Website should now work with mystmd.

Author: lunebellec

.github/workflows/deploy-book.yml

@@ -23,19 +23,14 @@ jobs:
       run: |
         pip install -r content/requirements.txt
 
-    # Fetch ORCID records
-    - name: Fetch ORCID records
-      run: |
-        cd content; python orcid_to_bib.py
-
     # Build the page
     - name: Build the book
       run: |
-        jupyter-book build content/
+        myst build --html
 
     # Push the book's HTML to github-pages
     - name: GitHub Pages action
       uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./content/_build/html
+        publish_dir: _build/html

README.md

@@ -1,6 +1,6 @@
 # simexp.github.io
 Website of the laboratory for brain simulation and exploration (SIMEXP). The codebase of this website is licensed under a
-[Creative Commons Attribution 4.0 International License][cc-by].
+[Creative Commons Attribution 4.0 International License][cc-by] and is based on the [Myst Markdown](https://mystmd.org/) framework.
 
 ## Usage
 
@@ -11,18 +11,9 @@ If you'd like to develop and/or build the SIMEXP website, you should:
 1. Clone this repository
 2. Run `pip install -r content/requirements.txt` (it is recommended you do this within a virtual environment)
 3. (Optional) Edit the books source files located in the `content/` directory
-4. In a terminal, move to the `content` directory
-5. Run `python orcid_to_bib.py` to update the content of the publication section.
-4. Run `jupyter-book clean .` to remove any existing builds
-5. Run `jupyter-book build .` to create the book
+4. Run `myst build --html` to create the website
 
-A fully-rendered HTML version of the book will be built in `content/_build/html/`.
-
-### Hosting the book
-
-Please see the [Jupyter Book documentation](https://jupyterbook.org/publish/web.html) to discover options for deploying a book online using services such as GitHub, GitLab, or Netlify.
-
-For GitHub and GitLab deployment specifically, the [cookiecutter-jupyter-book](https://github.com/executablebooks/cookiecutter-jupyter-book) includes templates for, and information about, optional continuous integration (CI) workflow files to help easily and automatically deploy books online with GitHub or GitLab. For example, if you chose `github` for the `include_ci` cookiecutter option, your book template was created with a GitHub actions workflow file that, once pushed to GitHub, automatically renders and pushes your book to the `gh-pages` branch of your repo and hosts it on GitHub Pages when a push or pull request is made to the main branch.
+A fully-rendered HTML version of the book will be built in `_build/html/`. If a change is merged into `main`, a github action will automatically publish an updated version of the website. 
 
 ## Contributors
 

content/intro.md

@@ -1,8 +1,8 @@
 # SIMEXP
 
-![](images/banner.png)
+![](../images/banner.png)
 
-The laboratory for brain simulation and exploration (SIMEXP) is located in Montreal and affiliated with the [CRIUGM](https://criugm.qc.ca/), [CSS-MTL](https://ciusss-centresudmtl.gouv.qc.ca/) and [Université de Montréal](https://psy.umontreal.ca/accueil/). The main objective of the lab is to train artificial neural networks in order to jointly mimic individual human brain activity and behaviour. To achieve that goal, we lead an intensive effort of individual data collection in neuroimaging (fMRI, MEG), the Courtois project on neuronal modelling ([CNeuroMod](https://cneuromod.ca)). The SIMEXP lab also applies machine learning techniques to identify robust markers of brain disorders in multisite data.
+The laboratory for brain simulation and exploration (SIMEXP) is located in Montreal and affiliated with the [CRIUGM](https://criugm.qc.ca/), [CSS-MTL](https://ciusss-centresudmtl.gouv.qc.ca/) and [Université de Montréal](https://psy.umontreal.ca/accueil/). The main objective of the lab is to train artificial neural networks in order to jointly mimic individual human brain activity and behaviour, notably leading the Courtois project on neuronal modelling ([CNeuroMod](https://cneuromod.ca)). The SIMEXP lab also translates these models to identify markers of brain disorders using neuroimaging data.
 
 ::::{grid}
 

myst.yml

@@ -14,13 +14,12 @@ project:
     - file: content/manifesto.md
     - file: content/coc.md
     - file: content/members.md
-    - file: content/publications.md
     - file: content/contributing.md  
     - title: Alliance Canada
       children:
         - file: alliance_canada/quick_start.md
 site:
   template: book-theme
   options:
-    favicon: content/images/favicon.png
-    logo: content/images/simexp.png
+    favicon: images/favicon.png
+    logo: images/simexp.png