[CRAN Release]: v0.5.0

[donyunardi]

Blocked by

• Pre-release activities #506
• teal.slice example apps testing #526
• [CRAN Release]: v0.5.0 teal.code#188
• [CRAN Release]: v0.4.0 teal.data#226
• remove check_ellipsis #511
• 1033 drop support for list filter #517
• remove get_teal_bs_theme #519
• internal function topological_sort() is defined in teal.slice and teal.data #516
• reevaluate variable_types function #507
• clean up after pre-release-cleanup #537
• Move shiny to Imports #529
• options for strict tests; few enhancements #536 we'll merge after CRAN release.
• remove exports of filter panel utils #539 not doing it with this release

Pre-release

• Make sure that high priority bugs (label "priority" + "bug") have been resolved before going into the release.
• Review old/hanging PRs before going into the release.
• Revisit R-package's lifecycle badges (Optional).
• Release Manager: Discuss package dependencies, create a plan to sequentially close release activities and submit groups of packages for internal validation (Applicable only for regulatory release).
• Check Validation Pipeline dry-run results for the package.
• Make sure all relevant integration tests are green 2-3 days before the release. Look carefully through logs (check for warnings and notes).
• Inform about the soft code freeze, decide what gets merged in before starting release activities.
• remove examples for non-exported functions #548 We will try to submit with examples first and see.

Release

Prepare the release

• Create a new release candidate branch
  git checkout -b release-candidate-vX.Y.Z
• Update NEWS.md file: make sure it reflects a holistic summary of what has changed in the package, check README.
• Update README:
  • include CRAN download links. See teal.code for example.
  • Update installation instruction to install from CRAN. See teal.code for example.
• Remove the additional fields (Remotes) from the DESCRIPTION file where applicable.
• Make sure that the minimum dependency versions are updated in the DESCRIPTION file for the package.
• Increase versioned dependency on {package name} to >=X.Y.Z.
• Commit your changes and create the PR on GitHub (add "[skip vbump]" in the PR title). Add all updates, commit, and push changes:

# Make the necessary modifications to your files
# Stage the changes
git add <files your modified>
# Commit the changes
git commit -m "[skip vbump] <Your commit message>"
git push origin release-candidate-vX.Y.Z

Test the release

• Execute the manual tests on Shiny apps that are deployed on various hosting providers (Posit connect and shinyapps.io) - track the results in GitHub issue (Applicable only for frameworks that use Shiny).
• Monitor integration tests, if integration fails, create priority issues on the board.
• Execute UAT tests (Optional).

CRAN submission

• Tag the update(s) as a release candidate vX.Y.Z-rc (e.g. v0.5.3-rc1) on the release candidate branch (release-candidate-vX.Y.Z).

  # Create rc tag for submission for internal validation
  git tag vX.Y.Z-rc<iteration number>
  git push origin vX.Y.Z-rc<iteration number>
  

• Build the package locally using the command:R CMD build . which will generate a .tar.gz file necessary for the CRAN submission.
• Submit the package to https://win-builder.r-project.org/upload.aspx for testing, for more details please see "Building and checking R source packages for Windows": https://win-builder.r-project.org/.
• Once tested, send the package that was built in the previous steps to CRAN via this form: https://cran.r-project.org/submit.html.
• Address CRAN feedback, tag the package vX.Y.Z-rc(n+1) and repeat the submission to CRAN whenever necessary.
• Get the package accepted and published on CRAN.

Tag the release

• If the additional fields were removed, add them back in a separate PR, and then merge the PR back to main (add "[skip vbump]" in the PR title). If nothing was removed just merge the PR you created in the "Prepare the release" section to main. Note the commit hash of the merged commit. Note: additional commits might be added to the main branch by a bot or an automation - we do NOT want to tag this commit.

Make sure of the following before continuing with the release:

• CI checks are passing in GH.
• Shiny apps are deployable and there are no errors/warnings (Applicable only for frameworks that use Shiny).
• Create a git tag with the final version set to vX.Y.Z on the main branch. In order to do this:
  1. Checkout the commit hash.
     git checkout <commit hash>
  2. Tag the hash with the release version (vX.Y.Z).
     git tag vX.Y.Z
  3. Push the tag to make the final release.
     git push origin vX.Y.Z
• Update downstream package dependencies to (>=X.Y.Z) in {package name}.
  Note: Once the release tag is created, the package is automatically published to internal repositories.

Post-release

• Make sure that the package is published to internal repositories (Validated and/or Non-Validated repository).
• Review and update installation instructions for the package if needed.
• Make sure internal documentation/documentation catalogs are up to date.
• Notify the IDR team to start post-release/clean-up activities.
• Announce the release on 6 FEB 2024.

Decision tree

Click here to see the release decision tree.

[gogonzo]

@donyunardi we have MultiAssayExperiment and SummarizedExperiment in the package dependencies. We need to consider splitting teal.slice in two parts. teal.slice (to CRAN) and teal.bio (to Bioconductor with functions supporting MAE and SE).

[m7pr]

+1 for splitting !

[gogonzo]

@donyunardi @lcd2yyz @pawelru @chlebowa @kartikeyakirar @m7pr @vedhav @averissimo

1. teal.slice will be released as one of the first packages (after teal.data). I think we should first split it into two packages and release them separately to CRAN.
2. Other thing is that I've made a big simplification of the package code and there is currently PR here. I think this change is needed sooner or later in order to fix teal. We can postpone this PR to "after" release but then we will have to deal with deprecation process (there will be few). My question to @donyunardi and @lcd2yyz is, what is a deadline for teal.slice on CRAN? I wonder if it is worth to put more effort now on this PR or not. Functional-wise PR is almost ready. It needs more effort to explain "simplified" but still not so easy way to extend filter-panel. I believe team could be very helpful here. My estimate is that it can be successfully put on production in the middle of January.

[gogonzo]

Another question to everyone. What should be the name of the package on bioconductor.

• teal.slice.bio - extends teal.slice only
• teal.bio - could keep methods from multiple packages - currently it would be only teal.slice but in the future we might add some additional support for teal.data or teal.transform classes/methods.

If we decide we should ask IDR to create a github repo and prepare pipeline for bioconductor release (same as hermes)

[pawelru]

I vote for teal.slice.bio

[vedhav]

Me too, teal.slice.bio 👍🏽 . <package>.bio sounds like a nice nomenclature to follow for bioC components of our packages and I like that it's explicit to a package.

[kartikeyakirar]

Keeping a separate package with a .bio extension can indeed enhance clarity regarding the product functionality it holds instead of keeping everything with teal.bio.
so +1 for teal.slice.bio

[chlebowa]

It is unclear to me why support for classes defined in BioC packages should be taken out of teal.slice and kept in a separate package on BioC. One would have to attach both to use SE, for instance. Will BioC dependencies removed from teal.slice at least?