Merge remote-tracking branch 'upstream/main' into readme_update

* upstream/main:
  Update indexing material (xarray-contrib#192)
  Migrate to exercise syntax (xarray-contrib#196)
  Bump pangeo/base-image from 2023.06.20 to 2023.07.05 in /.devcontainer (xarray-contrib#193)
  Add Nebari-specific instructions for SciPy 2023 (xarray-contrib#195)
  Add contributors image (xarray-contrib#194)
  Computational pattern tutorial edits (xarray-contrib#186)
  Housekeeping + clean up sidebar (xarray-contrib#190)

Author: dcherian

.devcontainer/Dockerfile

@@ -1 +1 @@
-FROM pangeo/base-image:2023.06.20
+FROM pangeo/base-image:2023.07.05

.github/workflows/main.yaml

@@ -30,7 +30,7 @@ jobs:
         with:
           path: _build
           # NOTE: change key to "jupyterbook-DATE" to force rebuilding cache
-          key: jupyterbook-20230626
+          key: jupyterbook-20230707
 
       - name: Install Conda environment with Micromamba
         uses: mamba-org/setup-micromamba@v1

.github/workflows/preview.yaml

@@ -21,7 +21,7 @@ jobs:
         with:
           path: _build
           # NOTE: change key to "jupyterbook-DATE" to force rebuilding cache
-          key: jupyterbook-20230626
+          key: jupyterbook-20230707
 
       - name: Install Conda environment with Micromamba
         uses: mamba-org/setup-micromamba@v1

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.
 

README.md

@@ -33,3 +33,11 @@ jupyter lab
 ## Contributing
 
 Contributions are welcome and greatly appreciated! See our [CONTRIBUTING.md](./CONTRIBUTING.md) document.
+
+Thanks to our contributors so far!
+
+[![Contributors](https://contrib.rocks/image?repo=xarray-contrib/xarray-tutorial)](https://github.com/xarray-contrib/xarray-tutorial/graphs/contributors)
+
+## 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).

_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 +78,7 @@ sphinx:
 
     rediraffe_redirects:
       scipy-tutorial/00_overview.ipynb: overview/get-started.md
+      workshops/scipy2022/README.md: overview/fundamental-path/README.md
+      fundamentals/02.1_working_with_labeled_data.ipynb: fundamentals/02.1_indexing_Basic.ipynb
 
     bibtex_reference_style: author_year # or label, super, \supercite

_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:
@@ -17,7 +19,7 @@ parts:
           - file: fundamentals/01.1_io
       - file: fundamentals/02_labeled_data.md
         sections:
-          - file: fundamentals/02.1_working_with_labeled_data
+          - file: fundamentals/02.1_indexing_Basic.ipynb
           - file: fundamentals/02.2_manipulating_dimensions
       - file: fundamentals/03_computation.md
         sections:
@@ -35,11 +37,17 @@ parts:
   - caption: Intermediate
     chapters:
       - file: intermediate/01-high-level-computation-patterns
+      - file: intermediate/indexing/indexing
+        sections:
+          - file: intermediate/indexing/advanced-indexing.ipynb
+          - file: intermediate/indexing/boolean-masking-indexing.ipynb
       - file: intermediate/xarray_and_dask
       - 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 +89,8 @@ 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

advanced/backends/backends.md

@@ -22,7 +22,7 @@ Xarray bundles several backends internally for the following formats:
 External Backends that use the new backend API (xarray >= v0.18.0) that allows to add support for backend without any change to Xarray
 
 - [cfgrib](https://github.com/ecmwf/cfgrib) - GRIB
-- [tiledb](https://pythonrepo.com/repo/TileDB-Inc-TileDB-xarray) - TileDB
+- [tiledb](https://github.com/TileDB-Inc/TileDB-CF-Py) - TileDB
 - [rioxarray](https://corteva.github.io/rioxarray/stable/) - GeoTIFF, JPEG-2000, ESRI-hdr, etc (via GDAL)
 - [xarray-sentinel](https://github.com/bopen/xarray-sentinel) - Sentinel-1 SAFE
 - ...

data_cleaning/data_cleaning.md

@@ -0,0 +1,5 @@
+# Data Tidying
+
+```{tableofcontents}
+
+```