Merge branch 'main' into feature/582-skipna

.github/workflows/build_workflow.yml

@@ -95,7 +95,8 @@ jobs:
               run: |
                   mamba env update -n xcdat_ci -f conda-env/ci.yml
                   # Make sure the Python version in the env matches the current matrix version.
-                  mamba install -c conda-forge python=${{ matrix.python-version }}
+                  # Make sure numpy is not > 2.0.
+                  mamba install -c conda-forge python=${{ matrix.python-version }} "numpy>=1.23.0,<2.0"
 
             - name: Install xcdat
               # Source: https://github.com/conda/conda-build/issues/4251#issuecomment-1053460542

.gitignore

@@ -3,6 +3,8 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+.DS_Store
+
 # C extensions
 *.so
 
@@ -119,3 +121,6 @@ qa/
 
 # Custom Sphinx generated .txt files.
 docs/*.txt
+
+# ESGF wget script status files.
+*.sh.status

HISTORY.rst

@@ -2,6 +2,41 @@
 History
 =======
 
+v0.7.1 (24 June 2024)
+----------------------
+
+This patch release fixes a bug in the Regrid2 API where a static order of dimensions are
+incorrectly expected. It updates ``add_missing_bounds()`` to convert ``np.timedelta64``
+values to ``pandas.Timedelta`` objects to support Xarray's datetime component
+accessor.
+
+This release also includes numerous updates to the documentation, including adding
+a general guide to parallel computing with Dask notebook. It also ensures all existing
+notebooks and documentation are up to date with the latest and relevant information.
+
+Bug Fixes
+~~~~~~~~~
+
+- Fixes regrid2 mapping output to input ordering by `Jason Boutte`_
+  in https://github.com/xCDAT/xcdat/pull/653
+- Update ``add_missing_bounds()`` to convert ``np.timedelta64`` to ``pd.Timedelta``
+  to support Xarray's datetime component accessor `_Jiwoo Lee` in https://github.com/xCDAT/xcdat/pull/660
+
+Documentation
+~~~~~~~~~~~~~
+
+- Add JOSS paper by `Tom Vo`_ in https://github.com/xCDAT/xcdat/pull/567
+- Add Parallel Computing with Dask Jupyter Notebook by `Tom Vo`_ in https://github.com/xCDAT/xcdat/pull/489
+- Update regridding notebook for v0.7.0 by `Jill Chengzhu Zhang`_ in https://github.com/xCDAT/xcdat/pull/646
+- Update FAQs, HPC guide, and Gentle Introduction by `Tom Vo`_ in https://github.com/xCDAT/xcdat/pull/650
+- Simplify the contributing guide by `Tom Vo`_ in https://github.com/xCDAT/xcdat/pull/593
+- Update notebook env setup instructions with kernel by `Tom Vo`_ in https://github.com/xCDAT/xcdat/pull/652
+- Add instructions for setting `ESMFMKFILE` and update links to xESMF docs by `Tom Vo`_ in https://github.com/xCDAT/xcdat/pull/643
+- Temporal average notebooks maintanance by `Jiwoo Lee`_ in https://github.com/xCDAT/xcdat/pull/633
+- Review of spatial averaging and general dataset utilities by `Stephen Po-Chedley`_ in https://github.com/xCDAT/xcdat/pull/644
+
+**Full Changelog**: https://github.com/xCDAT/xcdat/compare/v0.7.0...v0.7.1
+
 v0.7.0 (10 April 2024)
 ----------------------
 
@@ -54,7 +89,7 @@ Deprecations
    -  Remove CDML/XML support from ``open_dataset()`` and
       ``open_mfdataset()`` since CDAT is EOL since Dec/2023
 
-**Full Changelog**: https://github.com/xCDAT/xcdat/compare/v0.6.1...0.7.0
+**Full Changelog**: https://github.com/xCDAT/xcdat/compare/v0.6.1...v0.7.0
 
 v0.6.1 (29 November 2023)
 -------------------------

README.rst

@@ -17,7 +17,7 @@
    +====================+======================================================+
    | Distribution       | |conda-forge| |platforms| |conda-downloads|          |
    +--------------------+------------------------------------------------------+
-   | Citation           | |zenodo-doi|                                         |
+   | Citation           | |zenodo-doi| |joss|                                  |
    +--------------------+------------------------------------------------------+
    | DevOps             | |CI/CD Build Workflow| |codecov| |docs|              |
    +--------------------+------------------------------------------------------+
@@ -36,6 +36,8 @@
    :target: https://anaconda.org/conda-forge/xcdat
 .. |zenodo-doi| image:: https://zenodo.org/badge/354103918.svg
    :target: https://zenodo.org/badge/latestdoi/354103918
+.. |joss| image:: https://joss.theoj.org/papers/10.21105/joss.06426/status.svg
+   :target: https://doi.org/10.21105/joss.06426
 .. |CI/CD Build Workflow| image:: https://github.com/xCDAT/xcdat/actions/workflows/build_workflow.yml/badge.svg
    :target: https://github.com/xCDAT/xcdat/actions/workflows/build_workflow.yml
 .. |docs| image:: https://readthedocs.org/projects/xcdat/badge/?version=latest
@@ -250,6 +252,14 @@ Environmental Research (`BER`_) within the `Department of Energy`_'s `Office of
 .. _Department of Energy: https://www.energy.gov/
 .. _Office of Science: https://science.osti.gov/
 
+.. raw:: html
+
+   <p align="center">
+      <img style="display: inline-block; width:200px" src="./docs/_static/e3sm-logo.jpg" alt="E3SM logo"/>
+      <img style="display: inline-block; width:200px" src="./docs/_static/pcmdi-logo.png" alt="PCMDI logo"/>
+      <img style="display: inline-block; width:200px" src="./docs/_static/seats-logo.png" alt="SEATS logo"/>
+   </p>
+
 Contributors
 ------------
 

conda-env/ci.yml

@@ -11,7 +11,7 @@ dependencies:
     - cftime
     - dask
     - netcdf4
-    - numpy >=1.23.0
+    - numpy >=1.23.0,<2.0
     - pandas
     - python-dateutil
     - xarray >=2022.02.0

conda-env/dev.yml

@@ -11,7 +11,7 @@ dependencies:
     - cftime
     - dask
     - netcdf4
-    - numpy >=1.23.0
+    - numpy >=1.23.0,<2.0
     - pandas
     - python-dateutil
     - xarray >=2022.02.0

docs/demos.rst

@@ -11,4 +11,9 @@ This page includes relevant xCDAT presentations, demos, and papers.
 
     AMS 2023 Abstract <https://ams.confex.com/ams/103ANNUAL/meetingapp.cgi/Paper/412648>
     demos/1-25-23-cwss-seminar/introduction-to-xcdat.ipynb
-    ESGF2 - A Gentle Introduction to xCDAT (video introduction) <https://youtu.be/sJpQ9vKDKa8?feature=shared>
+    ESGF2 - A Gentle Introduction to xCDAT (Video Introduction) <https://youtu.be/sJpQ9vKDKa8?feature=shared>
+    Journal of Open Source Software Paper  <https://joss.theoj.org/papers/10.21105/joss.06426>
+    DOE EESM Research Highlight <https://climatemodeling.science.energy.gov/research-highlights/xcdat-python-package-simple-and-robust-analysis-climate-data>
+    SciPy 2024 (Abstract) <https://cfp.scipy.org/2024/talk/VRACYW/>
+    SciPy 2024 (Presentation Notebook) <demos/24-07-11-scipy-2024/scipy-2024.ipynb>
+    DOE EESM PI Meeting Presentation <https://climatemodeling.science.energy.gov/presentations/xcdat-xarray-climate-data-analysis-tools-python-package-simple-and-robust-analysis>

docs/demos.yml

@@ -2,10 +2,30 @@
   path: https://ams.confex.com/ams/103ANNUAL/meetingapp.cgi/Paper/412648
   thumbnail: _static/thumbnails/ams-logo.jpg
 
-- title: LLNL Climate and Weather Seminar Series (01/25/2023) - A Gentle Introduction to xCDAT
+- title: LLNL Climate and Weather Seminar Series (01/25/23) - A Gentle Introduction to xCDAT
   path: demos/1-25-23-cwss-seminar/introduction-to-xcdat.ipynb
   thumbnail: _static/thumbnails/llnl-logo.png
 
-- title: ESGF2 - A Gentle Introduction to xCDAT (video introduction)
+- title: ESGF2 - A Gentle Introduction to xCDAT (Video Introduction, 03/23/23)
   path: https://youtu.be/sJpQ9vKDKa8?feature=shared
   thumbnail: _static/thumbnails/esgf2-logo.png
+
+- title: Journal of Open Source Software Paper (06/29/24)
+  path: https://joss.theoj.org/papers/10.21105/joss.06426
+  thumbnail: _static/thumbnails/joss-logo.jpg
+
+- title: DOE EESM Research Highlight (06/29/24)
+  path: https://climatemodeling.science.energy.gov/research-highlights/xcdat-python-package-simple-and-robust-analysis-climate-data
+  thumbnail: _static/thumbnails/doe-logo.jpg
+
+- title: SciPy 2024 (Abstract, 07/11/24)
+  path: https://cfp.scipy.org/2024/talk/VRACYW/
+  thumbnail: _static/thumbnails/scipy-logo.png
+
+- title: SciPy 2024 (Presentation Notebook, 07/11/24)
+  path: demos/24-07-11-scipy-2024/scipy-2024.ipynb
+  thumbnail: _static/thumbnails/scipy-logo.png
+
+- title: DOE EESM PI Meeting 2024 Presentation (08/08/24)
+  path: https://climatemodeling.science.energy.gov/presentations/xcdat-xarray-climate-data-analysis-tools-python-package-simple-and-robust-analysis
+  thumbnail: _static/thumbnails/doe-logo.jpg

docs/demos/1-25-23-cwss-seminar/introduction-to-xcdat.ipynb

@@ -1,7 +1,6 @@
 {
  "cells": [
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {
     "cell_style": "center",
@@ -1546,7 +1545,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {
     "slideshow": {
@@ -4867,7 +4865,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.11.9"
   },
   "rise": {
    "scroll": true,