Docs + restore JaCoCo coverage gate (#323) - #327
Merged
Conversation
Replace legacy build/publish references (launch.sh, make publish, nextflow-io/plugins PR flow, NXF_PLUGINS_TEST_REPOSITORY GitHub-release pinning, plugins/ subproject, buildSrc) with the new io.nextflow.nextflow-plugin workflow: make assemble/install/package/release and ./gradlew releasePlugin (NPR_API_KEY) for publishing to registry.nextflow.io. Add CHANGELOG bullets for the registry migration. Refs #323 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Reapply the pre-migration coverage gate that was dropped during the move to the io.nextflow.nextflow-plugin Gradle build. Adds the `jacoco` plugin, configures `jacocoTestReport` and `jacocoTestCoverageVerification` (70% line minimum, matching the previous threshold), and wires `check` to depend on the verification task. Restores the `coverage` and `verifyCoverage` Makefile targets. Refs #323 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
🦙 MegaLinter status: ✅ SUCCESS
See detailed report in MegaLinter reports
|
drernie
added a commit
that referenced
this pull request
Apr 30, 2026
## Summary First release published to the [Nextflow Plugin Registry](https://registry.nextflow.io). Bumps the plugin version to `1.0.0`, consolidating the unpublished `0.9.2` intermediate into the registry-migration release. This is the final PR in the migration tracked by #323. It bundles three previously-merged PRs: - #322 — Jackson `OffsetDateTime` serialization fix for Nextflow 24.10+ - #324 — Migrate to the new `io.nextflow.nextflow-plugin` Gradle build system - #327 — Docs refresh + restore JaCoCo 70% line-coverage gate ## Changes - `build.gradle`: `version = '0.9.2'` -> `'1.0.0'` - `CHANGELOG.md`: rename `[0.9.2]` section to `[1.0.0]` and add note about Nextflow Plugin Registry as the publishing channel - `README-DEV.md`: bump example `nf-quilt@0.9.2` references to `@1.0.0` The `dest-1.0.0` test package has been pre-published to `s3://udp-spec` so `QuiltPkgTest > should confirm contents of dest URI` passes in CI. ## Post-merge manual steps (human) The actual registry publish is intentionally NOT automated in this PR: 1. `git tag 1.0.0 && git push origin 1.0.0` 2. `export NPR_API_KEY=... && ./gradlew releasePlugin` 3. Verify the plugin appears on https://registry.nextflow.io 4. Close #321 with the registry URL ## Test plan - [x] `./gradlew test` passes - [x] `./gradlew check` passes (JaCoCo gate satisfied) - [x] `./gradlew packagePlugin` produces `build/distributions/nf-quilt-1.0.0.zip` - [x] `make pkg-test WRITE_BUCKET=udp-spec` published `nf-quilt/dest-1.0.0` to `udp-spec` - [ ] CI green Closes #323 Closes #321 🤖 Generated with [Claude Code](https://claude.com/claude-code) <!-- greptile_comment --> <h3>Greptile Summary</h3> This PR bumps the plugin version from `0.9.2` to `1.0.0` across `build.gradle`, `CHANGELOG.md`, and `README-DEV.md` in preparation for the first publish to the Nextflow Plugin Registry. All `0.9.2` references have been consistently updated and no stale occurrences remain in the repository. <h3>Confidence Score: 4/5</h3> Safe to merge — changes are purely a version bump with no functional code modifications. Only P2 finding (stale comment in build.gradle); no logic, security, or correctness issues present. No files require special attention beyond the minor stale comment in build.gradle line 17. <h3>Important Files Changed</h3> | Filename | Overview | |----------|----------| | build.gradle | Version bumped from 0.9.2 to 1.0.0; stale "until the 1.0.0 release" comment left in place (P2) | | CHANGELOG.md | Section heading renamed from [0.9.2] to [1.0.0]; registry publication note prepended — no issues found | | README-DEV.md | Four nf-quilt version references updated from 0.9.2 to 1.0.0 in example commands — no issues found | </details> <h3>Flowchart</h3> ```mermaid %%{init: {'theme': 'neutral'}}%% flowchart TD A["build.gradle\nversion = '1.0.0'"] --> B["./gradlew packagePlugin\nnf-quilt-1.0.0.zip"] B --> C["git tag 1.0.0\ngit push origin 1.0.0"] C --> D["./gradlew releasePlugin\nNPR_API_KEY set"] D --> E["Nextflow Plugin Registry\nregistry.nextflow.io"] F["CHANGELOG.md\n1.0.0 section"] -.-> B G["README-DEV.md\nnf-quilt at 1.0.0"] -.-> E ``` <sub>Reviews (1): Last reviewed commit: ["Release 1.0.0"](c7e63de) | [Re-trigger Greptile](https://app.greptile.com/api/retrigger?id=30280267)</sub> > Greptile also left **1 inline comment** on this PR. <!-- /greptile_comment --> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
PR 2 of the 4-PR migration to the Nextflow Plugin Registry (#323). PR 1 was the structural rewrite (#324). This PR is documentation + restoring the JaCoCo coverage gate; no version bump and no source/test changes.
launch.sh,make publish,nextflow-io/pluginsPR flow,NXF_PLUGINS_TEST_REPOSITORYGitHub-release pinning,plugins/subproject,buildSrc) inREADME-DEV.mdwith the newio.nextflow.nextflow-pluginworkflow:make assemble/install/package/releaseand./gradlew releasePlugin(requiresNPR_API_KEY) for publishing to registry.nextflow.io.README.mddid not contain stale references and was left as-is.[0.9.2] 2026-04-29section noting the registry migration, the new build system, droppednextflow-io/pluginsflow, doc updates, and JaCoCo restoration. No new version section (1.0.0 entry comes in the release PR).id 'jacoco'to the plugins block, configuredjacocoTestReportandjacocoTestCoverageVerification(70% line minimum, mirroring the pre-migration threshold), and wiredcheckto depend on the verification task. Restoredcoverage/verifyCoverageMakefile targets and updated.PHONY../gradlew checkpasses includingjacocoTestCoverageVerificationat the 70% bar — no threshold reduction needed.Refs #323
Test plan
./gradlew checkpasses locally with the 70% JaCoCo gate enabled