Author	SHA1	Message	Date
pat-s	77a2f1f04a	fix(ci): install RPostgres for audit workflows (#172) ... ## Summary - Install RPostgres before running the missing-binaries audit. - Install RPostgres before running weekly patch proposal and automatic patch workflows. ## Validation - `prek run --files .crow/auto-apply-patches.yaml .crow/weekly-audit-missing.yaml .crow/weekly-patch-proposals.yaml` - `crow lint .crow/` - `git diff --check` Reviewed-on: #172	2026-08-30 07:31:28 +00:00
pat-s	1e843523a0	fix(ci): gate the three ungated pipelines on their own variable (#155) ... ## Problem A manual `crow pipeline create` instantiates **every** pipeline in `.crow/`, and each one decides for itself whether to run. Three had nothing to decide with — their only manual condition was a bare `event: manual`: - `auto-apply-patches` — pushes to `auto/registry-patch-proposals` and opens/updates a PR - `weekly-patch-proposals` — posts and edits two Forgejo issues - `trial-build-registry` — starts a build per matrix row, on both arches So they fired on *any* manual trigger in this repo, whatever it was for. That is how they came to run alongside a manual `process-updates` run for `alpine-324-arm64` (#10723), which is also why that pipeline is marked failure. `repair-built-stamp.yaml` already documents the rule this breaks: > The gate variable is `repair_built_stamp`, not `target_arch` … Every pipeline here gates on a variable named after itself for exactly that reason. ## What this changes Each of the three gets a gate variable named after the pipeline, `evaluate`d on the manual event, defaulting to off: ```yaml variables: auto_apply_patches: description: 'Run the auto-patch proposer. Also gates this pipeline.' options: ['true', 'false'] default: 'false' when: - event: manual evaluate: 'auto_apply_patches == "true"' - event: cron cron: auto-apply-patches ``` Cron triggers are untouched, so the scheduled runs behave exactly as before. The run-manually comments in all three headers were also stale: they documented `--var task=<name>` with `woodpecker-cli`, and no pipeline evaluates a `task` variable. They now show the real invocation. ## Note on the sibling pipelines The already-gated pipelines use `default: all` (e.g. `weekly_rebuild_missing`). If Crow applies a declared default to a variable that an API-created pipeline never passed, those would match on an unrelated manual run too — `weekly-rebuild-missing` would be an expensive way to find out. I could not settle that from #10723 because its step logs have since expired, so I left them alone rather than guess. The three fixed here default to `'false'`, which is safe under either semantics. ## Verification `crow lint .crow/` passes. Auditing every pipeline that accepts a manual event now reports a gate on all ten: ``` build-all-versions-install-deps.yaml: gated auto-apply-patches.yaml: gated weekly-patch-proposals.yaml: gated weekly-audit-missing.yaml: gated repair-built-stamp.yaml: gated archive-missed-packages.yaml: gated weekly-rebuild-missing.yaml: gated trial-build-registry.yaml: gated build-all-versions.yaml: gated process-updates.yaml: gated ``` Reviewed-on: #155	2026-08-09 10:02:05 +00:00
pat-s	ee15c50f53	refactor: migrate package installation from pak to uvr (#147) ... `bincraft` dropped pak in favour of uvr (5.0.x, "Dependencies and their system requirements are now installed with `uvr` instead of pak during `build_binary_package()`"), so the pipelines, helper scripts and images in this repo move with it. ## Approach uvr is project-scoped in a way pak is not: `uvr add` refuses to run outside a project and always installs into `.uvr/library/`, and only `uvr sync` honours `--library`. So there is no one-line `pak::pak(...)` equivalent. `local/uvr-install.sh` encapsulates the dance — bootstrap a pinned uvr, mint a throwaway project under `TMPDIR`, `uvr add --no-install`, then `uvr sync --library <target>`. Keeping the project outside the checkout also keeps `uvr init`'s `.Rprofile` from hijacking `.libPaths()` for every other R call in the pipeline. This matches what bincraft itself does (`uvr sync --install-system-deps --library <lib>`), and bincraft requires `uvr` on `PATH`, which the bootstrap provides: every pipeline that calls `bincraft::` runs `install-bincraft.R` (and therefore the bootstrap) first. ## Changes | File | Change | | --- | --- | | `local/uvr-install.sh` | **New.** The single replacement for `pak::pak(...)`. Bootstraps uvr `v0.4.4`, resolves the R interpreter from `UVR_R_BIN`/`R_VERSION`/`PATH`, pins the manifest to that R's exact version, and syncs into `UVR_TARGET_LIB`/`R_LIBS_USER`. | | `local/install-bincraft.R` | Installs `forgejo::codefloe.com/rpkgs/bincraft@<tag>` instead of a `git::` URL; keeps the `git ls-remote` tag resolution. Exports `UVR_R_BIN`/`UVR_TARGET_LIB` from `R.home()`/`.libPaths()[1]` so the per-R-minor passes target their own R and library. | | `.crow/auto-apply-patches.yaml`, `.crow/weekly-patch-proposals.yaml`, `.crow/weekly-audit-missing.yaml`, `.crow/weekly-rebuild-missing.yaml`, `.crow/build-all-versions-install-deps.yaml` | `pak::pak(...)` → `UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh ...`. The explicit `UVR_R_BIN` matters in `build-all-versions-install-deps.yaml`, which has no `R_VERSION` in its step environment. | | `.crow/build-all-versions.yaml`, `.crow/process-updates.yaml`, `.crow/weekly-rebuild-missing.yaml` | `R_PKG_CACHE_DIR` → `UVR_CACHE_DIR` + `UVR_PACKAGES_DIR` on the same `/mnt/cache` volume, preserving the amd64-off/arm64-on split. Drops the `rm -rf .../pkgcache/_metadata/...` cleanup. | | `local/r-minor-helpers.R`, `local/build-all.R`, `local/tests/test-trim-pkgcache.R` | Removes `trim_pkgcache_metadata()`, its every-25-packages call and its tests. uvr's cache does not mint a fresh ~70 MB snapshot per `PACKAGES` change. | | `.crow/build-all-versions-install-deps.yaml` | Drops `pak::sysreqs_db_update()`; uvr resolves sysreqs from its vendored `r-system-requirements` rules via `--install-system-deps`. | | `docker/Containerfile-shiny-app` | Bootstraps uvr and drives both dependency installs through one uvr project with `UVR_LIBRARY` pointed at the image's R library. | | `docker/build-one.Dockerfile` | Ships `uvr-install.sh` at `/work/local/` so `install-bincraft.R` finds it. | | `docker/reprex/alpine.sh` | Replaces `pak::local_install_deps()` with DESCRIPTION parsing + `uvr add`. | | `local/test-package-loading.R` | Installs via the helper instead of `pak::pkg_install()`. | | `README.md` | Documents uvr for sysreq inference, archived-version installs and cache clearing. | | `renovate.json` | Tracks the `UVR_PIN` in `uvr-install.sh` via `github-releases`. | ## Behaviour notes - **`weekly-audit-missing` still takes bincraft from the default branch**, not the latest release tag, matching what the `git::` pak call did. Called out in a comment rather than silently changed. - **The uvr pin is repo-wide.** bincraft resolves `uvr` from `PATH` and pins no version of its own, so `UVR_PIN` in `uvr-install.sh` governs the whole pipeline. - **Persistent caches now also benefit bincraft**, which reads `UVR_CACHE_DIR`/`UVR_PACKAGES_DIR` from the inherited pipeline environment. - **`uvr sync` will not prune the shared library.** Pruning is disabled whenever `--library` is passed (`do_prune = prune && library_override.is_none()`), so `/mnt/cache/R-pkgs` keeps bincraft and its dependencies. The wipe-on-ABI-mismatch path is *not* similarly guarded, which is why the helper pins the manifest to the active R's exact version. - **`plans/` and `specs/` are untouched** — they are dated records of decisions made in June 2026 and describe bincraft's then-pak-based internals; rewriting them would misstate history. ## Verification `shellcheck`, all pre-commit hooks (on this commit's file range) and the `local/tests/` suite (100 assertions) pass. Not yet exercised in CI: the build-env images do not ship `uvr`, so the per-step `curl install.sh` bootstrap is untested against a real image. Worth a manual `build-all-versions-install-deps` run before merging. Reviewed-on: #147	2026-07-31 12:19:26 +00:00
pat-s	ed1485c542	ci: remove evaluate conditions	2026-07-15 16:51:15 +02:00
pat-s	1bca6004fd	chore(local): reuse FORGEJO_TOKEN for the auto-patch push (#125) ... Follow-up to #124 (merged): the auto-patch pipeline required a separate write-scoped `REPO_RW_TOKEN` to push the branch. Reuse the existing `FORGEJO_TOKEN` instead. - `propose-patches.R --open-pr` now pushes `auto/registry-patch-proposals` over HTTPS with `FORGEJO_TOKEN` (the same token used for the PR API); the read-only `origin` clone URL can't push, so it builds an authenticated URL explicitly. - Drop `REPO_RW_TOKEN` from `.crow/auto-apply-patches.yaml` and the docs. No new secret needed: the pipeline's secrets are now `PGPASS`, `REPO_RO_TOKEN`, and `FORGEJO_TOKEN` (all existing). `FORGEJO_TOKEN` must have repository write scope for the push to succeed. 105 tests pass; all pre-commit hooks pass. Reviewed-on: #125	2026-07-15 14:50:19 +00:00
pat-s	4bca17e4ac	feat(local): auto-apply registry patches with a build-env trial-build gate (#124) ... Closes the classifier loop (issue #115, step 3): turns the auto-proposable candidates into an actual PR, gated by a real trial build **in our own build-env images**. Chosen model (from the design discussion): **autonomous PR**, **PR-first with a CI trial-build gate**, **bounded top-N batch** per run. ## Creating the patch PR - `propose-patches.R` gains: - `--limit N` -- act on the top-N candidates by failure volume; the rest defer to the next run (logged). - `--open-pr` -- write the entries onto the reused `auto/registry-patch-proposals` branch, push (with `REPO_RW_TOKEN`), and open/update **one** PR via the Forgejo API (so re-runs update the same PR instead of piling up). - `.crow/auto-apply-patches.yaml` -- a single job that runs `--open-pr --limit` on a cron/manual trigger. Needs `FORGEJO_TOKEN` + a write-scoped `REPO_RW_TOKEN`. Novel source diffs and unknown signatures are still never proposed; nothing merges. ## The merge gate (our build-env images) - `.crow/trial-build-registry.yaml` -- matrixed over the real `OS/IMG` build-env matrix (alpine:3.24, redhat:8/9/10, ubuntu:jammy/noble/**resolute** for ubuntu-2604). Each platform runs `local/trial-build-registry.R`, which diffs the branch registry against `main` and trial-builds **only the entries the branch adds** that apply to that platform, inside `reg.devxy.io/rpkgs/build-env-*`. Green only if every new entry builds; a platform with no new entries is a fast no-op. Nothing is uploaded/archived/recorded. - The base-registry read **fails loud** if it can't read `registry.json` at `main`, rather than silently treating the base as empty and trial-building the whole registry. ## Notes / follow-up - The repo uses **no `pull_request` triggers**, so the gate runs manually or on a cron against the branch (`--var patch_branch=...`). Wiring it to fire automatically on the PR needs `event: pull_request` enabled on the Forgejo webhook -- a one-line addition once that's on. - Two new crons to register in the crow UI: `auto-apply-patches` and `trial-build-registry`. New secret needed: `REPO_RW_TOKEN` (write scope) for the push. ## Verification - New pure helpers `entry_applies_to_os()` / `new_registry_packages()` covered by tests (platform codename/family/wildcard matching; added-vs-unchanged entry detection; per-platform filtering). - `--limit` smoke (stubbed DB): top-2 by volume proposed, 3 deferred, candidate registry validates. - Full suite: 105 tests pass; all pre-commit hooks pass (air, prettier, markdownlint, yamllint, validate-patches). Reviewed-on: #124	2026-07-15 08:28:15 +00:00