Merge pull request #3933 from clarissecheung/GH-3710-fix-broken-documentation-links

Fix broken documentation links (#3710)

Author: infotroph

CHANGELOG.md

@@ -25,6 +25,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - Added `PEcAn.data.land::to_co2e()` for converting SOC change, CH4, and N2O to CO2-equivalent emissions using IPCC Global Warming Potential values.
 
 ### Fixed
+- Fixed broken pecanproject.github.io, pecan.gitbooks.io, and other outdated documentation links across book_source, tutorials, models, modules, web, and shiny files (#3710).
 - Added note to DEV-INTRO.md documenting Traefik workaround for Apple Silicon (ARM64) Macs: use `traefik:v2.11` with `platform: linux/arm64` to fix 404 errors (#3910)
 - Fixed `web/08-finished.php`: show database info instead of "Still running" when workflow folder doesn't exist locally (#3501).
 

DEV-INTRO.md

@@ -253,7 +253,7 @@ A better way of doing this is developed as part of GSOC, in which case you can l
 
 ## PEcAn URLs
 
-You can check the RabbitMQ server used by pecan using <https://rabbitmq.pecan.localhost> on the same server that the docker stack is running on. You can use rstudio either with <http://server/rstudio> or at <http://rstudio.pecan.localhost>. To check the traefik dashboard you can use <http://traefik.pecan.localhost>.
+You can check the RabbitMQ server used by pecan using <https://rabbitmq.pecan.localhost> on the same server that the docker stack is running on. You can use rstudio either with `http://server/rstudio` or at <http://rstudio.pecan.localhost>. To check the traefik dashboard you can use <http://traefik.pecan.localhost>.
 
 If the stack is running on a remote machine, you can use ssh and port forwarding to connect to the server. For example `ssh -L 8000:localhost:80` will allow you to use <http://rabbitmq.pecan.localhost:8000/> in your browser to connect to the remote PEcAn server RabbitMQ.
 

base/utils/R/datasets.R

@@ -2,7 +2,7 @@
 #' Standardized variable names and units for PEcAn
 #'
 #' A lookup table giving standard names, units and descriptions for variables in PEcAn input/output files.
-#' Originally based on the \href{https://nacp.ornl.gov/MsTMIP_variables.shtml}{MsTMIP} standards,
+#' Originally based on the \href{https://nacp-prod.ornl.gov/MsTMIP_variables.shtml}{MsTMIP} standards,
 #' with additions to accomodate a wider range of model inputs and outputs.
 #' The standard_vars table replaces both `mstmip_vars` and `mstmip_local`,
 #' both of which are now deprecated.
@@ -13,7 +13,7 @@
 #' @format data frame, all columns character
 #' \describe{
 #'  \item{Variable.Name}{Short name suitable for programming with}
-#'  \item{standard_name}{Name used in the NetCDF \href{http://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html}{CF metadata conventions} }
+#'  \item{standard_name}{Name used in the NetCDF \href{https://cf-convention.github.io/Data/cf-standard-names/current/build/cf-standard-name-table.html}{CF metadata conventions} }
 #'  \item{Units}{Standard units for this variable. Do not call variables by these names if they are in different units.
 #'    See `ud_convert` for conversions to and from non-standard units}
 #'  \item{Long.Name}{Human-readable variable name, suitable for e.g. axis labels}

base/utils/R/read.output.R

@@ -11,7 +11,7 @@
 #' surface runoff (Qs), subsurface runoff (Qsb), and rainfall (Rainf).
 #'
 #' For more details, see the [MsTMIP
-#' variables](http://nacp.ornl.gov/MsTMIP_variables.shtml)
+#' variables](https://nacp-prod.ornl.gov/MsTMIP_variables.shtml)
 #' documentation.
 #'
 #' @param runid the ID distinguishing the model run. Can be omitted

base/utils/man/read.output.Rd

@@ -81,8 +81,8 @@ We have no strict rules about this, but it's useful to have tags that give some
 If section organization changes, it is fine to move header tags, but **avoid altering existing tags** as this will break all the links pointing to that tag.
 (Note that it is also possible to link to section headings by their exact title. However, this is not recommended because these section titles could change, which would break the links.)
 
-When referring to PEcAn packages or specific functions, it is a good idea to link to the [rendered package documentation](https://pecanproject.github.io/pkgdocs.html).
-For instance, here are links to the [`models/ed`](https://pecanproject.github.io/models/ed/docs/index.html) package, the [`PEcAn.ED2::modify_ed2in`](https://pecanproject.github.io/models/ed/docs/reference/modify_ed2in.html) function, and the PEcAnRTM package [vignette](https://pecanproject.github.io/modules/rtm/docs/articles/pecanrtm.vignette.html).
+When referring to PEcAn packages or specific functions, it is a good idea to link to the [rendered package documentation](https://pecanproject.github.io/package-documentation/develop/).
+For instance, here are links to the [`PEcAn.ED2`](https://pecanproject.github.io/package-documentation/develop/PEcAn.ED2/) package, the [`PEcAn.ED2::modify_ed2in`](https://pecanproject.github.io/package-documentation/develop/PEcAn.ED2/reference/modify_ed2in.html) function, and the PEcAnRTM package [vignette](https://pecanproject.github.io/package-documentation/develop/PEcAnRTM/articles/pecanrtm.vignette.html).
 If necessary, you can also link directly to specific lines or blocks in the source code on GitHub, [like this](https://github.com/PecanProject/pecan/blob/develop/models/ed/R/create_veg.R#L11-L25).
 (To get a link to a line, click its line number. To then select a block, shift-click another line number.)
 

base/utils/man/standard_vars.Rd

@@ -283,7 +283,7 @@ If you would like to make changes to a release branch, you must follow a differe
 
 #### Tags
 
-Git supports two types of tags: lightweight and annotated. For more information see the [Tagging Chapter in the Git documentation](http://git-scm.com/book/ch2-6.html).
+Git supports two types of tags: lightweight and annotated. For more information see the [Tagging Chapter in the Git documentation](https://git-scm.com/book/en/v2/Git-Basics-Tagging).
 
 Lightweight tags are useful, but here we discuss the annotated tags that are used for marking stable versions, major releases, and versions associated with published results. 
 
@@ -312,7 +312,7 @@ To tag an earlier commit, just append the commit SHA to the command, e.g.
 * GitHub help pages,
 [https://help.github.com](https://help.github.com)/
 * Main GIT page
-[http://git-scm.com/documentation](http://git-scm.com/documentation)
+[https://git-scm.com/doc](https://git-scm.com/doc)
 * Another set of pages about branching,
 [http://sandofsky.com/blog/git-workflow.html](http://sandofsky.com/blog/git-workflow.html)
 * [Stackoverflow highest voted questions tagged "git"](http://stackoverflow.com/questions/tagged/git?sort=votes&pagesize=50)
@@ -322,8 +322,7 @@ To tag an earlier commit, just append the commit SHA to the command, e.g.
 
 When in doubt, the first step is to click the "Help" button at the top of the page.
 
-* [GitHub Flow](http://scottchacon.com/2011/08/31/github-flow.html) by
-Scott Chacon (Git evangelist and Ruby developer working on GitHub.com)
+* [GitHub Flow](https://docs.github.com/en/get-started/quickstart/github-flow)
 * [GitHub FAQ](https://help.github.com/)
 * [Using Pull Requests](https://help.github.com/articles/using-pull-requests)
 * [SSH Keys](https://help.github.com/articles/generating-ssh-keys)

book_source/01_introduction/03_how_to_use_book.Rmd

@@ -45,7 +45,7 @@ Note:
 
 
 (from The Pragmatic Programmer, available as
-[ebook](http://proquestcombo.safaribooksonline.com/0-201-61622-X/223)
+[ebook](https://github.com/lighthousand/books/blob/master/the-pragmatic-programmer.pdf)
 through UI libraries, hardcopy on David’s bookshelf)\
 
 * focus on “user stories”, e.g. specific use cases

book_source/02_demos_tutorials_workflows/05_developer_workflows/02_git/01_using-git.Rmd

@@ -34,7 +34,7 @@ ProxyPassReverse         /bety/ http://pecan.localhost/bety/
 RedirectMatch permanent ^/bety$ /bety/
 ```
 
-Once this modified we can restart apache using `systemctl restart apache2`. At this point BETY is running in a container and is accessable trough the webserver at http://server/bety/.
+Once this modified we can restart apache using `systemctl restart apache2`. At this point BETY is running in a container and is accessable trough the webserver at `http://server/bety/`.
 
 
 To upgrade to a new version of BETY you can now use the docker commands. You can use the following commands to stop BETY, pull the latest image down, migrate the database (you made a backup correct?) and start BETY again.