Follow Python standard packaging guidelines

[jan-janssen]

Summary by CodeRabbit

• Chores
  • Updated project build configuration and continuous integration workflows to reflect project structure reorganization.

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

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request migrates the project package structure from a top-level layout to a src-layout. Path references across CI workflows and the build configuration are updated to reflect the new location of the package under a src/ directory, including updates to version file paths and build tool configurations.

Changes

Cohort / File(s)	Summary
CI Workflow Files .github/workflows/deploy.yml, .github/workflows/pipeline.yml	Updated file paths to reference the new src/pyiron_lammps/ location in git ignore rules and Black formatter configuration
Build Configuration pyproject.toml	Updated Hatch build configuration, version file paths, and coverage settings to use the new src/pyiron_lammps/ layout instead of top-level pyiron_lammps/

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Possibly related PRs

• Use hatchling rather than versioneer #239 — Directly overlaps with this PR's migration of package paths to src-layout and updates to CI workflow file paths alongside hatchling packaging migration.

Poem

🐰 Hop, hop, the package takes flight,
To src/ it moves, oh what a sight!
Workflows and configs all in a row,
New paths to follow, watch it grow! 📦✨

🚥 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 'Follow Python standard packaging guidelines' accurately reflects the main change: migrating the project to a src-layout structure, which is indeed a Python standard packaging guideline.
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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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 81.95%. Comparing base (202ec5d) to head (bee5111).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #292       +/-   ##
===========================================
- Coverage   92.75%   81.95%   -10.80%     
===========================================
  Files           8       10        +2     
  Lines         980     1125      +145     
===========================================
+ Hits          909      922       +13     
- Misses         71      203      +132     

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (1)

pyproject.toml (1)

74-76: Review the coverage configuration change.

The coverage configuration has changed from using omit to using source. Based on the AI summary, the previous configuration excluded pyiron_lammps/_version.py and tests/* from coverage reports. The new configuration only specifies the source but doesn't exclude these files.

Consider whether you want to preserve the exclusions for auto-generated files:

[tool.coverage.run]
source = ["pyiron_lammps"]
command_line = "-m unittest discover tests"
omit = ["src/pyiron_lammps/_version.py"]

Including auto-generated version files in coverage reports is typically not desired as they artificially lower coverage metrics.

📜 Review details

Configuration used: defaults

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 202ec5d and bee5111.

📒 Files selected for processing (14)

• .github/workflows/deploy.yml
• .github/workflows/pipeline.yml
• pyproject.toml
• src/pyiron_lammps/__init__.py
• src/pyiron_lammps/_version.py
• src/pyiron_lammps/compatibility/__init__.py
• src/pyiron_lammps/compatibility/calculate.py
• src/pyiron_lammps/compatibility/constraints.py
• src/pyiron_lammps/compatibility/file.py
• src/pyiron_lammps/compatibility/structure.py
• src/pyiron_lammps/output.py
• src/pyiron_lammps/potential.py
• src/pyiron_lammps/structure.py
• src/pyiron_lammps/units.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). (1)

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

🔇 Additional comments (8)

.github/workflows/pipeline.yml (2)

16-16: LGTM! Black path updated correctly for src-layout.

The Black source path has been correctly updated to reflect the new src-layout structure.

---

32-32: LGTM! Consistent path update.

The Black source path in the auto-fix job is correctly updated to match the new src-layout structure.

.github/workflows/deploy.yml (1)

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

The git ignore path correctly reflects the new location of the version file under the src-layout structure.

pyproject.toml (5)

52-55: LGTM! Build include path updated correctly.

The include path correctly specifies the package location under the src-layout structure.

---

57-58: LGTM! Version file path updated correctly.

The version file path correctly reflects its new location in the src-layout structure.

---

60-63: LGTM! Source distribution include path updated correctly.

The sdist target correctly includes the package from its new src-layout location.

---

70-72: LGTM! Version path updated correctly.

The version path correctly reflects the new src-layout structure, consistent with the VCS hook configuration.

---

65-68: The current configuration is correct. For Hatch projects using src-layout, the packages directive in [tool.hatch.build.targets.wheel] should include the src/ prefix. This is the documented and correct approach: packages = ["src/pyiron_lammps"] properly configures Hatch to package files from src/pyiron_lammps as the pyiron_lammps package in the wheel.

Likely an incorrect or invalid review comment.