[Cvicnaire]

Release 1.1.0: dev -> master. Checklist copied from #267 (state as of opening; it is kept current there). Pairs with montilab/SigRepo_Server release PR; both merge in the same window and production rebuilds once afterwards. #273 (DESCRIPTION 1.1.0) is still to merge into dev and will appear here when it does.

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Release checklist for the next dev -> master pull request. One line per merged pull request, with what to exercise on staging and what a correct result looks like. Tick a box only after doing it. Paired with montilab/SigRepo_Server release issue montilab/SigRepo_Server#154 (the server one): the two release pull requests merge in the same window, and production rebuilds its image once, after both are in.

Why both repositories, and in which order

• Client dev changes runHypeR() so organism and test are required and method, msigdb_species and split_by_direction are gone (hypeR-native annotation client, plotting and annotation tutorial #223). The production server's MCP run_enrichment tool still calls the old signature (mcp/lib/queries.R on server master). Releasing the client alone and rebuilding the production image would break that tool. Server dev withdrew the tool (SigRepo_Server#139), so the server release must land no later than the client release.
• Server dev rebuilt the Shiny Annotate and Home tabs on the new client (SigRepo_Server#148, package touch ups #153). They call getHypeRGenesets(), hypeRToExcel(), plotHypeRDots(), plotHypeREnrichment(), hypeRDotData(), hypeREnrichmentData() and hypeRSignatureKey(), none of which exist on client master. Releasing the server alone would break staging's Annotate tab the moment production rebuilt. So the client release must land no later than the server release.
• Everything else on client dev is client-only: it reaches users through install_github() and the server does not call it.

Net: merge both release pull requests, then rebuild montilab/sigrepo:latest once. The Dockerfile clones client master at build time, so the rebuild must come after the client merge.

Before anything can be tested on staging

• Merge Ask SigRepo_Server to rebuild the staging image when this package changes #241 (client change dispatches a staging image rebuild; pairs with SigRepo_Server#122 which is already on server dev). Until this is in, a push to client dev never reaches montilab.bu.edu and the boxes below cannot honestly be ticked. (Client changes never reach the staging instance #240.)
• Confirm the dispatched build ran and montilab/sigrepo:dev carries the current client: inside the staging API container, packageDescription("SigRepo")$RemoteSha matches origin/dev.

Coupled with the server release (test on staging, which runs the dev image)

• hypeR-native annotation client, plotting and annotation tutorial #223 hypeR-native annotation client. In the staging Shiny Annotate tab, run LLFS_Aging_Gene_2023 against MSigDB Hallmarks with hypergeometric, kstest and fgsea. Each produces a table and plots; the Excel export opens. From R against the staging database: runHypeR(conn_handler = conn, signature_name = "LLFS_Aging_Gene_2023", organism = "Homo sapiens", test = "fgsea", genesets = "msigdb") returns a hyp object with no error. Calling it without organism errors with a message that names the argument.
• connect-sigrepo-mcp skill: stop listing run_enrichment among the MCP tools #251 connect-sigrepo-mcp skill no longer lists run_enrichment. Staging MCP tool list (mcp/) has no run_enrichment; the skill text matches.

Client-only (test from an R session with remotes::install_github("montilab/SigRepo@dev"))

• Add searchExternal(): query Rummagene, RummaGEO and CORESH from a SigRepo signature #266 searchExternal(). searchExternal(conn_handler = conn, signature_name = "LLFS_Aging_Gene_2023", limit = 10) returns a named list of three data frames with the same first twelve columns; the verbose lines say "165 of 169 features mapped" and "N of M matching hits returned (limit = 10)"; attr(x$coresh, "job_url") opens a CORESH results page in a browser. source = "rummagene", direction = "both" returns a stacked frame with direction up/down. A mouse signature from the database runs RummaGEO against the mouse background (attr(x$rummageo, "query")$organism_code == "mmu").
• Add writeSignatureSearchScript(), which writes a LINCS search script #256 writeSignatureSearchScript(). Writes an R script for a human transcriptomics signature with at least 10 features in each direction; the script sources without error where signatureSearch is installed (or: the generated file reads correctly and refuses a signature with too few features with a clear message).
• Add mergeDifexp() to merge signatures' difexp tables into one matrix #264 mergeDifexp() (open; include only if merged before the release PR opens). Two signatures with difexp merge into one matrix with collapse = "min"; a signature without difexp is reported, not silently dropped.
• Fix missing rollback in addSignatureWithID on partial failure #188 addSignatureWithID() rolls back on partial failure. Deposit a signature whose feature step is forced to fail on the staging database; no orphan row remains in signatures.
• Remove R/hypeR_examples.R, a Shiny module that was never part of the package #249 R/hypeR_examples.R removed. R CMD check passes on the release candidate; nothing imports the removed module.

Process and CI (no user-visible behaviour; confirm they still work after the release)

• Run R CMD check and validation on the dev branch #235 R CMD check and validation run on dev and on the release PR; all green on the release PR.
• Document the dev branch, the release pull request and the staging tunnel #237, Say when Closes #NNN actually fires under the dev model #239 CONTRIBUTING describes the dev model and when Closes #NNN fires. Still accurate after this release; update the "what is live" sentence if needed.
• Close linked issues when a pull request merges into dev #254 close-linked-issues workflow. Issues named by the release PR body are not re-closed or spammed (the PR body should not say Closes for already-closed issues).

Release steps

• Bump Version in DESCRIPTION to 1.1.0 (the runHypeR() interface change is breaking; decide whether that warrants 2.0.0 instead and note the decision here).
• Rename the # SigRepo (development version) header in NEWS.md to # SigRepo 1.1.0 and check every merged PR since 1.0.0 has a bullet or a no-changelog label.
• Open the release PR dev -> master with this checklist copied into the body. No Closes lines.
• Merge the client release PR and the server release PR (SigRepo_Server#154) in the same window; the server one may go first or second but production must not rebuild between them.
• Trigger the production image rebuild once both are merged (the :latest build clones client master and OmicSignature main; this is also what finally ships OmicSignature 1.4.1 to production).
• Tag v1.1.0 on master.
• Merge master back into dev the same day (CONTRIBUTING rule).
• Close idea Connect to CORESH #82 with a pointer to Add searchExternal(): query Rummagene, RummaGEO and CORESH from a SigRepo signature #266 and this release.
• Update https://montilab.github.io/SigRepo/ (pkgdown runs on master).

Out of this release

• Nothing on dev is excluded. If a line above cannot be ticked, open a bug with what was run, what happened and the error, link it here, and label this issue blocked until it closes.

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[Cvicnaire]

Closing and reopening to make GitHub pick up dev's new head (3ae0ecd, the #276 docs fix); the PR did not synchronise on its own.