Migrate to pyproject.toml and ruff (#31)

.pre-commit-config.yaml

@@ -4,29 +4,18 @@ repos:
     hooks:
       - id: absolufy-imports
         name: absolufy-imports
-  - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
-        language_version: python3
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
-    hooks:
-      - id: pyupgrade
-        args:
-          - --py38-plus
   - repo: https://github.com/psf/black
     rev: 23.12.1
     hooks:
       - id: black
         language_version: python3
         args:
           - --target-version=py38
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.14
     hooks:
-      - id: flake8
-        language_version: python3
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.8.0
     hooks:

HOW_TO_RELEASE

@@ -13,32 +13,31 @@ Time required: about an hour.
       git commit -a -m 'Release v0.X.Y'
  5. Tag the release:
       git tag -a v0.X.Y -m 'v0.X.Y'
- 6. Build source for pypi:
-      python setup.py sdist
- 7. Use twine to register and upload the release on pypi. Be careful, you can't
-    take this back!
-      twine upload dist/xarray_extras-0.X.Y*
-    You will need to be listed as a package owner at
-    https://pypi.python.org/pypi/xarray_extras for this to work.
- 8. Push your changes to main:
+ 6. Push your changes to main:
       git push origin main
       git push origin --tags
- 9. Update the stable branch (used by ReadTheDocs) and switch back to main:
+ 7. Update the stable branch (used by ReadTheDocs) and switch back to main:
       git checkout stable
       git rebase main
       git push origin stable
       git checkout main
     It's OK to force push to 'stable' if necessary.
     We also update the stable branch with `git cherrypick` for documentation
     only fixes that apply the current released version.
-10. Add a section for the next release (v.X.(Y+1)) to doc/whats-new.rst.
-11. Commit your changes and push to main again:
+ 8. Add a section for the next release (v.X.(Y+1)) to doc/whats-new.rst.
+ 9. Commit your changes and push to main again:
       git commit -a -m 'Revert to dev version'
       git push origin main
     You're done pushing to main!
-12. Issue the release on GitHub. Open https://github.com/crusaderky/xarray_extras/releases;
+10. Issue the release on GitHub. Open https://github.com/crusaderky/xarray_extras/releases;
     the new release should have automatically appeared. Otherwise, click on
     "Draft a new release" and paste in the latest from whats-new.rst.
+11. Download the .tar.gz package for the release
+12. Use twine to register and upload the release on pypi. Be careful, you can't
+    take this back!
+      twine upload xarray_extras-*.tar.gz
+    You will need to be listed as a package owner at
+    https://pypi.python.org/pypi/xarray_extras for this to work.
 13. Update the docs. Login to https://readthedocs.org/projects/xarray_extras/versions/
     and switch your new release tag (at the bottom) from "Inactive" to "Active".
     It should now build automatically.

doc/develop.rst

@@ -59,9 +59,8 @@ Test using ``py.test``:
 Code Formatting
 ---------------
 
-xarray_extras uses several code linters (flake8, black, isort, pyupgrade, mypy),
-which are enforced by CI. Developers should run them locally before they submit a PR,
-through the single command
+xarray_extras uses several code linters (black, ruff, mypy), which are enforced by CI.
+Developers should run them locally before they submit a PR, through the single command
 
 .. code-block:: bash
 

doc/whats-new.rst

@@ -24,6 +24,8 @@ v0.6.0 (Unreleased)
 - Added support for Python 3.10 and 3.11
 - Added support for recent versions of Pandas (tested up to 2.2) and xarray
 - Added support for :cls:`pathlib.Path` in function arguments
+- Migrated from setup.cfg to pyproject.toml
+- Migrated from flake8+isort+pyupgrade to ruff
 
 .. _whats-new.0.5.0:
 

pyproject.toml

@@ -0,0 +1,118 @@
+[project]
+name = "xarray_extras"
+authors = [{name = "Guido Imperiale", email = "[email protected]"}]
+license = {text = "Apache"}
+description = "Advanced / experimental algorithms for xarray"
+keywords = ["xarray"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+requires-python = ">=3.8"
+dependencies = [
+    "dask >= 2022.6",
+    "numba >= 0.56",
+    "numpy >= 1.23",
+    "pandas >= 1.5",
+    "scipy >= 1.9",
+    "xarray >= 2022.6.0",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/crusaderky/xarray_extras"
+
+[tool.setuptools]
+packages = ["xarray_extras"]
+zip-safe = false  # https://mypy.readthedocs.io/en/latest/installed_packages.html
+include-package-data = true
+
+[tool.setuptools_scm]
+# Use hardcoded version when .git has been removed and this is not a package created
+# by sdist. This is the case e.g. of a remote deployment with PyCharm.
+fallback_version = "9999"
+
+[tool.setuptools.package-data]
+xarray_extras = [
+    "py.typed",
+    "tests/data/*",
+]
+
+[build-system]
+requires = [
+    "setuptools>=66",
+    "setuptools_scm[toml]",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+addopts = "--strict-markers --strict-config -v -r sxfE --color=yes"
+xfail_strict = true
+python_files = ["test_*.py"]
+testpaths = ["xarray_extras/tests"]
+
+[tool.coverage.report]
+show_missing = true
+exclude_lines = [
+    "pragma: nocover",
+    "pragma: no cover",
+    "TYPE_CHECKING",
+    "except ImportError",
+    "@overload",
+    '@(abc\.)?abstractmethod',
+    '@(numba\.)?jit',
+    '@(numba\.)?vectorize',
+    '@(numba\.)?guvectorize',
+]
+
+[tool.ruff]
+builtins = ["ellipsis"]
+exclude = [".eggs"]
+target-version = "py38"
+
+[tool.ruff.lint]
+ignore = [
+  "E402",  # module level import not at top of file
+  "SIM108",  # use ternary operator instead of if-else block
+]
+select = [
+  "F",    # Pyflakes
+  "B",    # flake8-bugbear
+  "C4",   # flake8-comprehensions
+  "ISC",  # flake8-implicit-str-concat
+  "SIM",  # flake8-simplify
+  "E",    # Pycodestyle
+  "W",    # Pycodestyle
+  "I",    # isort
+  "N",    # pep8-naming
+  "UP",   # Pyupgrade
+  "RUF",  # unused-noqa
+  "EXE001",  #  Shebang is present but file is not executable
+]
+
+[tool.ruff.lint.isort]
+known-first-party = ["xarray_extras"]
+
+[tool.mypy]
+allow_incomplete_defs = false
+allow_untyped_decorators = false
+allow_untyped_defs = false
+ignore_missing_imports = true
+no_implicit_optional = true
+show_error_codes = true
+warn_redundant_casts = true
+warn_unused_ignores = true
+warn_unreachable = true
+
+[[tool.mypy.overrides]]
+module = ["*.tests.*"]
+allow_untyped_defs = true

setup.py

@@ -1,10 +1,7 @@
-#!/usr/bin/env python
 from setuptools import Extension, setup
 
 setup(
-    # Use hardcoded version when .git has been removed and this is not a package created
-    # by sdist. This is the case e.g. of a remote deployment with PyCharm.
-    use_scm_version={"fallback_version": "999"},
+    use_scm_version=True,
     # Compile CPython extensions
     ext_modules=[
         Extension(

xarray_extras/csv.py

@@ -18,7 +18,7 @@
 __all__ = ("to_csv",)
 
 if TYPE_CHECKING:
-    # TODO remove TYPE_CHECKING (requires dask >=2023.9.1)
+    # TODO: remove TYPE_CHECKING (requires dask >=2023.9.1)
     from dask.typing import DaskCollection, Key
 
 
@@ -76,7 +76,7 @@ def to_csv(
     and concatenate the partial outputs.
     """
     if not isinstance(x, xarray.DataArray):
-        raise ValueError("first argument must be a DataArray")
+        raise TypeError("first argument must be a DataArray")
 
     # Health checks
     if not isinstance(path, (str, Path)):
@@ -86,7 +86,7 @@ def to_csv(
 
     if x.ndim not in (1, 2):
         raise ValueError(
-            "cannot convert arrays with %d dimensions into " "pandas objects" % x.ndim
+            "cannot convert arrays with %d dimensions into pandas objects" % x.ndim
         )
 
     if nogil and x.dtype.kind not in "if":

xarray_extras/interpolate.py

@@ -169,7 +169,7 @@ def splev(
             dims = [tck.spline_dim]
         else:
             raise ValueError(
-                "N-dimensional x_new is only supported if " "x_new is a DataArray"
+                "N-dimensional x_new is only supported if x_new is a DataArray"
             )
         x_new = xarray.DataArray(x_new, dims=dims, coords={tck.spline_dim: x_new})
 

xarray_extras/kernels/csv.py

@@ -44,7 +44,7 @@ def to_csv(
         x_pd = pd.DataFrame(x, index, columns)
     else:
         # proper ValueError already raised in wrapper
-        assert False, "unreachable"  # pragma: nocover
+        raise AssertionError("unreachable")  # pragma: nocover
 
     encoding = kwargs.pop("encoding", "utf-8")
     header = kwargs.pop("header", True)
@@ -83,7 +83,7 @@ def to_csv(
     elif x.dtype.kind == "f":
         body_bytes = snprintcsvd(x, index_csv, sep, fmt, na_rep)
     else:
-        raise NotImplementedError("only int and float are supported when " "nogil=True")
+        raise NotImplementedError("only int and float are supported when nogil=True")
 
     if header is not False:
         header_bytes = (

xarray_extras/kernels/cumulatives.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 """Numba kernels for :mod:`cumulatives`
 """
 import numpy as np
@@ -39,7 +38,7 @@ def compound_mean(x: np.ndarray, c: np.ndarray, y: np.ndarray) -> None:
     """
     acc = 0
     j = 0  # Initialise j explicitly for when x.shape == (0, )
-    for j, i in enumerate(c):
+    for j, i in enumerate(c):  # noqa: B007
         if i == -1:
             break
         acc += x[i]