From b01c12e7b30f50635a09f05c7374fddc4e9d6a58 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= Date: Thu, 8 Jan 2026 15:18:15 +0100 Subject: [PATCH] Follow Python standard packaging guidelines --- .github/workflows/deploy.yml | 2 +- .github/workflows/pipeline.yml | 4 ++-- pyproject.toml | 10 +++++----- {structuretoolkit => src/structuretoolkit}/__init__.py | 0 {structuretoolkit => src/structuretoolkit}/_version.py | 0 .../structuretoolkit}/analyse/__init__.py | 0 .../structuretoolkit}/analyse/distance.py | 0 .../structuretoolkit}/analyse/dscribe.py | 0 .../structuretoolkit}/analyse/neighbors.py | 0 .../structuretoolkit}/analyse/phonopy.py | 0 .../structuretoolkit}/analyse/pyscal.py | 0 .../structuretoolkit}/analyse/snap.py | 0 .../structuretoolkit}/analyse/spatial.py | 0 .../structuretoolkit}/analyse/strain.py | 0 .../structuretoolkit}/analyse/symmetry.py | 0 .../structuretoolkit}/build/__init__.py | 0 .../structuretoolkit}/build/aimsgb.py | 0 .../structuretoolkit}/build/compound.py | 0 .../structuretoolkit}/build/mesh.py | 0 .../structuretoolkit}/build/sqs.py | 0 .../structuretoolkit}/build/surface.py | 0 .../structuretoolkit}/common/__init__.py | 0 .../structuretoolkit}/common/error.py | 0 .../structuretoolkit}/common/helper.py | 0 .../structuretoolkit}/common/phonopy.py | 0 .../structuretoolkit}/common/pymatgen.py | 0 .../structuretoolkit}/common/pyscal.py | 0 .../structuretoolkit}/visualize.py | 0 28 files changed, 8 insertions(+), 8 deletions(-) rename {structuretoolkit => src/structuretoolkit}/__init__.py (100%) rename {structuretoolkit => src/structuretoolkit}/_version.py (100%) rename {structuretoolkit => src/structuretoolkit}/analyse/__init__.py (100%) rename {structuretoolkit => src/structuretoolkit}/analyse/distance.py (100%) rename {structuretoolkit => src/structuretoolkit}/analyse/dscribe.py (100%) rename {structuretoolkit => src/structuretoolkit}/analyse/neighbors.py (100%) rename {structuretoolkit => src/structuretoolkit}/analyse/phonopy.py (100%) rename {structuretoolkit => src/structuretoolkit}/analyse/pyscal.py (100%) rename {structuretoolkit => src/structuretoolkit}/analyse/snap.py (100%) rename {structuretoolkit => src/structuretoolkit}/analyse/spatial.py (100%) rename {structuretoolkit => src/structuretoolkit}/analyse/strain.py (100%) rename {structuretoolkit => src/structuretoolkit}/analyse/symmetry.py (100%) rename {structuretoolkit => src/structuretoolkit}/build/__init__.py (100%) rename {structuretoolkit => src/structuretoolkit}/build/aimsgb.py (100%) rename {structuretoolkit => src/structuretoolkit}/build/compound.py (100%) rename {structuretoolkit => src/structuretoolkit}/build/mesh.py (100%) rename {structuretoolkit => src/structuretoolkit}/build/sqs.py (100%) rename {structuretoolkit => src/structuretoolkit}/build/surface.py (100%) rename {structuretoolkit => src/structuretoolkit}/common/__init__.py (100%) rename {structuretoolkit => src/structuretoolkit}/common/error.py (100%) rename {structuretoolkit => src/structuretoolkit}/common/helper.py (100%) rename {structuretoolkit => src/structuretoolkit}/common/phonopy.py (100%) rename {structuretoolkit => src/structuretoolkit}/common/pymatgen.py (100%) rename {structuretoolkit => src/structuretoolkit}/common/pyscal.py (100%) rename {structuretoolkit => src/structuretoolkit}/visualize.py (100%) diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index f132c4553..50964b64c 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -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 structuretoolkit/_version.py + git update-index --assume-unchanged pyproject.toml src/structuretoolkit/_version.py hatchling build -t sdist -t wheel - name: Publish distribution 📦 to PyPI uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/pipeline.yml b/.github/workflows/pipeline.yml index 2a1fc7208..fd5b3e3ac 100644 --- a/.github/workflows/pipeline.yml +++ b/.github/workflows/pipeline.yml @@ -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] @@ -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" diff --git a/pyproject.toml b/pyproject.toml index fe9cc604f..27b1e9bfb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -106,22 +106,22 @@ ignore = [ ] [tool.hatch.build.hooks.vcs] -version-file = "structuretoolkit/_version.py" +version-file = "src/structuretoolkit/_version.py" [tool.hatch.build.targets.sdist] include = [ - "structuretoolkit" + "src/structuretoolkit" ] [tool.hatch.build.targets.wheel] packages = [ - "structuretoolkit" + "src/structuretoolkit" ] [tool.hatch.version] source = "vcs" -path = "structuretoolkit/_version.py" +path = "src/structuretoolkit/_version.py" [tool.coverage.run] -omit = ["structuretoolkit/_version.py", "tests/*"] +source = ["structuretoolkit"] command_line = "-m unittest discover tests" diff --git a/structuretoolkit/__init__.py b/src/structuretoolkit/__init__.py similarity index 100% rename from structuretoolkit/__init__.py rename to src/structuretoolkit/__init__.py diff --git a/structuretoolkit/_version.py b/src/structuretoolkit/_version.py similarity index 100% rename from structuretoolkit/_version.py rename to src/structuretoolkit/_version.py diff --git a/structuretoolkit/analyse/__init__.py b/src/structuretoolkit/analyse/__init__.py similarity index 100% rename from structuretoolkit/analyse/__init__.py rename to src/structuretoolkit/analyse/__init__.py diff --git a/structuretoolkit/analyse/distance.py b/src/structuretoolkit/analyse/distance.py similarity index 100% rename from structuretoolkit/analyse/distance.py rename to src/structuretoolkit/analyse/distance.py diff --git a/structuretoolkit/analyse/dscribe.py b/src/structuretoolkit/analyse/dscribe.py similarity index 100% rename from structuretoolkit/analyse/dscribe.py rename to src/structuretoolkit/analyse/dscribe.py diff --git a/structuretoolkit/analyse/neighbors.py b/src/structuretoolkit/analyse/neighbors.py similarity index 100% rename from structuretoolkit/analyse/neighbors.py rename to src/structuretoolkit/analyse/neighbors.py diff --git a/structuretoolkit/analyse/phonopy.py b/src/structuretoolkit/analyse/phonopy.py similarity index 100% rename from structuretoolkit/analyse/phonopy.py rename to src/structuretoolkit/analyse/phonopy.py diff --git a/structuretoolkit/analyse/pyscal.py b/src/structuretoolkit/analyse/pyscal.py similarity index 100% rename from structuretoolkit/analyse/pyscal.py rename to src/structuretoolkit/analyse/pyscal.py diff --git a/structuretoolkit/analyse/snap.py b/src/structuretoolkit/analyse/snap.py similarity index 100% rename from structuretoolkit/analyse/snap.py rename to src/structuretoolkit/analyse/snap.py diff --git a/structuretoolkit/analyse/spatial.py b/src/structuretoolkit/analyse/spatial.py similarity index 100% rename from structuretoolkit/analyse/spatial.py rename to src/structuretoolkit/analyse/spatial.py diff --git a/structuretoolkit/analyse/strain.py b/src/structuretoolkit/analyse/strain.py similarity index 100% rename from structuretoolkit/analyse/strain.py rename to src/structuretoolkit/analyse/strain.py diff --git a/structuretoolkit/analyse/symmetry.py b/src/structuretoolkit/analyse/symmetry.py similarity index 100% rename from structuretoolkit/analyse/symmetry.py rename to src/structuretoolkit/analyse/symmetry.py diff --git a/structuretoolkit/build/__init__.py b/src/structuretoolkit/build/__init__.py similarity index 100% rename from structuretoolkit/build/__init__.py rename to src/structuretoolkit/build/__init__.py diff --git a/structuretoolkit/build/aimsgb.py b/src/structuretoolkit/build/aimsgb.py similarity index 100% rename from structuretoolkit/build/aimsgb.py rename to src/structuretoolkit/build/aimsgb.py diff --git a/structuretoolkit/build/compound.py b/src/structuretoolkit/build/compound.py similarity index 100% rename from structuretoolkit/build/compound.py rename to src/structuretoolkit/build/compound.py diff --git a/structuretoolkit/build/mesh.py b/src/structuretoolkit/build/mesh.py similarity index 100% rename from structuretoolkit/build/mesh.py rename to src/structuretoolkit/build/mesh.py diff --git a/structuretoolkit/build/sqs.py b/src/structuretoolkit/build/sqs.py similarity index 100% rename from structuretoolkit/build/sqs.py rename to src/structuretoolkit/build/sqs.py diff --git a/structuretoolkit/build/surface.py b/src/structuretoolkit/build/surface.py similarity index 100% rename from structuretoolkit/build/surface.py rename to src/structuretoolkit/build/surface.py diff --git a/structuretoolkit/common/__init__.py b/src/structuretoolkit/common/__init__.py similarity index 100% rename from structuretoolkit/common/__init__.py rename to src/structuretoolkit/common/__init__.py diff --git a/structuretoolkit/common/error.py b/src/structuretoolkit/common/error.py similarity index 100% rename from structuretoolkit/common/error.py rename to src/structuretoolkit/common/error.py diff --git a/structuretoolkit/common/helper.py b/src/structuretoolkit/common/helper.py similarity index 100% rename from structuretoolkit/common/helper.py rename to src/structuretoolkit/common/helper.py diff --git a/structuretoolkit/common/phonopy.py b/src/structuretoolkit/common/phonopy.py similarity index 100% rename from structuretoolkit/common/phonopy.py rename to src/structuretoolkit/common/phonopy.py diff --git a/structuretoolkit/common/pymatgen.py b/src/structuretoolkit/common/pymatgen.py similarity index 100% rename from structuretoolkit/common/pymatgen.py rename to src/structuretoolkit/common/pymatgen.py diff --git a/structuretoolkit/common/pyscal.py b/src/structuretoolkit/common/pyscal.py similarity index 100% rename from structuretoolkit/common/pyscal.py rename to src/structuretoolkit/common/pyscal.py diff --git a/structuretoolkit/visualize.py b/src/structuretoolkit/visualize.py similarity index 100% rename from structuretoolkit/visualize.py rename to src/structuretoolkit/visualize.py