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Follow Python standard packaging guidelines #389

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Merged
merged 2 commits into from
Oct 20, 2025
Merged

Follow Python standard packaging guidelines #389

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ef2a017
Follow Python standard packaging guidelines
jan-janssen Oct 20, 2025
d720293
Merge branch 'main' into refactor
jan-janssen Oct 20, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/deploy.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ jobs:
run: |
cp .ci_support/environment-old.yml environment.yml
python .ci_support/release.py; cat pyproject.toml
git update-index --assume-unchanged pyproject.toml pylammpsmpi/_version.py
git update-index --assume-unchanged pyproject.toml src/pylammpsmpi/_version.py
hatchling build -t sdist -t wheel
- name: Publish distribution 📦 to PyPI
uses: pypa/gh-action-pypi-publish@release/v1
4 changes: 2 additions & 2 deletions .github/workflows/pipeline.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
- uses: psf/black@stable
with:
options: "--check --diff"
src: ./${{ github.event.repository.name }}
src: ./src/${{ github.event.repository.name }}

black_fix: # in most cases pre-commit is faster
needs: [black]
Expand All @@ -29,7 +29,7 @@ jobs:
uses: psf/black@stable
with:
options: ""
src: "./${{ github.event.repository.name }}"
src: "./src/${{ github.event.repository.name }}"
- name: commit
run: |
git config --local user.email "pyiron@mpie.de"
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10 changes: 5 additions & 5 deletions pyproject.toml
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Expand Up @@ -48,7 +48,7 @@ include = [
]

[tool.hatch.build.hooks.vcs]
version-file = "pylammpsmpi/_version.py"
version-file = "src/pylammpsmpi/_version.py"

[tool.ruff]
exclude = [".ci_support", "docs", "notebooks", "setup.py", "_version.py"]
Expand Down Expand Up @@ -91,18 +91,18 @@ ignore = [

[tool.hatch.build.targets.sdist]
include = [
"pylammpsmpi"
"src/pylammpsmpi"
]

[tool.hatch.build.targets.wheel]
packages = [
"pylammpsmpi"
"src/pylammpsmpi"
]

[tool.hatch.version]
source = "vcs"
path = "pylammpsmpi/_version.py"
path = "src/pylammpsmpi/_version.py"

[tool.coverage.run]
omit = ["pylammpsmpi/_version.py", "tests/*"]
source = ["pylammpsmpi"]
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⚠️ Potential issue | 🔴 Critical

Coverage source path not updated to src-layout.

Line 106 still references the old package location ["pylammpsmpi"] instead of ["src/pylammpsmpi"]. This will cause coverage collection to fail after migration to the src-layout structure, as it won't find source files in their new location.

Apply this fix:

 [tool.coverage.run]
-source = ["pylammpsmpi"]
+source = ["src/pylammpsmpi"]
 command_line = "-m unittest discover tests"
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
source = ["pylammpsmpi"]
[tool.coverage.run]
source = ["src/pylammpsmpi"]
command_line = "-m unittest discover tests"
🤖 Prompt for AI Agents 
In pyproject.toml around line 106, the coverage source path still points to the
old package root ["pylammpsmpi"] but the repository uses src-layout; update the
path to ["src/pylammpsmpi"] so coverage tools can find sources under the src/
directory and regenerate/verify coverage by running the coverage collection/test
command after the change.

command_line = "-m unittest discover tests"
0 pylammpsmpi/__init__.py → src/pylammpsmpi/__init__.py
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0 pylammpsmpi/_version.py → src/pylammpsmpi/_version.py
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0 pylammpsmpi/mpi/__init__.py → src/pylammpsmpi/mpi/__init__.py
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0 pylammpsmpi/mpi/lmpmpi.py → src/pylammpsmpi/mpi/lmpmpi.py
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0 pylammpsmpi/wrapper/__init__.py → src/pylammpsmpi/wrapper/__init__.py
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0 pylammpsmpi/wrapper/ase.py → src/pylammpsmpi/wrapper/ase.py
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0 pylammpsmpi/wrapper/base.py → src/pylammpsmpi/wrapper/base.py
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0 pylammpsmpi/wrapper/concurrent.py → src/pylammpsmpi/wrapper/concurrent.py
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0 pylammpsmpi/wrapper/extended.py → src/pylammpsmpi/wrapper/extended.py
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