Add shed-tools validate subcommand#237
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Drop the run-data-managers comment claiming Galaxy 26.0 requires a history to execute tools (it doesn't; the failure was a session without an associated history), and trim the verbose galaxy-app pin comment in dev-requirements. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
No-install, no-Galaxy validation of tools files / .yml.lock against a Tool Shed. Structural check reuses RepositoryInstallTargets/read_tools; shed check asserts each repo exists and every pinned changeset_revision is installable. --structural-only skips network for offline pre-commit. Closes #236. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
extra=forbid on RepositoryInstallTarget(s) so a typo'd key (e.g. revision vs revisions) fails structurally instead of silently passing with the pin unchecked. read_tools now rejects a non-mapping/empty YAML root with a clear error instead of a TypeError from **-splatting None; validate() catches it. Install path is unaffected (reads raw YAML, not the model). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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@arash77 this looks interesting. Can you please point John to the scripts that you have been cooking - removing the non-installable revisions etc? Maybe that is interesting for whatever @jmchilton is cooking here. |
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Sure! You can find the scripts for filtering out the non-installable tool revisions in this PR: usegalaxy-eu/usegalaxy-eu-tools#929 |
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Should we also allow/validate the top-level |
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What
Adds a
shed-tools validatesubcommand: no-install, no-Galaxy validation of a tools file /.yml.lockagainst a Tool Shed. Closes #236.RepositoryInstallTargetspydantic model viaread_tools(same parsing as install).--structural-onlyskips all network access — suitable for offline pre-commit / CI on revision-pinned lock files.Hardening (second commit)
extra=forbidonRepositoryInstallTarget(s)so a typo'd key (e.g.revision:forrevisions:) fails structurally instead of silently passing with the pin unchecked — the failure mode the validator exists to catch. Safe: the install path reads raw YAML and does not use the model; the only model consumers arevalidate, the IDC generator (known keys only), and tests.read_toolsrejects a non-mapping / empty YAML root with a clear error instead of aTypeErrorfrom**-splattingNone.Tests
tests/test_shed_tools_validate.pyfakes the Tool Shed via monkeypatch (no network): structural-only good/bad, full good/bad-revision, missing file, no input, unknown-key rejection, empty/non-mapping root, query-once-per-repo. mypy clean.Comment cleanup (rolled in from #238)
Per @mvdbeek's review on #238, the first commit tidies two comments that landed with that merge: drops the run-data-managers comment wrongly claiming Galaxy 26.0 requires a history to execute tools (the real cause was a session without an associated history), and trims the verbose
galaxy-apppin comment indev-requirements.txt.🤖 Generated with Claude Code