[pull] main from NCAR:main

.github/workflows/ci.yml

@@ -47,7 +47,7 @@ jobs:
 
       - name: tests
         run: |
-          python -m pytest
+          python -m pytest --mpl
 
   link-check:
     runs-on: ubuntu-latest

.github/workflows/pypi.yaml

@@ -49,7 +49,7 @@ jobs:
           python -m twine check dist/*
 
       - name: Publish package to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.9.0
+        uses: pypa/gh-action-pypi-publish@v1.12.4
         with:
           skip-existing: true
           verbose: true

.pre-commit-config.yaml

@@ -1,22 +1,28 @@
 repos:
--   repo: https://github.com/pre-commit/mirrors-yapf    # To format the code to conform YAPF
-    rev: v0.31.0
+-   repo: https://github.com/google/yapf    # To format the code to conform YAPF
+    rev: v0.43.0
     hooks:
       - id: yapf
         args: ['--in-place', '--recursive', '--style', 'google']
+        require_serial: true
 
--   repo: https://github.com/myint/docformatter    # To format the doc strings to conform PEP257
-    rev: v1.4
-    hooks:
-    - id: docformatter
-      args: [--in-place]
-
+# -   repo: https://github.com/PyCQA/docformatter    # To format the doc strings to conform PEP257
+#     rev: v1.7.5
+#     hooks:
+#     - id: docformatter
+#       args: [--in-place]
+#
 -   repo: https://github.com/pre-commit/pre-commit-hooks    # Some common pre-commit hooks
-    rev: v3.4.0
+    rev: v5.0.0
     hooks:
     - id: check-yaml               # Checks the syntax of .yaml files.
       args: [--allow-multiple-documents]
       exclude: 'meta.yaml'    # Exclude this because it gives an error for '%' in Line 1 and couldn't fix yet
     - id: end-of-file-fixer        # Makes sure files end with a newline.
     - id: trailing-whitespace      # Checks for any tabs or spaces after the last non-whitespace character on the line.
     - id: check-docstring-first    # Checks that code comes after the docstrings.
+    - id: check-yaml               # Check valid yml file
+
+ci:
+    autofix_prs: false
+    autoupdate_schedule: monthly

CODE_OF_CONDUCT.md

@@ -25,7 +25,7 @@ Examples of behaviors that contribute to a positive environment include:
 Examples of unacceptable behavior include, but are not limited to:
 
 - Harassment, intimidation, or discrimination in any form
-- Physical, verbal, or written abuse by anyone to anyone, including repeated use of pronouns other than those requested
+- Physical, verbal, or written abuse by anyone to anyone
 - Unwelcome sexual attention or advances
 - Personal attacks directed at other guests, members, participants, etc.
 - Publishing others’ private information, such as a physical or electronic address, without explicit permission
@@ -68,9 +68,8 @@ Upon receipt of a complaint, the project administrator(s) may take any action de
 circumstances. Such action can include things such as: removing, editing, or rejecting comments, commits, code, wiki edits,
 email, issues, and other contributions that are not aligned to this Code of Conduct, or banning temporarily or permanently
 any contributor for other behaviors that are deemed inappropriate, threatening, offensive, or harmful. Project administrators
-also have the right to report violations to UCAR HR and/or UCAR’s Office of Diversity, Equity and Inclusion (ODEI), as well
-as a participant’s home institution and/or law enforcement. In the event an incident is reported to UCAR, UCAR will follow
-its Harassment Reporting and Complaint Procedure.
+also have the right to report violations to UCAR HR, as well as a participant’s home institution and/or law enforcement. In 
+the event an incident is reported to UCAR, UCAR will follow its Harassment Reporting and Complaint Procedure.
 
 ## Attribution
 
@@ -79,4 +78,4 @@ Participant Code of Conduct, which also borrows from the American Geophysical Un
 Code of Conduct applies to both UCAR employees as well as participants in activities run by UCAR. The original version of this
 for all software projects that have strong management from UCAR or UCAR staff is available on the UCAR website at
 [https://doi.org/10.5065/6w2c-a132](https://doi.org/10.5065/6w2c-a132). The date that it was adopted by this project was 2
-October 2023. When responding to complaints, UCAR HR and ODEI will do so based on the latest published version.
+October 2023. When responding to complaints, UCAR HR will do so based on the latest published version.

build_envs/docs.yml

@@ -13,7 +13,7 @@ dependencies:
   - myst-nb
   - nbsphinx
   - sphinx-design
-  - xarray
+  - xarray!=2024.11.0
   - geocat-datafiles
   - pip:
       - -e ..

docs/citation.rst

@@ -11,33 +11,24 @@ users to access older releases. This ensures that users are not only able to cit
 software version through DOIs but are also able to download & use the corresponding release for
 reproducibility purposes.
 
-Please find DOIs for all the GeoCAT-viz versions `here
-<https://zenodo.org/search?page=1&size=20&q=conceptrecid:%226678345%22&sort=-version&all_versions=True>`_.
+DOIs for all the GeoCAT-viz versions can be found `here on Zenodo
+<https://zenodo.org/search?q=parent.id%3A6678345&f=allversions%3Atrue&l=list&p=1&s=10&sort=version>`_.
 
+Example citations
+^^^^^^^^^^^^^^^^^
 
-If you would like to cite GeoCAT-viz as a whole (without referring to a specific version), use
-the following text:
-
-    **Visualization & Analysis Systems Technologies. (2020).
-    Geoscience Community Analysis Toolkit: GeoCAT-viz [Software].
-    Boulder, CO: NSF NCAR Computational and Information Systems Lab. doi:10.5281/zenodo.6678345.**
-
-Instead, if you would like to cite a specific version of GeoCAT-viz, use the following text:
-
-    **Visualization & Analysis Systems Technologies. (\<Year\>).
-    Geoscience Community Analysis Toolkit: GeoCAT-viz (v\<version\>) [Software].
-    Boulder, CO, USA: NSF NCAR Computational and Information Systems Lab. doi:\<DOI\>.**
-
-In the above citation text, update the year, GeoCAT-viz version, and DOI as appropriate. For
-example:
+Citing a specific version of GeoCAT-viz:
 
     **Visualization & Analysis Systems Technologies. (2022).
     Geoscience Community Analysis Toolkit: GeoCAT-viz (v2022.05.0) [Software].
     Boulder, CO, USA: NSF NCAR Computational and Information Systems Lab. doi:10.5281/zenodo.6678351.**
 
-Please note: The DOI minting service, Zenodo, might be suggesting their own citation text (as
-they are the publisher of such DOIs) in their website. We prefer the text we recommend here to be used;
-however, either way is acceptable.
+.. attention::
+
+   Requires updating the year, GeoCAT-viz version, and DOI
+
+Citing GeoCAT-viz without referring to a specific version:
 
-For further information, please refer to
-`GeoCAT homepage - Citation <https://geocat.ucar.edu/pages/citation.html>`_.
+    **Visualization & Analysis Systems Technologies. (2020).
+    Geoscience Community Analysis Toolkit: GeoCAT-viz [Software].
+    Boulder, CO: NSF NCAR Computational and Information Systems Lab. doi:10.5281/zenodo.6678345.**

docs/conf.py

@@ -212,20 +212,30 @@ def __getattr__(cls, name):
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-html_theme_options = dict(
-    # analytics_id=''  this is configured in rtfd.io
-    # canonical_url="",
-    repository_url="https://github.com/NCAR/geocat-viz",
-    repository_branch="main",
-    path_to_docs="docs",
-    use_edit_page_button=True,
-    use_repository_button=True,
-    use_issues_button=True,
-    home_page_in_toc=False,
-    navbar_footer_text="",
-    extra_footer=
-    "<em>This material is based upon work supported by the NSF National Center for Atmospheric Research, a major facility sponsored by the U.S. National Science Foundation and managed by the University Corporation for Atmospheric Research. Any opinions, findings and conclusions or recommendations expressed in this material do not necessarily reflect the views of the U.S. National Science Foundation.</em>",
-)
+html_theme_options = {
+    "repository_url":
+        "https://github.com/NCAR/geocat-viz",
+    "repository_branch":
+        "main",
+    "path_to_docs":
+        "docs",
+    "use_edit_page_button":
+        True,
+    "use_repository_button":
+        True,
+    "use_issues_button":
+        True,
+    "home_page_in_toc":
+        False,
+    "navbar_footer_text":
+        "",
+    "logo": {
+        "image_light": '_static/images/logos/NSF_NCAR_light.svg',
+        "image_dark": '_static/images/logos/NSF_NCAR_dark.svg',
+    },
+    "extra_footer":
+        "<em>This material is based upon work supported by the NSF National Center for Atmospheric Research, a major facility sponsored by the U.S. National Science Foundation and managed by the University Corporation for Atmospheric Research. Any opinions, findings and conclusions or recommendations expressed in this material do not necessarily reflect the views of the U.S. National Science Foundation.</em>",
+}
 
 # Add any paths that contain custom themes here, relative to this directory.
 #html_theme_path = []
@@ -237,15 +247,6 @@ def __getattr__(cls, name):
 # A shorter title for the navigation bar.  Default is the same as html_title.
 #html_short_title = None
 
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-html_theme_options = {
-    "logo": {
-        "image_light": '_static/images/logos/NSF_NCAR_light.svg',
-        "image_dark": '_static/images/logos/NSF_NCAR_dark.svg',
-    }
-}
-
 # The name of an image file (relative to this directory) to use as a favicon of
 # the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.

docs/index.rst

@@ -86,7 +86,6 @@ plotting packages.
 
    Release Notes <release-notes.rst>
    Contributor's Guide <contrib.rst>
-   Roadmap <https://geocat.ucar.edu/pages/roadmap.html>
 
 .. toctree::
    :maxdepth: 2

docs/release-notes.rst

@@ -5,12 +5,20 @@
 Release Notes
 =============
 
-v2024.07.0 (unreleased)
+v2024.xx.0 (unreleased)
 ---------------------------
 
+Documentation
+^^^^^^^^^^^^^
+* Remove link to broken NCL_vector_5.py example by `Katelyn FitzGerald`_ in (pr::`249`)
+* Fix documentation theme configuration by `Katelyn FitzGerald`_ in (pr::`253`)
+* Minor updates and removal of broken link on citation page by`Katelyn FitzGerald`_ in (pr::`260`)
+
 Internal Changes
 ^^^^^^^^^^^^^^^^
+* Update pre-commit versions and configuration by `Katelyn FitzGerald`_ in (:pr:`247`)
 * Remove M1 workaround for CI and tokens that are no longer needed by `Katelyn FitzGerald`_ in (:pr:`232`)
+* Modify tests to avoid hitting an unrelated Xarray bug and turn on image comparison testing by `Katelyn FitzGerald`_ in (:pr:`257`)
 
 Testing
 ^^^^^^^

src/geocat/viz/taylor.py

@@ -506,7 +506,8 @@ def add_ygrid(self,
 
         *arr*.
 
-        This method will be deprecated in favor of `TaylorDiagram.add_std_grid()`
+        This method will be deprecated in favor of
+        `TaylorDiagram.add_std_grid()`
         """
 
         warnings.warn(

src/geocat/viz/util.py

@@ -282,8 +282,6 @@ def add_height_from_pressure_axis(ax,
     - `NCL_h_lat_6.py <https://geocat-examples.readthedocs.io/en/latest/gallery/Contours/NCL_h_lat_6.html?highlight=add_height_from_pressure_axis>`_
 
     - `NCL_h_lat_7.py <https://geocat-examples.readthedocs.io/en/latest/gallery/Contours/NCL_h_lat_7.html?highlight=add_height_from_pressure_axis>`_
-
-    - `NCL_h_vector_5.py <https://geocat-examples.readthedocs.io/en/latest/gallery/Vectors/NCL_vector_5.html?highlight=add_height_from_pressure_axis>`_
     """
 
     # Create the right hand axis, inheriting from the left

tests/test_taylor.py

@@ -6,9 +6,7 @@
 from geocat.viz.taylor import TaylorDiagram
 
 
-@pytest.mark.mpl_image_compare(tolerance=0.02,
-                               remove_text=True,
-                               style='default')
+@pytest.mark.mpl_image_compare(tolerance=2, remove_text=True, style='default')
 def test_add_model_set():
     fig = plt.figure(figsize=(10, 10))
     taylor = TaylorDiagram(fig=fig, label='REF')
@@ -21,9 +19,7 @@ def test_add_model_set():
     return fig
 
 
-@pytest.mark.mpl_image_compare(tolerance=0.02,
-                               remove_text=True,
-                               style='default')
+@pytest.mark.mpl_image_compare(tolerance=2, remove_text=True, style='default')
 def test_add_legend():
     fig = plt.figure(figsize=(10, 10))
     taylor = TaylorDiagram(fig=fig, label='REF')
@@ -50,9 +46,7 @@ def test_add_legend():
     return fig
 
 
-@pytest.mark.mpl_image_compare(tolerance=0.02,
-                               remove_text=True,
-                               style='default')
+@pytest.mark.mpl_image_compare(tolerance=2, remove_text=True, style='default')
 def test_add_bias_legend():
     fig = plt.figure(figsize=(10, 10))
     taylor = TaylorDiagram(fig=fig, label='REF')
@@ -72,9 +66,7 @@ def test_add_bias_legend():
     return fig
 
 
-@pytest.mark.mpl_image_compare(tolerance=0.02,
-                               remove_text=True,
-                               style='default')
+@pytest.mark.mpl_image_compare(tolerance=2, remove_text=True, style='default')
 def test_add_model_name():
     fig = plt.figure(figsize=(10, 10))
     taylor = TaylorDiagram(fig=fig, label='REF')
@@ -94,9 +86,7 @@ def test_add_model_name():
     return fig
 
 
-@pytest.mark.mpl_image_compare(tolerance=0.02,
-                               remove_text=True,
-                               style='default')
+@pytest.mark.mpl_image_compare(tolerance=2, remove_text=True, style='default')
 def test_add_corr_grid():
     fig = plt.figure(figsize=(10, 10))
     taylor = TaylorDiagram(fig=fig, label='REF')
@@ -116,9 +106,7 @@ def test_add_corr_grid():
     return fig
 
 
-@pytest.mark.mpl_image_compare(tolerance=0.02,
-                               remove_text=True,
-                               style='default')
+@pytest.mark.mpl_image_compare(tolerance=2, remove_text=True, style='default')
 def test_add_contours():
     fig = plt.figure(figsize=(10, 10))
     taylor = TaylorDiagram(fig=fig, label='REF')