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- Updated template-branch from v0.8.16 to v0.9.5 - Removed orphaned workflow files (dep_compat_test, deptry, license, pip_audit, pre-commit, security, semgrep, typecheck, validate, renovate_rhiza_sync) - Added new workflow files (rhiza_weekly.yml, semgrep.yml) - Added new rhiza files (CODE_OF_CONDUCT.md, CONTRIBUTING.md, test_docs_targets.py) - Removed obsolete docs and templates - Resolved merge conflict in rhiza_ci.yml (upload-artifact condition + version) - Kept local .rhiza/.env (excluded from template management) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Automatically synced template files after updating .rhiza/template.yml Co-Authored-By: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Pull request overview
Syncs this repository with the upstream Rhiza template updates (v0.8.16 → v0.9.5), modernizing CI/workflow layout and migrating documentation tooling toward an MkDocs-based “book” build.
Changes:
- Bumped Rhiza template version to
v0.9.5and applied upstream sync (including additions/removals under.rhiza/and.github/workflows/). - Consolidated CI responsibilities (more jobs in
rhiza_ci.yml) and added a new weekly workflow. - Reorganized documentation structure and introduced a base MkDocs config under
docs/.
Reviewed changes
Copilot reviewed 58 out of 65 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
| ruff.toml | Updates Ruff per-file ignores to target notebook locations. |
| docs/mkdocs-base.yml | Adds a base MkDocs configuration for Rhiza-based projects. |
| docs/index.md | Adds MkDocs landing page via snippet include. |
| docs/development/TESTS.md | Adds testing documentation (property/benchmark/stress). |
| docs/development/MARIMO.md | Updates Marimo notebook documentation and paths. |
| docs/assets/rhiza-logo.svg | Adds documentation logo asset. |
| docs/adr/0000-adr-template.md | Adds ADR template document. |
| docs/SECURITY.md | Removes docs-local security policy (root SECURITY.md remains). |
| docs/QUICK_REFERENCE.md | Removes quick reference doc (moved/removed by template sync). |
| docs/GLOSSARY.md | Removes glossary doc (moved/removed by template sync). |
| docs/DEMO.md | Removes demo doc (moved/removed by template sync). |
| docs/CUSTOMIZATION.md | Removes customization doc (moved/removed by template sync). |
| docs/BOOK.md | Removes book doc (moved/removed by template sync). |
| docs/ARCHITECTURE.md | Removes architecture doc (moved/removed by template sync). |
| book/marimo/notebooks/rhiza.py | Removes a Marimo showcase notebook from the previous location. |
| SECURITY.md | Updates supported versions; currently contains a placeholder instruction line. |
| Makefile | Removes local semgrep/license targets; keeps ADR target. |
| .rhiza/tests/sync/conftest.py | Updates sync test setup (removes docs.mk split). |
| .rhiza/tests/security/test_security_patterns.py | Tightens security policy location check to root SECURITY.md only. |
| .rhiza/tests/integration/test_marimushka.py | Removes marimushka integration tests (target removed). |
| .rhiza/tests/integration/test_docs_targets.py | Adds integration tests for MkDocs extra-packages support in book.mk. |
| .rhiza/tests/integration/test_book_targets.py | Updates expectations around available book-related targets. |
| .rhiza/tests/api/test_makefile_targets.py | Adds dry-run assertions for new/adjusted targets (license, suppression-audit). |
| .rhiza/tests/api/conftest.py | Removes docs.mk from expected synced makefiles list. |
| .rhiza/tests/README.md | Removes mention of marimushka test. |
| .rhiza/templates/minibook/custom.html.jinja2 | Removes old minibook HTML template (MkDocs-based approach). |
| .rhiza/template.yml | Bumps template branch to v0.9.5. |
| .rhiza/template.lock | Updates locked template ref/sha and synced file list. |
| .rhiza/rhiza.mk | Updates stated purpose (drops docs/marimushka mentions). |
| .rhiza/requirements/docs.txt | Switches docs deps toward MkDocs tooling. |
| .rhiza/requirements/README.md | Updates docs deps description (now slightly out of sync with docs.txt). |
| .rhiza/make.d/quality.mk | Adds license + suppression-audit targets and config var LICENSE_FAIL_ON. |
| .rhiza/make.d/marimo.mk | Removes marimushka target; retains marimo run/validate. |
| .rhiza/make.d/docs.mk | Removes legacy pdoc/mkdocs targets file. |
| .rhiza/make.d/book.mk | Replaces minibook assembly with MkDocs-based build and report/notebook copying/export. |
| .rhiza/make.d/agentic.mk | Switches analyse-repo implementation to Claude-based agent invocation. |
| .rhiza/make.d/README.md | Removes docs.mk reference and outdated external link. |
| .rhiza/docs/WORKFLOWS.md | Updates dependency rationale link path. |
| .rhiza/docs/CONFIG.md | Updates workflow list (removes deptry/typecheck entries). |
| .rhiza/CONTRIBUTING.md | Adds contributing guide under .rhiza/. |
| .rhiza/CODE_OF_CONDUCT.md | Adds code of conduct under .rhiza/. |
| .rhiza/.env | Minor change (newline); remains present and now appears template-managed per lockfile. |
| .pre-commit-config.yaml | Bumps tool revisions and tweaks YAML check exclusions. |
| .gitignore | Adds ignores for generated docs notebooks/reports and LaTeX artifacts. |
| .github/workflows/rhiza_weekly.yml | Adds weekly workflow for dep-compat, semgrep, pip-audit, link checking. |
| .github/workflows/rhiza_validate.yml | Removes standalone validate workflow (now folded into unified CI). |
| .github/workflows/rhiza_typecheck.yml | Removes standalone typecheck workflow (now folded into unified CI). |
| .github/workflows/rhiza_sync.yml | Reworks sync workflow to handle Renovate pushes vs scheduled/manual PR syncs. |
| .github/workflows/rhiza_semgrep.yml | Removes standalone semgrep workflow (weekly workflow added). |
| .github/workflows/rhiza_security.yml | Removes standalone security workflow (now folded into unified CI). |
| .github/workflows/rhiza_release.yml | Updates uv versions and adds git-cliff release notes generation. |
| .github/workflows/rhiza_pre-commit.yml | Removes standalone pre-commit workflow (now folded into unified CI). |
| .github/workflows/rhiza_pip_audit.yml | Removes standalone pip-audit workflow (now in weekly workflow). |
| .github/workflows/rhiza_marimo.yml | Updates uv setup action/version. |
| .github/workflows/rhiza_license.yml | Removes standalone license workflow (now folded into unified CI). |
| .github/workflows/rhiza_deptry.yml | Removes standalone deptry workflow (now folded into unified CI). |
| .github/workflows/rhiza_dep_compat_test.yml | Removes standalone dep-compat workflow (now in weekly workflow). |
| .github/workflows/rhiza_codeql.yml | Updates CodeQL action version and docs path reference. |
| .github/workflows/rhiza_ci.yml | Expands CI responsibilities and updates uv/action versions. |
| .github/workflows/rhiza_book.yml | Updates uv/action versions for book build + pages deployment steps. |
| .github/workflows/renovate_rhiza_sync.yml | Removes old Renovate sync workflow (logic moved into rhiza_sync.yml). |
| .github/workflows/copilot-setup-steps.yml | Updates uv setup action/version. |
| .github/semgrep.yml | Adds local Semgrep rules configuration under .github/. |
| .github/copilot-instructions.md | Updates Copilot agent instructions (removes some references). |
| .github/agents/analyser.md | Updates analyser output format to a scored rubric table. |
Comments suppressed due to low confidence (2)
docs/development/MARIMO.md:43
- The example command uses
marimo edit docs/notebooks/rhiza.py, but that file/path doesn’t exist in the current repo layout. Adjust the example to point at an existing notebook location (e.g., underbook/marimo/) or add the notebook at the documented path.
docs/development/MARIMO.md:36 - This references notebooks living in
docs/notebooks, but that directory isn’t present in the repo (current Marimo notebooks appear underbook/marimo/). Update the documented notebook directory (or move notebooks accordingly) somake marimomatches reality.
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| @printf "${GREEN}[SUCCESS] Book built at $(BOOK_OUTPUT)/${RESET}\n" | ||
| @tree $(BOOK_OUTPUT) |
| @@ -0,0 +1,2 @@ | |||
| --8<-- "README.md" | |||
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| nav: | ||
| - Home: index.md | ||
| - Notebooks: notebooks.md | ||
| - Reports: reports.md | ||
| - Paper: paper/rhiza.pdf |
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| - **tests.txt** - Testing dependencies (pytest, pytest-cov, pytest-html, pytest-mock, PyYAML, defusedxml, hypothesis, pytest-benchmark, pygal) | ||
| - **marimo.txt** - Marimo notebook dependencies | ||
| - **docs.txt** - Documentation generation dependencies (pdoc) | ||
| - **tools.txt** - Development tools (pre-commit, python-dotenv) | ||
| - **docs.txt** - Documentation generation dependencies (pdoc, interrogate, mkdocs, mkdocs-material, mkdocstrings) | ||
| - **tools.txt** - Development tools (pre-commit, python-dotenv, typer, ty) |
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@copilot apply changes based on this feedback
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Updated the README in commit 9f74d36 — removed pdoc from the docs.txt description so it now accurately reflects the actual contents: (interrogate, mkdocs, mkdocs-material, mkdocstrings).
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| include: [] | ||
| exclude: | ||
| - .rhiza/.env | ||
| exclude: [] |
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| @if [ -d "$(MARIMO_FOLDER)" ]; then \ | ||
| for nb in $(MARIMO_FOLDER)/*.py; do \ | ||
| name=$$(basename "$$nb" .py); \ | ||
| printf "${BLUE}[INFO] Exporting $$nb${RESET}\n"; \ | ||
| abs_output="$$(pwd)/docs/notebooks/$$name.html"; \ | ||
| mkdir -p docs/notebooks; \ | ||
| (cd "$$(dirname "$$nb")" && ${UV_BIN} run marimo export html --sandbox "$$(basename "$$nb")" -o "$$abs_output"); \ | ||
| done; \ |
S101 (assert) and RUF001 (ambiguous unicode) were flagged in book/marimo/*.py because the existing '**/notebooks/*.py' glob didn't match that path. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Move Balanced.py, monkey.py, OneAssetFadingOut.py, pairs.py into book/marimo/notebooks/ so they are matched by the existing '**/notebooks/*.py' ruff glob. Remove the now-redundant 'book/marimo/*.py' per-file-ignores entry. Update MARIMO_FOLDER in .rhiza/.env accordingly. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Notebooks moved from book/marimo/ to book/marimo/notebooks/, so the path to the project root gains one extra level. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Keeps data files co-located with the notebooks that use them. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Automatically synced template files after updating .rhiza/template.yml Co-Authored-By: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Automatically synced template files after updating .rhiza/template.yml Co-Authored-By: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Automatically synced template files after updating .rhiza/template.yml Co-Authored-By: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Automatically synced template files after updating .rhiza/template.yml Co-Authored-By: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Agent-Logs-Url: https://github.com/cvxgrp/simulator/sessions/e433a7b4-63dd-4293-9050-a4f0427830a4 Co-authored-by: tschm <2046079+tschm@users.noreply.github.com>
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Summary
template-branchfromv0.8.16tov0.9.5in.rhiza/template.ymlrhiza syncto apply all upstream template changes.github/workflows/rhiza_ci.yml: took upstream condition (matrix.os == 'ubuntu-latest') andupload-artifact@v7.rhiza/.env: kept local version (file is excluded from rhiza management)Key changes from v0.8.16 → v0.9.5
Workflows removed (consolidated into unified CI):
renovate_rhiza_sync.yml,rhiza_dep_compat_test.yml,rhiza_deptry.yml,rhiza_license.yml,rhiza_pip_audit.yml,rhiza_pre-commit.yml,rhiza_security.yml,rhiza_semgrep.yml,rhiza_typecheck.yml,rhiza_validate.ymlWorkflows added:
rhiza_weekly.ymlFiles reorganised:
CODE_OF_CONDUCT.md/CONTRIBUTING.mdmoved into.rhiza/.semgrep.ymlmoved to.github/semgrep.ymldocs/development/,docs/adr/,docs/assets/Test plan
rhiza validatereports no issues🤖 Generated with Claude Code