pat-s
930a4acd12bincraft v5.5.1 dropped lubridate, dplyr, purrr, data.table and others from its imports, so the pipelines' own calls now depend on whatever the build-env image's site library or the shared R_LIBS_USER cache happens to hold. The arm64 redhat:9 image has no progressr under R 4.4.3, which fails every process-cran-updates-redhat-9-arm64 run since v5.5.1. - Install progressr and lubridate for process-updates, which call them inline. - Install purrr for packages-to-build.R and data.table for the weekly audit. - Drop the unused dplyr and progressr library() calls from packages-to-build.R. - Install RPostgres in every pipeline that talks to the metadata DB, since bincraft silently skips the DB (and the per-minor index aborts) without it. - Reinstall bincraft in the prune re-index step, whose /tmp library does not survive from the prune step.
206 lines
7.6 KiB
YAML
206 lines
7.6 KiB
YAML
# Re-index and purge after weekly-rebuild-missing.
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#
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# weekly-rebuild-missing runs three shards per slot. Each of them replaces
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# objects in place, so the slot's index still advertises the old MD5 and, for
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# anything that had been served from source, no Built stamp. Re-indexing from
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# inside a shard would mean three concurrent `upload_package_index()` calls on
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# one prefix: each lists the live bucket, so an early lister that uploads last
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# publishes an index missing its siblings' work.
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#
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# So it happens exactly once per slot, here, after every shard has finished.
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# `runs_on: [success, failure]` keeps that true when a shard fails; only an
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# explicit cancel skips it, and this pipeline can then be triggered on its own.
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variables:
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# Mirrors the gate on weekly-rebuild-missing so a manual run re-indexes
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# exactly the slots it rebuilt. A manual pipeline creation instantiates every
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# file in .crow/, so the default must match no matrix row.
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weekly_rebuild_missing:
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description: "Manual run target: a specific <os>-<arch>, 'all' to run every os/arch in parallel, or 'none' to run nothing."
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options:
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- none
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- all
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- alpine-323-amd64
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- alpine-323-arm64
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- alpine-324-amd64
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- alpine-324-arm64
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- redhat-8-amd64
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- redhat-8-arm64
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- redhat-9-amd64
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- redhat-9-arm64
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- redhat-10-amd64
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- redhat-10-arm64
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- ubuntu-2204-amd64
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- ubuntu-2204-arm64
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- ubuntu-2404-amd64
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- ubuntu-2404-arm64
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- ubuntu-2604-amd64
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- ubuntu-2604-arm64
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default: none
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when:
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- event: cron
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cron: weekly-rebuild-missing-${OS}-${ARCH}
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- event: manual
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evaluate: 'weekly_rebuild_missing == "all" || weekly_rebuild_missing == "${OS}-${ARCH}"'
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depends_on:
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- weekly-rebuild-missing
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runs_on: [success, failure]
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skip_clone: true
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labels:
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group: rpkgs-${ARCH}
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matrix:
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include:
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- OS: alpine-323
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ARCH: amd64
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R_VERSION: 4.5.3
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IMG: alpine:3.23
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- OS: alpine-323
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ARCH: arm64
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R_VERSION: 4.5.3
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IMG: alpine:3.23
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- OS: alpine-324
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ARCH: amd64
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R_VERSION: 4.5.3
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IMG: alpine:3.24
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- OS: alpine-324
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ARCH: arm64
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R_VERSION: 4.5.3
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IMG: alpine:3.24
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- OS: redhat-8
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ARCH: amd64
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R_VERSION: 4.4.3
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IMG: redhat:8
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- OS: redhat-8
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ARCH: arm64
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R_VERSION: 4.4.3
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IMG: redhat:8
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- OS: redhat-9
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ARCH: amd64
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R_VERSION: 4.4.3
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IMG: redhat:9
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- OS: redhat-9
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ARCH: arm64
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R_VERSION: 4.4.3
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IMG: redhat:9
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- OS: redhat-10
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ARCH: amd64
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R_VERSION: 4.5.3
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IMG: redhat:10
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- OS: redhat-10
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ARCH: arm64
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R_VERSION: 4.5.3
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IMG: redhat:10
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- OS: ubuntu-2204
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ARCH: amd64
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R_VERSION: 4.4.3
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IMG: ubuntu:jammy
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- OS: ubuntu-2204
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ARCH: arm64
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R_VERSION: 4.4.3
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IMG: ubuntu:jammy
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- OS: ubuntu-2404
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ARCH: amd64
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R_VERSION: 4.4.3
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IMG: ubuntu:noble
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- OS: ubuntu-2404
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ARCH: arm64
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R_VERSION: 4.4.3
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IMG: ubuntu:noble
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- OS: ubuntu-2604
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ARCH: amd64
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R_VERSION: 4.4.3
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IMG: ubuntu:resolute
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- OS: ubuntu-2604
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ARCH: arm64
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R_VERSION: 4.4.3
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IMG: ubuntu:resolute
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steps:
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- name: 'Re-index the slot'
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image: reg.devxy.io/rpkgs/build-env-${IMG}
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pull: true
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environment:
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OTEL_R_TRACES_EXPORTER: none
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OTEL_R_LOGS_EXPORTER: none
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OTEL_R_METRICS_EXPORTER: none
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RED_HAT_DEV_PW:
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from_secret: RED_HAT_DEV_PW
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B2_S3_ACCESS_KEY:
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from_secret: B2_S3_ACCESS_KEY
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B2_S3_SECRET_KEY:
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from_secret: B2_S3_SECRET_KEY
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# The index build reads the ABI classifier cache to decide which packages
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# may be carried from the flat slot into a per-minor one. Without the
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# password that query fails, and it fails soft, so the run still succeeds
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# while quietly using an empty risky set: exactly the state the cache was
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# added to fix. It logs one connection error per slot.
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PGPASS:
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from_secret: PGPASS
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REPO_RO_TOKEN:
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from_secret: REPO_RO_TOKEN
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# bincraft reads the DESCRIPTION of every new or replaced tarball from
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# the CRAN mirror on raw.githubusercontent.com, and authenticates with
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# this token when it is set. A slot whose published index cannot be read
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# is re-read in full, ~25k requests, which the anonymous rate limit would
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# cut short.
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GITHUB_PAT:
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from_secret: GITHUB_PAT
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GIT_USER: pat-s
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R_LIBS_USER: /mnt/cache/R-pkgs
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R_VERSION: ${R_VERSION}
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PLATFORM: ${OS}
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ARCH: ${ARCH}
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commands:
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- git clone -q https://pat-s:$$REPO_RO_TOKEN@git.devxy.io/devxy/build-cran-binaries.git .
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- mkdir -p /mnt/cache/R-pkgs
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- rm -rf /mnt/cache/R-pkgs/00LOCK-*
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- /opt/R/$R_VERSION/bin/Rscript local/install-bincraft.R
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- UVR_R_BIN=/opt/R/$R_VERSION/bin/R local/uvr-install.sh RPostgres
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# The codename is detected from the image's /etc/os-release.
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- /opt/R/$R_VERSION/bin/R -q -e 'library(bincraft); upload_package_index(s3_endpoint = "https://s3.eu-central-003.backblazeb2.com", s3_region = "eu-central-003", s3_bucket = "devxy-rpkgs-binaries", s3_access_key_id = Sys.getenv("B2_S3_ACCESS_KEY"), s3_secret_access_key = Sys.getenv("B2_S3_SECRET_KEY"))'
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- |
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FAILED_MINORS=""
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for RBIN in /opt/R/[0-9]*/bin/R; do
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RMINOR=$(basename "$(dirname "$(dirname "$RBIN")")" | cut -d. -f1-2)
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/opt/R/$R_VERSION/bin/R -q -e "library(bincraft); upload_package_index(r_minor = '$RMINOR', s3_endpoint = 'https://s3.eu-central-003.backblazeb2.com', s3_region = 'eu-central-003', s3_bucket = 'devxy-rpkgs-binaries', s3_access_key_id = Sys.getenv('B2_S3_ACCESS_KEY'), s3_secret_access_key = Sys.getenv('B2_S3_SECRET_KEY'), metadata_db_host = 'r-binaries.devxy.io', metadata_db_name = 'build_metadata', metadata_db_port = 15432L, metadata_db_user = 'rpkgs', metadata_db_password = Sys.getenv('PGPASS'), metadata_db_sslmode = 'verify-full')" || FAILED_MINORS="$FAILED_MINORS $RMINOR"
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done
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if [ -n "$FAILED_MINORS" ]; then
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echo "Could not republish the per-minor index for:$FAILED_MINORS" >&2
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exit 1
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fi
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- name: Purge CDN cache
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image: reg.devxy.io/docker.io/library/alpine:3.24
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environment:
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OTEL_R_TRACES_EXPORTER: none
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OTEL_R_LOGS_EXPORTER: none
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OTEL_R_METRICS_EXPORTER: none
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BUNNYNET_API_KEY:
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from_secret: BUNNYNET_API_KEY
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# cran.rpkgs.com and cran.allianceswisspass.devxy.io are on separate
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# Bunny pull zones, so both must be purged after the shared origin changes.
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# The staging zone is listed too. It shares the B2 origin, so an index
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# it still holds is a stale copy of the same object, and its
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# cache_expiration_time is the same ~370 days: without a purge here it
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# serves pre-reindex indexes indefinitely and any verification run
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# against it measures the past.
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BUNNY_PULLZONES: '3857050 cran.allianceswisspass.devxy.io cran-rpkgs-test.b-cdn.net'
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commands:
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- apk add --no-cache -q bash curl jq
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# Crow carries the checkout from the re-index step into this step.
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- bash scripts/purge_cdn_zone.sh "$BUNNYNET_API_KEY" $BUNNY_PULLZONES
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# Runs on every row rather than on one designated slot: a cron fires only
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# its own slot's row, so gating on a named slot would leave every other
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# slot unpurged. A manual "all" run therefore purges the zone 18 times,
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# which is a cheap API call and rare.
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#
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# Run it even when the re-index above failed: the objects were still
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# replaced, and a stale edge is exactly what keeps them hidden.
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when:
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- status: [success, failure]
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