Rhiza v0 18 8

[tschm]

run 'make sync'

1. This will read .rhiza/template.yml
2. It will sync with the template repo declared in that file
3. It will update .rhiza and a few files at root level. It will not (yet) touch .github, src and tests

[Copilot]

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

This PR appears to sync in the latest Rhiza template updates and establish a standardized developer tooling baseline (Makefile API, lint/format config, docs config, security utilities, and a comprehensive pytest suite).

Changes:

• Added Ruff, pytest, and pre-commit configuration plus MkDocs base configuration/docs.
• Introduced/updated Rhiza Makefile infrastructure under .rhiza/ (split makefiles, utilities, completions, requirements).
• Added an extensive .rhiza/tests/ suite covering structure, API, integration, sync, shell, and stress testing.

Reviewed changes

Copilot reviewed 59 out of 62 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
ruff.toml	Adds Ruff lint/format configuration and per-path ignores.
pytest.ini	Adds pytest defaults (paths, logs, timeout, markers).
docs/mkdocs-base.yml	Adds a base MkDocs Material configuration for Rhiza projects.
docs/development/MARIMO.md	Adds documentation for running and maintaining Marimo notebooks.
Makefile	Switches to always include .rhiza/rhiza.mk and sets template overrides/vars.
.rhiza/utils/suppression_audit.py	Adds a utility to audit inline suppressions and optionally validate stale CVE suppressions.
.rhiza/utils/pip_audit_policy.py	Adds a tiered pip-audit policy script (fail runtime CVEs, warn tooling CVEs).
.rhiza/tests/utils/test_git_repo_fixture.py	Adds tests validating the git_repo fixture behavior.
.rhiza/tests/test_utils.py	Adds shared helpers for running make, stripping ANSI, and setting up a git repo.
.rhiza/tests/sync/test_readme_validation.py	Adds tests that execute README code blocks and validate bash syntax blocks.
.rhiza/tests/sync/test_docstrings.py	Adds doctest discovery/execution across source modules.
.rhiza/tests/sync/conftest.py	Adds sync-test environment setup fixture (temp repo, Makefiles, template.yml, etc.).
.rhiza/tests/structure/test_requirements.py	Adds structure tests for .rhiza/requirements contents.
.rhiza/tests/structure/test_pyproject.py	Adds strong validation of pyproject.toml structure and version/tag alignment.
.rhiza/tests/structure/test_project_layout.py	Adds structure tests for expected root files/dirs and CI directory presence.
.rhiza/tests/stress/conftest.py	Adds stress-test CLI options and fixtures.
.rhiza/tests/stress/init.py	Adds stress test package marker module.
.rhiza/tests/stress/README.md	Documents stress test purpose and how to run them.
.rhiza/tests/shell/test_scripts.sh	Adds a bash test harness to validate key shell scripts and their syntax.
.rhiza/tests/integration/test_virtual_env_unexport.py	Adds integration test for unexport VIRTUAL_ENV behavior in Makefiles.
.rhiza/tests/integration/test_test_mk.py	Adds integration test for test.mk behavior when no tests exist.
.rhiza/tests/integration/test_docs_targets.py	Adds integration tests for MKDOCS_EXTRA_PACKAGES behavior in book.mk.
.rhiza/tests/integration/test_book_targets.py	Adds integration tests for book targets and resilience when book assets are missing.
.rhiza/tests/conftest.py	Adds core test fixtures including a sandbox git repo and mocked tool binaries.
.rhiza/tests/api/test_makefile_targets.py	Adds API tests asserting Makefile targets and command emissions (mostly dry-run).
.rhiza/tests/api/test_makefile_api.py	Adds tests for Makefile API extension/override mechanisms.
.rhiza/tests/api/test_make_variable_overrides.py	Adds tests for Makefile variable override behavior.
.rhiza/tests/api/test_github_targets.py	Adds GitHub-target dry-run tests (help presence and target invocations).
.rhiza/tests/api/conftest.py	Adds shared setup for API tests (copy Makefile/split makefiles, chdir, env).
.rhiza/tests/README.md	Documents the test suite layout and usage conventions.
.rhiza/template.yml	Bumps template ref to v0.18.8.
.rhiza/template.lock	Adds lockfile capturing synced template files + sync metadata.
.rhiza/semgrep.yml	Adds Semgrep rules (NumPy security/repro/stability checks).
.rhiza/rhiza.mk	Adds core Rhiza Makefile (targets, variables, sync/validate behavior, help).
.rhiza/requirements/tools.txt	Adds tool requirements list.
.rhiza/requirements/tests.txt	Adds test requirements list.
.rhiza/requirements/marimo.txt	Adds Marimo requirements list.
.rhiza/requirements/docs.txt	Adds docs requirements list.
.rhiza/requirements/README.md	Documents the requirements file purpose and usage.
.rhiza/make.d/test.mk	Adds split makefile for test/benchmark/security/docs coverage/stress/etc.
.rhiza/make.d/releasing.mk	Adds split makefile for bump/release workflows and hooks.
.rhiza/make.d/quality.mk	Adds split makefile for fmt/deptry/security/license/semgrep/suppression audit.
.rhiza/make.d/marimo.mk	Adds split makefile for Marimo validate/server targets.
.rhiza/make.d/doctor.mk	Adds split makefile for prerequisite diagnostics.
.rhiza/make.d/custom-task.mk	Adds example custom task and hook extension.
.rhiza/make.d/custom-env.mk	Adds example custom env/variable overrides.
.rhiza/make.d/bootstrap.mk	Adds split makefile for uv bootstrap + install/clean targets.
.rhiza/make.d/book.mk	Adds split makefile for MkDocs book build/serve and notebook export.
.rhiza/completions/rhiza-completion.zsh	Adds zsh completion for Make targets and common variables.
.rhiza/completions/rhiza-completion.bash	Adds bash completion for Make targets and common variables.
.rhiza/completions/README.md	Documents installing/using shell completion scripts.
.rhiza/assets/rhiza-logo.svg	Adds Rhiza SVG logo asset for docs/branding.
.rhiza/.rhiza-version	Pins Rhiza toolchain version.
.rhiza/.gitignore	Adds Rhiza-specific ignore rules (notably allowing .env).
.rhiza/.env	Adds Rhiza environment defaults (MARIMO_FOLDER, SOURCE_FOLDER, OS matrix).
.rhiza/.cfg.toml	Adds bumpversion configuration/settings.
.python-version	Adds project Python version file.
.pre-commit-config.yaml	Adds pre-commit hooks for linting, formatting, security, lockfile, etc.
.gitignore	Replaces/expands ignore rules for Python/dev/docs artifacts and project outputs.
.github/dependabot.yml	Adds Dependabot configuration for uv + GitHub Actions.
.editorconfig	Adds EditorConfig defaults for consistent formatting across file types.
.bandit	Adds Bandit basic config (skip B101).

Comments suppressed due to low confidence (4)

Makefile:1

• Using a non-optional include .rhiza/rhiza.mk will hard-fail make on first run or in any environment where .rhiza/rhiza.mk hasn’t been materialized yet (e.g., partial checkouts, shallow template consumers, or before a sync step). Consider reverting to -include .rhiza/rhiza.mk plus a small bootstrap target/guard (like the previous conditional sync) or emitting a clear error message instructing how to materialize .rhiza/rhiza.mk.
  .rhiza/tests/api/test_makefile_targets.py:1
• These assertions assume the dry-run output starts with the literal uvx, but the Makefiles compute UVX_BIN via command -v uvx, which commonly expands to an absolute path (e.g., /usr/bin/uvx). This will make the tests fail even when the Makefile is correct. A more robust assertion is to check for the -p <version> + command_fragment sequence (and optionally accept any prefix ending in uvx).
  .rhiza/tests/conftest.py:1
• git checkout -b master can fail if the clone already has an unborn master branch (or if git creates it based on remote HEAD). To make the fixture idempotent across git versions/configurations, use a command that overwrites/creates deterministically (e.g., git checkout -B master or git switch -C master).
  ruff.toml:1
• Ruff is configured for py311, but the repo includes a .python-version set to 3.12 and the Makefile defaults/tooling appear to target 3.12+ in places. This mismatch can cause Ruff to flag/ignore syntax incompatibly. Align target-version with the project’s actual minimum supported Python (or explicitly document why Ruff is pinned to 3.11).

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[tschm]

@alihaskar once you have merged this into your master branch you have rhiza's Makefile system in place. You can try (from the command line or even better directly from Claude):

• make docs-coverage
• make test
• make fmt
• make typecheck
• make all

or just

• make

No changes in src or tests at this stage at all. To get an idea where this is heading checkout jebel-quant/jquantstats or cvxgrp/cvxcla or tschm/pyhrp

[tschm]

@alihaskar once you have merged this into your master branch you have rhiza's Makefile system in place. You can try (from the command line or even better directly from Claude):

• make docs-coverage
• make test
• make fmt
• make typecheck
• make all

or just

• make

No changes in src or tests at this stage at all. To get an idea where this is heading checkout jebel-quant/jquantstats or cvxgrp/cvxcla or tschm/pyhrp