* Fix release-progress badges to read native issue-level Priority field
The Project Priority board field was consolidated into a Priority field
managed at the issue level (GitHub's org-wide custom issue fields), which
the GraphQL API mirrors into projects as ProjectV2ItemIssueFieldValue
instead of ProjectV2ItemFieldSingleSelectValue. The badge script's query
had no fragment for that type, so it silently found zero priority values
and would raise ProjectFieldMissingError on every run.
* Show TBD on the Next Release badge when no milestone due date is set
Previously the badge silently omitted any due-date annotation when the
milestone had none, which read as if the badge just hadn't picked one up.
* Update release-schedule image and plantuml source from add-next-release-badge branch
* Don't flag CODEOWNERS auto-assignment as a manual reviewer add on a PR's first pass
GitHub's own CODEOWNERS engine fires an identical review_requested webhook
(sender type User, not Bot) when it auto-assigns owners at PR-open time. If
one of those survives the cancel-in-progress race as the run that actually
executes, it was mistaken for a human deliberately requesting that reviewer,
permanently flagging them "manually added" and requiring separate approval —
e.g. a catch-all "*" owner also named on a touched area's CODEOWNERS line got
flagged on every PR touching that area, even though no human ever picked them.
Gate the manual-add detection and the sticky per-area assignment on
!isFirstCoordinationPass (no checklist comment posted yet), since that's
exactly the window where GitHub's own auto-assignment is indistinguishable
from a real human pick.
Checkout deliberately uses persist-credentials: false so the workflow
token never lands in git config, but the add-and-commit step never got
a token of its own to push with -- it silently relied on credentials
checkout no longer leaves behind. Every push to any branch failed with
"could not read Username for 'https://github.com'" once clang-format
found something to fix, regardless of the repo's Actions write-permission
setting.
The hdf5_vol_rest_fetchcontent job fails at "Install HSDS dependencies"
because HSDS pins numpy==2.4.6, which publishes no distributions for
Python 3.10:
ERROR: Could not find a version that satisfies the requirement
numpy==2.4.6 (from versions: ... 2.2.5, 2.2.6)
numpy 2.4.6 declares requires_python >= 3.11, and HSDS's pyproject.toml
now says requires-python = ">=3.11". Move the matrix to Python 3.12,
which is what HSDS uses for its own unix-socket test job - the same
configuration this job exercises.
Also drop the "Fix requests version" step that force-downgraded to
requests==2.31.0. HSDS now pins requests-unixsocket==0.4.1, which fixed
the requests 2.32 breakage that step worked around, so the downgrade only
fights HSDS's own pins. Upstream HSDS has already commented the same step
out of its socket-test job.
Fixes#6657
Claude-Session: https://claude.ai/code/session_011qUw9C11arB1WftiT56EA4
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
The issue_comment trigger let every PR comment boot a full runner just
to make one API call checking draft status, even though the only
comments that matter are ones on PRs already labeled draft-stale. That
label snapshot is already present in the webhook payload, so gate the
job on it directly and drop the now-redundant draft-status API step.
Address all zizmor 1.25.2 findings in the Maven/Java-themed workflows
with no behavioral change:
- template-injection: move attacker-controllable ${{ }} expressions
(matrix.*, runner.workspace, github.actor, github.base_ref,
steps.*.outputs.*, needs.*.outputs.*) out of run: script bodies into
step-level env: blocks referenced as shell/pwsh variables.
- artipacked: add persist-credentials: false to all actions/checkout
steps (none of these workflows push to git).
- excessive-permissions: add/tighten explicit permissions. Reduce
overly broad workflow-level packages:/pull-requests: grants to
contents: read, granting minimal packages: read/write only to the
specific jobs that need it.
- secrets-inherit (release.yml): remove secrets: inherit on the
test-maven-packages.yml call, which declares no workflow_call secrets.
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Harden workflow checkout credential hygiene + permissions
Address zizmor static-analysis findings:
- artipacked: add `persist-credentials: false` to actions/checkout
steps in codeql.yml (2), test-binary-installation.yml (2),
clang-format-check.yml, freebsd.yml, h5py.yml, openbsd.yml,
signed-plugins.yml, and update-progress.yml. None of these jobs
push to git, so dropping the persisted checkout credential is safe.
- excessive-permissions: restrict call-workflows.yml top-level
permissions to `contents: read`, and grant `packages: write` /
`pull-requests: write` only on the two jobs that call the
maven-staging reusable workflow (which declares those needs).
No behavioral change.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* Removed extra blank lines.
---------
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Harden scheduled/downstream build workflows against zizmor findings
Fix all zizmor static-analysis findings in the scheduled/downstream build
workflows without changing behavior:
- template-injection: move ${{ }} expressions out of run: script bodies
into step-level env: blocks referenced as shell variables
- artipacked: add persist-credentials: false to actions/checkout steps
(none of these jobs push to git)
- excessive-permissions: add top-level 'permissions: contents: read' to
macos-26-matrix.yml (other files already restrict permissions)
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
* Address Copilot review comments on PR #6544
- Drop unnecessary command substitution in daily-schedule.yml's
FILE_NAME_BASE assignment
- Name the two env-block steps in daily-build.yml that previously ran
unnamed (easier to scan in logs)
- Quote $GITHUB_OUTPUT in the getinputs step
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
* Remove extra blank lines.
---------
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Address GitHub Actions static-analysis (zizmor/CodeQL) findings in the
S3 publishing workflows:
- publish-release.yml: hoist every inputs/secrets/vars value used inside
run blocks into job-level env vars and reference plain shell variables
($USE_TAG, $FILE_NAME, $TARGET_DIR, $S3_BUCKET, $TARGET_PATH, $DRY_RUN),
eliminating 41 template-injection findings. Add persist-credentials:
false to the checkout (artipacked).
- publish-branch.yml: add persist-credentials: false to the checkout
(artipacked); its S3 sync already used env vars.
No behavioral change: the same values are used, only via the shell
environment instead of direct ${{ }} expansion into the script body.
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
GitHub-hosted runners have no real InfiniBand, and the Open MPI bundled
with NVIDIA HPC-X intermittently has UCX select a non-functional verbs
interface (e.g. ud_verbs/mana_0), causing:
ucp_worker.c:1487 UCX ERROR uct_iface_open(ud_verbs/mana_0:1) failed
pml_ucx.c:319 Error: Failed to create UCP worker
MPI_INIT has failed because at least one MPI process is unreachable
which fails h5_api_test_parallel_* tests in the "Run Tests" step. This
only affects nvhpc.yml (HPC-X's bundled Open MPI ships UCX); main-par.yml
uses Ubuntu's openmpi-bin package, which doesn't use UCX and is unaffected.
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>
* Add Fortran ABI compatibility check to abi-report workflow
Mirrors the existing C/HL/C++ abi-dumper + abi-compliance-checker
steps for libhdf5_fortran.so, plus a supplementary nm-based exported
symbol diff since gfortran's mangled names don't encode argument
lists and DWARF-based diffing has not been validated against
Fortran-specific constructs (array descriptors, derived types).
* Auto-detect ABI reference release instead of hardcoding it
file_ref was pinned to '2.0.0' in both daily-build.yml and release.yml
and had gone stale across two releases (2.1.0, 2.1.1) without being
bumped, silently comparing against a two-versions-old baseline. Have
abi-report.yml query the GitHub API for the latest published
HDFGroup/hdf5 release when file_ref isn't explicitly given, so callers
no longer need to remember to update a pinned tag after every release.
Verified the resolution command returns 2.1.1 against the live API.
Also documents the expected false-positive pattern in the new Fortran
ABI check: abi-dumper misreads gfortran's DWARF encoding of
assumed-shape array descriptors as fixed array bounds, producing bulk
Low-severity noise on the KIND/RANK-generated H5_gen.F90 procedures
that isn't a real interface change.
Generate the Doxygen tag file inside the html output directory
(hdf5lib_docs/html/hdf5.tag) instead of at the build root. The S3
documentation publishing (daily "latest", release zip, and
publish-release) all derive from the docs-doxygen artifact, which is
uploaded from the build-tree html directory. Placing the tag file there
makes it flow to every destination, e.g.
https://support.hdfgroup.org/documentation/hdf5/latest/hdf5.tag
Since the tag file now lives inside html/, the existing DIRECTORY install
already installs it to ${HDF5_INSTALL_DOC_DIR}/html/hdf5.tag, so the
redundant standalone install(FILES ...) is removed (it would otherwise
reference a file that no longer exists at the build root).
* Add Next Release badge and Medium/Low priority progress badges
Adds a "Next Release" badge (in-development version from H5public.h)
and extends the existing Critical/High priority progress badges with
Medium (P2) and Low (P3) priority tracking, all fed from the same
GitHub Project #39 gist-based badge pipeline.
* Remove in-progress 2.0 entry from release schedule diagram
The Release Schedule chart is meant to show only past releases that
have reached end of life; the in-development series is now tracked
separately by the Release Progress badges. Regenerate the PNG from
the updated PlantUML source and clarify the README wording.
* Add Latest Release badge and milestone target date to Next Release
Fetches the most recent published release in the current major
version series from the GitHub Releases API (e.g. "2.1.1
(2026-03-23)") and exposes it as a new "Latest Release" badge.
Also looks up the target due date of the matching GitHub milestone
(e.g. "HDF5 2.2.0") and appends it to the existing Next Release
badge when one is set. Both lookups are independent of the
project-board query and degrade gracefully to "N/A" on failure.
* ci: skip draft-pr-policy checkout on issue-only comments
The issue_comment event fires for comments on both issues and PRs;
draft-pr-policy only cares about PR draft-staleness, so short-circuit
before checkout when the comment is on a plain issue. Also switch all
three jobs to a sparse, shallow checkout since they only need
.github/scripts to load the github-script payload.
* ci: also skip draft-pr-policy on bot-authored PR comments
draft-pr-policy.js already excludes Bot comments when deciding whether
a draft was revived, so a bot comment (e.g. review-checklist posting
its checklist) can never do anything meaningful here — it still ran
checkout + API calls only to no-op. Filter it out at the same if:
using the free github.event.comment.user.type field.
* ci: skip checkout for draft-pr-policy on non-draft PR comments
Even after filtering out issue-only and bot comments, a human comment
on any non-draft PR still paid for a full checkout just to have the
script itself discover pr.draft is false and return. Add a cheap
pulls.get-only pre-check step (no checkout required) and gate the real
checkout + script load on its result.
These workflows use pull_request_target / workflow_run with elevated
permissions (pull-requests: write, issues: write). Because GitHub
copies workflow files into forks, any fork with Actions enabled was
independently running these privileged workflows against its own
PRs, e.g. https://github.com/sp26-hdfgroup/hdf5-sandbox/pull/2.
Add the same github.repository == 'HDFGroup/hdf5' guard already used
in review-checklist-test.yml so the job-level if short-circuits
before doing anything in a fork's copy of the workflow.
actions/checkout v7.0.0 (bumped in #6500) added a blanket check that
blocks checkout on pull_request_target/workflow_run events, even when
no fork ref is checked out. This workflow only ever checks out the
base branch (develop), so opt in via allow-unsafe-pr-checkout.
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
- action's hash pin has mismatched or missing version comment
- credential persistence through GitHub Actions artifacts: does not set
persist-credentials: false
The HDF-EOS5 compatibility test downloads a source tarball from
git.earthdata.nasa.gov, an external host that has proven unreliable and
frequently times out, causing spurious PR-check failures unrelated to the
code under review.
Move the test off the pull_request/push triggers onto a daily schedule
(plus workflow_dispatch) so transient network failures no longer block PR
merges, while still catching genuine HDF-EOS5 regressions on a daily
cadence. Guard the job with an owner check so it does not run on forks.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* Fix runExecute.cmake: restore ERROR_APPEND and fix zero-or-more mask patterns
Three bugs were introduced when runTest.cmake was refactored into runExecute.cmake:
1. ERROR_APPEND=1 support was dropped. Tests that redirect their error-stack
output to stderr and rely on ERROR_APPEND to combine it with stdout before
comparison (e.g. H5TEST-err_compat, H5TEST-error_test) fail silently because
the reference file never matches the truncated actual output.
2. " line [0-9]*" uses zero-or-more digits, so it matches " line " (with zero
digits) in already-masked reference text like " line (number)", prepending
another "(number)" and producing " line (number)(number)".
3. "HDF5 [1-9]*[.][0-9]*..." has the "HDF5 " prefix and uses [1-9]* (zero-or-
more), so it does not match "2.2.0" in actual output (blocked by the leading
"("), and double-masks "version (number)" in the reference.
"H5Eget_auto[1-2]*" / "H5Eset_auto[1-2]*" have the same zero-or-more issue,
double-masking "(1 or 2)" already present in reference files.
Fix: restore ERROR_APPEND handling; change * to + for all digit/char class
quantifiers that can match zero occurrences in already-masked reference text;
remove the "HDF5 " prefix from the version pattern. Same fix applied to
HDF5Examples/config/cmake/runExecute.cmake which has identical bugs.
* Fix AOCC CI: source setenv_AOCC.sh from its actual install location
install.sh generates setenv_AOCC.sh inside the aocc-compiler-VERSION/
directory (where it runs from), not in the repo root one level up.
* Fix AOCC CI: replace hardcoded runner paths with GITHUB_WORKSPACE
All /home/runner/work/hdf5/hdf5/ paths were hardcoded to the HDFGroup/hdf5
repo name. Running the workflow in any fork (e.g. brtnfld/hdf5_swmr_2)
puts the checkout under a different path, breaking AOCC/OpenMPI install,
configure, and build steps. Use $GITHUB_WORKSPACE / ${{ github.workspace }}
so the paths resolve correctly regardless of repo name.
* fix(aocc): source setenv_AOCC.sh from workspace root, not compiler subdir
install.sh places setenv_AOCC.sh in the workspace root, not inside the
aocc-compiler-X.X.X/ directory.
* Fix runExecute.cmake: anchor HDF5 version regex to full token
Replace the over-broad version pattern with one that matches the complete
'HDF5 (x.y.z)' token, preventing over-matching of IP addresses and other
version-like strings, and avoiding nested substitution artifacts in .err
reference comparisons. Applied identically to both copies of the file.
* ci: replace actions/stale with bot-aware mark-stale script
actions/stale uses updatedAt to measure inactivity, so any bot event
(e.g. the /remove-reviewer acknowledgment comment) resets the stale
countdown even when there has been no meaningful human activity for
months. PR #6332 was last touched by a human on 2026-04-02 but was
not flagged because a reviewer-removal on 2026-06-11 refreshed the
timestamp.
Replace the actions/stale step with a custom mark-stale.js script
(same pattern as alert-stale.js) that only counts non-bot comments,
non-bot review submissions, and commits as meaningful activity. The
script also removes the stale label if such activity occurs after the
label was applied.
* ci: fix draft-stale keepalive for external contributors
Two bugs with the keepalive checkbox on draft-stale PRs:
1. External contributors (fork authors) lack write access to edit the
bot's comment, so clicking the checkbox silently fails for them.
Fix: also treat a new non-bot comment posted after the keepalive
comment as a sufficient keepalive signal.
2. The stale label could take up to 24 hours to be removed (daily cron
only). Fix: add an issue_comment.created trigger so draft-pr-policy
fires immediately when someone comments on a stale draft PR.
mark-stale and alert-stale are guarded to only run on
schedule/workflow_dispatch, not on every comment.
Also fix lastRealActivityAt to exclude bot comments (matching
mark-stale.js), so the keepalive and "Thanks for confirming" bot
comments don't count as real activity when measuring staleness.
Add PullRequest inline fragment to the project items GraphQL query
so PRs in the GitHub Project are counted alongside issues when
calculating release blocker/must-do progress.
* Add stale PR/issue policy with assignee alerts instead of auto-close
Ready PRs/issues use actions/stale to label inactivity (30/60 days).
Draft PRs get a longer 90-day window and only reset on an explicit
"still working on this" comment, since pushes/CI activity alone
shouldn't make an abandoned draft look fresh. Nothing is auto-closed:
once a staleness label has persisted past its alert threshold, a
custom script pings the assignee (falling back to requested
reviewers, then the author) to decide whether to keep it open or
close it.
* Scope stale policy to PRs only, not issues
Issue staleness is disabled (days-before-issue-stale: -1) and the
alert script now skips any non-PR item defensively, since this
workflow is meant to address PRs sitting unmerged/unreviewed, not
issue triage.
* Draft stale window 60 days (was 90); drop dead pull_request branch
alert-stale.js's pickAlertTargets is now only ever called with PR
items (filtered upstream in runAlertStale), so the pull_request
check around the requested-reviewers lookup was dead code.
* Set persist-credentials: false on checkout steps
Fixes two zizmor notes: these checkouts only need to read local
script files for github-script's require(), so there's no reason
to persist the GITHUB_TOKEN in git config afterward.
* Use a keep-alive checkbox instead of a magic comment phrase for drafts
Checking a box in the bot's own stale-notice comment is more
discoverable than requiring an exact phrase, and the live checkbox
state can be read straight off that comment's current body on each
run instead of scanning new comments for a regex match.
---------
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
* CI: fix buildBody to accept any owner approval, not only the assigned reviewer
PR #6446 narrowed the approver lookup to effectiveReviewers (the confirmed-
requested subset), inadvertently breaking the case where a non-assigned owner
approves. Restore the original intent: any CODEOWNER's approval signs off an
area; fall back to effectiveReviewers only when no CODEOWNER is assigned.
* text updates
* CI: add tests for non-CODEOWNER reviewer sign-off path (#6446)
Three tests cover the nonOwnerReviewers fallback introduced in #6446:
- pending mention when a non-owner is manually assigned
- non-owner approval signs off an area with no CODEOWNER assigned
- non-owner approval does NOT sign off when a CODEOWNER was assigned
* CI: restore review_requested/review_request_removed triggers
These were dropped in #6453 when ready_for_review was added, breaking
automatic checklist updates on manual reviewer changes.
Both events fall through to the preserve-existing path in
coordinateReviewers when a checklist already exists, so the checklist
body is simply rebuilt with the current requested_reviewers set.
Also extend the opening-race detection (previously called isFirstSyncRace)
to cover review_requested: for any PR, CODEOWNERS auto-assignment fires
review_requested shortly after opened, and with cancel-in-progress: true
that run can cancel the opened run. If no checklist exists yet, treat the
review_requested event as a new-PR event and run full selection.
* CI: show only one reviewer per checklist area
Each area's pending mention now shows the primary (first) effective reviewer
rather than all confirmed-requested owners joined with commas.
* CI: revert to showing all confirmed reviewers per checklist area
A manually added person who is also a CODEOWNER for that area should be
shown alongside the load-balanced pick, not hidden. "One reviewer per area"
only describes chooseReviewers' default selection, not a display constraint.
* CI: skip reviewer removal when they have already submitted a review
GitHub's API rejects removeRequestedReviewers for users who have already
reviewed; detect that case upfront via listReviews and report it clearly
instead of surfacing a cryptic API error.
* CI: defer reviewer assignment for draft PRs until ready for review
Add ready_for_review to the pull_request_target trigger so the workflow
fires when a draft is promoted. In the script, skip requestReviewers
(and the CODEOWNERS auto-assignment cleanup second pass) while the PR is
a draft; still assign the PR author and strip any reviewers GitHub
auto-assigned. When the PR is marked ready, treat it like a fresh open
and run the full load-balanced reviewer selection.
* CI: fix synchronize race — treat first synchronize as new PR when opened was cancelled
When a fork PR is created, GitHub fires both opened and synchronize.
With cancel-in-progress: true the synchronize run often wins, and the
opened run (which clears CODEOWNERS auto-assignments) is cancelled before
it completes. Detect this: if synchronize fires but no checklist comment
exists yet, run the full new-PR path (enforceSelection + load-balanced
reviewer assignment) instead of silently carrying forward all auto-assigned
reviewers.
* CI: enforce reviewer selection before posting @mentions
On synchronize, run enforceSelection against the ideal load-balanced
pick before building the checklist body so the @mentions are never
sent until the reviewer list is actually correct. Re-fetch the PR
after cleanup so confirmedRequested reflects reality, not the pre-
cleanup snapshot.
For workflow_run (review submitted), reviewer assignment is intentionally
left unchanged but @mentions are filtered to the ideal selection so
CODEOWNERS extras don't generate spurious notifications on comment edits.
* CI: preserve manually added reviewers on synchronize
Reverting the enforceSelection call on the non-first-run synchronize
path. There is no API way to distinguish CODEOWNERS auto-assignments
from manually added reviewers, so enforcing the load-balanced selection
on every synchronize would silently remove intentional additions.
The initial cleanup (opened or first-synchronize via openedWasSkipped)
already produces a correct reviewer list; subsequent synchronize and
workflow_run events carry it forward unchanged.
* CI: pin actions/github-script to commit hash in remove-reviewer.yml
zizmor requires actions to be pinned to a commit hash rather than a tag.
Use the same pinned hash (ed597411d8f924073f98dfc5c65a23a2325f34cd, v8.0.0)
already used in review-checklist.yml.
* CI: refactor review-checklist.js for readability
Extract the reviewer coordination logic out of the monolithic run()
function into named module-level helpers:
checklistExists() — single responsibility: does a checklist
comment already exist on the PR?
removeUnselected() — remove CODEOWNERS auto-assignments not in
the load-balanced selection set
requestReviewers() — request each reviewer individually so one
bad login cannot block the rest
removeUnselectedAfterDelay() — 15-second wait + re-fetch + re-enforce
for GitHub's async auto-assignment race
coordinateReviewers() — top-level dispatcher; the four event paths
(read-only, synchronize-normal, new-PR/draft,
new-PR/non-draft) are now explicit branches
with labelled comments instead of nested ifs
run() is now a straight pipeline of 8 numbered steps with no nested
async functions. Behaviour is unchanged.
* CI: extract convertGlobToRegex and use github.paginate consistently
Extract glob-to-regex conversion into a standalone helper and replace
manual pagination loops for listFiles and listReviews with github.paginate,
matching the existing style used for listComments and pulls.list.
* CI: restrict remove-reviewer workflow to main repo only
Adds a github.repository guard so the job does not run in forks,
preventing unintended resource consumption and command execution
against fork PRs.
* CI: restrict test-maven-packages workflow to main repo only
Adds github.repository guards to all three jobs so the workflow
does not evaluate in forks, preventing spurious "workflow file issue"
failures on push events in forked repositories.
* Revert "CI: restrict test-maven-packages workflow to main repo only"
This reverts commit cc1208226d.
* CI: fix template injection in workflow_dispatch run: blocks
Move workflow_dispatch inputs that appeared directly in run: scripts
into step-level env: blocks, then reference them as plain shell
variables. This is the pattern zizmor recommends and eliminates the
injection vector.
Only workflow_dispatch inputs are fixed here — workflow_call inputs
in reusable files are not attacker-controlled (they come from the
calling workflow) so no changes are needed there.
Files changed:
- publish-branch.yml: local_dir, target_dir in aws s3 sync
- java-implementation-test.yml: java_versions, platforms, test_mode
- maven-staging.yml: test_maven_deployment, java_implementation,
platforms, use_snapshot_version
- maven-build-test.yml: test_deployment, java_implementation,
platforms, test_examples
- test-maven-packages.yml: version, repository_url throughout
- test-binary-installation.yml: maven_repository, maven_version,
install_method
* CI: move remaining GHA expressions from run: blocks to env: vars
* CI: exclude pure reusable workflows from zizmor template-injection scan
Pure reusable workflows (workflow_call only, no workflow_dispatch/pull_request/
push/schedule/release triggers) can never be triggered directly by external
users. Template-injection findings against inputs.* in those files are false
positives — inputs arrive from the trusted calling workflow, not from attackers.
Scanning only files with user-facing triggers keeps Security tab alerts
meaningful and prevents developers from dismissing real findings.
* Update Visual Studio versions in workflows
* Revert change to Windows ARM workflows
* Pin Intel OneAPI workflows to windows-2025
* Update more instances of issues
* review-checklist: show non-CODEOWNER reviewer when no owner is assigned
If the only assigned CODEOWNER is removed and a non-CODEOWNER is manually
added in their place, that person previously got no checklist mention and
their approval did not check the box.
For any area with no CODEOWNER in the requested set, fall back to
non-CODEOWNER reviewers (anyone assigned who is not an owner of any
touched area). They are shown in the mention and their approval counts
as sign-off for that area.
* review-checklist: update checklist on reviewer add/remove
Adding or removing a reviewer did not trigger a workflow run, leaving
the checklist comment stale until the next push.
Add review_requested and review_request_removed to the pull_request_target
activity types so the checklist updates immediately when a reviewer is
manually added or removed.
* review-checklist: show all requested owners per area in checklist
buildBody was using area.owners.find() — picking the first CODEOWNERS-listed
owner in the requested set. This broke reviewer swaps (removing @A and adding
@B would show @C, the next CODEOWNERS entry, not @B) and also failed to
reflect GitHub's CODEOWNERS auto-assignment, which requests all owners.
Switch to area.owners.filter() so every requested owner for an area is
mentioned in that row. Approval logic is unchanged: any owner approval
still checks the box.
* review-checklist: enforce one load-balanced reviewer per area
GitHub's CODEOWNERS auto-assignment requests all owners of touched files
when a PR opens, before the workflow runs. The script was then seeing them
already assigned and skipping its own selection entirely.
On opened/reopened: select one load-balanced reviewer per area (ignoring
GitHub's pre-assigned set), remove any auto-assigned CODEOWNERS not in the
selection, then add the chosen reviewer. Only code owners are removed —
manually-added non-owner reviewers are left untouched.
On synchronize: keep existing assignments (reviewer may have already started).
confirmedRequested now starts empty and is populated only with the script's
selection, so the checklist only mentions owners that were explicitly chosen.
* review-checklist: retry reviewer cleanup to handle GitHub auto-assign race
GitHub's CODEOWNERS auto-assignment can fire after the workflow starts,
re-adding extra reviewers after we remove them. Add a 15-second wait
followed by a second cleanup pass on opened/reopened events.
Extract the removal loop into enforceSelection() so both passes share
the same logic.
* zizmor: suppress template-injection for PR #6356 workflow files
Add zizmor_config.yml to ignore template-injection findings in the
setup-jextract action and maven/ctest workflow files introduced in
PR #6356, where inputs are caller-controlled but not user-controlled.
* review-checklist: don't re-assign reviewers on synchronize
On synchronize, chooseReviewers saw no owner assigned (because the
reviewer was manually removed) and re-added one via requestReviewers,
overriding the manual removal.
Reviewer assignment now only happens on opened/reopened. Synchronize
only updates the checklist display based on whoever is currently
assigned — manual removals are respected.
* zizmor: skip upload-sarif failure on fork PRs
* zizmor: move config out of workflows dir to fix GitHub Actions parse error
GitHub Actions parses all .yml files in .github/workflows/ as workflow
files; zizmor_config.yml there caused "unexpected value 'rules'" because
rules: is not valid workflow syntax. Moved to .github/zizmor.yml and
updated the --config path in zizmor.yml accordingly.
* review-checklist: retry on transient 401 from GitHub API
GitHub's API intermittently returns 401 on write operations
(issues.addAssignees, issues.createComment) even when the token has
Issues: write and PullRequests: write — read-only calls succeed in the
same run. The github-script action excludes 401 from retries by default.
Removing 401 from retry-exempt-status-codes and setting retries: 3
handles these transient failures with exponential backoff.
* review-checklist: fix checklist mention when non-requested owner approves
The mention in each checklist row was derived from the approver (if any),
so when a different area owner happened to approve first, the mention
changed from the assigned reviewer to the approver. Fix by decoupling
sign-off detection from display: signedOff now uses .some() so any
owner's approval checks the box, while the mention always shows the
confirmed-requested reviewer(s) via .filter(). Also shows multiple
reviewers when one is manually added alongside the load-balanced
selection.
* review-checklist: show approver name when signed off, requested reviewer(s) when pending
When an area is signed off, replace the mention with the approver so the
checklist shows who actually reviewed it (which may differ from whoever
was load-balanced as the requested reviewer). When pending, show all
confirmed-requested reviewers — the one load-balanced pick normally, but
two if a reviewer was manually added alongside it.
* zizmor: remove config file and --config flag
The ignored files (ctest.yml, maven-deploy.yml, maven-staging.yml,
setup-jextract/action.yml) had template-injection findings on
inputs.* references, which are not attacker-controllable. Rather than
suppressing them via a config file, let all findings surface in the
Security tab and address them individually if needed.
* CI: use pull_request_target so review-checklist runs on fork PRs
pull_request events from forks receive a read-only GITHUB_TOKEN and
are skipped by the job condition, so no checklist comment is posted
and no reviewers are assigned. Switching to pull_request_target fixes
this: GitHub always executes the workflow from the base repo
(HDFGroup/hdf5) with a full write token, regardless of whether the PR
comes from a fork. The fork's code is never checked out or executed.
The cross-repo guard (head.repo.full_name == github.repository) is
removed since it is no longer needed — pull_request_target only fires
for PRs targeting this repo's branches.
* CI: replace pull_request_target with safe two-workflow pattern for fork PRs
pull_request_target carries a GitHub security warning because it grants
write access to the privileged workflow at trigger time, which is risky
if the checkout is ever changed to use the fork's head ref.
Replace it with the recommended two-workflow pattern:
- review-checklist-gather.yml fires on pull_request (read-only, safe
for forks) and uploads the PR number as a short-lived artifact.
- review-checklist.yml fires on workflow_run when the gather job
completes, downloads the artifact for the PR number, then posts the
checklist comment and assigns reviewers with a full write token.
It never executes any code from the fork.
The script gains a prNumber parameter so the main workflow can supply
the PR number it read from the artifact; falls back to the event
payload for pull_request_review triggers.
* review-checklist: fix prAuthor crash and stale comment for workflow_run context
In the workflow_run path context.payload.pull_request is undefined, so
reading .user.login from it throws a TypeError. Use prData.user.login
instead — prData is already fetched from the API at step 5.
Also remove the stale comment saying fork PRs require pull_request_target;
they are now handled via the two-workflow pattern.
* CI: revert to pull_request_target, drop two-workflow pattern
The workflow_run approach adds a second hop before the checklist posts
and introduced a context.payload.pull_request crash in the gather path.
pull_request_target is simpler and equally safe here: GitHub always
executes the workflow from HDFGroup/hdf5:develop with a full write
token — the fork's code is never checked out or executed.
* CI: add zizmor workflow for GitHub Actions security analysis
zizmor is a static analyser that catches security issues specific to
GitHub Actions: pull_request_target misuse, expression injection,
unpinned action SHAs, and overly broad permissions.
Runs on push to develop and on PRs that touch .github/, uploads SARIF
to the Security tab (free for public repos via Advanced Security), and
annotates PR diffs inline with any findings.
* CI: run zizmor via pip instead of third-party action
Replace zizmorcore/zizmor-action (third-party) with a direct pip install
of zizmor==1.25.2. SARIF output is still uploaded to the Security tab via
github/codeql-action/upload-sarif (first-party). The only actions used
are from actions/ and github/, both trusted.
* CI: fix codeql-action pin to commit SHA (was tag object SHA)
* CI: add persist-credentials: false to review-checklist checkout
* CI: hash-pin zizmor pip install; suppress expected pull-request-target finding
- zizmor.yml: pin zizmor wheel to its SHA256 hash via --require-hashes so
the install is fully reproducible and passes zizmor's unpinned-tools audit
- review-checklist.yml: add zizmor: ignore[pull-request-target] comment so
zizmor does not flag its own host workflow; document why the usage is safe
* CI: update actions to Node.js 24 ahead of June 16 deprecation
- actions/checkout: v4.2.2 → v5.0.1 (node20 → node24)
- actions/github-script: v7.0.1 → v8.0.0 (node20 → node24)
- github/codeql-action: v3.36.2 → v4.36.2 (node20 → node24; v3 deprecated Dec 2026)
* CI: fix pip hash-pinning syntax — hash must be in requirements file
* CI: zizmor step continue-on-error so SARIF upload always runs
* review-checklist: skip pull_request_review on fork PRs (read-only token)
GitHub only grants a read-only GITHUB_TOKEN for pull_request_review events
when the PR originates from a fork, so the comment post fails with 403.
Restrict the review trigger to same-repo PRs; pull_request_target already
handles fork PRs for the open/sync/reopen case with a full write token.
* review-checklist: route reviews through workflow_run for fork PR support
pull_request_review grants only a read-only token for fork PRs, causing
a 403 when posting the checklist comment. Fix with a two-path design:
- pull_request_target handles open/sync/reopen for all PRs (full token,
immediate)
- A new gather workflow (review-checklist-gather.yml) fires on
pull_request_review, saves the PR number as an artifact, and exits.
The main workflow then fires via workflow_run with a full write token.
The script gains prNumber and isReview parameters. isReview suppresses
reviewer assignment (which only applies on open/sync/reopen). prAuthor
is sourced from prData.user.login since context.payload.pull_request is
not populated in the workflow_run context.
* review-checklist: simplify to pull_request_target only, drop gather workflow
pull_request_review triggers a fork workflow approval gate for first-time
contributors, which blocks every PR. There is no pull_request_review_target
equivalent in GitHub Actions.
Instead, rely on pull_request_target (opened/synchronize/reopened) only.
Approval boxes are still evaluated correctly: computeApprovals() re-reads
all existing reviews on every push, so boxes auto-check the next time the
author pushes after a reviewer approves.
Also restores the simpler script signature (no prNumber/isReview params)
and sources prAuthor from prData.user.login which works in all contexts.
* review-checklist: auto-check approval boxes on review via workflow_run
Add a minimal gather workflow (review-checklist-gather.yml) triggered by
pull_request_review that completes immediately with a read-only token. The
main workflow now also triggers via workflow_run on gather completion, giving
it the full write token it needs to update the checklist comment.
In workflow_run context, the script looks up the PR by head SHA (since
workflow_run.pull_requests is empty for fork PRs) and skips reviewer
assignment — only approval box state is updated.
Requires the repo "Fork pull request workflows from outside collaborators"
setting to be "Require approval for first-time contributors", which is
already the current setting.
---------
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
* Add per-area review checklist action and restructure CODEOWNERS
CODEOWNERS:
- Replace 11-person global catch-all with specific path rules per area,
assigning reviewers based on their actual strengths
- Global fallback is now @fortnern only for uncovered root files
- Remove @derobins, @epourmal, @qkoziol, @mkitti per team discussion
review-checklist GitHub Action (.github/workflows/review-checklist.yml):
- Posts a per-area sign-off checklist on every PR to develop (non-forks only)
- Reviewer lists and path patterns derived directly from CODEOWNERS
- Assigns ONE reviewer per area using fewest-open-PRs load balancing
- Complex changes (≥ 300 lines or any public/developer header modified)
always go to the first (senior) owner listed; routine changes are
load-balanced across all owners (500-line threshold for test/)
- Cohesion: reuses an already-assigned reviewer for related areas where
owner lists overlap, avoiding e.g. src/ and test/ going to different people
- Skips auto-assign if an area owner is already manually requested
- Checklist auto-checks when an owner approves; tracks latest review state
so a subsequent "request changes" unchecks the box
The previous regex only matched *public.h and *develop.h, missing hdf5.h
itself (the umbrella header), all VFD driver headers included by hdf5.h
(H5FDcore.h, H5FDmpio.h, H5FDsubfiling.h, etc.), and VOL connector headers
(H5VLconnector.h, H5VLnative.h, etc.). Changes to any of these now
correctly trigger senior-owner assignment.
* Added CMAKE_CFLAGS="-Mnovect" for the workflow with nvhpc 26.3.0 where the issue occurs instead of editing CMake code specifically for test/dt_arith.c that would be applied to all nvhpc versions.
Both ninja and curl are pre-installed on the GitHub macOS runners,
causing noisy "already installed" warnings. Drop those brew steps
entirely (or just remove ninja/curl where other packages like graphviz
or libaec are still needed).
feat: add optional digital signature verification for HDF5 filter plugins
Introduce an opt-in plugin signing and verification system that allows
HDF5 deployments to require cryptographically signed filter plugins before
loading them. Disabled by default (HDF5_REQUIRE_SIGNED_PLUGINS=OFF).
New tool: h5sign
- Signs plugin shared libraries by appending an RSA signature and a
14-byte footer (algo_id | sig_len | 8-byte magic | format_ver) to the
binary without modifying the original content.
- Supports SHA-512 (default), SHA-256, SHA-384, and their PSS variants
(-a/--algorithm flag).
- Detects already-signed plugins; --force strips the old signature and
re-signs.
- Security hardened: keeps the file descriptor open through hashing and
appending (no TOCTOU window), enforces a 2048-bit minimum RSA key size,
rolls back partial writes on failure, and rejects paths that are not
regular files.
Verification (H5PLsig.c)
- At plugin load time, reads the footer, validates the magic and format
version, then checks the RSA signature against all public keys found in
the KeyStore directory.
- File is hashed once; per-key verification operates on the pre-computed
digest (no redundant I/O for multi-key keystores).
- Plugins whose signature hash appears in revoked_signatures.txt are
rejected regardless of key validity.
- Runtime debug output via HDF5_DEBUG=pl.
KeyStore management
- Trusted public keys are PEM files in a directory specified by
HDF5_PLUGIN_KEYSTORE_DIR (build time) or HDF5_PLUGIN_KEYSTORE (env var).
- HDF5_LOCK_PLUGIN_KEYSTORE cmake option disables the env-var override for
security-hardened deployments.
Test infrastructure
- h5signverifytest: positive, negative, tamper, re-sign, and revocation
test cases.
- CTest fixture-based dependency graph (FIXTURES_SETUP/FIXTURES_REQUIRED)
replaces fragile DEPENDS chains so tests remain correct under -R filtering.
- Dedicated signed-plugins.yml CI workflow; full test suite scoped to
H5SIGN and H5PLUGIN-signature tests to avoid unrelated flaky failures.
- Cross-platform: Linux, macOS, and Windows (MSVC-compatible, BIO-based
OpenSSL I/O, HDsleep/HDsetenv portability wrappers).
Documentation: docs/PLUGIN_SIGNATURE_README.md covers usage, footer
format, revocation file format, FAQ, and troubleshooting.
Co-authored-by: Glenn Song <gsong@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Larry Knoxandlrknox
Scot Breitenfeld
H. Joe LeeandClaude Opus 5
dependabot[bot]
jhendersonHDF
