From a7c854974993afa3eb633791845e57a852622c32 Mon Sep 17 00:00:00 2001 From: Ariel Rokem Date: Tue, 15 Oct 2024 10:14:04 -0700 Subject: [PATCH] Initial commit --- .github/workflows/draft-paper.yml | 23 + .gitignore | 135 ++++++ LICENSE | 674 ++++++++++++++++++++++++++++++ README.md | 29 ++ binder/data_requirement.json | 3 + binder/requirements.txt | 4 + binder/runtime.txt | 1 + content/00-simple_markdown.md | 10 + content/01-simple_notebook.ipynb | 95 +++++ content/02-simple-myst.md | 64 +++ content/_config.yml | 52 +++ content/_toc.yml | 9 + content/neurolibre-logo.png | Bin 0 -> 4614 bytes paper.bib | 10 + paper.md | 79 ++++ 15 files changed, 1188 insertions(+) create mode 100644 .github/workflows/draft-paper.yml create mode 100644 .gitignore create mode 100644 LICENSE create mode 100644 README.md create mode 100644 binder/data_requirement.json create mode 100644 binder/requirements.txt create mode 100644 binder/runtime.txt create mode 100644 content/00-simple_markdown.md create mode 100644 content/01-simple_notebook.ipynb create mode 100644 content/02-simple-myst.md create mode 100644 content/_config.yml create mode 100644 content/_toc.yml create mode 100644 content/neurolibre-logo.png create mode 100644 paper.bib create mode 100644 paper.md diff --git a/.github/workflows/draft-paper.yml b/.github/workflows/draft-paper.yml new file mode 100644 index 0000000..75ed661 --- /dev/null +++ b/.github/workflows/draft-paper.yml @@ -0,0 +1,23 @@ +on: [push] + +jobs: + paper: + runs-on: ubuntu-latest + name: Paper Draft + steps: + - name: Checkout + uses: actions/checkout@v3 + - name: Build draft PDF + uses: neurolibre/neurolibre-draft-action@master + with: + journal: neurolibre + # This should be the path to the paper within your repo. + paper-path: paper.md + - name: Upload + uses: actions/upload-artifact@v1 + with: + name: paper + # This is the output path where Pandoc will write the compiled + # PDF. Note, this should be the same directory as the input + # paper.md + path: paper.pdf diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..518cfea --- /dev/null +++ b/.gitignore @@ -0,0 +1,135 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# OSX +.DS_Store +__pycache__ +*~ +.ipynb_checkpoints + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +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/ + +# 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 +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.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 + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__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/ diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md new file mode 100644 index 0000000..aaba9b1 --- /dev/null +++ b/README.md @@ -0,0 +1,29 @@ +## Preprint template + +Template repository for NeuroLibre reproducibe preprint submissions. + +### Step 1: Click `Use this template button` and name your new repository + +### Step 2: Do the following changes in [_config.yml](content/_config.yml) + +```yaml +title : "NeuroLibre preprint template" # Add your title +author : John Doe, Jane Doe # Add author names +``` +```yaml +repository: + url: https://github.com/neurolibre/template # The URL to your new repository +``` +> At this stage, you are ready to use [RoboNeuro preview service](https://roboneuro.herokuapp.com/) to get your first book build. +--- +### Step 3: Add your executable content under the `content` directory + +* ✅ You can add a mixture of `Jupyter Notebooks`, `MyST` formatted markdown and plain text markdown files. +* ✅ You can organize your content in subfolders. +* ❌ We don't accept (non-executable) plain text markdown files alone. + +### Step 4: Edit [_toc.yml](content/_toc.yml) according to your new content + +### Step 5: Define your execution environment under the `binder` directory + +You can use any [BinderHub configuration files](https://mybinder.readthedocs.io/en/latest/using/config_files.html) that you need. diff --git a/binder/data_requirement.json b/binder/data_requirement.json new file mode 100644 index 0000000..410e0d0 --- /dev/null +++ b/binder/data_requirement.json @@ -0,0 +1,3 @@ +{ "src": "from nilearn import datasets; datasets.fetch_development_fmri(data_dir=_dst, n_subjects=1);", + "dataLayout": "neurolibre", + "projectName": "agah_template"} diff --git a/binder/requirements.txt b/binder/requirements.txt new file mode 100644 index 0000000..f674c1d --- /dev/null +++ b/binder/requirements.txt @@ -0,0 +1,4 @@ +plotly==5.14.1 +plotly-express==0.4.1 +repo2data>=2.6.0 +jupyter-book==0.14.0 \ No newline at end of file diff --git a/binder/runtime.txt b/binder/runtime.txt new file mode 100644 index 0000000..1d5ee4a --- /dev/null +++ b/binder/runtime.txt @@ -0,0 +1 @@ +Python-3.8 \ No newline at end of file diff --git a/content/00-simple_markdown.md b/content/00-simple_markdown.md new file mode 100644 index 0000000..bc7e0aa --- /dev/null +++ b/content/00-simple_markdown.md @@ -0,0 +1,10 @@ +# How to organize the preprint content? + +NeuroLibre expects all the preprint content (except for `paper.md` and `preprint.md`) under +the `content` folder. You can add subfolders to organize your content as you see fit. + +The `_toc.yml` file determines the structure of your Book. Please visit the [official documentation](https://jupyterbook.org/customize/toc.html) for details. + +## How to configure Book settings? + +The `_config.yml` defines the majority Book configurations. Please visit the [official documentation]https://jupyterbook.org/customize/config.html?highlight=_config%20yml) for details. \ No newline at end of file diff --git a/content/01-simple_notebook.ipynb b/content/01-simple_notebook.ipynb new file mode 100644 index 0000000..91a850b --- /dev/null +++ b/content/01-simple_notebook.ipynb @@ -0,0 +1,95 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# How to make a code cell collapsible in the Jupyter Book? \n", + "\n", + "1. In the title bar above: `View` --> `Cell Toolbar` --> `Edit Metadata`\n", + "\n", + "2. An `Edit Metadata` button will appear on the upper right corner of all the cells. Click that button for the cell you would like to expand/collapse in your preprint.\n", + "\n", + "3. Make the following addition:\n", + "\n", + "```json\n", + "{\n", + " \"tags\": [\n", + " \"hide-input\"\n", + " ]\n", + "}\n", + "```\n", + "\n", + "Please visit [Jupyter Book documentation](https://jupyterbook.org/content/index.html) for more information about the Book content and syntax. " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "tags": [ + "hide-input" + ] + }, + "outputs": [], + "source": [ + "print(\"This code cell will be hidden in the Jupyter Book.\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## How to render interactive figures?\n", + "\n", + "The code cell below uses `Plotly` to generate a simple interactive figure. When the Jupyter Book is built, the example figure will be rendered." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import plotly.express as px\n", + "from plotly.offline import plot\n", + "from IPython.core.display import HTML\n", + "\n", + "# Example dataset \n", + "df = px.data.gapminder()\n", + "\n", + "# Scatter plot with slider\n", + "fig = px.scatter(df.query(\"year==2007\"), x=\"gdpPercap\", y=\"lifeExp\", size=\"pop\", color=\"continent\",\n", + " hover_name=\"country\", log_x=True, size_max=60)\n", + "\n", + "# fig.show() # You can use this command for inline rendering as you are developing your notebook.\n", + "\n", + "plot(fig, filename = 'example_figure.html')\n", + "display(HTML('example_figure.html'))" + ] + } + ], + "metadata": { + "celltoolbar": "Edit Metadata", + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.16" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/content/02-simple-myst.md b/content/02-simple-myst.md new file mode 100644 index 0000000..f428b04 --- /dev/null +++ b/content/02-simple-myst.md @@ -0,0 +1,64 @@ +--- +jupytext: + formats: md:myst + text_representation: + extension: .md + format_name: myst + format_version: 0.13 + jupytext_version: 1.11.5 +kernelspec: + display_name: Python 3 + language: python + name: python3 +--- + +# What is MyST Markdown? + +In addition to Jupyter Notebooks, Jupyter Book also supports a special flavour of Markdown called MyST (or Markedly Structured Text). It is designed to make it easier to create publishable computational documents written with Markdown notation. + +The following sections present the same content in the Jupyter Book (`01-simple_notebook.ipynb`) in MyST format. + +## How to make a code cell collapsible in the Jupyter Book? + +In MyST, a code cell is defined as follows: + +```{code-cell} python3 + +print("This is a code cell using Python3 kernel.") + +``` + +To hide a code cell, you can simply add `:tags: [hide-cell]` expression to the beginning of a code cell: + +```{code-cell} python3 +:tags: [hide-cell] + +print("This code cell will be hidden in the Jupyter Book.") + +``` + +Please visit [Jupyter Book documentation](https://jupyterbook.org/content/index.html) for more information about the [MyST Markdown](https://jupyterbook.org/content/myst.html). + +## How to render interactive figures? + +The code cell below uses `Plotly` to generate a simple interactive figure. When the Jupyter Book is built, the example figure will be rendered. + +```{code-cell} python3 + +import plotly.express as px +from plotly.offline import plot +from IPython.core.display import HTML + +# Example dataset +df = px.data.gapminder() + +# Scatter plot with slider +fig = px.scatter(df.query("year==2007"), x="gdpPercap", y="lifeExp", size="pop", color="continent", + hover_name="country", log_x=True, size_max=60) + +# fig.show() # You can use this command for inline rendering as you are developing your notebook. + +plot(fig, filename = 'example_figure.html') +display(HTML('example_figure.html')) + +``` diff --git a/content/_config.yml b/content/_config.yml new file mode 100644 index 0000000..fda9776 --- /dev/null +++ b/content/_config.yml @@ -0,0 +1,52 @@ +####################################################################################### +# A default configuration that will be loaded for all jupyter books +# Users are expected to override these values in their own `_config.yml` file. +# This is also the "master list" of all allowed keys and values. + +####################################################################################### +# Book settings +title : "NeuroLibre preprint template" # The title of the book. Will be placed in the left navbar. +author : Robo Neuro # The author of the book +copyright : "2021" # Copyright year to be placed in the footer +logo : "neurolibre-logo.png" # A path to the book logo +exclude_patterns : [] # Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb") + +####################################################################################### +# Execution settings +execute: + execute_notebooks : auto # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off") + cache : "" # A path to the jupyter cache that will be used to store execution artifacs. Defaults to `_build/.jupyter_cache/` + exclude_patterns : [] # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time) + timeout : -1 # remove restriction on execution time +####################################################################################### +# HTML-specific settings +html: + favicon : "" # A path to a favicon image + use_edit_page_button : false # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in + use_repository_button : false # Whether to add a link to your repository button + use_issues_button : false # Whether to add an "open an issue" button + extra_navbar : Powered by Jupyter Book # Will be displayed underneath the left navbar. + extra_footer : "" # Will be displayed underneath the footer. + google_analytics_id : "" # A GA id that can be used to track book views. + home_page_in_navbar : true # Whether to include your home page in the left Navigation Bar + baseurl : "" # The base URL where your book will be hosted. Used for creating image previews and social links. e.g.: https://mypage.com/mybook/ + +####################################################################################### +# Launch button settings +launch_buttons: + notebook_interface : classic # The interface interactive links will activate ["classic", "jupyterlab"] + binderhub_url : https://test.conp.cloud # The URL of the Neurolibre BinderHub + thebe : false # Add a thebe button to pages (requires the repository to run on Binder) + +repository: + url : https://github.com/agahkarakuzu/template # The URL to your book's repository + path_to_book : "content" # A path to your book's folder, relative to the repository root. + branch : main # Which branch of the repository should be used when creating links + + +html_theme_options: + logo: + image_light: "neurolibre-logo.png" + image_dark: "neurolibre-logo.png" + +####################################################################################### diff --git a/content/_toc.yml b/content/_toc.yml new file mode 100644 index 0000000..ab06c26 --- /dev/null +++ b/content/_toc.yml @@ -0,0 +1,9 @@ +format: jb-book +root: 00-simple_markdown +parts: + - caption: Ipynb + chapters: + - file: 01-simple_notebook + - caption: MyST + chapters: + - file: 02-simple-myst \ No newline at end of file diff --git a/content/neurolibre-logo.png b/content/neurolibre-logo.png new file mode 100644 index 0000000000000000000000000000000000000000..6e51a5140f7dac010099a8aee14de894a5fc3335 GIT binary patch literal 4614 zcmZu#cRU;1*No`XDmdtHH$Kd!y*{xZN zfHz+6QySg9yqVMsettc3J`Mc6FyG$#>~wE${xZx(I_BBw!Q8yhSD)|=%;K2_Qv#`T z7eD_yU?Fm%WBLad4Qbp8cnSix1~(+3Q9D*S+=#Dyg(qoJw;$V)v;7L>pVbA2y8O;z zMGO^M#SIX7GG&vx>lC~6HCr$ViUWO#8;gfaylt~}ah0jY)gBVem#-&huJUEWc0%(& zC>DJ>gNDYG!i|yA8CHnQd@^m?_++mZMlP*x!!=ZXp*=fJv2k)U={L>|pvMnOEO%8? 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(2021)" +* `[@author:2021]` -> "(Author et al., 2021)" +* `[@author1:2021; @author2:2001]` -> "(Author1 et al., 2021; Author2 et al., 2021)" + +This is an example citation [@neurolibre:2021]. + +# Figures + +Figures can be included like this: + +![Caption for example figure.\label{fig:example}](images/example_figure.png) + +You can reference figure from text using \autoref{fig:example}. + +Figure sizes can be customized by adding an optional second parameter: + +![Caption for example figure.](images/example_figure.png){ width=20% } + +# Acknowledgements + +NeuroLibre is sponsored by Canadian Open Neuroscience Platform (CONP), Brain Canada, Quebec Bioimaging Network, Cancer Computing and Healthy Brains & Healthy Life. + +# References