Expand linting/styling QC

[jonasfreimuth]

For my intended coming changes addressing #27, I wanted to make sure tools for styling/linting md and toml files are available.

Summary by CodeRabbit

• Documentation

  • README updated with an additional descriptive line about the catalog.

• Chores

  • Reorganized project configuration to centralize style and lint tooling.
  • Consolidated build task formatting and simplified quality-check command mappings.
  • Added dedicated style and lint task groups covering Python, Markdown, and TOML.

[Copilot]

Pull request overview

This PR expands the project’s Pixi-based quality-control tooling to support linting/formatting not only Python, but also Markdown and TOML—preparing the repo for upcoming documentation work related to #27.

Changes:

• Refactors qc / apply-qc tasks and introduces a style feature with dedicated lint/format tasks for Python, Markdown, and TOML.
• Adds a separate Pixi environment (style) to install optional formatting/linting tools.
• Updates the lockfile accordingly and applies a minor README formatting tweak.

Reviewed changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 3 comments.

File	Description
pixi.toml	Adds a style feature + environment and new lint/style task graph; updates top-level QC tasks.
pixi.lock	Captures the new style environment resolution and dependency set.
README.md	Adds a blank line after the title.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: b46400da-7c35-45a1-b9cb-6e2932aeee65

📥 Commits

Reviewing files that changed from the base of the PR and between 2345969 and e6a8a10.

⛔ Files ignored due to path filters (1)

• pixi.lock is excluded by !**/*.lock

📒 Files selected for processing (2)

• README.md
• pixi.toml

📝 Walkthrough

Walkthrough

Updated README with a one-line descriptive subtitle; reworked pixi.toml to move style tooling and tasks into a feature-scoped configuration, introducing feature-based dependencies, grouped style/lint tasks, and a style environment.

Changes

Cohort / File(s)	Summary
Documentation Update README.md	Added one-line subtitle: "An automatically updated catalog of Snakemake plugins and their documentation".
Build / CI Configuration pixi.toml	Removed public qc/apply-qc task entries; moved ruff out of top-level [dependencies] into a new [feature.style.dependencies] and added mdformat, mdformat-gfm, fd-find, tombi; introduced [feature.style.tasks] with _style-python, _style-md, _style-toml; added _lint-* and _style-* task entries and composite style and lint tasks that depend on them; added [environments] style = { features = ["style"], no-default-feature = true }; minor formatting change to tasks.build-single value.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Expand linting/styling QC' accurately describes the main changes in the PR, which involve adding linting and styling tools/tasks to the QC configuration.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

pixi.toml (1)

29-34: Verify ruff version and consider pinning mdformat versions.

1. ruff version >=0.12.11,<0.13: This version range seems unusually high. Please verify this is the intended version.

2. Unpinned mdformat dependencies: Using "*" for mdformat and mdformat-gfm may lead to reproducibility issues if breaking changes are introduced in future versions. Consider adding version constraints similar to other dependencies.

,

What is the latest version of ruff Python linter?

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@pixi.toml` around lines 29 - 34, Verify the ruff version range and pin the
mdformat packages: confirm the intended ruff constraint (the current key "ruff"
should be validated against the latest ruff release) and adjust it if it's too
restrictive or incorrect (e.g., set a realistic upper bound like <0.13 only if
you verified compatibility), and replace the wildcard "*" for "mdformat" and
"mdformat-gfm" with explicit version constraints (e.g., lock to a tested
minor/patch range) to ensure reproducible builds; update the entries for the
keys ruff, mdformat, and mdformat-gfm accordingly after checking the latest ruff
release and the compatible mdformat versions.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@pixi.toml`:
- Around line 11-12: The qc and apply-qc tasks reference target tasks (lint and
style) that are defined under feature.style.tasks and thus aren't available in
the default environment because no-default-feature = true; fix this by moving
the lint and style task definitions from [feature.style.tasks] into the global
[tasks] section so qc and apply-qc can delegate to them without requiring
--environment style, update any feature-specific settings accordingly, and keep
qc and apply-qc entries as-is to preserve CI usage of pixi run qc.

---

Nitpick comments:
In `@pixi.toml`:
- Around line 29-34: Verify the ruff version range and pin the mdformat
packages: confirm the intended ruff constraint (the current key "ruff" should be
validated against the latest ruff release) and adjust it if it's too restrictive
or incorrect (e.g., set a realistic upper bound like <0.13 only if you verified
compatibility), and replace the wildcard "*" for "mdformat" and "mdformat-gfm"
with explicit version constraints (e.g., lock to a tested minor/patch range) to
ensure reproducible builds; update the entries for the keys ruff, mdformat, and
mdformat-gfm accordingly after checking the latest ruff release and the
compatible mdformat versions.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 01178378-d14e-4134-b392-ec269ffaa977

📥 Commits

Reviewing files that changed from the base of the PR and between 93de4d9 and 5eee92e.

⛔ Files ignored due to path filters (1)

• pixi.lock is excluded by !**/*.lock

📒 Files selected for processing (2)

• README.md
• pixi.toml

[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@pixi.toml`:
- Around line 49-53: The pixi task aliases currently use string values ("qc" =
"lint" and "apply-qc" = "style") which Pixi treats as shell commands; change
these keys to use depends-on task references instead so they point to the
existing tasks "lint" and "style" (i.e., replace the string assignments for qc
and apply-qc with depends-on references that list the target task names) so
running the alias executes the referenced task rather than a shell command.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 1557496e-3971-4842-ae15-a1fd7c9c3415

📥 Commits

Reviewing files that changed from the base of the PR and between 5eee92e and 2345969.

⛔ Files ignored due to path filters (1)

• pixi.lock is excluded by !**/*.lock

📒 Files selected for processing (1)

• pixi.toml

[johanneskoester]

Cool!