diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 6883b4e6..5d3ed768 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,18 +1,22 @@ -## Contributing +# Contributing Guide -This repository is a great opportunity to start contributing to Xarray. +This tutorial repository is a great opportunity to start contributing to Xarray. -- Report bugs, request features or submit feedback as a [GitHub Issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues). First check existing issues: https://github.com/xarray-contrib/xarray-tutorial/issues ! +- Report bugs, request features or submit feedback as a [GitHub Issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues). First check existing [issues](https://github.com/xarray-contrib/xarray-tutorial/issues) ! - Make fixes, add content or improvements using [GitHub Pull Requests](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests), the sections below go over this process in more detail: +```{seealso} +The Project Pythia Foundations material on [Github](https://foundations.projectpythia.org/foundations/getting-started-github.html) and Github workflows is a great place to start if you are new to this. +``` + ## Content Guidelines Please note that examples submitted to this repository should follow these guidelines: 1. Run top-to-bottom without intervention from the user -1. Not require external data sources that may disappear over time (external data sources that are highly unlikely to disappear are fine) +1. Not require external data sources that may disappear over time (external data sources that are highly unlikely to disappear are fine). Small datasets for tutorial purposes can be added [here](https://github.com/pydata/xarray-data/) if necessary. 1. Not be resource intensive, and should run within 2GB of memory 1. Be clear and contain enough prose to explain the topic at hand 1. Be concise and limited to one or two topics, such that a reader can get through the example within a few minutes of reading @@ -31,7 +35,7 @@ cd xarray-tutorial You'll need `conda` or `mamba`, which can be installed from https://github.com/conda-forge/miniforge -We also use [conda-lock](https://conda-incubator.github.io/conda-lock/) to ensure we have reproducible environments across different operating systems +We also use [conda-lock](https://conda.github.io/conda-lock/) to ensure we have reproducible environments across different operating systems We also use [pre-commit hooks](https://pre-commit.com) to run styling and other checks before committing code. diff --git a/README.md b/README.md index 53414c51..58606948 100644 --- a/README.md +++ b/README.md @@ -33,3 +33,7 @@ jupyter lab ## Contributing Contributions are welcome and greatly appreciated! See our [CONTRIBUTING.md](./CONTRIBUTING.md) document. + +## Acknowledgements + +This website is the result of many contributions from the Xarray community! We're very grateful for everyone's volunteered effort as well as [sponsored development](https://xarray.dev/#sponsors). Funding for SciPy 2022, SciPy 2023 tutorial materialdevelopment specifically was supported by NASA's Open Source Tools, Frameworks, and Libraries Program (award 80NSSC22K0345). diff --git a/_config.yml b/_config.yml index 218dbff1..78978501 100644 --- a/_config.yml +++ b/_config.yml @@ -19,7 +19,8 @@ parse: # https://jupyterbook.org/content/content-blocks.html?highlight=myst%20substitution#define-substitutions-for-your-whole-book # https://jupyterbook.org/content/content-blocks.html#using-substitutions-in-links myst_substitutions: - xarray_docs: https://xarray.dev + xarray_homepage: https://xarray.dev + xarray_docs: https://docs.xarray.dev xarray_repo: https://github.com/pydata/xarray xarray_forum: https://github.com/pydata/xarray/discussions myst_enable_extensions: @@ -68,6 +69,7 @@ sphinx: - sphinxext.rediraffe - sphinx_exercise config: + language: en # accessibility # application/vnd.holoviews_load.v0+json, application/vnd.holoviews_exec.v0+json suppress_warnings: ['mystnb.unknown_mime_type', 'misc.highlighting_failure'] notfound_context: @@ -76,5 +78,6 @@ sphinx: rediraffe_redirects: scipy-tutorial/00_overview.ipynb: overview/get-started.md + workshops/scipy2022/README.md: overview/fundamental-path/README.md bibtex_reference_style: author_year # or label, super, \supercite diff --git a/_toc.yml b/_toc.yml index 33d72793..6e8ea89e 100644 --- a/_toc.yml +++ b/_toc.yml @@ -6,7 +6,9 @@ parts: chapters: - file: overview/get-started.md - file: overview/xarray-in-45-min - - file: overview/fundamental-path/README.md + - file: overview/learning-paths.md + sections: + - file: overview/fundamental-path/README.md - caption: Fundamentals chapters: @@ -39,7 +41,9 @@ parts: - file: intermediate/xarray_ecosystem - file: intermediate/hvplot - file: intermediate/cmip6-cloud - - file: data_cleaning/ice_velocity.ipynb + - file: data_cleaning/data_cleaning.md + sections: + - file: data_cleaning/ice_velocity - caption: Advanced chapters: @@ -81,16 +85,8 @@ parts: - file: workshops/online-tutorial-series/02_indexing - file: workshops/online-tutorial-series/03_computation - - caption: Domain Specific - chapters: - - url: https://anopheles-genomic-surveillance.github.io/workshop-5/module-1-xarray.html - title: Genomics - - url: https://predictablynoisy.com/posts/2019/2019-10-22-xarray-neuro/ - title: Electrophysiology - - caption: Reference chapters: + - file: CONTRIBUTING - file: reference/resources - file: reference/glossary - - file: reference/bibliography - - file: reference/acknowledgements diff --git a/data_cleaning/data_cleaning.md b/data_cleaning/data_cleaning.md new file mode 100644 index 00000000..154064a1 --- /dev/null +++ b/data_cleaning/data_cleaning.md @@ -0,0 +1,5 @@ +# Data Tidying + +```{tableofcontents} + +``` diff --git a/images/alignment_schematic.png b/images/alignment_schematic.png index 9b04ab07..b9c91245 100644 Binary files a/images/alignment_schematic.png and b/images/alignment_schematic.png differ diff --git a/images/broadcasting.png b/images/broadcasting.png index 67b6a5bd..4bdd88ad 100644 Binary files a/images/broadcasting.png and b/images/broadcasting.png differ diff --git a/images/broadcasting_schematic.png b/images/broadcasting_schematic.png index ecdfeb81..034950ab 100644 Binary files a/images/broadcasting_schematic.png and b/images/broadcasting_schematic.png differ diff --git a/images/logo.png b/images/logo.png index 4c2042c5..8fa32d2a 100644 Binary files a/images/logo.png and b/images/logo.png differ diff --git a/images/scipylogo.png b/images/scipylogo.png index 6303d6d1..59c34332 100644 Binary files a/images/scipylogo.png and b/images/scipylogo.png differ diff --git a/images/xarray-data-structures.png b/images/xarray-data-structures.png index c472423e..8f4d4ae7 100644 Binary files a/images/xarray-data-structures.png and b/images/xarray-data-structures.png differ diff --git a/intro.md b/intro.md index c3b03257..aec20724 100644 --- a/intro.md +++ b/intro.md @@ -35,4 +35,16 @@ Ask questions on the Xarray Discussion Forum ```` +## Citation + ✏️ To cite this material, you can use the recommended [Xarray citation](https://docs.xarray.dev/en/stable/getting-started-guide/faq.html#how-should-i-cite-xarray): {cite:p}`hoyerhamman2017`, {cite:p}`xarray_v202230`. + +## Acknowledgements + +This website is the result of many contributions from the Xarray community! We're very grateful for everyone's volunteered effort as well as [sponsored development](https://xarray.dev/#sponsors). Funding for SciPy 2022, SciPy 2023 tutorial material development specifically was supported by NASA's Open Source Tools, Frameworks, and Libraries Program (award 80NSSC22K0345). + +## Bibliography + +```{bibliography} +:style: plain +``` diff --git a/overview/fundamental-path/README.md b/overview/fundamental-path/README.md index 359a240c..7c768049 100644 --- a/overview/fundamental-path/README.md +++ b/overview/fundamental-path/README.md @@ -1,4 +1,4 @@ -# Fundamental Learning Path +# Fundamentals Learning Path This syllabus comes from Scipy 2022 tutorial workshop. This path covers fundamental Xarray concepts with diff --git a/overview/learning-paths.md b/overview/learning-paths.md new file mode 100644 index 00000000..9e7922e4 --- /dev/null +++ b/overview/learning-paths.md @@ -0,0 +1,11 @@ +# Learning Paths + +Learning Paths are guided tours through the material on the site. +These paths were originally built for in-person tutorials at the SciPy conference. +They are useful if you would like to work through the material in an organized manner. + +Follow the links below to try out each path. + +```{tableofcontents} + +``` diff --git a/reference/acknowledgements.md b/reference/acknowledgements.md deleted file mode 100644 index c2f90d25..00000000 --- a/reference/acknowledgements.md +++ /dev/null @@ -1,3 +0,0 @@ -# Acknowledgements - -This website is the result of many contributions from the Xarray community! We're very grateful for everyone's volunteered effort as well as [sponsored development](https://xarray.dev/#sponsors). Funding for 2022 SciPy tutorial development specifically was supported by NASA's Open Source Tools, Frameworks, and Libraries Program (award 80NSSC22K0345) diff --git a/reference/bibliography.md b/reference/bibliography.md deleted file mode 100644 index c4375e2c..00000000 --- a/reference/bibliography.md +++ /dev/null @@ -1,5 +0,0 @@ -# Bibliography - -```{bibliography} -:style: plain -``` diff --git a/reference/resources.md b/reference/resources.md index 8b6a611c..ae61724e 100644 --- a/reference/resources.md +++ b/reference/resources.md @@ -5,7 +5,14 @@ demonstrate real-world applications of Xarray in a variety of use cases. These need not be explored in any particular sequence, instead they are meant to provide a sampling of what Xarray can be used for. -## Weather/Climate Model Data +```{seealso} +1. The [Xarray blog](https://xarray.dev/blog) has a number of user stories showcasing Xarray in +many scientific domains. +2. [Project Pythia Foundations](https://foundations.projectpythia.org/) is a great collection of +material on Xarray and related packages. +``` + +## Weather and Climate 1. [Global Mean Surface Temperature from CMIP6](https://gallery.pangeo.io/repos/pangeo-gallery/cmip6/): Start with `global_mean_surface_temp.ipynb` then feel free to explore the @@ -14,10 +21,9 @@ provide a sampling of what Xarray can be used for. 1. [National Water Model Streamflow Analysis](https://gallery.pangeo.io/repos/rsignell-usgs/esip-gallery/): Start with `02_National_Water_Model.ipynb` then feel free to explore the rest of the notebooks. - -## Satellite Data - -1. [Planetary Computer Examples](https://github.com/microsoft/PlanetaryComputerExamples) +1. The [Project Pythia Cookbooks](https://cookbooks.projectpythia.org/) are a great collection of + resources showcasing use of Xarray with real world datasets. +1. [Examples using the Microsoft Planetary Computer](https://github.com/microsoft/PlanetaryComputerExamples) ## Bayesian Statistical Modeling @@ -25,3 +31,11 @@ provide a sampling of what Xarray can be used for. Start with `multilevel_modeling.ipynb` then feel free to explore the rest of the notebooks. Also checkout [Arviz](https://arviz-devs.github.io/arviz/) which uses Xarray as its data model. + +## Genomics + +1. [From "data analysis for genomic surveillance of African malaria vectors" ](https://anopheles-genomic-surveillance.github.io/workshop-5/module-1-xarray.html) + +## Electrophysiology + +1. ["Analyzing intracranial electrophysiology data with xarray"](https://chrisholdgraf.com/blog/2019/2019-10-22-xarray-neuro/)