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Update to devel versions and add hpaSearch() function - #36
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# Conflicts: # DESCRIPTION
Bioconductor's git.bioconductor.org/packages/HPAanalyze devel branch had diverged from this GitHub repo: it carries two automatic version-bump commits (1.29.1 -> 1.30.0 -> 1.31.0) applied when the RELEASE_3_23 branch was cut, which never made it back here. Merging that history in and bumping to 1.31.1 keeps this branch a fast-forward of Bioconductor's actual devel history so it can be pushed cleanly. Also consolidates the NEWS entry for the hpaSearch()/hpaXmlParse() work under the new version, and repoints check-bioc.yml's Bioconductor docker image/BiocManager version from the stale RELEASE_3_18 to devel so BiocCheck runs against the version this package will actually be built against.
Badges were plain images with no click-through; wire each one to the page it summarizes (GitHub Actions run history, or the relevant anchor on the Bioconductor package page / check results / stats page). Also mention the two functions added this cycle (hpaSearch, hpaXmlParse) in the README overview, and bump the stale 2018-2025 copyright range.
Part of updating the bundled data to HPA version 25.1 (released 2026-05-25); the binary data files (hpa_histology_data.rda, R/sysdata.rda) are regenerated in a follow-up commit once the R toolchain finishes installing in this session.
Re-ran data_raw/create_internal_data.R and data_raw/example_data.R against the live v25.proteinatlas.org endpoints (which now serve the 25.1 point release; HPA archives point releases in place under the same major-version subdomain rather than minting a new one) to refresh R/sysdata.rda (gene/Ensembl lookup table + download list) and data/hpa_histology_data.rda (bundled example dataset). Row counts for normal_tissue/pathology/subcellular_location and the gene/Ensembl lookup table are unchanged from 25.0, consistent with a point release; the download list URLs are untouched since they already targeted the v25 subdomain.
Verified via R CMD check: package installs, loads, and the full testthat suite passes against the regenerated data.
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Pull request overview
This PR updates HPAanalyze to Bioconductor/R devel targets, refreshes release metadata (version/news), and updates user-facing documentation to reflect new API/query and XML parsing capabilities.
Changes:
- Bumped package version to 1.31.2 and updated NEWS accordingly.
- Updated README badges/links and added documentation blurbs for
hpaXmlParse()andhpaSearch(). - Switched BiocCheck GitHub Actions workflow matrix to R devel / Bioconductor devel, updating cache keys and artifact naming.
- Updated example data metadata to HPA version 25.1.
Reviewed changes
Copilot reviewed 6 out of 8 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| README.Rmd | Updates CI/Bioconductor badges to be clickable and documents hpaXmlParse() / hpaSearch(); updates copyright year. |
| README.md | Mirrors README.Rmd badge/link updates and new function descriptions; updates copyright year. |
| NEWS | Adds entries for 1.31.1/1.31.2 describing new functionality and maintenance fixes. |
| DESCRIPTION | Version bump to 1.31.2 (and release date retained/updated). |
| data_raw/example_data.R | Updates embedded example metadata to HPA version 25.1. |
| .github/workflows/check-bioc.yml | Moves CI matrix to devel (R/Bioc), updates cache keys and artifact naming. |
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actions/upload-artifact@master was an unpinned moving target; pin to the stable v4 major to avoid unexpected breakage and reduce supply chain risk. The "in bioc" badge's alt text was split across two lines, which can render incorrectly in Markdown.
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Summary
Prepares HPAanalyze for a Bioconductor devel push and adds
hpaSearch().Key changes
git.bioconductor.org/packages/HPAanalyze) had already auto-bumped to 1.31.0 when theRELEASE_3_23branch was cut; this branch merges that history in so it stays a clean fast-forward of Bioconductor's actual devel branch, then adds 1.31.1 (new features) and 1.31.2 (data refresh).hpaSearch()to query the HPA search API, andhpaXmlParse()to generically parse an entire imported XML document into a flat, joinable list of tibbles (with a new vignette).data_raw/pipeline against live HPA data; verified with a fullR CMD checkincluding the testthat suite).check-bioc.ymlmoved from a stale pinned Bioconductor 3.18/R 4.3 matrix todevel/devel, andactions/upload-artifactpinned to@v4instead of the unpinned@master.Notable details
bioconductor/bioconductor_docker:develcontainer.devel/develmatrix.https://claude.ai/code/session_01U2tzwP213Nf1qrCZ9jkPQ9