docrev 0.9.13 → 0.9.14

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (126) hide show
  1. package/.claude/settings.local.json +9 -9
  2. package/.gitattributes +1 -1
  3. package/CHANGELOG.md +149 -149
  4. package/PLAN-tables-and-postprocess.md +850 -850
  5. package/README.md +391 -391
  6. package/bin/rev.js +11 -11
  7. package/bin/rev.ts +145 -145
  8. package/completions/rev.bash +127 -127
  9. package/completions/rev.ps1 +210 -210
  10. package/completions/rev.zsh +207 -207
  11. package/dev_notes/stress2/build_adversarial.ts +186 -186
  12. package/dev_notes/stress2/drift_matcher.ts +62 -62
  13. package/dev_notes/stress2/probe_anchors.ts +35 -35
  14. package/dev_notes/stress2/project/discussion.before.md +3 -3
  15. package/dev_notes/stress2/project/discussion.md +3 -3
  16. package/dev_notes/stress2/project/methods.before.md +20 -20
  17. package/dev_notes/stress2/project/methods.md +20 -20
  18. package/dev_notes/stress2/project/rev.yaml +5 -5
  19. package/dev_notes/stress2/project/sections.yaml +4 -4
  20. package/dev_notes/stress2/sections.yaml +5 -5
  21. package/dev_notes/stress2/trace_placement.ts +50 -50
  22. package/dev_notes/stresstest_boundaries.ts +27 -27
  23. package/dev_notes/stresstest_drift_apply.ts +43 -43
  24. package/dev_notes/stresstest_drift_compare.ts +43 -43
  25. package/dev_notes/stresstest_drift_v2.ts +54 -54
  26. package/dev_notes/stresstest_inspect.ts +54 -54
  27. package/dev_notes/stresstest_pstyle.ts +55 -55
  28. package/dev_notes/stresstest_section_debug.ts +23 -23
  29. package/dev_notes/stresstest_split.ts +70 -70
  30. package/dev_notes/stresstest_trace.ts +19 -19
  31. package/dev_notes/stresstest_verify_no_overwrite.ts +40 -40
  32. package/dist/lib/build.d.ts +38 -1
  33. package/dist/lib/build.d.ts.map +1 -1
  34. package/dist/lib/build.js +68 -30
  35. package/dist/lib/build.js.map +1 -1
  36. package/dist/lib/commands/build.d.ts.map +1 -1
  37. package/dist/lib/commands/build.js +38 -5
  38. package/dist/lib/commands/build.js.map +1 -1
  39. package/dist/lib/commands/utilities.js +164 -164
  40. package/dist/lib/commands/word-tools.js +8 -8
  41. package/dist/lib/grammar.js +3 -3
  42. package/dist/lib/pdf-comments.js +44 -44
  43. package/dist/lib/plugins.js +57 -57
  44. package/dist/lib/pptx-themes.js +115 -115
  45. package/dist/lib/spelling.js +2 -2
  46. package/dist/lib/templates.js +387 -387
  47. package/dist/lib/themes.js +51 -51
  48. package/eslint.config.js +27 -27
  49. package/lib/anchor-match.ts +276 -276
  50. package/lib/annotations.ts +644 -644
  51. package/lib/build.ts +1300 -1251
  52. package/lib/citations.ts +160 -160
  53. package/lib/commands/build.ts +833 -801
  54. package/lib/commands/citations.ts +515 -515
  55. package/lib/commands/comments.ts +1050 -1050
  56. package/lib/commands/context.ts +174 -174
  57. package/lib/commands/core.ts +309 -309
  58. package/lib/commands/doi.ts +435 -435
  59. package/lib/commands/file-ops.ts +372 -372
  60. package/lib/commands/history.ts +320 -320
  61. package/lib/commands/index.ts +87 -87
  62. package/lib/commands/init.ts +259 -259
  63. package/lib/commands/merge-resolve.ts +378 -378
  64. package/lib/commands/preview.ts +178 -178
  65. package/lib/commands/project-info.ts +244 -244
  66. package/lib/commands/quality.ts +517 -517
  67. package/lib/commands/response.ts +454 -454
  68. package/lib/commands/section-boundaries.ts +82 -82
  69. package/lib/commands/sections.ts +451 -451
  70. package/lib/commands/sync.ts +706 -706
  71. package/lib/commands/text-ops.ts +449 -449
  72. package/lib/commands/utilities.ts +448 -448
  73. package/lib/commands/verify-anchors.ts +272 -272
  74. package/lib/commands/word-tools.ts +340 -340
  75. package/lib/comment-realign.ts +517 -517
  76. package/lib/config.ts +84 -84
  77. package/lib/crossref.ts +781 -781
  78. package/lib/csl.ts +191 -191
  79. package/lib/dependencies.ts +98 -98
  80. package/lib/diff-engine.ts +465 -465
  81. package/lib/doi-cache.ts +115 -115
  82. package/lib/doi.ts +897 -897
  83. package/lib/equations.ts +506 -506
  84. package/lib/errors.ts +346 -346
  85. package/lib/format.ts +541 -541
  86. package/lib/git.ts +326 -326
  87. package/lib/grammar.ts +303 -303
  88. package/lib/image-registry.ts +180 -180
  89. package/lib/import.ts +911 -911
  90. package/lib/journals.ts +543 -543
  91. package/lib/merge.ts +633 -633
  92. package/lib/orcid.ts +144 -144
  93. package/lib/pdf-comments.ts +263 -263
  94. package/lib/pdf-import.ts +524 -524
  95. package/lib/plugins.ts +362 -362
  96. package/lib/postprocess.ts +188 -188
  97. package/lib/pptx-color-filter.lua +37 -37
  98. package/lib/pptx-template.ts +469 -469
  99. package/lib/pptx-themes.ts +483 -483
  100. package/lib/protect-restore.ts +520 -520
  101. package/lib/rate-limiter.ts +94 -94
  102. package/lib/response.ts +197 -197
  103. package/lib/restore-references.ts +240 -240
  104. package/lib/review.ts +327 -327
  105. package/lib/schema.ts +417 -417
  106. package/lib/scientific-words.ts +73 -73
  107. package/lib/sections.ts +335 -335
  108. package/lib/slides.ts +756 -756
  109. package/lib/spelling.ts +334 -334
  110. package/lib/templates.ts +526 -526
  111. package/lib/themes.ts +742 -742
  112. package/lib/trackchanges.ts +247 -247
  113. package/lib/tui.ts +450 -450
  114. package/lib/types.ts +550 -550
  115. package/lib/undo.ts +250 -250
  116. package/lib/utils.ts +69 -69
  117. package/lib/variables.ts +179 -179
  118. package/lib/word-extraction.ts +806 -806
  119. package/lib/word.ts +643 -643
  120. package/lib/wordcomments.ts +817 -817
  121. package/package.json +137 -137
  122. package/scripts/postbuild.js +28 -28
  123. package/skill/REFERENCE.md +431 -431
  124. package/skill/SKILL.md +258 -258
  125. package/tsconfig.json +26 -26
  126. package/types/index.d.ts +525 -525
package/lib/scientific-words.ts CHANGED
@@ -1,73 +1,73 @@
1
- /**
2
- * Common scientific and academic words not in standard dictionaries
3
- * These words are accepted by Word's spellchecker
4
- */
5
-
6
- export const scientificWords = new Set([
7
- // Biology/Ecology
8
- 'abiotic', 'biotic', 'biogeographic', 'biogeography', 'phenotypic', 'phenotype',
9
- 'anthropogenic', 'propagule', 'propagules', 'herbivory', 'herbivore', 'herbivores',
10
- 'ruderal', 'ruderals', 'refugia', 'refugium', 'hotspot', 'hotspots',
11
- 'biodiversity', 'ecosystem', 'ecosystems', 'ecotype', 'ecotypes',
12
- 'taxonomic', 'phylogenetic', 'phylogeny', 'morphological', 'morphology',
13
- 'allometric', 'allometry', 'biomass', 'biome', 'biomes',
14
- 'invasibility', 'invasive', 'invasives', 'neophyte', 'neophytes',
15
- 'archaeophyte', 'archaeophytes', 'naturalisation', 'naturalization',
16
- 'colonisation', 'colonization', 'dispersal', 'fecundity',
17
- 'phenology', 'phenological', 'ontogeny', 'ontogenetic',
18
- 'mesic', 'xeric', 'hydric', 'riparian', 'riverine',
19
- 'subalpine', 'alpine', 'boreal', 'temperate', 'tropical',
20
- 'heathland', 'heathlands', 'scrubland', 'scrublands', 'grassland', 'grasslands',
21
- 'broadleaf', 'broadleaved', 'coniferous', 'deciduous', 'evergreen',
22
- 'autochory', 'autochorous', 'zoochory', 'zoochorous',
23
- 'anemochory', 'anemochorous', 'hydrochory', 'hydrochorous',
24
- 'anthropochory', 'anthropochorous', 'hemerochor', 'hemerochorist',
25
- 'helophyte', 'helophytes', 'hydrophyte', 'hydrophytes',
26
- 'therophyte', 'therophytes', 'geophyte', 'geophytes',
27
- 'chamaephyte', 'chamaephytes', 'phanerophyte', 'phanerophytes',
28
-
29
- // Statistics
30
- 'logit', 'logistic', 'probit', 'frequentist', 'bayesian',
31
- 'overdispersion', 'underdispersion', 'heteroscedasticity', 'homoscedasticity',
32
- 'multicollinearity', 'autocorrelation', 'covariate', 'covariates',
33
- 'parameterization', 'parameterisation', 'reparameterization',
34
- 'bootstrapping', 'resampling', 'imputation', 'interpolation',
35
- 'standardized', 'standardised', 'normalized', 'normalised',
36
- 'discretized', 'discretised', 'categorized', 'categorised',
37
-
38
- // Compound words
39
- 'overrepresentation', 'underrepresentation', 'overrepresented', 'underrepresented',
40
- 'outcompete', 'outcompetes', 'outcompeted', 'outcompeting',
41
- 'subdataset', 'subgroup', 'subgroups', 'subtype', 'subtypes',
42
- 'dataset', 'datasets', 'datapoint', 'datapoints',
43
- 'spatiotemporal', 'spatio', 'geospatial',
44
- 'timestep', 'timesteps', 'timeframe', 'timeframes',
45
- 'warmup', 'backend', 'frontend', 'workflow', 'workflows',
46
- 'fallback', 'fallbacks', 'tradeoff', 'tradeoffs',
47
-
48
- // Academic writing
49
- 'interpretability', 'reproducibility', 'replicability',
50
- 'hypothesise', 'hypothesised', 'hypothesize', 'hypothesized',
51
- 'analyse', 'analysed', 'analyze', 'analyzed',
52
- 'prioritise', 'prioritised', 'prioritize', 'prioritized',
53
- 'characterise', 'characterised', 'characterize', 'characterized',
54
- 'generalise', 'generalised', 'generalize', 'generalized',
55
- 'parameterise', 'parameterised', 'parameterize', 'parameterized',
56
- 'visualise', 'visualised', 'visualize', 'visualized',
57
- 'modelling', 'modeling', 'modelled', 'modeled',
58
-
59
- // Geography
60
- 'unvegetated', 'landform', 'landforms', 'topographic', 'topography',
61
- 'elevational', 'latitudinal', 'longitudinal', 'altitudinal',
62
-
63
- // Technical
64
- 'doi', 'dois', 'pdf', 'pdfs', 'csv', 'xlsx',
65
- 'pandoc', 'markdown', 'bibtex', 'crossref',
66
-
67
- // R packages and tools
68
- 'brms', 'cmdstanr', 'rstanarm', 'lme', 'glmm', 'glmer', 'lmer',
69
- 'ggplot', 'dplyr', 'tidyr', 'tidyverse', 'rmarkdown',
70
-
71
- // Common in papers
72
- 'foci', 'et', 'al', 'cf', 'eg', 'ie', 'vs',
73
- ]);
1
+ /**
2
+ * Common scientific and academic words not in standard dictionaries
3
+ * These words are accepted by Word's spellchecker
4
+ */
5
+
6
+ export const scientificWords = new Set([
7
+ // Biology/Ecology
8
+ 'abiotic', 'biotic', 'biogeographic', 'biogeography', 'phenotypic', 'phenotype',
9
+ 'anthropogenic', 'propagule', 'propagules', 'herbivory', 'herbivore', 'herbivores',
10
+ 'ruderal', 'ruderals', 'refugia', 'refugium', 'hotspot', 'hotspots',
11
+ 'biodiversity', 'ecosystem', 'ecosystems', 'ecotype', 'ecotypes',
12
+ 'taxonomic', 'phylogenetic', 'phylogeny', 'morphological', 'morphology',
13
+ 'allometric', 'allometry', 'biomass', 'biome', 'biomes',
14
+ 'invasibility', 'invasive', 'invasives', 'neophyte', 'neophytes',
15
+ 'archaeophyte', 'archaeophytes', 'naturalisation', 'naturalization',
16
+ 'colonisation', 'colonization', 'dispersal', 'fecundity',
17
+ 'phenology', 'phenological', 'ontogeny', 'ontogenetic',
18
+ 'mesic', 'xeric', 'hydric', 'riparian', 'riverine',
19
+ 'subalpine', 'alpine', 'boreal', 'temperate', 'tropical',
20
+ 'heathland', 'heathlands', 'scrubland', 'scrublands', 'grassland', 'grasslands',
21
+ 'broadleaf', 'broadleaved', 'coniferous', 'deciduous', 'evergreen',
22
+ 'autochory', 'autochorous', 'zoochory', 'zoochorous',
23
+ 'anemochory', 'anemochorous', 'hydrochory', 'hydrochorous',
24
+ 'anthropochory', 'anthropochorous', 'hemerochor', 'hemerochorist',
25
+ 'helophyte', 'helophytes', 'hydrophyte', 'hydrophytes',
26
+ 'therophyte', 'therophytes', 'geophyte', 'geophytes',
27
+ 'chamaephyte', 'chamaephytes', 'phanerophyte', 'phanerophytes',
28
+
29
+ // Statistics
30
+ 'logit', 'logistic', 'probit', 'frequentist', 'bayesian',
31
+ 'overdispersion', 'underdispersion', 'heteroscedasticity', 'homoscedasticity',
32
+ 'multicollinearity', 'autocorrelation', 'covariate', 'covariates',
33
+ 'parameterization', 'parameterisation', 'reparameterization',
34
+ 'bootstrapping', 'resampling', 'imputation', 'interpolation',
35
+ 'standardized', 'standardised', 'normalized', 'normalised',
36
+ 'discretized', 'discretised', 'categorized', 'categorised',
37
+
38
+ // Compound words
39
+ 'overrepresentation', 'underrepresentation', 'overrepresented', 'underrepresented',
40
+ 'outcompete', 'outcompetes', 'outcompeted', 'outcompeting',
41
+ 'subdataset', 'subgroup', 'subgroups', 'subtype', 'subtypes',
42
+ 'dataset', 'datasets', 'datapoint', 'datapoints',
43
+ 'spatiotemporal', 'spatio', 'geospatial',
44
+ 'timestep', 'timesteps', 'timeframe', 'timeframes',
45
+ 'warmup', 'backend', 'frontend', 'workflow', 'workflows',
46
+ 'fallback', 'fallbacks', 'tradeoff', 'tradeoffs',
47
+
48
+ // Academic writing
49
+ 'interpretability', 'reproducibility', 'replicability',
50
+ 'hypothesise', 'hypothesised', 'hypothesize', 'hypothesized',
51
+ 'analyse', 'analysed', 'analyze', 'analyzed',
52
+ 'prioritise', 'prioritised', 'prioritize', 'prioritized',
53
+ 'characterise', 'characterised', 'characterize', 'characterized',
54
+ 'generalise', 'generalised', 'generalize', 'generalized',
55
+ 'parameterise', 'parameterised', 'parameterize', 'parameterized',
56
+ 'visualise', 'visualised', 'visualize', 'visualized',
57
+ 'modelling', 'modeling', 'modelled', 'modeled',
58
+
59
+ // Geography
60
+ 'unvegetated', 'landform', 'landforms', 'topographic', 'topography',
61
+ 'elevational', 'latitudinal', 'longitudinal', 'altitudinal',
62
+
63
+ // Technical
64
+ 'doi', 'dois', 'pdf', 'pdfs', 'csv', 'xlsx',
65
+ 'pandoc', 'markdown', 'bibtex', 'crossref',
66
+
67
+ // R packages and tools
68
+ 'brms', 'cmdstanr', 'rstanarm', 'lme', 'glmm', 'glmer', 'lmer',
69
+ 'ggplot', 'dplyr', 'tidyr', 'tidyverse', 'rmarkdown',
70
+
71
+ // Common in papers
72
+ 'foci', 'et', 'al', 'cf', 'eg', 'ie', 'vs',
73
+ ]);