Initial commit

.github/workflows/deploy.yml

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+name: MyST GitHub Pages Deploy
+on:
+  push:
+    # Runs on pushes targeting the default branch
+    branches: [main]
+env:
+  # `BASE_URL` determines the website is served from, including CSS & JS assets
+  # You may need to change this to `BASE_URL: ''`
+  BASE_URL: /${{ github.event.repository.name }}
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: 'pages'
+  cancel-in-progress: false
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+      # Set up Python
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      # Install Python dependencies
+      - name: Install Python dependencies
+        run: |
+          python -m venv venv
+          source venv/bin/activate
+          pip install -r binder/requirements.txt
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 18.x
+      - name: Install MyST Markdown
+        run: npm install -g mystmd
+      - name: Build HTML Assets
+        run: myst build --execute --html
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: './_build/html'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+_build/
+# C extensions
+*.so
+.DS_Store
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+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
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# 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/

LICENSE

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+MIT License
+
+Copyright (c) 2024 NeuroLibre
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# mystical-article
+
+This repository provides a NeuroLibre-compatible article template using MyST (Markedly Structured Text) for creating interactive scientific preprints.
+
+https://events.neurolibre.org/mystical-article
+
+## Learn the ropes of MyST through GitHub Actions
+
+This repository includes a GitHub Actions workflow that builds the MyST-formatted preprint and publishes it to GitHub Pages. 
+
+> [!TIP]
+> To enable this, you need to enable GitHub Pages in the repository settings (select GitHub Actions as the `Build and deployment` source).
+
+Once you push your changes to the `main` branch, the GitHub Actions workflow will build the MyST-formatted preprint and publish it to your GitHub Pages.
+
+> [!WARNING]
+> The actions file (`.github/workflows/deploy.yml`) attempts to **execute** the executable content in this preprint. However, this doesn't always work smoothly in the GitHub Actions environment, as it requires starting a Jupyter Server and connecting to it. In other words, it may not generate the interactive figures as intended. Nevertheless, any changes you make to the **narrative** content will be reflected in the preprint.
+
+The ultimate guide for authoring narrative and executable content in MyST documents is the [MyST Guide](https://mystmd.org/guide). 
+
+## The real deal: NeuroLibre workflow
+
+Below is a decision tree guiding you through the process of preparing your living preprint before submitting it to the [NeuroLibre](https://neurolibre.org) for publication.
+
+![Decision tree](https://github.com/neurolibre/brand/blob/main/png/myst_flow.png?raw=true)
+
+
+> [!NOTE]
+> This template includes executable content (simple Python code to generate interactive figures) and needs some data to be used as input. Let's take a look at how they are managed.
+
+### The `binder` folder
+
+* `runtime.txt` declares `python-3.10` as the Python version.
+* `requirements.txt` declares the Python packages that will be installed in your reproducible runtime environment.
+* `data_requirement.json` declares a download source (a simple csv file), which will be downloaded to a folder named `neurolibre-demo-dataset` (project-name). 
+    * In your runtime environment the data will be mounted to `data/neurolibre-demo-dataset`, relative to the base if your repository.
+
+> [!TIP]
+> Feel free to make small modifications to runtime dependencies and change your code to work with the [provided data](https://raw.githubusercontent.com/plotly/datasets/master/hobbs-pearson-trials.csv). However, if you need to work with a new data, [let us know](https://github.com/neurolibre/info/issues/new?assignees=agahkarakuzu&labels=DOWNLOAD&projects=&template=data_cache.md&title=)
+
+The complete list of REES configuration files for different programming languages can be found [here](https://mybinder.readthedocs.io/en/latest/using/config_files.html).
+
+### NeuroLibre preview Binder X RoboNeuro preview service
+
+We provide a [public Binder instance](https://binder-preview.conp.cloud/) to help you create reproducible, interactive computing environments. Upon successfully building a Binder, a Docker image is pushed to our private registry, tagged with the `commit hash` of your repository.
+
+NeuroLibre can use that Docker image over and over again to build new versions of your living preprint. So hold onto that `commit hash` and keep pushing commits to work on your narrative and executable content! Unless you need to install new dependencies or modify your input data, you don't need to build a new Binder.
+
+![](https://github.com/neurolibre/brand/blob/main/png/let_it_go.png?raw=true)
+
+RoboNeuro will be glad to build the `latest` version of your preprint (from the `main` branch) at each request!
+
+Once you are happy with the current shape and form of your living print, submit it to NeuroLibre! Our team will start a technical screening to ensure that your preprint is ready for publication with the help of RoboNeuro on a GitHub issue.
+

_toc.yml

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+format: jb-book
+root: paper.md
+chapters:
+  - file: content/figure_1.ipynb
+  - file: content/figure_2.md

binder/data_requirement.json

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+{ "src": "https://raw.githubusercontent.com/plotly/datasets/master/hobbs-pearson-trials.csv",
+  "dst": "../data",
+  "projectName": "neurolibre-demo-dataset"
+}

binder/requirements.txt

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+plotly
+networkx
+pandas

binder/runtime.txt

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+python-3.10