GHA refactor, Claude setup, umccr -> tidywf renaming#46
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LinkML: add schema support, mermaid ER utilities
GitHub Actions: refactor deploy wf for dev/main
precommit: add air formatter
Claude Code setup
* change gh org * change anaconda org * change anaconda org
* gha: use gh app for branch protection override * gha: use app email
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Pull request overview
This PR refactors nemo’s tool configuration system to use per-tool LinkML schemas, adds utilities/docs to visualize schemas as Mermaid ER diagrams, and updates project metadata + CI/deploy/docs to the tidywf org with a version bump.
Changes:
- Replace the previous raw/tidy YAML config approach with a single LinkML
schema.yamlper tool and updateConfighelpers accordingly. - Add
schema_to_mermaid()/schema_versions()plus a new “Schema” vignette and pkgdown nav/reference entries. - Update repo URLs, conda/deploy configs, workflows, and documentation for the
tidywfmove and version0.0.3.9007.
Reviewed changes
Copilot reviewed 35 out of 36 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
| vignettes/structure.Rmd | Update referenced child-package GitHub URLs to tidywf. |
| vignettes/schema.qmd | New vignette documenting LinkML schema structure + Mermaid visualization. |
| vignettes/devnotes.qmd | Update DVC example URL to tidywf. |
| vignettes/NEWS.qmd | Update repo URL and add new dev changelog entries. |
| tests/testthat/test-roxytest-testexamples-utils.R | Update roxytest-generated line references. |
| tests/testthat/test-roxytest-testexamples-Config.R | Update roxytest-generated line references. |
| pkgdown/_pkgdown.yml | Update site URL, enable development mode auto, add Schema article + schema functions to reference. |
| man/schema_versions.Rd | New Rd for schema_versions(). |
| man/schema_to_mermaid.Rd | New Rd for schema_to_mermaid(). |
| man/nemo-package.Rd | Update GitHub/docs URLs and bug-report link. |
| man/Config.Rd | Update Config docs to reflect LinkML schema-based configuration. |
| inst/documentation/notes/pixi.md | Update conda channel examples from umccr to tidywf. |
| inst/documentation/installation/_r.qmd | Update GitHub install instructions to tidywf and new version tag. |
| inst/documentation/installation/_pixi.qmd | Update Pixi install instructions to tidywf and new version pin. |
| inst/documentation/installation/_conda.qmd | Update conda install instructions to tidywf and new version pin. |
| inst/config/tools/tool1/schema.yaml | Add Tool1 LinkML schema (raw/tidy classes, versions, patterns). |
| deploy/conda/recipe/recipe.yaml | Bump conda recipe version and update project URLs to tidywf. |
| deploy/conda/env/yaml/pkgdown.yaml | Update channels/dependency pin for pkgdown env. |
| deploy/conda/env/yaml/nemo.yaml | Update channels/dependency pin for the nemo env. |
| deploy/conda/env/lock/conda-linux-64.lock | Regenerated conda lockfile for updated env/version. |
| README.qmd | Update docs/action/anaconda links to tidywf and installation pointers. |
| README.md | Re-rendered README content with new links/version/tag (but see review comment on version output). |
| R/utils.R | Add LinkML helper functions + type remapping; update tidywigits repo URL in dispatcher. |
| R/mermaid.R | Add exported functions to generate Mermaid ER diagrams and list schema versions. |
| R/Config.R | Refactor Config to read LinkML schema.yaml and expose raw/tidy schemas accordingly. |
| NAMESPACE | Export schema_to_mermaid and schema_versions. |
| Makefile | Add phony targets, adjust build behavior, add bump target to trigger bump workflow. |
| DESCRIPTION | Bump version to 0.0.3.9007 and update URL/BugReports to tidywf. |
| CLAUDE.md | Add repo-specific engineering guidance (architecture, schema conventions, CI, testing workflow). |
| .pre-commit-config.yaml | Switch to air-format pre-commit hook setup and keep other hooks. |
| .github/workflows/deploy.yaml | Replace inline deploy logic with reusable workflows; include dev branch; bump version input. |
| .github/workflows/claude.yml | Add workflow to run Claude Code action when tagged in comments/reviews/issues. |
| .github/workflows/claude-code-review.yml | Add automated PR code review workflow using Claude Code plugins. |
| .github/workflows/bump.yaml | Add workflow_dispatch wrapper that calls shared bump workflow. |
| .claude/skills/nemotool/SKILL.md | Add a Claude skill definition for scaffolding a new nemo tool. |
| .bumpversion.toml | Update bumpversion config for new deploy workflow fields and enable commit. |
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Pull request overview
Copilot reviewed 27 out of 28 changed files in this pull request and generated 8 comments.
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pdiakumis
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Need to clean this one up.