deps(actions)(deps): bump the github-actions group with 3 updates

.github/workflows/ci.yml

@@ -21,19 +21,19 @@ jobs:
     # GitHub-hosted, change this line to: runs-on: ubuntu-latest
     runs-on: [self-hosted, orion]
     steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
       # JDK 21: the io.nextflow.nextflow-plugin toolchain builds with a JDK 21
       # toolchain (sources still target Java 17). Provide 21 so Gradle uses it
       # rather than downloading one.
       - name: Setup JDK 21
-        uses: actions/setup-java@1bcf9fb12cf4aa7d266a90ae39939e61372fe520 # v5
+        uses: actions/setup-java@03ad4de0992f5dab5e18fcb136590ce7c4a0ac95 # v5.6.0
         with:
           distribution: temurin
           java-version: '21'
 
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@48b5f213c81028ace310571dc5ec0fbbca0b2947 # v4
+        uses: gradle/actions/setup-gradle@48b5f213c81028ace310571dc5ec0fbbca0b2947 # v4.4.3
 
       - name: Build
         run: ./gradlew assemble --no-daemon
@@ -43,3 +43,14 @@ jobs:
       # main safety net and were previously never executed in CI.
       - name: Test
         run: ./gradlew test --no-daemon
+
+      # The half of pin hygiene that needs the network, so it can't live in the
+      # (hermetic) Spock suite: does each pin's `# vX.Y.Z` comment actually name
+      # the tag its SHA carries? A wrong label is worse than none — it makes a
+      # major-version jump read as a routine same-line bump, which is exactly how
+      # a checkout v6 -> v7.0.1 bump nearly landed labelled `# v6`.
+      #
+      # Read-only (git ls-remote), no auth. Runs on PRs, so a Dependabot bump that
+      # mislabels a pin is caught before merge rather than after.
+      - name: Verify pin comments match their SHAs
+        run: ./scripts/verify-pins.sh

.github/workflows/release.yml

@@ -15,17 +15,17 @@ jobs:
     name: Build and publish plugin
     runs-on: [self-hosted, orion]
     steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
       # JDK 21 — see ci.yml (the nextflow-plugin toolchain builds on JDK 21).
       - name: Setup JDK 21
-        uses: actions/setup-java@1bcf9fb12cf4aa7d266a90ae39939e61372fe520 # v5
+        uses: actions/setup-java@03ad4de0992f5dab5e18fcb136590ce7c4a0ac95 # v5.6.0
         with:
           distribution: temurin
           java-version: '21'
 
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@48b5f213c81028ace310571dc5ec0fbbca0b2947 # v4
+        uses: gradle/actions/setup-gradle@48b5f213c81028ace310571dc5ec0fbbca0b2947 # v4.4.3
 
       # Sanity-check the tag matches build.gradle's version, so the artifact and
       # the release tag never drift.
@@ -46,7 +46,7 @@ jobs:
       # Use the action rather than the gh CLI — the self-hosted runner container
       # has no gh installed.
       - name: Publish release
-        uses: softprops/action-gh-release@3bb12739c298aeb8a4eeaf626c5b8d85266b0e65 # v2
+        uses: softprops/action-gh-release@3d0d9888cb7fd7b750713d6e236d1fcb99157228 # v3.0.2
         with:
           files: build/distributions/nf-spawn-*.zip
           generate_release_notes: true

.github/workflows/security.yml

@@ -18,7 +18,7 @@ jobs:
     name: Secret Scan (gitleaks)
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           fetch-depth: 0 # full history so leaked-then-removed secrets are caught
       # Run the gitleaks BINARY directly (MIT-licensed, free for orgs). The
@@ -37,7 +37,7 @@ jobs:
     name: Trivy Security Scan
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
       - name: Trivy filesystem scan (vulns + secrets)
         uses: aquasecurity/trivy-action@ed142fd0673e97e23eac54620cfb913e5ce36c25 # v0.36.0
         with:
@@ -60,7 +60,7 @@ jobs:
     container:
       image: semgrep/semgrep
     steps:
-      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
       # Enforcing: fails the build on findings. Triaged false-positives are
       # annotated inline with `# nosemgrep: <rule-id> -- <reason>` (#368).
       - name: Semgrep scan

CHANGELOG.md

@@ -21,7 +21,28 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   `nextflow-plugin` toolchain, already a release behind. A new
   `SpawnCiHygieneTest` fails the build if a pin is reverted or an entry dropped.
 
+### Changed
+- **Actions bumped, and every pin's version comment now states the truth (#83).**
+  `actions/checkout` → v7.0.1, `actions/setup-java` → v5.6.0,
+  `softprops/action-gh-release` → v3.0.2. The bumps arrived from Dependabot
+  labelled `# v6` on all five `checkout` refs — but the SHA it moved to
+  (`3d3c42e`) is **v7.0.1**, so a three-major jump read as a routine same-line
+  bump; `gradle/actions/setup-gradle` had likewise carried a bare `# v4` while
+  pinning v4.4.3. Comments now name exact versions. Nothing in the majors affects
+  this repo: `action-gh-release@v3` requires the Node 24 runtime, which the orion
+  runner (2.336.0) provides and `checkout@v6.0.3` was already using, and
+  `checkout@v7`'s one behavior change only blocks fork checkouts under
+  `pull_request_target`/`workflow_run`, neither of which appears here.
+
 ### Fixed
+- **A pin's version comment can no longer silently misstate what CI runs (#83).**
+  `SpawnCiHygieneTest` required only that *some* `# vN` comment be present, so the
+  mislabelled `checkout` bump above passed it. It now requires an exact `vX.Y.Z`,
+  and a new `scripts/verify-pins.sh` — wired into CI, so it gates PRs — resolves
+  each SHA against the tag its comment claims and fails if they disagree. The
+  network half lives in the script to keep the Spock suite hermetic. Both accept
+  annotated-tag pins (the tag object *or* the commit it points at); an earlier
+  draft compared against only one form and called a correct pin mislabelled.
 - **`./gradlew test` no longer reports success without running the tests when only
   CI config changed (#80).** Gradle's up-to-date check considered just the Groovy
   sources, so a commit touching only `.github/` or `build.gradle` would skip

scripts/verify-pins.sh

@@ -0,0 +1,87 @@
+#!/usr/bin/env bash
+# Verify every action pin's `# vX.Y.Z` comment actually names the tag its SHA
+# carries.
+#
+# This is the half of pin hygiene that needs the network, so it is NOT in the
+# Spock suite (which must stay offline and hermetic). SpawnCiHygieneTest enforces
+# the offline half: every pin is a 40-hex SHA with an exact vX.Y.Z comment.
+#
+# Why it exists: a pin's comment can be silently false. Dependabot bumped
+# actions/checkout to 3d3c42e — which is v7.0.1 — while leaving `# v6` on all
+# five refs, and a stale `# v4` on gradle/actions/setup-gradle (really v4.4.3)
+# had sat on main for months. Both read as fine. A wrong label is worse than no
+# label: it makes a major-version jump look like a routine same-line bump.
+#
+# Read-only: git ls-remote only. No auth, no writes, no side effects.
+#
+# Usage: scripts/verify-pins.sh
+set -euo pipefail
+
+cd "$(dirname "$0")/.."
+
+fail=0
+found=0
+
+while IFS= read -r line; do
+    # file:lineno:  ... uses: owner/action@<sha> # vX.Y.Z
+    loc=${line%%:*}
+    rest=${line#*:}
+    lineno=${rest%%:*}
+
+    ref=$(printf '%s\n' "$line" | sed -nE 's/.*uses:[[:space:]]*([^[:space:]]+@[0-9a-f]{40}).*/\1/p')
+    ver=$(printf '%s\n' "$line" | sed -nE 's/.*@[0-9a-f]{40}[[:space:]]*#[[:space:]]*(v[0-9][^[:space:]]*).*/\1/p')
+    [ -n "$ref" ] && [ -n "$ver" ] || continue
+
+    action=${ref%@*}
+    sha=${ref#*@}
+    # gradle/actions/setup-gradle is a subdirectory action: the repo is the first
+    # two path segments, so trim anything deeper before querying.
+    repo=$(printf '%s\n' "$action" | cut -d/ -f1,2)
+
+    found=$((found + 1))
+
+    # Resolve the claimed tag to BOTH acceptable SHAs and accept either.
+    #
+    # For an annotated tag, `refs/tags/vX` is the tag OBJECT and `refs/tags/vX^{}`
+    # the commit it points at, and the two differ. Both are legitimate pins —
+    # gradle/actions/setup-gradle@48b5f21 is v4.4.3's tag object, actions/checkout
+    # pins the commit — and GitHub resolves either. Comparing against just one form
+    # reports a correct pin as mislabeled (which this script did on its first run,
+    # absurdly printing "comment says v4.4.3 ... SHA is actually v4.4.3").
+    claimed=$(git ls-remote "https://github.com/$repo" \
+        "refs/tags/$ver" "refs/tags/$ver^{}" 2>/dev/null | awk '{print $1}')
+
+    if [ -z "$claimed" ]; then
+        printf '  MISSING TAG  %s:%s  %s @ %.12s  — tag %s does not exist in %s\n' \
+            "$loc" "$lineno" "$action" "$sha" "$ver" "$repo"
+        fail=1
+    elif ! printf '%s\n' "$claimed" | grep -qFx "$sha"; then
+        # Name what the SHA really is, so the fix is obvious rather than a puzzle.
+        actual=$(git ls-remote --tags "https://github.com/$repo" 2>/dev/null \
+            | awk -v s="$sha" '$1==s {gsub("refs/tags/",""); gsub(/\^\{\}$/,"",$2); print $2}' \
+            | sort -u | paste -sd, -)
+        printf '  MISLABELED   %s:%s  %s @ %.12s  — comment says %s (that tag is %.12s); SHA is actually %s\n' \
+            "$loc" "$lineno" "$action" "$sha" "$ver" "$(printf '%s' "$claimed" | head -1)" \
+            "${actual:-untagged}"
+        fail=1
+    else
+        printf '  ok           %s:%s  %s %s\n' "$loc" "$lineno" "$action" "$ver"
+    fi
+done < <(grep -rn 'uses:.*@[0-9a-f]\{40\}' .github/workflows/)
+
+# Anti-vacuous: a grep that stops matching would otherwise report success forever.
+if [ "$found" -eq 0 ]; then
+    echo "verify-pins: found no SHA-pinned actions under .github/workflows — the check" >&2
+    echo "matched nothing, which is a parser problem, not a clean bill of health." >&2
+    exit 1
+fi
+
+if [ "$fail" -ne 0 ]; then
+    echo
+    echo "verify-pins: FAIL — a pin's version comment does not match its SHA." >&2
+    echo "Fix the comment to name the tag the SHA really carries (or move the SHA)." >&2
+    exit 1
+fi
+
+echo
+echo "verify-pins: OK — all $found pins' comments match their SHAs."

src/test/groovy/io/nextflow/spawn/SpawnCiHygieneTest.groovy

@@ -83,6 +83,35 @@ class SpawnCiHygieneTest extends Specification {
                 '\nUse: uses: owner/action@<40-hex-sha> # vX.Y.Z'
     }
 
+    def 'every version comment names an exact patch version, not a bare major'() {
+        // The comment is the only human-readable part of a pin, and a bare `# v6`
+        // is not just vague — it can be actively false, which is worse than absent.
+        // Dependabot bumped checkout to 3d3c42e (which is v7.0.1) while leaving the
+        // comment reading `# v6` on all five refs. The pin was correct; the label
+        // said it was a major version behind what it actually ran, and the previous
+        // spec passed because it only required SOME `# vN` to be present. A stale
+        // `# v4` on setup-gradle (really v4.4.3) had sat on main the same way.
+        //
+        // Requiring X.Y.Z is the strongest version of this claim checkable offline:
+        // a bare major can silently keep meaning something new as the pin moves,
+        // whereas an exact version either matches the SHA or is a visible lie, and
+        // reviewers can resolve it. Verifying comment-vs-tag needs the network, so
+        // it stays out of the unit suite — see scripts/verify-pins.sh.
+        given:
+        def exact = Pattern.compile(/^[^@\s]+@[0-9a-f]{40}\s+#\s*v\d+\.\d+\.\d+\s*$/)
+        def refs = usesRefs()
+
+        expect: 'anti-vacuous — if the parser stops matching, this would pass forever'
+        !refs.isEmpty()
+
+        and:
+        def vague = refs.findAll { !exact.matcher(it[2] as String).matches() }
+        assert vague.isEmpty(), 'these pins do not name an exact vX.Y.Z, so the comment ' +
+                'cannot be checked against the SHA and may silently misstate what CI runs:\n' +
+                vague.collect { "    ${it[0]}:${it[1]}  ${it[2]}" }.join('\n') +
+                '\nResolve the SHA to its tag and write that: # vX.Y.Z'
+    }
+
     def 'Dependabot has a github-actions entry whose group patterns cover every action'() {
         // The other half of pinning. A SHA never moves, including past a security
         // fix, so pinning without Dependabot trades a mutable-tag hole for a