Windows: get OpenMS from a reusable workflow instead of a contrib build - #409
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… build Add .github/workflows/openms-windows.yml (workflow_call). Installer mode repackages bin/ and share/ of the official OpenMS Windows installer; source mode builds a branch or fork with the vcpkg preset windows-x64-release and CPack ZIP. Both upload the openms-package artifact build-executable already consumes, after a --help smoke test of the kept TOPP tools. build-windows-executable-app.yaml now calls it in installer mode for 3.5.0, dropping contrib, the Qt install and the cibuild/citest/cipackage steps. A temporary workflow exercises source mode against OpenMS develop on this branch; it is removed before review. Part of OpenMS/OpenMS#10327 (step C2). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01ALo85PSS7JaNtrk18Au5qs
main (a9a3c7a) is red on Pylint (probe.py E1136) and on the assert-invariants doc-link check, independently of this PR. This is the change of #408, verbatim, so this PR's CI can go green; it no-ops once #408 is merged. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01ALo85PSS7JaNtrk18Au5qs
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Pylint / build and Build and Test / assert-invariants failed on 1e7d90d, but those failures aren't from this PR.
#408 fixes both. I ported its change verbatim in 6b68902, and it becomes a no-op once #408 merges. I ran Generated by Claude Code |
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Build and Test / test-nginx (simple, arm64, ubuntu-24.04-arm) failed on 6b68902. The cause is a race in the kind test's "Install nginx ingress controller" step, which this PR doesn't touch (it changes only the Windows workflows and docs):
Proposed patch (not applied here, to keep this PR on topic). A Deployment exists as soon as - kubectl wait --namespace ingress-nginx --for=condition=ready pod --selector=app.kubernetes.io/component=controller --timeout=90s
+ kubectl rollout status --namespace ingress-nginx deployment/ingress-nginx-controller --timeout=90sGenerated by Claude Code |
Source mode ran against OpenMS develop on this branch: cold 2h50m (vcpkg dependencies 1h23m, OpenMS compile 1h24m), warm 8m12s. The temporary workflow that ran it is no longer needed. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01ALo85PSS7JaNtrk18Au5qs
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Build and Test / build-simple-amd64 failed on 39a1989, at
The failure is an upstream download and happened before any test ran. No fix is needed in the repo. I'll re-run the job once when the run completes. Generated by Claude Code |
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📝 WalkthroughWalkthroughThe pull request adds a reusable Windows OpenMS workflow with installer and source-build modes. It updates the executable workflow to call it, adds packaging and smoke-test steps, and documents its inputs and artifact. It also updates Markdown link checks and a pylint annotation. ChangesWindows OpenMS packaging
Markdown reference updates
Lint annotation
Sequence Diagram(s)sequenceDiagram
participant Caller as Executable workflow caller
participant OpenMSWorkflow as openms-windows workflow
participant Release as OpenMS release
participant WindowsRunner as Windows runner
participant Artifacts as GitHub artifact storage
Caller->>OpenMSWorkflow: Pass version, mode, tools, and artifact name
OpenMSWorkflow->>Release: Find release and Windows installer
Release-->>OpenMSWorkflow: Return installer asset
OpenMSWorkflow->>WindowsRunner: Install or extract OpenMS
WindowsRunner->>Artifacts: Upload packaged ZIP
Suggested reviewers: Change: Feature 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
Full details: Docstring CoverageExplanation Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 2 functions across 2 files. (6 skipped: 6 unsupported.) ✨ Finishing Touches 💡 1📝 Generate docstrings 💡
🧪 Generate unit tests (beta)
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Inline comments:
Review comments at @.github/scripts/ci-assertions.sh:
- Around line 938-940: Update the loop that sets _ci_sibling in the
relative-reference link check so it validates the target separately for each
citing Markdown file instead of accepting a citation when any file has a
matching sibling. Report each citing file whose relative target does not
resolve.
Review comments at @.github/workflows/openms-windows.yml:
- Line 212: Pass the ref through an environment variable instead of embedding
the GitHub expression in the Bash script, and use that variable in the error
message in the vcpkg preset check. Apply the same change to the ref expansions
at the locations identified in the comment.
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.claude/skills/interview-parameters/probe.py.github/scripts/ci-assertions.sh.github/workflows/build-windows-executable-app.yaml.github/workflows/openms-windows.ymlCLAUDE.mdREADME.mddocs/notebook-to-webapp-design.mddocs/openms-windows-workflow.md
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…n run
ci-assertions.sh: a reference that resolves only relative to its citing
file's directory now has to resolve for every file citing it, not just for
one; the failure names only the citing files that do not resolve it. This
exposed three skill references that pointed at scaffold-workflow-app/ files
from another skill's directory; they now name that directory.
openms-windows.yml: the source ref and the release tag and asset names reach
the run scripts through env instead of ${{ }} expansion, so a ref containing
$(...) or backticks is never evaluated by bash.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01ALo85PSS7JaNtrk18Au5qs
2 participants
Part of OpenMS/OpenMS#10327 (step C2).
Before: the
build-openmsjob ofbuild-windows-executable-app.yamlcompiled OpenMSrelease/3.5.0against thecontribarchive withtools/ci/{cibuild,citest,cipackage}.cmake. It can't build OpenMS 3.6 or develop: those scripts were removed in OpenMS/OpenMS#9523, and contrib is being retired in favour of vcpkg.After: the job calls a new reusable workflow,
.github/workflows/openms-windows.yml(on: workflow_call). The workflow uploads the same artifactbuild-executablealready consumes:openms-package, a zip ofopenms-package/{bin,share}.build-executableis unchanged. The six app repos can call it asOpenMS/streamlit-template/.github/workflows/openms-windows.yml@<ref>.Modes
installer(default, used here for 3.5.0): finds the OpenMS GitHub release and downloads its Windows.exewithghandgithub.token. It tries the tagsv<ver>(thev*schemerelease.ymluses from 3.6 on), thenrelease/<ver>, thenRelease<ver>. The installer is installed silently (/S /allusers /D=…), with 7-Zip extraction as the fallback. Thenbin/andshare/are repackaged. No compile, no contrib, no Qt.source: for FLASHApp, OpenDIAKiosk and other forks or branches. It checks outopenms-repository@openms-refwith only thevcpkgandTHIRDPARTYsubmodules, then runsvs-shell+ Ninja andcmake --preset windows-x64-releasewith a TOPP-only set of options (WITH_GUI=OFF,ENABLE_DOCS=OFF, no tests). The optional vcpkg features match OpenMS'swindows-x64-ci. It packages with CPackPACKAGE_TYPE=zipand uses THIRDPARTY asSEARCH_ENGINES_DIRECTORY. The vcpkgfilesbinary cache and ccache are kept withactions/cache. The job fails with a clear message if the sources have no vcpkg presets: that means 3.6+, or develop from about 2026-08 on. A fork of an older develop must rebase first.In both modes, the kept tools are filtered by
topp-tools(each listed tool must exist). The job then checks thatshare/OpenMS/THIRDPARTY/*is present and not empty, because the app's.batputs those folders onPATH. It adds any MSVC/OpenMP runtime DLL the package lacks, and runs<tool> --helpfor each kept tool with a bare systemPATH, so a DLL missing frombin/fails the job. The inputs areopenms-version,mode,openms-repository,openms-ref,topp-tools,artifact-nameandruns-on, documented indocs/openms-windows-workflow.md.Changes to this repo's workflow
OPENMS_CONTRIB_VERSION, the Qt install, THIRDPARTY setup, and thecibuild/citest/cipackagesteps.OPENMS_VERSIONmoves into the call'swith:block asopenms-version: "3.5.0", becausewith:of a reusable-workflow call can't readenv. A tinyconfigjob passesTOPP_TOOLSthrough as an output, so it stays defined in one place.--helpsmoke test above.Validation
Installer mode, in this PR's
Build executable for Windowsrun: the OpenMS 3.5.0 installer installed silently without the 7-Zip fallback.FeatureFinderMetabo,FeatureLinkerUnlabeledKDandSiriusExportpassed--helpwith a barePATH. The artifact is 224 MB.build-openmstakes about 1.5 min, andbuild-executablethen built the MSI unchanged in about 7 min.Source mode against OpenMS
develop, onwindows-2025with the same three tools. It ran from a temporary workflow on this branch only, never on PRs, removed in 39a1989 (run 36548083206, attempt 1 cold, attempt 2 warm). Both attempts passed the smoke test and produced a 205 MB artifact.vcpkg/THIRDPARTYsubmodulesvcpkg install+ CMake)--parallel 2)Other commits
mainis red on Pylint (probe.pyE1136) and on the doc-link assertion, independently of this change. The port becomes a no-op once Make main's lint and doc-link checks pass again #408 merges.test-nginx (simple, arm64)failed once, due to a race inkubectl wait --selectorright afterkubectl apply, and passed on re-run. This comment has a proposed fix; I haven't applied it, to keep this PR on topic.Decisions for a maintainer
@main. If you want a tag, the apps need one to point at, e.g. a movingopenms-windows-v1. I have not created one.windows-2025(OpenMS's own CI runner).build-executablestays onwindows-2022.Overlap with open PRs (not modified)
All of these edit
build-windows-executable-app.yaml, and whichever merges second needs a rebase:build-executable. Its steps consume the sameopenms-bin/sharelayout, so it should rebase cleanly apart from theenv/build-openmshunk.🤖 Generated with Claude Code
https://claude.ai/code/session_01ALo85PSS7JaNtrk18Au5qs
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