Feature #3416 proofread

[JohnHalleyGotway]

Related to #3416

Summary

Proofreads the MET documentation. Reading every page also turned up about 50 content errors, which this PR fixes. Each one was checked against the source code, the default config files, the header column tables, or the unit tests.

This branch is based on develop, so it can be reviewed in parallel with the link check PR, #3457. It has 16 commits and changes 48 files. One of them is a source file, tc_diag.cc, where only the usage string changes. The two PRs edit some of the same lines in 7 files, so whichever one merges second will need those conflicts resolved. The changes themselves don't overlap: each conflicting line just needs both the link fix and the proofread fix.

Changes

Proofreading (11 commits)

Typos, grammar, punctuation, names, option names in examples, and citations (checked against Crossref) across the Contributor's Guide, the front matter, the configuration options, and every tool chapter and appendix.

• Commas after "e.g." and "i.e.": added consistently throughout the docs (156 places), following standard US style. Code and literal blocks were left unchanged. Also fixed "e.g," in tc-pairs.rst.
• Tabs replaced with spaces: in appendixA.rst (about 410 lines, mostly code blocks in the FAQ), 4 other .rst files, make.bat, and _static/theme_override.css. The tabs in the .rst files were expanded at 8-column stops, which is how docutils reads them, so the rendered pages are unchanged. Only the tabs that make requires in docs/Makefile remain.
• Consistent code block indentation: the content of every code-block (805) and :: literal block (12) is now indented 2 spaces past its directive or paragraph, the depth about 85% of them already used. Before, depths ranged from 1 to 16 spaces, and most of the FAQ examples in appendixA.rst were indented 16. This is whitespace only, in 14 files.

Garbled or truncated text

• point-stat.rst: "the center of the grid is." → "...is at the origin (0, 0)."
• ensemble-stat.rst: "constant points are and" → "constant points are included and".
• grid-stat.rst: "must be on a common grid" → "are already on a common grid". The old wording contradicted the next sentence.
• wavelet-stat.rst:
  • Restored the lost "½" thresholds.
  • Restored the summation signs in the MSE and En2 formulas.
  • Added the missing "[" in the En2 relative difference.
• appendixD.rst: "of the question" → "in the equation above"; filled in the empty "estimates, ." with the variance estimate; removed a repeated sentence.
• appendixA.rst: a dangling "Set" and a stray code block; a garbled environment variable sentence.
• appendixC.rst: the Kendall's Tau total and discordant pair counts.
• reformat_point.rst: the -goes_qc 0,1,2 description.
• data_io.rst: rewrote the NetCDF performance paragraph, which also said "compression" where it meant "decompression".
• overview.rst: the security sentence said the opposite of what was meant.
• Contributors_Guide/testing.rst: "fields and fields" → "input files".

Option, config, and command names

• masking.rst: input_file → input_grid.
• wavelet-stat.rst: wavelet_flag/wavelet_k → wavelet.type/wavelet.member.
• series-analysis.rst: -input → -aggr.
• tc-diag.rst: nc_rng_azi_flag → nc_cyl_grid_flag.
• tc-stat.rst: -prob_thresh → -probrirw_thresh (no default; the job exits if it isn't set), and -prob_exact → -probrirw_exact (default false, not true).
• mode-analysis.rst: the -lookin description was copied from Stat-Analysis. It now describes MODE _obj.txt files.
• rmw-analysis.rst: "TC-RMW reads" → "RMW-Analysis reads".
• appendixA.rst:
  • Added the now-required -type poly to the gen_vx_mask example.
  • The FAQ said there is no -mask_sid option, but Stat-Analysis supports it.
• appendixF.rst: the 4 gen_ens_prod examples were missing -ens.
• appendixB.rst: max_range_km → range_max_km.
• tc-diag.rst and tc_diag.cc: the usage synopsis now says -deck source, matching the description in both the docs and the tool's own usage message.

Text that didn't match the tables, defaults, or math

• point-stat.rst: PJC is "Joint and Conditional factorization" (it was "Joint/Continuous").
• ensemble-stat.rst:
  • ME_LT_OBS is strictly less than.
  • SSVAR FSTDEV/OSTDEV are the forecast and observation standard deviations.
• mode.rst: object IDs are FNNN/ONNN (it was FNN/ONN).
• mode-td.rst:
  • The min_volume default is 2,000 (it was 10,000), and the arithmetic in the example is updated to match.
  • The time centroid delta is computed as observed minus forecast (3d_att.cc), unlike the other deltas, and the text now says so.
• appendixC.rst:
  • "Ferro and Stephenson, 2011" now links to a new Ferro and Stephenson (2011) entry in refs.rst, instead of to Stephenson et al. (2008).
  • The column name is EIQR (it was IQR).
  • p_i (it was rho_i).
  • The PDF and CDF symbols are no longer swapped.
  • The RPS columns now point to the RPS table, not the ECNT table.
• release-notes.rst: the upgrade instructions now say "12.2.0 to 13.0.0".
• config_options.rst:
  • The NDBC complete stations link pointed to airnow.gov.
  • The 5 uncentered bins example included 0.9.
  • The text said there is "only one" point weighting option, then listed two.
• appendixA.rst: the CTS filter FAQ said CNT, and its line counts didn't match the log.
• tc-stat.rst: now links to the TC-Pairs output section.
• plotting.rst: the two MODE verification figure references were swapped.

File names, units, labels

• File names:
  • nam.grb → nam.grib
  • ioda2nc.log → run_ioda2nc.log
  • sample_pb.ps → sample_data.ps
  • sum.nc → Sum.nc, and "12-hour" → "24-hour" for the summed field
  • a mismatched /d1/SBU/GFS/... path
• code_profiling.rst: the timestamp is appended to the file name, not prepended, and "ISO 1806" → "ISO 8601".
• Units: km/m**2 → kg/m**2, and the degree sign removed from a km value.
• Names and labels: HFWI → HWFI, suggested_external_utiliites → suggested_external_utilities, and "station ID's" → "station IDs".

For the developers: Kendall's Tau

Not changed in this PR. appendixC.rst presents Kendall's Tau as tau-a, (N_C − N_D) / (n(n − 1)/2). But compute_cntinfo() in src/libcode/vx_statistics/compute_stats.cc (around line 530) computes the tie-corrected tau-b, (N_C − N_D) / sqrt((N_C + N_D + extra_f)(N_C + N_D + extra_o)), where extra_f and extra_o count the pairs tied only in the observation or only in the forecast. The two agree only when there are no ties. One of them should be updated so the docs and the code agree.

Expected Differences

• Do these changes introduce new tools, command line arguments, or configuration file options? [No]
  
  If yes, please describe:
  

• Do these changes modify the structure of existing or add new output data types (e.g. statistic line types or NetCDF variables)? [No]
  
  If yes, please describe:
  

Pull Request Testing

• Describe testing already performed for these changes:
  
  I built the docs with Sphinx 8.2.3 in nitpicky mode (-n) before and after these changes. Neither build has warnings, and only the content of the 30 edited pages changed. I checked the rendered math, the restored "½" thresholds, and the new Ferro (2011) links. Option names and defaults were checked against the tool source and data/config/*_default. The only source change is the tc_diag usage string. After adding the commas after "e.g." and "i.e.", I rebuilt the docs with Sphinx 8.2.3 in nitpicky mode (-n) before and after that commit. Neither build has warnings, and only the 31 pages with comma edits changed. For the tab-to-space change, I built the docs before and after in nitpicky mode: neither build has warnings, and every rendered page is byte-for-byte identical, apart from the checksum in the theme_override.css link. The code block indentation change was checked the same way: no warnings, and all rendered pages are byte-for-byte identical.

• Recommend testing for the reviewer(s) to perform, including the location of input datasets, and any additional instructions:
  
  Review the diff against develop. Pay particular attention to the tc-stat.rst PROBRIRW options, the mode-td.rst time centroid delta note, and the Kendall's Tau note above.

• 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 MET test suite? [No]
  
  If yes, describe the new output and/or changes to the existing output:
  

• Will this PR result in changes to existing METplus Use Cases? [No]
  
  If yes, create a new Update Truth METplus issue to describe them.

• 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.

• 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: METplus-X.Y Support project for bugfix releases or MET-X.Y Development project for the next coordinated release
• 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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Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

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