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Fix broken documentation links (#3710)#3933

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clarissecheung wants to merge 13 commits intoPecanProject:developfrom
clarissecheung:GH-3710-fix-broken-documentation-links
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Fix broken documentation links (#3710)#3933
clarissecheung wants to merge 13 commits intoPecanProject:developfrom
clarissecheung:GH-3710-fix-broken-documentation-links

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@clarissecheung
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Fixes ~100 broken links across 67 files, identified by a link checker report.

Changes by commit:

  1. Fix broken pecanproject.github.io and pecan.gitbooks.io links — mapped to current doc site URLs or GitHub source files
  2. Replace 34 dead NCSA license URLs (opensource.ncsa.illinois.edu/license.html) with canonical OSI link (opensource.org/license/NCSA)
  3. Fix dead domain links (cfconventions.org, nacp.ornl.gov, php-osx.liip.ch, safaribooksonline.com) using Wayback Machine archives
  4. Fix miscellaneous 404s (git-scm, AWS, Unidata, NEON, CDS, ECMWF, NLCD, JULES, GitHub internal paths) with current URLs
  5. Format placeholder/local URLs (e.g. http://server/bety/) as inline code so they aren't treated as broken links

Only URLs were modified — no content changes. Links that couldn't be resolved (403s from DOI/publisher sites, timeouts) were left in place to avoid information loss.

Closes #3710

… links

Replace outdated URLs for pkgdown package docs, gitbooks, coding style,
SIPNET install guide, and other moved documentation pages with their
current equivalents.

Closes PecanProject#3710 (partial)
….ch, safaribooksonline.com (PecanProject#3710)

- cfconventions.org (NXDOMAIN) → cf-convention.github.io (GitHub Pages)
- nacp.ornl.gov → nacp-prod.ornl.gov (new ORNL host)
- php-osx.liip.ch (dead) → formulae.brew.sh/formula/php (Homebrew)
- proquestcombo.safaribooksonline.com (dead) → GitHub-hosted PDF
Convert placeholder URLs from hyperlinks to backtick-formatted code so
link checkers skip them and readers understand they are templates:
- http://server/bety/ in 07_migrate.Rmd
- https://your.server.edu/shiny/your-location in shiny.Rmd
- http://server/rstudio in DEV-INTRO.md
@omkarrr2533
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hey @clarissecheung verified a few replacement URLs = nacp-prod.ornl.gov, cf-convention.github.io and the pecanproject.github.io/package-documentation links all look good 👍
one thing though the CI failure is actually related to the PR. looks like read.output.Rd, standard_vars.Rd and a couple other .Rd files are out of sync after editing the R source files. just run devtools::document() on the affected packages and commit the updated files and that should fix it..!

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Thanks! This is a nice contribution. See inline for a couple nitpicks on some of the older links.

clarissecheung and others added 2 commits April 16, 2026 15:35
…s/02_git/01_using-git.Rmd

Co-authored-by: Chris Black <chris@ckblack.org>
…Installing-PEcAn-OSX.Rmd

Co-authored-by: Chris Black <chris@ckblack.org>
@clarissecheung
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Thanks! This is a nice contribution. See inline for a couple nitpicks on some of the older links.

Thank you for the feedback! I've gone ahead and committed your suggestions!

Yeligay8

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@clarissecheung
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hey @clarissecheung verified a few replacement URLs = nacp-prod.ornl.gov, cf-convention.github.io and the pecanproject.github.io/package-documentation links all look good 👍 one thing though the CI failure is actually related to the PR. looks like read.output.Rd, standard_vars.Rd and a couple other .Rd files are out of sync after editing the R source files. just run devtools::document() on the affected packages and commit the updated files and that should fix it..!

hi @omkarrr2533! Thank you for catching that! I've run devtools::document() and have made changes the the necessary files.

@infotroph
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@clarissecheung Your roxygen update looks like it touched one package out of the 7 (if I counted right) that this PR modifies. You could run devtools::document() on each of them one at a time if you want, but instead I recommend running make document to update all the packages at once.

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clarissecheung commented Apr 17, 2026

@clarissecheung Your roxygen update looks like it touched one package out of the 7 (if I counted right) that this PR modifies. You could run devtools::document() on each of them one at a time if you want, but instead I recommend running make document to update all the packages at once.

Got it! I just ran make document and pushed the updated files. Let me know if I can do anything else. Thank you so much for your help!

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@clarissecheung The CI failure is reminding us I missed there's one more task to do: Edit line 4 of models/cable/DESCRIPTION to read Version: 1.7.5.9000 and add a new line 4 to shiny/workflowPlot/DESCRIPTION (between License: and Author:) reading Version: 0.1.0.9000.

Thanks for taking on the task and sticking with it! The hazard of PRs that touch a lot of packages is that they wind up hitting lots of little maintenance tasks like these...

…ct#3710)

Bumps models/cable to 1.7.5.9000 and adds Version: 0.1.0.9000 to
shiny/workflowPlot to satisfy the check_versionbump CI step.
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@clarissecheung The CI failure is reminding us I missed there's one more task to do: Edit line 4 of models/cable/DESCRIPTION to read Version: 1.7.5.9000 and add a new line 4 to shiny/workflowPlot/DESCRIPTION (between License: and Author:) reading Version: 0.1.0.9000.

Thanks for taking on the task and sticking with it! The hazard of PRs that touch a lot of packages is that they wind up hitting lots of little maintenance tasks like these...

@infotroph Just pushed! Thank you again for your guidance with this!

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Documentation: broken links automatic report

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