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README.md

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# <img src="https://www.pyopensci.org/images/logo.png" width=100 /> pyOpenSci Lessons
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[![All Contributors](https://img.shields.io/github/all-contributors/pyOpenSci/lessons?color=ee8449)](#contributors-)
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![GitHub release (latest by date)](https://img.shields.io/github/v/release/pyopensci/lessons?color=purple&display_name=tag&style=plastic)
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[![DOI](https://zenodo.org/badge/855935338.svg)](https://doi.org/10.5281/zenodo.13910245)
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[![CircleCI](https://circleci.com/gh/pyOpenSci/lessons.svg?style=svg)](https://circleci.com/gh/pyOpenSci/lessons)
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[![Binder](https://binder.opensci.2i2c.cloud/badge_logo.svg)](https://binder.opensci.2i2c.cloud/v2/gh/pyopensci/lessons/HEAD)
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## What is pyOpenSci?
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pyOpenSci is devoted to building diverse, supportive community around
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[pyOpenSci](https://pyopensci.org) is devoted to building diverse, supportive community around
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the Python open source tools that drive open science. We do this through:
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* open peer review
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## About this repo
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This repo contains a set of lessons being developed for pyOpenSci training
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events. as of early October 2024 it is a new repo being rapidly developed.
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This repo contains lessons being developed for pyOpenSci training
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events. This living repo is under active development.
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Please expect the contents to change at any time!
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With that said all contributions are always welcome!
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## Contributing statement
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## How to setup
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This repository contains the source files for the [pyOpenSci Tutorials](https://pyopensci.org/lessons).
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## Code formatting in Jupyter
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If yo are working on the notebooks, you may want to apply ruff for code formatting. Instructions on how to set this up in Jupyter Lab are below:
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<https://gist.github.com/jbwhit/eecdd1cac2756df85ad165f437445b0b>
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## Build the guidebook locally
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Our guidebook is built with [Sphinx](https://sphinx-doc.org) which is a documentation tool and uses the pyos-sphinx-theme which customizes the pydata-sphinx-theme.
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The easiest way to build our documentation is to use [the `nox` automation tool](https://nox.thea.codes/),
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a tool for quickly building environments and running
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commands within them.
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Using `nox` ensures that your environment has all the dependencies needed to build the documentation.
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To build, follow these steps:
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1. Install `nox`
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```console
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python -m pip install nox
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```
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### Using Binder for workshops
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2. Build the documentation:
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```console
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nox -s docs
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```
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This should create a local environment in a `.nox` folder, build the documentation (as specified in the `noxfile.py` configuration), and the output will be in `_build/html`.
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1. Click on the Binder badge at the top of this README.
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2. Wait 15-60 seconds and Binder will open a Jupyter Lab instance for you to use.
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3. We use [Jupytext](https://jupytext.readthedocs.io/en/latest/) to author our notebooks and lessons.
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These lessons are stored as Markdown (`.md`) files.
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4. To open a Markdown (Jupytext file) file, highlight the file in the left sidebar and right click to
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bring up a context sensitive menu. Select "Open with Jupytext".
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5. Enjoy discovering and learning in the notebook. **Remember** Shift-Enter or the play button executes
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a highlighted cell
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To build live documentation that updates when you update local files, run the following command:
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### Using Codespaces for workshops
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```console
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nox -s docs-live
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```
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We use [Codespaces](https://github.com/features/codespaces) in some lessons to offer a fully configured, general coding environment for users.
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## Contributing to pyOpenSci lessons
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## Gratitude
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We welcome and issues and pull requests to improve the content of this guide.
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If you'd like to see an improvement, please [open an issue](https://github.com/pyOpenSci/lessons/issues/new/choose).
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Thank you to [2i2c](https://2i2c.org/) for providing a Binder instance that we can use for workshops.
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We're grateful for the work that they are doing to support open learning and discovery.
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## Contributors ✨
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This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
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## Star History
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## Contributing
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[![Star History Chart](https://api.star-history.com/svg?repos=pyOpenSci/lessons&type=Date)](https://star-history.com/#pyOpenSci/lessons&Date)
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We welcome and issues and pull requests to improve the content of these lessons.
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If you'd like to see an improvement, please [open an issue](https://github.com/pyOpenSci/lessons/issues/new/choose).
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## Gratitude
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### Getting started
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Thank you to [2i2c](https://2i2c.org/) for providing a Binder instance that we can use for workshops.
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We're grateful for the work that they are doing to support open learning and discovery.
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This repository contains the source files for the [pyOpenSci Tutorials](https://pyopensci.org/lessons). We use Jupytext, MystMarkdown and Sphinx to maintain these lessons.
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### Workshop access to Binder
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### Build the guidebook locally
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1. Click on the Binder badge at the top of this README.
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2. Wait 15-60 seconds and Binder will open a Jupyter Lab instance for you to use.
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3. We use [Jupytext](https://jupytext.readthedocs.io/en/latest/) to author our notebooks and lessons.
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These lessons are stored as Markdown (`.md`) files.
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4. To open a Markdown (Jupytext file) file, highlight the file in the left sidebar and right click to
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bring up a context sensitive menu. Select "Open with Jupytext".
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5. Enjoy discovering and learning in the notebook. **Remember** Shift-Enter or the play button executes
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a highlighted cell
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Our guidebook is built with [Sphinx](https://sphinx-doc.org) which is a documentation tool and uses the pyos-sphinx-theme which customizes the pydata-sphinx-theme.
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The easiest way to build our documentation is to use [the `nox` automation tool](https://nox.thea.codes/),
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a tool for quickly building environments and running
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commands within them.
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Using `nox` ensures that your environment has all the dependencies needed to build the documentation.
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To build, follow these steps:
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1. Install `nox`
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```console
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python -m pip install nox
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```
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2. Build the documentation:
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```console
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nox -s docs-test
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```
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This should create a local environment in a `.nox` folder, build the documentation (as specified in the `noxfile.py` configuration), and the output will be in `_build/html`.
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To build live documentation that updates when you update local files, run the following command:
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```console
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nox -s docs-live
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```
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### Code formatting in Jupyter
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If you are working on the notebooks, you may want to apply ruff for code formatting. Instructions on how to set this up in Jupyter Lab are below:
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<https://gist.github.com/jbwhit/eecdd1cac2756df85ad165f437445b0b>
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## Star History
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[![Star History Chart](https://api.star-history.com/svg?repos=pyOpenSci/lessons&type=Date)](https://star-history.com/#pyOpenSci/lessons&Date)

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