Migrated to pyproject.toml and ruff.

.github/workflows/actions.yml

@@ -14,17 +14,18 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - name: dependencies
+    - name: install
+      if: always()
       run: |
-        cd ${GITHUB_WORKSPACE}/scripts && ./dependencies.sh
-    - name: lint
+        cd ${GITHUB_WORKSPACE}/scripts && ./install.sh
+    - name: format
       if: always()
       run: |
-        cd ${GITHUB_WORKSPACE}/scripts && ./lint.sh
-    - name: install
+        cd ${GITHUB_WORKSPACE}/scripts && ./format.sh
+    - name: lint
       if: always()
       run: |
-        cd ${GITHUB_WORKSPACE}/scripts && ./install.sh
+        cd ${GITHUB_WORKSPACE}/scripts && ./lint.sh
     - name: test
       if: always()
       run: |

README.md

@@ -2,7 +2,7 @@
 
 ![Build status](https://github.com/SINGROUP/dscribe/actions/workflows/actions.yml/badge.svg)
 [![Coverage Status](https://coveralls.io/repos/github/SINGROUP/dscribe/badge.svg?branch=master)](https://coveralls.io/github/SINGROUP/dscribe?branch=master)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 DScribe is a Python package for transforming atomic structures into fixed-size
 numerical fingerprints. These fingerprints are often called "descriptors" and

dscribe/__init__.py

@@ -13,4 +13,5 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 from dscribe.core.system import System

dscribe/core/__init__.py

@@ -13,5 +13,6 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 from dscribe.core.system import System
 from dscribe.core.lattice import Lattice

dscribe/core/lattice.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 
 

dscribe/core/system.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 from ase import Atoms
 import ase.geometry
 import numpy as np

dscribe/descriptors/__init__.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 from dscribe.descriptors.acsf import ACSF
 from dscribe.descriptors.mbtr import MBTR
 from dscribe.descriptors.valleoganov import ValleOganov

dscribe/descriptors/acsf.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 from ase import Atoms
 

dscribe/descriptors/coulombmatrix.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 from ase import Atoms
 import ase.geometry.cell

dscribe/descriptors/descriptor.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 from abc import ABC, abstractmethod
 
 import numpy as np

dscribe/descriptors/descriptorglobal.py

@@ -10,6 +10,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 import sparse as sp
 from ase import Atoms

dscribe/descriptors/descriptorlocal.py

@@ -10,6 +10,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 from ase import Atoms
 

dscribe/descriptors/descriptormatrix.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 from numpy.random import RandomState
 

dscribe/descriptors/ewaldsummatrix.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import math
 
 import numpy as np

dscribe/descriptors/lmbtr.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import sys
 import math
 

dscribe/descriptors/mbtr.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import sys
 import math
 import numpy as np

dscribe/descriptors/sinematrix.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 
 from ase import Atoms

dscribe/descriptors/soap.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 from warnings import warn
 
 import numpy as np

dscribe/kernels/__init__.py

@@ -13,5 +13,6 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 from dscribe.kernels.averagekernel import AverageKernel
 from dscribe.kernels.rematchkernel import REMatchKernel

dscribe/kernels/averagekernel.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 from dscribe.kernels.localsimilaritykernel import LocalSimilarityKernel
 

dscribe/kernels/localsimilaritykernel.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 from abc import ABC, abstractmethod
 
 import numpy as np

dscribe/kernels/rematchkernel.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 from dscribe.kernels.localsimilaritykernel import LocalSimilarityKernel
 

dscribe/utils/dimensionality.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 
 

dscribe/utils/geometry.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 
 import scipy.sparse

dscribe/utils/species.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 import numpy as np
 import ase.data
 

dscribe/utils/stats.py

@@ -13,6 +13,7 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
+
 from ase import Atoms
 from dscribe.core.system import System
 import numpy as np

pyproject.toml

@@ -0,0 +1,105 @@
+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel",
+    "pybind11>=2.4"
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = 'dscribe'
+version = '2.1.1'
+description = 'A Python package for creating feature transformations in applications of machine learning to materials science.'
+readme = "README.md"
+license = { file = "LICENSE" }
+requires-python = ">=3.8"
+dependencies = [
+    "numpy",
+    "scipy",
+    "ase>=3.19.0",
+    "scikit-learn",
+    "joblib>=1.0.0",
+    "sparse",
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Physics",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: MacOS",
+    "Operating System :: Unix",
+    "Programming Language :: C",
+    "Programming Language :: C++",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3 :: Only",
+]
+keywords = ['descriptor', 'machine learning', 'atomistic structure', 'materials science']
+
+[project.urls]
+Documentation = 'https://singroup.github.io/dscribe/latest/'
+Source = "https://singroup.github.io/dscribe"
+
+[project.optional-dependencies]
+dev = [
+    "coverage",
+    "ruff",
+    "coveralls",
+    "pymatgen",
+    "sphinx",
+    "sphinx_rtd_theme",
+    "sphinxcontrib-bibtex",
+    "pytest",
+]
+
+[tool.setuptools.packages.find]
+include = ["dscribe*"]
+exclude = ["tests*"]
+
+[tool.ruff]
+include = ["dscribe/*.py", "tests/*.py"]
+
+# Same as Black
+line-length = 88
+indent-width = 4
+
+[tool.ruff.lint]
+select = [
+    "E", # pycodestyle
+    "W", # pycodestyle
+    "PL", # pylint
+]
+ignore = [
+    "E501", # Line too long ({width} > {limit} characters)
+    "E701", # Multiple statements on one line (colon)
+    "E731", # Do not assign a lambda expression, use a def
+    "E402", # Module level import not at top of file
+    "E741", # Ambiguous variable name
+    "W605", # Invalid escape sequence
+    "PLR0911", # Too many return statements
+    "PLR0912", # Too many branches
+    "PLR0913", # Too many arguments in function definition
+    "PLR0915", # Too many statements
+    "PLR2004", # Magic value used instead of constant
+    "PLW0603", # Using the global statement
+    "PLW2901", # redefined-loop-name
+    "PLR1714", # consider-using-in
+    "PLR5501", # else-if-used
+]
+fixable = ["ALL"]
+
+[tool.ruff.format]
+# indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"

scripts/format.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+cd ..
+ruff format --check
+
+

scripts/install.sh

@@ -1,3 +1,7 @@
+# Update pip and setuptools
+pip install pip --upgrade
+pip install setuptools --upgrade
+
 # Make a source distribution
 cd ..
 python setup.py sdist
@@ -8,4 +12,4 @@ version=`python setup.py --version`
 cd dist
 tar xvzf dscribe-$version.tar.gz
 cd dscribe-$version
-pip install .
+pip install .[dev]

scripts/lint.sh

@@ -1,3 +1,4 @@
 #!/usr/bin/env bash
 cd ..
-black --check dscribe tests
+ruff check
+