Feature #584 proofread

[JohnHalleyGotway]

Related to #584

Summary

Proofreads the METplotpy documentation, and corrects file names, config settings, setup steps, links, and descriptions found while reading every page.

This branch is based on feature_584_linkcheck (#587). Until #587 is merged, this PR also shows its 4 commits (the link check workflow, Sphinx update, and spacing changes). After #587 is merged, only the 8 commits for this PR remain: 36 files changed.

Changes

Proofreading

• Spelling and grammar: for example "dependancies", "specifed", "usally", "Documenation", "latititude", doubled words, subject-verb agreement, and "Replace X with".
• Names: GitHub and GitHub Actions capitalized consistently, Madden-Julian, the Cooperative Institute for Research in the Atmosphere (CIRA), Naval Research Laboratory, the JTTI expansion, METdatadb → METdataio.
• Copied text: removed "line plot" and "performance diagram" text that had been copied onto the bar, box, spread-skill, and wind rose pages; a repeated sentence and phrases; stray text ("is66TAW"); "Cost/Lost" → "Cost/Loss".

File and Config Names in the Plot Instructions

The instructions named files that don't exist in the repository. They now use the actual names:

• ECLV: eclv_defaults.yaml, ./eclv.data.
• Box and line: minimal_box.yaml, custom_line.yaml, minimal_line.yaml (the files used in the commands).
• Scatter: edit $WORKING_DIR/custom_scatter.yaml (where the page copies it), the data file reformatted_data_for_scatter.data, and the output setting in custom_scatter.yaml.
• Taylor diagram: the directory $METPLOTPY_BASE/test/taylor_diagram, the data file plot_dlwr_sample.data (all 5 references), and minimal_taylor_diagram.yaml.
• Performance diagram: minimal_performance_diagram.yaml, and the .points1 file.
• Wind rose: the test/wind_rose directory, wind_rose_defaults.yaml, wind_rose.py, minimal_wind_rose.yaml, and wind_rose_custom.yaml (the page said custom_performance_diagram.yaml).
• Reliability diagram: reliability_defaults.yaml and minimal_reliability.yaml (the page said minimal_box.yaml).
• Histograms: rank_hist.yaml, prob_hist.yaml, and rel_hist.yaml (the page listed rank_hist.yaml three times), and dump_points_2.
• Stratosphere plots: stratosphere_plots.py (was .py.py).

TCMPR Setup

• The log levels are listed from most to least verbose as DEBUG, INFO, WARNING, ERROR (INFO and DEBUG were swapped).
• The number of colors, not columns, must match the number of series.
• Fixed the /path/to/METplotpy_source_code path, and the METcalcpy step now sets METCALCPY_BASE to the METcalcpy source (it set METPLOTPY_BASE to METplotpy), with valid csh setenv syntax.

Descriptions, Links, and References

• stratosphere_plots.rst: obar is described as the observed mean plotted as contour lines over the bias. The previous text ("frequency of occurrence of each cluster") was copied from the weather regime page.
• difficulty_index.rst: the link text said "METviewer documentation" but links to a METplus use case.
• make_maki_enso.rst: the sentence pointing to the MJO_ENSO use case ended with ":" and no link; the use case is now linked.
• mjo_rmm_omi.rst: compute_mjo_indices.py is in METcalcpy (metcalcpy/contributed/rmm_omi), not METplotpy.
• references.rst: removed the Hoaglin et al. (1983) DOI, which resolves to a 1984 review of the book in The Statistician, not the book.
• index.rst: completed the NCAR sentence ("NCAR is sponsored by NSF"), as in the other components.
• release-notes.rst: "histogramm" → "histogram", matching the title of Remove plotly: Update bar, box, and histogram plot #558.

Pull Request Testing

• Describe testing already performed for these changes:
  
  Full HTML builds of the docs (including the sphinx-gallery example) with Sphinx 8.2.3 in nitpicky mode (-n), before and after these changes, both have no warnings, and the content of exactly the edited pages changed. Each corrected file, directory, config, and script name was checked against the files in the repository and the code (for example, histogram_2d.py reads dump_points_2).

• Recommend testing for the reviewer(s) to perform, including the location of input datasets, and any additional instructions:
  
  Review the diff against feature_584_linkcheck (or against develop after Feature #584 linkcheck #587 is merged), especially the file names in the plot instructions and the TCMPR setup steps.

• Do these changes include sufficient documentation updates, ensuring that no errors or warnings exist in the build of the documentation? [Yes]

• Do these changes include sufficient testing updates? [Yes]

• Will this PR result in changes to the test suite? [No]
  
  If yes, describe the new output and/or changes to the existing output:
  

• Do these changes introduce new SonarQube findings? [No]
  
  If yes, please describe:

• Please complete this pull request review by [Fill in date].
  

Pull Request Checklist

See the METplus Workflow for details.

• Add any new Python packages to the METplus Components Python Requirements table.
• Review the source issue metadata (required labels, projects, and milestone).
• Complete the PR definition above.
• Ensure the PR title matches the feature or bugfix branch name.
• Define the PR metadata, as permissions allow.
  Select: Reviewer(s) and Development issue
  Select: Milestone as the version that will include these changes
  Select: Coordinated METplus-X.Y Support project for bugfix releases or METplotpy-X.Y.Z Development project for official releases
• After submitting the PR, select the ⚙️ icon in the Development section of the right hand sidebar. Search for the issue that this PR will close and select it, if it is not already selected.
• After the PR is approved, merge your changes. If permissions do not allow this, request that the reviewer do the merge.
• Close the linked issue and delete your feature or bugfix branch from GitHub.

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