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format C++ code with clang format #728

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Bai-Li-NOAA and others added 5 commits January 17, 2025 07:07
@Bai-Li-NOAA @k-doering-NOAA @kellijohnson-NOAA
fix call-calc-coverage workflow
b050b96 
* update the DESCRIPTION file and set Config/testthat/parallel to false.
  This addresses the GHA run-time issue.
* skip parallel tests when running covr::package_coverage(), as these tests
  don't contribute to increasing code coverage and are redundant due to
  the reuse of wrapper functions. Integration tests are sufficient for
  coverage calculation.
* update GHA build triggers.

Co-authored-by: Kathryn Doering <[email protected]>
@kellijohnson-NOAA
fix(allcontributors): alphabetical = TRUE
1fe4c7c 
Now that the fix to allcontributors is in. Thanks @iantaylor-NOAA

Changes commit message to "chore: Updates contributors" to add a descriptor and make the tense present.

PR on dev rather than main, which main is the default and nothing was declared. But we don't want any PR to main.

Updates to use v4 of actions and v7 of create-pull-request
@k-doering-NOAA @Bai-Li-NOAA @kellijohnson-NOAA
Update GitHub Actions: Build Triggers, upload-artifact (#720)
9cc8ee0 
fix(GHA): Updates GHA build triggers

* update to v4 of upload-artifact gha
* fix(clang-format): v18 of workflow; allows for the newest version of clang-format to always be used by removing the clang-format version specification. This might be causing the issues with clang-format reordering the libraries and things
crashing on the R side when the package is tested.
* refactor(build-doxygen): Uses one file with an if statement to know if the doxygen workflow should deploy after building now that it is built on changes to both dev and main.
* fix(call-calc-coverage): Ignores paths on push and PR; it was ignoring paths just on workflow dispatch. Now the ignore calls are there for both PR and pushes.
* Adds dependabot.yml file to update GitHub actions
* Removes tags as trigger in package down
* Formats the GitHub action yml files consistently; moves summary above name: and arrange on in alphabetical order, as well as branch names and files are now in order too. This standardizes the way that the files are written.

References:
* https://kevsoft.net/2020/06/10/running-github-action-steps-and-jobs-only-on-push-to-master.html
* https://stackoverflow.com/questions/58139406/only-run-job-on-specific-branch-with-github-actions

Co-authored-by: Bai-Li-NOAA <[email protected]>
Co-authored-by: kellijohnson-NOAA <[email protected]>
@kellijohnson-NOAA
fix(dependabot.yml): Moves it to .github
bfb9b5d
@kellijohnson-NOAA
style R code
d21d2e9 
results <- styler::style_pkg() which uses 4 spaces but it will be okay
until it adopts the new new rules.
@Andrea-Havron-NOAA
* add FIMS_dmultinom distribution to match TMB
fcff594 
* update tests to use FIMS_dmultinom for length comps

* remove TODO comments
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5 participants
@ChristineStawitz-NOAA @Bai-Li-NOAA @kellijohnson-NOAA @k-doering-NOAA @Andrea-Havron-NOAA