Merge pull request #224 from BioVisionCenter/fix/ci-nodejs20

cleanup ci with legacy node

Author: lorenzocerrone

.github/TEST_FAIL_TEMPLATE.md

@@ -0,0 +1,60 @@
+# Opens (or updates) the [test-bot] issue for a failing scheduled run.
+#
+# Replaces JasonEtco/create-an-issue, which is still `using: node20`. Composite, so
+# it pulls in no Node runtime at all; `gh` and `jq` are preinstalled on the ubuntu,
+# macos and windows runners, and `shell: bash` gives Git Bash on windows.
+name: Report failure
+description: Open a [test-bot] issue for a failing scheduled run, or update the open one.
+
+inputs:
+  title:
+    description: Issue title. An open issue with this exact title is updated in place.
+    required: true
+  platform:
+    description: Runner platform the failure was seen on.
+    required: true
+  python:
+    description: Python environment label, e.g. `test11` or `py3.13, pip stable`.
+    required: true
+  token:
+    description: Token carrying issues-write permission. Needed explicitly because checkout runs without persisted credentials.
+    required: true
+
+runs:
+  using: composite
+  steps:
+    - shell: bash
+      # Every caller-supplied value goes through `env:` rather than `${{ }}`
+      # interpolation into the script body, so nothing can be injected into it.
+      env:
+        GH_TOKEN: ${{ inputs.token }}
+        TITLE: ${{ inputs.title }}
+        PLATFORM: ${{ inputs.platform }}
+        PYTHON: ${{ inputs.python }}
+      run: |
+        set -euo pipefail
+
+        # printf rather than a heredoc: a heredoc body inside this block scalar
+        # would carry its YAML indentation into the issue text.
+        body=$(printf '%s\n' \
+          "The ${GITHUB_WORKFLOW} workflow failed on $(date -u '+%Y-%m-%d %H:%M') UTC" \
+          "" \
+          "The most recent failing test was on ${PLATFORM} (${PYTHON})" \
+          "with commit: ${GITHUB_SHA}" \
+          "" \
+          "Full run: ${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}" \
+          "" \
+          "(This post will be updated if another test fails, as long as this issue remains open.)")
+
+        # Match the title exactly rather than relying on `--search`, whose tokenizer
+        # does not treat the leading "[test-bot]" as a literal.
+        number=$(gh issue list --state open --label bug --limit 100 --json number,title \
+          | jq -r --arg t "${TITLE}" 'map(select(.title == $t)) | .[0].number // empty')
+
+        if [ -n "${number}" ]; then
+          echo "Updating existing issue #${number}"
+          gh issue edit "${number}" --body "${body}"
+        else
+          echo "Opening a new issue"
+          gh issue create --title "${TITLE}" --label bug --body "${body}"
+        fi

.github/actions/report-failure/action.yml

@@ -35,7 +35,14 @@ jobs:
       - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: "3.13"
-      - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
+      # prek is a drop-in reimplementation of pre-commit; its action caches the hook
+      # environments itself, unlike pre-commit/action, which is maintenance-only and
+      # hardcodes actions/cache@v4 (Node 20) internally.
+      # `prek-version` defaults to `latest` — pin it, and keep it in step with the
+      # `prek` version resolved in pixi.lock so CI and `pixi run -e dev lint` agree.
+      - uses: j178/prek-action@4e14d07f9231acabce116ccfca13b13dd9755ece # v3.0.0
+        with:
+          prek-version: "0.4.12"
 
   check-manifest:
     # check-manifest is a tool that checks that all files in version control are
@@ -191,16 +198,12 @@ jobs:
       # If something goes wrong with scheduled tests, open an issue in the repo
       - name: 📝 Report Failures
         if: failure() && github.event_name == 'schedule'
-        uses: JasonEtco/create-an-issue@1b14a70e4d8dc185e5cc76d3bec9eab20257b2c5 # v2.9.2
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          PLATFORM: ${{ matrix.platform }}
-          PYTHON: ${{ matrix.environment }}
-          RUN_ID: ${{ github.run_id }}
-          TITLE: "[test-bot] Scheduled tests are failing"
+        uses: ./.github/actions/report-failure
         with:
-          filename: .github/TEST_FAIL_TEMPLATE.md
-          update_existing: true
+          title: "[test-bot] Scheduled tests are failing"
+          platform: ${{ matrix.platform }}
+          python: ${{ matrix.environment }}
+          token: ${{ github.token }}
 
       - name: Coverage
         if: success() && matrix.platform == 'ubuntu-latest' && matrix.environment == 'test11'

.github/workflows/ci.yml

@@ -65,16 +65,12 @@ jobs:
 
       - name: 📝 Report Failures
         if: failure() && github.event_name == 'schedule'
-        uses: JasonEtco/create-an-issue@1b14a70e4d8dc185e5cc76d3bec9eab20257b2c5 # v2.9.2
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          PLATFORM: ubuntu-latest
-          PYTHON: "3.13 (pip stable)"
-          RUN_ID: ${{ github.run_id }}
-          TITLE: "[test-bot] pip stable tests are failing"
+        uses: ./.github/actions/report-failure
         with:
-          filename: .github/TEST_FAIL_TEMPLATE.md
-          update_existing: true
+          title: "[test-bot] pip stable tests are failing"
+          platform: ubuntu-latest
+          python: "py3.13, pip stable"
+          token: ${{ github.token }}
 
   test-pip-pre:
     name: pip (--pre)
@@ -118,13 +114,9 @@ jobs:
 
       - name: 📝 Report Failures
         if: failure()
-        uses: JasonEtco/create-an-issue@1b14a70e4d8dc185e5cc76d3bec9eab20257b2c5 # v2.9.2
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          PLATFORM: ubuntu-latest
-          PYTHON: "3.13 (pip --pre)"
-          RUN_ID: ${{ github.run_id }}
-          TITLE: "[test-bot] pip --pre tests are failing"
+        uses: ./.github/actions/report-failure
         with:
-          filename: .github/TEST_FAIL_TEMPLATE.md
-          update_existing: true
+          title: "[test-bot] pip --pre tests are failing"
+          platform: ubuntu-latest
+          python: "py3.13, pip --pre"
+          token: ${{ github.token }}

.github/workflows/ci_upstream.yml

@@ -1,11 +1,6 @@
-# enable pre-commit.ci at https://pre-commit.ci/
-# it adds:
-# 1. auto fixing pull requests
-# 2. auto updating the pre-commit configuration
-ci:
-  autoupdate_schedule: monthly
-  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
-  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+# Hooks are run by `prek` (a drop-in reimplementation of pre-commit), both in the
+# `lint` CI job and via `pixi run -e dev lint`. Bump the `rev:` pins with
+# `prek auto-update`.
 
 # Vendored third-party files, kept byte-identical to what upstream ships. The SIL OFL
 # text in particular should not be rewritten by the whitespace hooks.

.pre-commit-config.yaml

@@ -12,6 +12,11 @@
 - `atomic_add_image` / `atomic_remove_image` warn on Windows that their lock is best-effort: `filelock` can hand it to two writers at once, so concurrent ones can lose an update — `v1.0.0` lost it silently. A single writer is unaffected.
 - Lock files moved to a `<store>.ngio-locks/` directory beside the store, one per group path. Nothing is written inside the Zarr store any more, and groups differing only after a dot (`foo.bar`, `foo.baz`) no longer share a lock. A `≤1.0.0` writer takes the old paths, so upgrade all writers to a plate together.
 
+### Chores
+
+- Linting moves from `pre-commit` to [`prek`](https://github.com/j178/prek), a drop-in reimplementation. `.pre-commit-config.yaml` is unchanged apart from dropping a `ci:` block for pre-commit.ci, which was never enabled. `pixi run -e dev lint` is still the entry point; `pre-commit autoupdate` becomes `prek auto-update`.
+- CI no longer depends on any Node 20 action, which GitHub now warns about on every run. `pre-commit/action` is maintenance-only and pins `actions/cache@v4` internally, so it is replaced by `j178/prek-action`; `JasonEtco/create-an-issue` is `using: node20`, so the scheduled-failure issue reporter moves to a local composite action at `.github/actions/report-failure` (and `.github/TEST_FAIL_TEMPLATE.md` goes with it).
+
 ## [v1.0.0]
 
 First stable release. Everything deprecated in `v0.5.0` (each warned "will be removed in `ngio=0.6`") is now removed — that release became `1.0.0`.