feat: bioconductor improvements #944
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this makes `bioconductor-skeleton update-all-packages` idempotent, which is convenient when the update process fails halfway for some reason.
bgruening
approved these changes
Dec 3, 2023
bulk ci only runs if `[ci run]` in the commit message, so by default builds are skipped
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Also, just to document this, there was a suggestion by @mfansler to run unit tests whenever possible when including |
daler
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Mar 19, 2024
🤖 I have created a release \*beep\* \*boop\* --- ## [2.12.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.11.1...v2.12.0) (2024-03-18) ### Features * add support for excluding otherwise-selected recipes ([#962](https://www.github.com/bioconda/bioconda-utils/issues/962)) ([3946732](https://www.github.com/bioconda/bioconda-utils/commit/3946732eb6129f6905e53b62d76287e09d4bef36)) * bioconductor improvements ([#944](https://www.github.com/bioconda/bioconda-utils/issues/944)) ([b007d34](https://www.github.com/bioconda/bioconda-utils/commit/b007d34e6c723f7f9d6fcb5a6f58e072d4618cdf)) * Bulk build failure wiki ([#948](https://www.github.com/bioconda/bioconda-utils/issues/948)) ([18f988d](https://www.github.com/bioconda/bioconda-utils/commit/18f988d70966f6f6296170d96cc1ced51ad10392)) ### Bug Fixes * Do not emit cython_needs_compiler if compiler("cxx") is set ([#927](https://www.github.com/bioconda/bioconda-utils/issues/927)) ([8255afd](https://www.github.com/bioconda/bioconda-utils/commit/8255afdd9e5c0fd3cb09cb11269f5ff3397c959e)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Ryan Dale <[email protected]>
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Some fixes identified when preparing for the Bioconductor 3.18 updates:
run_exports.
bioconductor-skeletonnow adds run_exports to the recipes it builds. Since it's unclear to what extent all bioconductor developers adhere to semantic versioning, I opted formax_pin="x.x", even in the cases where versions start with0..Better build numbers.
bioconductor-skeleton update-all-packageswill now only modify the build number if it's needed. It checks what's available in the channel. So running the command multiple times (sometimes needed if the update process flakes out partway through) will not keep bumping the build number. This also uses the same check as the linting, which will hopefully reduce the frequency of build number adjustments in bulk.Fix manual build failure annotation. Allow category & reason to show up in manual build failure yaml via
bioconda-utils annotate-build-failuresCLIMore flexible dag.
bioconda-utils dagnow supports globs. So now withbioconda-utils dag --packages bioconductor-* | grep -v INFO > dag.gmland then loadingdag.gmlinto Gephi, you can visually identify which packages should be prioritized for building first. This example sizes nodes by out-degree and labels only those with >125 outgoing edges.And minor stuff. The pinning for bioconductor-data-packages needed a space; there was a build-failure yaml that was empty which crashed osx builds.