GEOPY-1362: replace black and a few linters with Ruff

.pre-commit-config.yaml

@@ -11,29 +11,20 @@ ci:
     autoupdate_schedule: monthly
 
 repos:
--   repo: https://github.com/psf/black
-    rev: 23.10.0
+-   repo: https://github.com/hadialqattan/pycln
+    rev: v2.4.0
     hooks:
-    -   id: black
--   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    -   id: pycln
+        args: [ --config=pyproject.toml ]
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
     hooks:
-    -   id: isort
-        additional_dependencies: [tomli] # to read config from pyproject.toml
--   repo: https://github.com/humitos/mirrors-autoflake
-    rev: v1.1
-    hooks:
-    -   id: autoflake
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
-    hooks:
-    -   id: flake8
--   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
-    hooks:
-    -   id: pyupgrade
-        args: [--py39-plus]
-#        exclude: plates
+    -   id: ruff
+        args:
+        -   --fix
+        -   --exit-non-zero-on-fix
+#        -   --unsafe-fixes
+    -   id: ruff-format
 -   repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.6.1
     hooks:

devtools/add_url_tag_sha256.py

@@ -22,6 +22,7 @@
 from pathlib import Path
 from urllib import request
 
+
 _url_filename_re = re.compile(".*/([^/]*)")
 
 

devtools/check-copyright.py

@@ -12,6 +12,7 @@
 import sys
 from datetime import date
 
+
 if __name__ == "__main__":
     current_year = date.today().year
     copyright_re = re.compile(

devtools/git_message_hook.py

@@ -124,8 +124,7 @@ def check_commit_message(filepath: str) -> tuple[bool, str]:
     if branch_jira_id and message_jira_id and branch_jira_id != message_jira_id:
         return (
             False,
-            "Different JIRA ID in commit message %s and in branch name %s."
-            % (message_jira_id, branch_jira_id),
+            f"Different JIRA ID in commit message {message_jira_id} and in branch name {branch_jira_id}.",
         )
 
     stripped_message_line = ""
@@ -140,8 +139,8 @@ def check_commit_message(filepath: str) -> tuple[bool, str]:
     if len(stripped_message_line) < min_required_length:
         return (
             False,
-            "First line of commit message must be at least %s characters long, "
-            "beyond the JIRA ID." % min_required_length,
+            f"First line of commit message must be at least {min_required_length} characters long, "
+            "beyond the JIRA ID.",
         )
 
     return True, ""
@@ -156,9 +155,8 @@ def check_commit_msg(filepath: str) -> None:
     (is_valid, error_message) = check_commit_message(filepath)
     if not is_valid:
         print(
-            """commit-msg hook: **ERROR** %s
-            Message has been saved to %s."""
-            % (error_message, filepath)
+            f"""commit-msg hook: **ERROR** {error_message}
+            Message has been saved to {filepath}."""
         )
         sys.exit(1)
 

devtools/rename_my_app.py

@@ -15,6 +15,7 @@
 import subprocess
 from pathlib import Path
 
+
 logger = logging.getLogger(__name__)
 
 THIS_FILE = Path(__file__).resolve()

devtools/run_conda_lock.py

@@ -33,6 +33,7 @@
 from add_url_tag_sha256 import patch_pyproject_toml
 from ruamel.yaml import YAML
 
+
 env_file_variables_section_ = """
 variables:
   KMP_WARNINGS: 0
@@ -167,9 +168,10 @@ def patch_none_hash(self) -> None:
         )
         with tempfile.TemporaryDirectory(dir=str(self.lock_file.parent)) as tmpdirname:
             patched_file = Path(tmpdirname) / self.lock_file.name
-            with open(patched_file, mode="w", encoding="utf-8") as patched, open(
-                self.lock_file, encoding="utf-8"
-            ) as f:
+            with (
+                open(patched_file, mode="w", encoding="utf-8") as patched,
+                open(self.lock_file, encoding="utf-8") as f,
+            ):
                 for line in f:
                     match = none_hash_re.match(line)
                     if not match:
@@ -202,9 +204,10 @@ def remove_pip_hashes(self) -> None:
 
         with tempfile.TemporaryDirectory(dir=str(self.lock_file.parent)) as tmpdirname:
             patched_file = Path(tmpdirname) / self.lock_file.name
-            with open(patched_file, mode="w", encoding="utf-8") as patched, open(
-                self.lock_file, encoding="utf-8"
-            ) as f:
+            with (
+                open(patched_file, mode="w", encoding="utf-8") as patched,
+                open(self.lock_file, encoding="utf-8") as f,
+            ):
                 for line in f:
                     patched_line = self.sha_re.sub(r"\1", line)
                     patched.write(patched_line)

docs/source/conf.py

@@ -7,7 +7,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = "plate-simulation"
-copyright = "2024, Benjamin Kary"
+project_copyright = "2024, Mira Geoscience"
 author = "Benjamin Kary"
 release = "2024"
 

plate_simulation/__init__.py

@@ -8,6 +8,7 @@
 
 from pathlib import Path
 
+
 __version__ = "0.1.0-alpha.1"
 
 

plate_simulation/mesh/params.py

@@ -36,7 +36,7 @@ def octree_params(
             "Refinement B levels": "4, 2",
             "Refinement B type": "radial",
         }
-        for plate, letter in zip(plates, string.ascii_uppercase[2:]):
+        for plate, letter in zip(plates, string.ascii_uppercase[2:], strict=False):
             refinements.update(
                 {
                     f"Refinement {letter} object": plate,

plate_simulation/models/events.py

@@ -13,6 +13,7 @@
 from trimesh import Trimesh
 from trimesh.proximity import ProximityQuery
 
+
 # pylint: disable=too-few-public-methods
 
 

plate_simulation/models/params.py

@@ -17,6 +17,7 @@
     model_validator,
 )
 
+
 T = TypeVar("T")
 
 
@@ -101,7 +102,7 @@ def center(
         :param surface: surface object to reference plate depth from.
         :param depth_offset: Additional offset to be added to the depth of the plate.
         """
-        return self._get_xy(survey) + [self._get_z(surface, depth_offset)]
+        return [*self._get_xy(survey), self._get_z(surface, depth_offset)]
 
     def _get_xy(self, survey: ObjectBase) -> list[float]:
         """Return true or relative locations in x and y."""

plate_simulation/models/series.py

@@ -18,6 +18,7 @@
 
 from .events import Anomaly, Erosion, Overburden
 
+
 if TYPE_CHECKING:
     from .events import Deposition, Event
 

plate_simulation/simulations/params.py

@@ -15,6 +15,7 @@
 from simpeg_drivers.params import InversionBaseParams
 from simpeg_drivers.potential_fields.gravity.params import GravityParams
 
+
 # pylint: disable=import-outside-toplevel, too-few-public-methods
 
 

pyproject.toml

@@ -93,16 +93,40 @@ readthedocs-sphinx-ext = "*"
 platforms = ['win-64', 'linux-64']
 channels = ['conda-forge']
 
-[tool.isort]
-# settings for compatibility between ``isort`` and ``black`` formatting
-multi_line_output = 3
-include_trailing_comma = true
-force_grid_wrap = 0
-use_parentheses = true
-line_length = 88
-
-[tool.black]
-# defaults are just fine
+[tool.ruff]
+target-version = "py310"
+
+[tool.ruff.lint]
+ignore = [
+    "B028",  # no-explicit-stacklevel for warnings.warn()
+    "E501",  # line-too-long - code is reformatted (do not care about comments and docstring)
+    "F401",  # unsused-import - covered by pycln
+]
+select = [
+    "A",  # flake8-builtins
+    "B",  # flake8-bugbear
+    "B006",  # Do not use mutable data structures for argument defaults
+    "B9",  # flake8-bugbear opiniated warnings
+    "BLE",  # flake8-blind-except
+    "C4",  # flake8-comprehensions
+    "C9",  # mccabe
+    "E",  # pycodestyle errors
+    "F",  # pyflakes
+    "I",  # isort
+    "RUF",  # ruff rules
+    "TID", # flake8-tidy-imports
+    "UP",  # pyupgrade
+    "W",  # pycodestyle warnings
+]
+
+[tool.ruff.lint.mccabe]
+max-complexity = 18
+
+[tool.ruff.lint.isort]
+lines-after-imports = 2
+
+[tool.ruff.format]
+# default formatting is just fine
 
 [tool.mypy]
 warn_unused_configs = true

tests/assets_path_test.py

@@ -14,4 +14,4 @@ def test_assets_directory_exist():
 
 def test_uijson_files_exists():
     assert (assets_path() / "uijson").is_dir()
-    assert list((assets_path() / "uijson").iterdir())[0].is_file()
+    assert next(iter((assets_path() / "uijson").iterdir())).is_file()

tests/runtest/driver_test.py

@@ -29,6 +29,7 @@
 
 from . import get_survey, get_topography
 
+
 # pylint: disable=duplicate-code
 
 
@@ -112,7 +113,7 @@ def test_plate_simulation(tmp_path):
     with Workspace(result.options["geoh5"]) as ws:
         data = ws.get_entity(result.options["data_object"]["value"].uid)[0]
         mesh = ws.get_entity(result.options["mesh"]["value"].uid)[0]
-        model = [k for k in mesh.children if k.name == "starting_model"][0]
+        model = next(k for k in mesh.children if k.name == "starting_model")
 
         assert len(data.property_groups) == 3
         assert all(