Follow Python standard packaging guidelines

[jan-janssen]

Summary by CodeRabbit

Release Notes

• Chores
  • Updated build and release pipeline configuration to align with project structure.
  • Modified packaging and versioning settings in build configuration.

_{✏️ Tip: You can customize this high-level summary in your review settings.}

[coderabbitai]

📝 Walkthrough

Walkthrough

The changes reorganize the project to adopt a src/ directory structure. Updates include modifying workflow files to reference the new src/structuretoolkit path, updating pyproject.toml to point version and package files to the src/ layout, and adjusting git assume-unchanged to include the new version file path.

Changes

Cohort / File(s)

Summary

Project Layout Migration to src/ Directory .github/workflows/deploy.yml, .github/workflows/pipeline.yml, pyproject.toml

Migrated project from flat structure to src/ directory layout. Updated workflow paths from ./${{ github.event.repository.name }} to ./src/${{ github.event.repository.name }} in black formatter and pipeline steps. Updated pyproject.toml version source path from structuretoolkit/_version.py to src/structuretoolkit/_version.py across hatch vcs, sdist, and wheel configurations. Updated deploy workflow to assume-unchanged on the versioned file at new location. Adjusted coverage configuration source reference.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Possibly related PRs

• Switch from versioneer to hatchling #379: Updates packaging and workflow files to reference the new src/structuretoolkit structure, including version file path and assume-unchanged git configuration.

Poem

🐰 Hop hop, the code now finds its home,
In src/ directories to roam,
Version files tucked away just right,
Workflows updated, bright with light! ✨
Structure perfect, what a sight!

🚥 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 accurately describes the main purpose of the pull request, which reorganizes the project structure to follow Python's src-layout standard packaging convention.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

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📜 Recent review details

Configuration used: defaults

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 960b95a and b01c12e.

📒 Files selected for processing (28)

• .github/workflows/deploy.yml
• .github/workflows/pipeline.yml
• pyproject.toml
• src/structuretoolkit/__init__.py
• src/structuretoolkit/_version.py
• src/structuretoolkit/analyse/__init__.py
• src/structuretoolkit/analyse/distance.py
• src/structuretoolkit/analyse/dscribe.py
• src/structuretoolkit/analyse/neighbors.py
• src/structuretoolkit/analyse/phonopy.py
• src/structuretoolkit/analyse/pyscal.py
• src/structuretoolkit/analyse/snap.py
• src/structuretoolkit/analyse/spatial.py
• src/structuretoolkit/analyse/strain.py
• src/structuretoolkit/analyse/symmetry.py
• src/structuretoolkit/build/__init__.py
• src/structuretoolkit/build/aimsgb.py
• src/structuretoolkit/build/compound.py
• src/structuretoolkit/build/mesh.py
• src/structuretoolkit/build/sqs.py
• src/structuretoolkit/build/surface.py
• src/structuretoolkit/common/__init__.py
• src/structuretoolkit/common/error.py
• src/structuretoolkit/common/helper.py
• src/structuretoolkit/common/phonopy.py
• src/structuretoolkit/common/pymatgen.py
• src/structuretoolkit/common/pyscal.py
• src/structuretoolkit/visualize.py

⏰ 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). (4)

• GitHub Check: codecov/patch
• GitHub Check: unittest_matrix (macos-latest, 3.13, osx-64-py-3-13)
• GitHub Check: unittest_matrix (windows-latest, 3.13, win-64-py-3-13)
• GitHub Check: unittest_old

🔇 Additional comments (5)

.github/workflows/pipeline.yml (1)

16-16: LGTM! Black formatter targets updated correctly.

The black formatter paths have been properly updated to target the new src/ directory structure. Both the check and fix jobs now correctly reference ./src/${{ github.event.repository.name }}.

Also applies to: 32-32

.github/workflows/deploy.yml (1)

35-35: LGTM! Version file path updated correctly.

The git assume-unchanged command now correctly includes the version file at its new location src/structuretoolkit/_version.py, which aligns with the src/ layout migration.

pyproject.toml (3)

109-109: LGTM! Version file path updated correctly.

The hatch VCS hook now correctly points to the version file at src/structuretoolkit/_version.py.

---

123-123: LGTM! Version path updated correctly.

The hatch version source path now correctly points to src/structuretoolkit/_version.py.

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126-126: LGTM! Coverage source configuration is correct.

The coverage source correctly specifies "structuretoolkit" as the package name to track. This is appropriate since the source parameter refers to the package import name, not the filesystem path, and the package will be imported as structuretoolkit regardless of the src/ layout.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.91%. Comparing base (63b3ec8) to head (b01c12e).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #445      +/-   ##
==========================================
+ Coverage   82.78%   82.91%   +0.12%     
==========================================
  Files          24       25       +1     
  Lines        1807     1820      +13     
==========================================
+ Hits         1496     1509      +13     
  Misses        311      311              

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