Swapped to ruff for formatting and checking (#68)

* Fixed some complaints

docs/source/conf.py

@@ -14,20 +14,20 @@
 import os.path
 import sys
 
-sys.path.insert(0, os.path.abspath("../.."))
-sys.path.insert(0, os.path.abspath("../../../py-pde"))
+sys.path.insert(0, os.path.abspath("../.."))  # noqa: PTH100
+sys.path.insert(0, os.path.abspath("../../../py-pde"))  # noqa: PTH100
 sys.path.insert(0, ".")
 
 from datetime import date
 
-import sphinx_simplify_typehints  # @UnresolvedImport @UnusedImport
+import sphinx_simplify_typehints
 
 # -- Project information -----------------------------------------------------
 
 project = "py-droplets"
 module_name = "droplets"
 author = "David Zwicker"
-copyright = f"{date.today().year}, {author}"  # @ReservedAssignment
+copyright = f"{date.today().year}, {author}"  # noqa: A001
 
 # The short X.Y version
 import droplets

docs/source/quickstart/contributing.rst

@@ -19,8 +19,9 @@ define a droplet class that stores additional information by subclassing
 
 Coding style
 """"""""""""
-The coding style is enforced using `isort <https://timothycrosley.github.io/isort/>`_
-and `black <https://black.readthedocs.io/>`_. Moreover, we use `Google Style docstrings
+The coding style is enforced using `ruff <https://docs.astral.sh/ruff/>`_, based on the
+styles suggest by `isort <https://timothycrosley.github.io/isort/>`_ and
+`black <https://black.readthedocs.io/>`_. Moreover, we use `Google Style docstrings
 <https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings>`_,
 which might be best `learned by example
 <https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html>`_.

docs/source/run_autodoc.py

@@ -4,10 +4,11 @@
 import logging
 import os
 import subprocess as sp
+from pathlib import Path
 
 logging.basicConfig(level=logging.INFO)
 
-OUTPUT_PATH = "packages"
+OUTPUT_PATH = Path("packages")
 
 
 def replace_in_file(infile, replacements, outfile=None):
@@ -26,21 +27,21 @@ def replace_in_file(infile, replacements, outfile=None):
     if outfile is None:
         outfile = infile
 
-    with open(infile) as fp:
+    with infile.open() as fp:
         content = fp.read()
 
     for key, value in replacements.items():
         content = content.replace(key, value)
 
-    with open(outfile, "w") as fp:
+    with outfile.open("w") as fp:
         fp.write(content)
 
 
 def main(folder="droplets"):
     # remove old files
-    for path in glob.glob(f"{OUTPUT_PATH}/*.rst"):
+    for path in OUTPUT_PATH.glob("*.rst"):
         logging.info("Remove file `%s`", path)
-        os.remove(path)
+        path.unlink()
 
     # run sphinx-apidoc
     sp.check_call(
@@ -50,7 +51,7 @@ def main(folder="droplets"):
             "--maxdepth",
             "4",
             "--output-dir",
-            OUTPUT_PATH,
+            str(OUTPUT_PATH),
             "--module-first",
             f"../../{folder}",  # path of the package
             f"../../{folder}/tests",  # ignored path
@@ -59,7 +60,7 @@ def main(folder="droplets"):
     )
 
     # replace unwanted information
-    for path in glob.glob(f"{OUTPUT_PATH}/*.rst"):
+    for path in OUTPUT_PATH.glob("*.rst"):
         logging.info("Patch file `%s`", path)
         replace_in_file(path, {"Submodules\n----------\n\n": ""})
 

droplets/droplet_tracks.py

@@ -328,7 +328,7 @@ def _write_hdf_dataset(self, hdf_path, key: str = "droplet_track"):
 
         else:
             # create empty dataset to indicate empty emulsion
-            dataset = hdf_path.create_dataset(key, shape=tuple())
+            dataset = hdf_path.create_dataset(key, shape=())
             dataset.attrs["droplet_class"] = "None"
 
         return dataset
@@ -549,7 +549,7 @@ def match_tracks(
                         tracks.append(DropletTrack(droplets=[droplet], times=[time]))
 
                 if found_multiple_overlap:
-                    logger.debug(f"Found multiple overlapping droplet(s) at t={time}")
+                    logger.debug("Found multiple overlapping droplet(s) at t=%g", time)
 
         elif method == "distance":
             # track droplets by their physical distance
@@ -591,11 +591,11 @@ def match_tracks(
                         tracks.append(DropletTrack(droplets=[droplet], times=[time]))
 
         else:
-            raise ValueError(f"Unknown tracking method {method}")
+            raise ValueError("Unknown tracking method `%s`", method)
 
         # check kwargs
         if kwargs:
-            logger.warning(f"Unused keyword arguments: {kwargs}")
+            logger.warning("Unused keyword arguments: %s", kwargs)
 
         # add all emulsions successively using the given algorithm
         t_last = None

droplets/droplets.py

@@ -192,7 +192,6 @@ def __eq__(self, other):
 
     def check_data(self):
         """Method that checks the validity and consistency of self.data."""
-        pass
 
     @property
     def _args(self):
@@ -1092,8 +1091,10 @@ def __init__(
             opt_modes = spherical.spherical_index_count(l) - 1
             logger.warning(
                 "The length of `amplitudes` should be such that all orders are "
-                f"captured for the perturbations with the highest degree ({l}). "
-                f"Consider increasing the size of the array to {opt_modes}."
+                "captured for the perturbations with the highest degree (%d). "
+                "Consider increasing the size of the array to %d.",
+                l,
+                opt_modes,
             )
 
     @preserve_scalars

droplets/emulsions.py

@@ -373,7 +373,7 @@ def _write_hdf_dataset(self, hdf_path, key: str = "emulsion"):
 
         else:
             # create empty dataset to indicate empty emulsion
-            dataset = hdf_path.create_dataset(key, shape=tuple())
+            dataset = hdf_path.create_dataset(key, shape=())
             dataset.attrs["droplet_class"] = "None"
 
         return dataset
@@ -675,15 +675,15 @@ def plot(
         if len(self) == 0:
             # empty emulsions can be plotted in all dimensions :)
             return PlotReference(ax, [], {})
+
         if self.dim is None or self.dim <= 1:
             raise NotImplementedError(
                 f"Plotting emulsions in {self.dim} dimensions is not implemented."
             )
-        elif self.dim > 2:
-            if Emulsion._show_projection_warning:
-                logger = logging.getLogger(self.__class__.__name__)
-                logger.warning("A projection on the first two axes is shown.")
-                Emulsion._show_projection_warning = False
+        elif self.dim > 2 and Emulsion._show_projection_warning:
+            logger = logging.getLogger(self.__class__.__name__)
+            logger.warning("A projection on the first two axes is shown.")
+            Emulsion._show_projection_warning = False
 
         # plot background and determine bounds for the droplets
         if field is not None:

droplets/image_analysis.py

@@ -107,7 +107,7 @@ def _locate_droplets_in_mask_cartesian(mask: ScalarField) -> Emulsion:
 
     # locate individual clusters in the padded image
     labels, num_labels = ndimage.label(mask.data)
-    grid._logger.info(f"Found {num_labels} cluster(s) in image")
+    grid._logger.info("Found %d cluster(s) in image", num_labels)
     if num_labels == 0:
         example_drop = SphericalDroplet(np.zeros(grid.dim), radius=0)
         return Emulsion.empty(example_drop)
@@ -164,11 +164,11 @@ def _locate_droplets_in_mask_cartesian(mask: ScalarField) -> Emulsion:
     emulsion = Emulsion(droplets)
     num_candidates = len(emulsion)
     if num_candidates < num_labels:
-        grid._logger.info(f"Only {num_candidates} candidate(s) inside bounds")
+        grid._logger.info("Only %d candidate(s) inside bounds", num_candidates)
 
     emulsion.remove_overlapping(grid=grid)
     if len(emulsion) < num_candidates:
-        grid._logger.info(f"Only {num_candidates} candidate(s) not overlapping")
+        grid._logger.info("Only %d candidate(s) not overlapping", num_candidates)
 
     return emulsion
 
@@ -212,8 +212,6 @@ def _locate_droplets_in_mask_spherical(mask: ScalarField) -> Emulsion:
 class _SpanningDropletSignal(RuntimeError):
     """Exception signaling that an untypical droplet spanning the system was found."""
 
-    ...
-
 
 def _locate_droplets_in_mask_cylindrical_single(
     grid: CylindricalSymGrid, mask: np.ndarray
@@ -299,7 +297,7 @@ def _locate_droplets_in_mask_cylindrical(mask: ScalarField) -> Emulsion:
         except _SpanningDropletSignal:
             pass
         else:
-            grid._logger.info(f"Found {len(candidates)} droplet candidates.")
+            grid._logger.info("Found %d droplet candidates.", len(candidates))
 
             # keep droplets that are inside the central area
             droplets = Emulsion()
@@ -310,7 +308,7 @@ def _locate_droplets_in_mask_cylindrical(mask: ScalarField) -> Emulsion:
                 if z_min <= droplet.position[2] <= z_max:
                     droplets.append(droplet)
 
-            grid._logger.info(f"Kept {len(droplets)} central droplets.")
+            grid._logger.info("Kept %d central droplets.", len(droplets))
 
             # filter overlapping droplets (e.g. due to duplicates)
             droplets.remove_overlapping()
@@ -373,7 +371,7 @@ def locate_droplets(
                 field,
                 threshold="auto",
                 refine=True,
-                refine_args={'vmin': None, 'vmax': None},
+                refine_args={"vmin": None, "vmax": None},
             )
 
         :code:`field` is the scalar field, in which the droplets are located. The
@@ -840,8 +838,9 @@ def get_length_scale(
             for window_size in [5, 1, 0.2]:
                 bracket = [max_est / window_size, max_est, max_est * window_size]
                 logger.debug(
-                    f"Search maximum of structure factor in interval {bracket} with "
-                    f"window_size={window_size}"
+                    "Seek maximal structure factor in interval %s with window_size=%g",
+                    bracket,
+                    window_size,
                 )
                 try:
                     result = optimize.minimize_scalar(
@@ -854,7 +853,8 @@ def get_length_scale(
                     if not result.success:
                         logger.warning(
                             "Maximization of structure factor resulted in the "
-                            f"following message: {result.message}"
+                            "following message: %s",
+                            result.message,
                         )
                     length_scale = 2 * np.pi / result.x
                     break  # found some answer, which we will use

droplets/resources/make_spheres_3d.py

@@ -54,4 +54,4 @@
                 num_list.add(num)
 
     # store the number of generated spheres
-    f.attrs["num_list"] = list(sorted(num_list))
+    f.attrs["num_list"] = sorted(num_list)

droplets/trackers.py

@@ -12,6 +12,7 @@
 from __future__ import annotations
 
 import math
+from pathlib import Path
 from typing import Any, Callable, Literal
 
 from pde.fields.base import FieldBase
@@ -112,7 +113,7 @@ def finalize(self, info: InfoDict | None = None) -> None:
             import json
 
             data = {"times": self.times, "length_scales": self.length_scales}
-            with open(self.filename, "w") as fp:
+            with Path(self.filename).open("w") as fp:
                 json.dump(data, fp)
 
 
@@ -153,7 +154,7 @@ def __init__(
             .. code-block:: python
 
                 droplet_tracker = DropletTracker(
-                    1, refine=True, refine_args={'vmin': None, 'vmax': None}
+                    1, refine=True, refine_args={"vmin": None, "vmax": None}
                 )
 
             :code:`field` is the scalar field, in which the droplets are located. The

examples/tutorial/Using the py-droplets package.ipynb

@@ -19,6 +19,7 @@
     "\n",
     "# import necessary packages\n",
     "import pde\n",
+    "\n",
     "import droplets"
    ]
   },

pyproject.toml

@@ -59,6 +59,41 @@ namespaces = false
 
 [tool.setuptools_scm]
 write_to = "droplets/_version.py"
+[tool.ruff]
+target-version = "py38"
+exclude = ["scripts/templates"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
+select = [
+    "UP",  # pyupgrade
+    "I",  # isort
+    "A",  # flake8-builtins 
+    "B",  # flake8-bugbear
+    "C4",  # flake8-comprehensions
+    "FA", # flake8-future-annotations
+    "ISC", # flake8-implicit-str-concat
+    "ICN", # flake8-import-conventions
+    "LOG", # flake8-logging
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "PT", # flake8-pytest-style
+    "Q", # flake8-quotes
+    "RSE", # flake8-raise
+    "RET", # flake8-return
+    "SIM", # flake8-simplify
+    "PTH", # flake8-use-pathlib
+]
+ignore = ["B007", "B027", "B028", "SIM108", "ISC001", "PT006", "PT011", "RET504", "RET505", "RET506"]
+
+[tool.ruff.lint.isort]
+section-order = ["future", "standard-library", "third-party", "first-party", "my-modules", "self", "local-folder"]
+
+[tool.ruff.lint.isort.sections]
+my-modules = ["pde"]
+self = ["droplets"]
 
 [tool.black]
 target_version = ["py39"]

scripts/format_code.sh

@@ -7,10 +7,10 @@ find . -name '*.py' -exec pyupgrade --py39-plus {} +
 popd > /dev/null
 
 echo "Formating import statements..."
-isort ..
+ruff check --fix --config=../pyproject.toml ..
 
 echo "Formating docstrings..."
 docformatter --in-place --black --recursive ..
 
 echo "Formating source code..."
-black ..
+ruff format --config=../pyproject.toml ..

tests/conftest.py

@@ -10,7 +10,7 @@
 from pde.tools.numba import random_seed
 
 
-@pytest.fixture(scope="function", autouse=False, name="rng")
+@pytest.fixture(autouse=False, name="rng")
 def init_random_number_generators():
     """Get a random number generator and set the seed of the random number generator.
 
@@ -21,8 +21,8 @@ def init_random_number_generators():
     return np.random.default_rng(0)
 
 
-@pytest.fixture(scope="function", autouse=True)
-def setup_and_teardown():
+@pytest.fixture(autouse=True)
+def _setup_and_teardown():
     """Helper function adjusting environment before and after tests."""
     # ensure we use the Agg backend, so figures are not displayed
     plt.switch_backend("agg")

tests/requirements.txt

@@ -1,11 +1,10 @@
 -r ../requirements.txt
-black>=24
 docformatter>=1.7
-isort>=5.1
 pyupgrade>=3
 pytest>=5.4
 pytest-cov>=2.8
 pytest-xdist>=1.30
 mypy>=0.770
+ruff>=0.6
 types-PyYAML
 types-tqdm