chore: reorganize CI workflow files

.woodpecker/process-updates-redhat-8-arm64.yaml

@@ -0,0 +1,122 @@
+when:
+  - event: [cron]
+    cron: process-cran-updates
+  - event: manual
+    evaluate: 'process_cran_updates == "all"'
+  - event: manual
+    evaluate: 'process_cran_updates == "redhat-8-arm64"'
+
+skip_clone: true
+
+steps:
+  - name: 'Warming up'
+    image: busybox:latest
+    failure: ignore
+    environment:
+      PLATFORM: ubuntu-2204
+      BLOCK: 21389:length(pkgs)
+      NCPUS: 2
+      STRATEGY: multisession
+    commands:
+      - sleep 1
+      - echo "Warmed Up"
+    backend_options:
+      kubernetes:
+        resources:
+          requests:
+            memory: 29Gi
+            cpu: 4000m
+          limits:
+            memory: 29Gi
+            cpu: 4000m
+        nodeSelector:
+          kubernetes.io/arch: arm64
+          node.kubernetes.io/instance-type: cax41
+        tolerations:
+          - key: 'CI'
+            operator: 'Equal'
+            value: 'true'
+            effect: 'NoSchedule'
+
+  - name: 'Processing Updates'
+    secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT]
+    image: docker.io/devxygmbh/arm64-binaries-r-${PLATFORM}
+    pull: true
+    environment:
+      GIT_USER: pat-s
+      # set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
+      R_PKG_CACHE_DIR: /mnt/cache/pkgcache
+      R_LIBS_USER: /mnt/cache/R-pkgs
+      CCACHE_DIR: /mnt/cache/ccache
+      PLATFORM: redhat-8
+      ARCH: arm64
+      NCPUS: 2
+      MEMORY: 29Gi
+      STRATEGY: multisession
+      INSTANCE_TYPE: cax41
+      INTERVAL: lubridate::interval(lubridate::today() - 3, lubridate::today() - 31)
+    volumes:
+      - arm64-binaries-r-dep-cache-${PLATFORM}:/mnt/cache
+    commands:
+      # download latest package version (avoid having to rebuild image every time)
+      - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git .
+      - rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR /mnt/cache/R-pkgs/00LOCK-RPostgres
+      # for some reason paks pkgcache is often corrupt
+      - rm -rf /mnt/cache/R-pkgs/pkgcache/ /mnt/cache/pkgcache/ /root/.cache/R/
+      - R -q -e 'pak::meta_update()'
+      - R CMD INSTALL .
+      - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
+      # set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
+      # options(future.globals.onReference = NULL): for some reason s3fs::file_delete() throws 'Error: Detected a non-exportable reference ('externalptr') in one of the globals ('FUN' of class 'function') used in the future expression' otherwise
+      - xvfb-run R -q -e "options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = 'error', repos = structure(c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'))); pkgs = tools::CRAN_package_db()[[1]][$BLOCK]; pkgs = setdiff(pkgs, c('biplotbootGUI', 'Rsymphony', 'PortfolioAnalytics', 'ROI.plugin.symphony', 'adea', 'RInno', 'skedastic', 'RPushbullet', 'SimNPH', 'SimDesign','simCAT', 'SIAmodules', 'shinytest2', 'shinyIRT', 'ShinyItemAnalysis', 'shiny.benchmark', 'scDIFtest', 'RSP', 'ROracle', 'ROI.plugin.qpoases', 'ROI.plugin.cplex', 'RmecabKo', 'rmarchingcubes', 'RcppMeCab', 'Rcplex', 'ravetools', 'Rbeast', 'Rblpapi', 'RcppEnsmallen', 'qtkit', 'priorCON', 'prior3D', 'PerFit', 'outlierensembles', 'nomnoml', 'mxfda', 'MultBiplotR', 'mstDIF', 'mdsr', 'makepipe', 'lordif', 'KSgeneral', 'kequate', 'jstager', 'jrt', 'irtreliability', 'irtQ', 'irtpwr', 'irtawsi', 'GRShiny', 'gpuR', 'googletraffic', 'giacR', 'gamstransfer', 'aflps', 'flow', 'filters', 'faoutlier', 'equateIRT', 'EnrichIntersect', 'EFA.dimensions', 'DFIT', 'D3mirt', 'ctgdist', 'CoTiMA', 'ConvertPar', 'clrng', 'bscui', 'BifactorIndicesCalculator', 'autoFC', 'airt')); library(bincraftR); future::plan('sequential'); options(progressr.enable = TRUE); progressr::handlers('cli'); progressr::handlers(global = TRUE); options(future.globals.onReference = NULL); process_cran_updates(interval = $INTERVAL, platform = 'redhat-8', process_updated = TRUE, process_new = TRUE)"
+    backend_options:
+      kubernetes:
+        ### PROD
+        resources:
+          requests:
+            memory: 29Gi
+            cpu: 4000m
+          limits:
+            memory: 29Gi
+            cpu: 4000m
+        # DEBUG
+        # resources:
+        #   requests:
+        #     memory: 4Gi
+        #     cpu: 2000m
+        #   limits:
+        #     memory: 4Gi
+        #     cpu: 2000m
+        nodeSelector:
+          kubernetes.io/arch: arm64
+          node.kubernetes.io/instance-type: cax41
+        tolerations:
+          - key: 'CI'
+            operator: 'Equal'
+            value: 'true'
+            effect: 'NoSchedule'
+
+  - name: 'ntfy'
+    image: codeberg.org/l-x/woodpecker-ntfy:1.3.1
+    when:
+      - status: [failure]
+    settings:
+      url: https://ntfy.devxy.io/ci-builds
+      token:
+        from_secret: ntfy_token
+      title: "CI '${CI_REPO}' failed"
+      actions: view, Open build, ${CI_PIPELINE_URL}, clear=false;
+      click: ${CI_BUILD_LINK}
+      message: |
+        Workflow: ${CI_WORKFLOW_NAME/\n//}
+        Commit message: ${CI_COMMIT_MESSAGE/\n//}
+        Commit Author: ${CI_COMMIT_AUTHOR/\n//}
+    backend_options:
+      kubernetes:
+        resources:
+          requests:
+            memory: 100Mi
+            cpu: 0m
+          limits:
+            memory: 300Mi
+            cpu: 200m