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Link to files, not topics #1109

Merged
merged 24 commits into from
Jun 26, 2020
Merged

Link to files, not topics #1109

merged 24 commits into from
Jun 26, 2020

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gaborcsardi
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@gaborcsardi gaborcsardi commented Jun 11, 2020 •
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External packages are simple, we just look up the file name and link to that.

Linking to the package being documented is harder, because at the time of the linking we don't know the file names yet. So we'll need to mark these parts in the docs, and post-process all files, ones the file names are known. These links do work with the topic, so we'll leave them alone.

  • Links to external packages.
  • Internal links, to the package being documented. Not needed.
  • Fix re-exported functions, if they need anything special
  • Improve warnings to contain file name and line number.
  • Throw warnings for non-existing package or topic, for re-exports.
  • Simplify links where the file name is the same as the topic name.
  • Refactor into its own file.
  • Can we link to another package w/o specifying its name? Yes, probably shouldn't, though. Not relevant.
  • Should we look up unqualified unknown link targets in dependent packages? Not just yet. Not releavant.
  • One warning only for non-local unqualified links. No warning at all, R CMD check will warn if it needs to.
  • Resolve links to the base package, automatically? No need, we'll just leave unqualified links alone.
  • Tests.
  • Docs. Not really needed.
  • News.
  • Fix links in inherited text.
  • Fix links in the text of the @inheritedDotParams intro.
  • Automatically remove package names from in-package references. This is e.g. useful for compat files that are copied to a number of packages. It does not need to be in this PR, just making a note here.

Closes #1108.

simonpcouch added a commit to tidymodels/broom that referenced this pull request Jun 11, 2020
@simonpcouch
link to man files rather than topics (r-lib/roxygen2#1109)
c5eedbe
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Do not link to file, if not needed
adb089d 
I.e. if the name of the topic is the same as the
name of the file, then we are ok.
@gaborcsardi
Link to files refactoring
a86e14c 
Also implement proper warnings, with file names
and line numbers, for re-exports as well.
@gaborcsardi
Add test to auto-linking to file
66f00cd
@gaborcsardi gaborcsardi mentioned this pull request Jun 12, 2020
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Actually, the approach in #1109 (comment) does not work, so we'll have to go with the more complicated solution.

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@hadley This is ready, fyi.

yutannihilation added a commit to yutannihilation/ggplot2 that referenced this pull request Jun 14, 2020
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Try r-lib/roxygen2#1109
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@hadley Can you pls take another look? Thanks!

echasnovski added a commit to echasnovski/pdqr that referenced this pull request Jun 18, 2020
@echasnovski
Roxygenize with 'roxygen2' version at 'r-lib/roxygen2/pull/1109' to a…
e7e7b3e 
…ccount for documentation handling in R-devel.
DavisVaughan added a commit to business-science/tibbletime that referenced this pull request Jun 18, 2020
@DavisVaughan
Redocument with r-lib/roxygen2#1109
fe6af31
jgabry added a commit to stan-dev/bayesplot that referenced this pull request Jun 18, 2020
@jgabry
fix R-devel warnings use dev version of roxygen2
0a9e235 
r-lib/roxygen2#1109
mattfidler added a commit to nlmixrdevelopment/nlmixr that referenced this pull request Jun 19, 2020
@mattfidler
Fix reexports using develpoment roxygen2
75753f7 
r-lib/roxygen2#1109
@sgratzl sgratzl mentioned this pull request Jun 21, 2020
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@smurching smurching mentioned this pull request Jun 22, 2020
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A few last smaller things; only bother with them if we don't hear back on R-package-devel in a couple of days. (And then I'll do a release on Thursday or Friday)

.github/workflows/R-CMD-check.yaml Outdated Show resolved Hide resolved
R/object-import.R Show resolved Hide resolved
R/rd-find-link-files.R Outdated Show resolved Hide resolved
R/rd-find-link-files.R Outdated Show resolved Hide resolved
tests/testthat/test-markdown-link.R Show resolved Hide resolved
@rpln rpln mentioned this pull request Jun 23, 2020
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chacalle added a commit to ihmeuw-demographics/demCore that referenced this pull request Jun 23, 2020
@chacalle
undo package links change since it is being fixed r-lib/roxygen2#1109
4e2f0e7
@gaborcsardi
Don't need dev rmarkdown any more
59bdd0f
@gaborcsardi
Close a dangling connection
e7de910
@gaborcsardi
Refactor link-to-file helpers
9947c05
@gaborcsardi
Do not qualify links to the current package
3dc1b0e 
R searches for topics in the linking package itself
first, so these are not need to be qualified.

Ignoring the 'mypackage::' part helps moving code
between packages, e.g. for compat files.
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@hadley: Thanks, this is ready to go.

@yutannihilation yutannihilation mentioned this pull request Jun 25, 2020
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@hadley hadley merged commit 65330c5 into master Jun 26, 2020
@hadley hadley deleted the fix/link-to-file branch June 26, 2020 17:44
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hadley commented Jun 26, 2020

Thanks!

pgpmartin pushed a commit to pgpmartin/NanoBAC that referenced this pull request Jul 4, 2020
modified help page of consmat2seq to link to specific help file, not …
cbae082 
…topic as indicated here r-lib/roxygen2#1109
@mjsteinbaugh mjsteinbaugh mentioned this pull request Jul 7, 2020
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clrpackages pushed a commit to clearlinux-pkgs/R-broom that referenced this pull request Jul 14, 2020
@fenrus75
R-broom: Autospec creation for update from version 0.5.6 to version 0…
1f4aafe 
….7.0

Grant McDermott (24):
      Add logitmfx tidiers
      Better regexp
      Add more examples
      Add probit tidiers (same as logit TBH)
      Updated NAMESPACE after adding new mfx tidiers
      Correct function name would be nice
      Just use logitmfx tidiers for probitmfx equivalents
      Catch cases where user doesn't specify atmean argument
      Add tests for mfxlogit
      Argh, correct function name again
      Better name
      Add probitmfx tests
      Squash into generic tidiers with various methods
      Missed on previous commit
      Right export names would help...
      Add contributor details
      Suggest packages
      Fix mfx rdnames and methods
      Retain SEs of input object
      mfx tidiers to NEWS.md
      Resolve Alex's PR commments
      Separate out betamfx tidiers
      Drop deprecated fix_data_frame function
      Update NAMESPACE

Greg Macfarlane (6):
      Write tidy method for sarlm models
      Add glance and augment for sarlm objects; document
      Simplify logic of spatial regression tidying
      Write tidy method for sarlm models
      Add glance and augment for sarlm objects; document
      Simplify logic of spatial regression tidying

Lukas Wallrich (3):
      Add option to return p.values to tidy.polr
      Update NEWS.md
      Update DESCRIPTION

Max Kuhn (1):
      0.7.0 revdeps

Petr Hrobar (2):
      model added
      model added

Simon Couch (61):
      restore .Rproj... oops🙈
      add svd return value alexpghayes/modeltests#26, document()
      check when entries don't result in docs
      work through failing return_* entries (closes #856)
      small build fixes
      fix `codecov` and `pkgdown` actions
      use lavaan extractors in glance.lavaan (#835)
      explicitly coerce to tibble (closes #824)
      tidyverse -> tidymodels in links (closes #832)
      pass ddf arg to confint (#839)
      adjust covr install re: 4.0.0 error
      update gh actions R version
      install tidytemplate for pkgdown
      correct nobs and norig in glance.lavaan (closes #835)
      note deprecation of fix_data_frame() (#806, #862)
      restore n column re: chest revdepcheck (#862)
      refresh docs with devel modeltests version
      restore .resid column to augment.nls output
      restore sparse matrix tidiers (closes #470)
      small build fixes
      use_tidy_style() (closes #640)
      document after use_tidy_style()
      last few fixes to evalRd return_*() calls
      deprecate fix_data_frame() (closes #629, closes #806)
      add contributors🙂
      glance.lm edge cases (closes #865)
      add helper for tidy methods
      small build fixes
      use modeltests for car:: unit tests
      unname columns generated from predict() (closes #866)
      for now, use devel modeltests for unit testing
      wait on modeltests release for car::Anova tests
      wait for modeltests release to check arguments
      document p.values arguments
      correct language about glance.aov changes (closes #864)
      warn on tidy_optim standard error (closes #529)
      deprecate summary.manova()
      address TODOs in NEWS.md
      spellcheck
      update to new tidyr::(un)nest() API (#831, closes #870)
      more vignette edits (closes #831)
      windows 3.6 build fix
      only manually install mnormt on windows
      windows 3.6 build failing re: new mnormt release
      add glance helper (#823)
      run document()
      refactor glance() methods (closes #823)
      a few more NEWS.md updates for 0.7.0
      rename helpers for internal consistency
      ensure no docs for map_as_tidy_tibble
      small vignette style edits (closes #831)
      restore unit tests re: modeltests v0.1.2 (closes #869)
      update fixest tidiers with new internal helpers and documentation
      document tidy.map return value (closes #481)
      small build fixes
      remove duplicate entry
      workshop NEWS.md
      fix merge conflict
      fix url formatting
      replace `iris` with `trees`, fix badges
      formatting/spellcheck

Simon P. Couch (54):
      resolve merge conflicts, use helpers in #847 tidiers
      recover original response name, clarify docs (#847)
      spellcheck/clarify automated docs
      add `spatialreg` contributions (#847)
      build fixes
      add unit testing for #847
      build fixes
      more build fixes
      correct documentation
      skip sarlm examples
      skip redundant examples
      improve errors for scam objects (closes #186)
      use conf.int idiom (closes #868)
      address package lint
      increment version number
      documentation updates re: lint
      update cran comments
      clean up pkgdown yaml
      add myself as author per alex's request
      submit to CRAN!
      fixes from CRAN pretest failure - new `fixest` version
      update timeline
      submit round 2!
      link to man files rather than topics (r-lib/roxygen2#1109)
      cran submission 3
      adjust docs for reexports
      specify base and stats namespaces
      explicitly export mfx aliased functions (#873)
      fix for internal .Rd linking
      more internal .Rd fixes
      link to quantreg file rather than topic
      note docs changes, update title
      clarify news re: new tidiers
      submission
      submit to CRAN
      update epi.2by2 tests
      submit to cran
      bump version
      write out iris in favor of modeldata::hpc_data
      update docs with reexports and iris -> hpc_data change
      bump version back
      soften deprecations
      adjust language about deprecations
      some check fixes re: deprecations
      tidy.dist fixes
      /dontrun examples with longest runtime
      update cran comments with new revdepchecks records
      restore finish_glance
      add deprecation notice to finish_glance
      more notes on reverse dependency checks
      submit to cran
      skip most unit tests on CRAN
      submit to cran
      accepted to CRAN🎉

karldw (10):
      Auto-remove trailing whitespace
      Start adding fixest
      Progress on fixest tidiers
      Progress on fixest tidiers
      Fixes to fixest tidiers
      Fix roxygen issues
      Address fixest PR comments
      Address additional fixest comments
      Bump required fixest version
      Remove deprecated `fix_data_frame`

petrhrobar (2):
      Another model support added (line 31)
      Another model support added (line 31)

topepo (1):
      revdeps on 05-26
@asfimport asfimport mentioned this pull request Jun 16, 2020
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@llrs llrs mentioned this pull request Aug 27, 2024
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Markdown links need to link to the file instead of the topic now
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