,7 @@ by [Jing-Hui Tong](https://orcid.org/0009-0002-7195-3071)
 :::
 
 :::{grid-item-card} Tutorial 2 - Integration with the scientific Python ecosystem 🐍: pandas and GeoPandas (tabular data 🗒️)
-:img-top: _images/7f18327908c8dd210197cc51845e45a933f356b9fd12bd029a4a8cbda080eb2b.png
+:img-top: \_images/7f18327908c8dd210197cc51845e45a933f356b9fd12bd029a4a8cbda080eb2b.png
 :link: ./tut02_spe_pd_gpd.html
 by [Yvonne Fröhlich](https://orcid.org/0000-0002-8566-0619)
 +++
@@ -47,13 +46,12 @@ by [Yvonne Fröhlich](https://orcid.org/0000-0002-8566-0619)
 ::::
 :::::
 
-
 :::::{grid-item}
 ::::{grid} 1 1 1 1
 :gutter: 1
 
 :::{grid-item-card} Tutorial 3 - Integration with the scientific Python ecosystem 🐍: Xarray (gridded data 🌐)
-:img-top: _images/a18fcb026fb0d0c83360f2b8382a360e552dd50db6aa2db5311259bf5223d3a2.png
+:img-top: \_images/a18fcb026fb0d0c83360f2b8382a360e552dd50db6aa2db5311259bf5223d3a2.png
 :link: ./tut03_spe_xarray.html
 by [Max Jones](https://orcid.org/0000-0003-0180-8928)
 +++
@@ -89,13 +87,12 @@ and [Yvonne Fröhlich](https://orcid.org/0000-0002-8566-0619)
 ::::
 :::::
 
-
 :::::{grid-item}
 ::::{grid} 1 1 1 1
 :gutter: 1
 
 :::{grid-item-card} Tutorial 5 - 3-D Topography (Planetary / Antarctic maps)
-:img-top: _images/0a6fc097b1fcaa99eff8632dab714787757564ed60e07f20825101c6a8e045ae.png
+:img-top: \_images/0a6fc097b1fcaa99eff8632dab714787757564ed60e07f20825101c6a8e045ae.png
 :link: ./tut05_topography.html
 by [Wei Ji Leong](https://orcid.org/0000-0003-2354-1988)
 and [André Belém](https://orcid.org/0000-0002-8865-6180)
@@ -109,7 +106,7 @@ and [André Belém](https://orcid.org/0000-0002-8865-6180)
 :::
 
 :::{grid-item-card} Tutorial 6 - Animations with GMT
-:img-top: _images/5847818951ca8fbc9b86a6f2c67389b6.png
+:img-top: \_images/5847818951ca8fbc9b86a6f2c67389b6.png
 :link: ./tut06_animation.html
 by [Federico Esteban](https://orcid.org/0000-0002-0641-7371)
 +++
@@ -124,15 +121,12 @@ by [Federico Esteban](https://orcid.org/0000-0002-0641-7371)
 ::::
 :::::
 
-
 ::::::
 
-
 Each tutorial is rendered on this website for easy viewing 👀, but they are all Jupyter
 notebooks designed to be ran interactively 💫. See the instructions below on how you can
 start running the tutorials in no time! 🚀
 
-
 # 🌠 Quickstart
 
 To run these notebooks in an interactive Jupyter session online, 🖱️ click on the button
@@ -181,18 +175,18 @@ Here's the instructions to install the `agu24workshop` environment:
 
 4. Run the following commands on the 🧑‍💻 command-line to create the virtual environment
 
-    ```bash
-    cd /path/to/agu24workshop
-    conda env create --name agu24workshop --file environment.yml
-    ```
+   ```bash
+   cd /path/to/agu24workshop
+   conda env create --name agu24workshop --file environment.yml
+   ```
 
 5. Once the installation is completed 🏁, launch
    [Jupyter Lab](https://jupyterlab.readthedocs.io) as follows:
 
-    ```bash
-    conda activate agu24workshop
-    jupyter lab
-    ```
+   ```bash
+   conda activate agu24workshop
+   jupyter lab
+   ```
 
    This should open up a page in your default browser. If not, you can click and open
    the 🔗 link that says `http://localhost:8888/lab?token=...` in your command-line
@@ -202,7 +196,7 @@ Here's the instructions to install the `agu24workshop` environment:
    https://www.generic-mapping-tools.org/agu24workshop/tut01_firstfigure.html) using
    either the download button on the ↗️ top right (select '.ipynb') or from GitHub at
    https://github.com/GenericMappingTools/agu24workshop/tree/main/book. Make sure to put
-   the *.ipynb file(s) inside of the 'agu24workshop' folder.
+   the \*.ipynb file(s) inside of the 'agu24workshop' folder.
 
 7. Open the Jupyter notebook in the left-pane file browser, e.g. by 🖱️ double-clicking
    on `first-figure.ipynb`. You are now ready to run through the course materials 🎉!