Follow Python standard packaging guidelines

[jan-janssen]

Summary by CodeRabbit

• Chores
  • Updated project build configuration and CI/CD pipelines to align with source directory restructuring.

[coderabbitai]

Walkthrough

The repository migrates from a root-level package structure to a src-layout by updating all path references in CI/CD workflows and packaging configuration to point to src/pysqa instead of pysqa.

Changes

Cohort / File(s)	Summary
GitHub Actions Workflows .github/workflows/deploy.yml, .github/workflows/pipeline.yml	Updated path references to reflect src-layout: changed pysqa/_version.py to src/pysqa/_version.py in deploy workflow; prepended ./src/ to black and mypy paths in pipeline workflow
Packaging Configuration pyproject.toml	Updated Hatch build configuration, VCS hooks, and coverage settings to reference src/pysqa instead of pysqa; modified coverage configuration from omit to source tracking

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

The changes follow a consistent, repetitive pattern of path updates across multiple files. No complex logic or control flow modifications are present—verification involves ensuring all occurrences of the package path were uniformly updated and no references were missed.

Possibly related PRs

• pyiron/pysqa#386: Modifies .github/workflows/pipeline.yml with workflow path reference updates
• pyiron/pysqa#447: Updates coverage configuration in both pyproject.toml and pipeline workflows

Poem

🐰 Hopping through paths, we reorganize,
src/ now holds our treasures, neat and wise,
From root to folder, a cleaner sight,
Our warren's structure, perfectly right! ✨

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title Check	✅ Passed	The pull request title "Follow Python standard packaging guidelines" is directly related to the changeset's primary objective. The modifications across all three files consistently refactor the package structure to move from a root-level layout to a src-layout (moving from pysqa/ to src/pysqa/), which is indeed a standard Python packaging best practice recommended by the Python Packaging Authority. While the title is somewhat broad and doesn't explicitly mention the specific "src-layout" structure change, it accurately captures the purpose of the refactoring and refers to a real and central aspect of the changeset.
Docstring Coverage	✅ Passed	No functions found in the changes. Docstring coverage check skipped.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch refactor

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.19%. Comparing base (25c4219) to head (cc1b600).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #469      +/-   ##
==========================================
- Coverage   92.46%   92.19%   -0.27%     
==========================================
  Files          17       19       +2     
  Lines        1008     1025      +17     
==========================================
+ Hits          932      945      +13     
- Misses         76       80       +4     

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (1)

.github/workflows/pipeline.yml (1)

56-58: Align mypy path format with Black for consistency.

The mypy invocation at line 56 uses src/${{ github.event.repository.name }} while the Black steps use ./src/${{ github.event.repository.name }}. Both formats resolve identically in shell, but aligning them to ./src/... would improve consistency and explicitness across the workflow.

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 72c68ca and cc1b600.

📒 Files selected for processing (3)

• .github/workflows/deploy.yml (1 hunks)
• .github/workflows/pipeline.yml (3 hunks)
• pyproject.toml (1 hunks)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (2)

• GitHub Check: unittest_matrix (windows-latest, 3.14)
• GitHub Check: unittest_slurm

🔇 Additional comments (6)

.github/workflows/pipeline.yml (1)

14-16: Black src paths correctly updated for src-layout.

Both Black steps properly reference ./src/${{ github.event.repository.name }} to check and format code in the new source layout.

Also applies to: 28-32

.github/workflows/deploy.yml (1)

34-34: Version file path correctly updated for src-layout.

The git update-index exclusion properly references src/pysqa/_version.py, aligning with the relocated version file in the packaging configuration.

pyproject.toml (4)

96-99: Hatch build include path correctly updated for src-layout.

The include directive now references src/pysqa as expected.

---

101-102: VCS version-file path correctly updated.

The version-file directive now references src/pysqa/_version.py as expected.

---

104-112: Source and wheel package paths correctly updated for src-layout.

Both sdist and wheel configurations now properly reference src/pysqa.

---

114-120: ****

The coverage source configuration at line 119 is actually correct and follows best practices for src-layout projects. According to coverage documentation, using the package name is often best with src-layout because coverage will only consider importable modules. The current configuration of source = ["pysqa"] appropriately references the package name rather than the directory path, which is the recommended approach. No changes are needed.

Likely an incorrect or invalid review comment.