Update pyproject.toml and enable minor Ruff rules (#2196)

Author: VeckoTheGecko

.github/ci/min_deps_check.py

@@ -60,8 +60,8 @@ def parse_requirements(fname) -> Iterator[tuple[str, int, int, int | None]]:
 
         try:
             version_tup = tuple(int(x) for x in version.split("."))
-        except ValueError:
-            raise ValueError("non-numerical version: " + row)
+        except ValueError as e:
+            raise ValueError("non-numerical version: " + row) from e
 
         if len(version_tup) == 2:
             yield (pkg, *version_tup, None)  # type: ignore[misc]

parcels/particle.py

@@ -51,9 +51,9 @@ def __init__(
 
         try:
             dtype = np.dtype(dtype)
-        except (TypeError, ValueError):
+        except (TypeError, ValueError) as e:
             if dtype is not _SAME_AS_FIELDSET_TIME_INTERVAL.VALUE:
-                raise TypeError(f"Variable dtype must be a valid numpy dtype. Got {dtype=!r}")
+                raise TypeError(f"Variable dtype must be a valid numpy dtype. Got {dtype=!r}") from e
 
         if to_write not in _TO_WRITE_OPTIONS:
             raise ValueError(f"to_write must be one of {_TO_WRITE_OPTIONS!r}. Got {to_write=!r}")

parcels/xgcm/grid.py

@@ -515,7 +515,7 @@ def check_neighbor(link, position):
                     try:
                         neighbor_link = face_links[idx][ax][correct_position]
                     except (KeyError, IndexError):
-                        raise KeyError(
+                        raise KeyError(  # noqa: B904
                             f"Couldn't find a face link for face {idx!r}in axis {ax!r} at position {correct_position!r}"
                         )
                     idx_n, ax_n, rev_n = neighbor_link

pyproject.toml

@@ -111,9 +111,6 @@ parcels = { path = ".", editable = true }
 [tool.setuptools]
 packages = ["parcels"]
 
-[tool.setuptools.package-data]
-parcels = ["parcels/include/*"]
-
 [tool.setuptools_scm]
 write_to = "parcels/_version_setup.py"
 local_scheme = "no-local-version"
@@ -193,15 +190,7 @@ ignore = [
     "D404",
     # 1 blank line required between summary line and description (requires writing of summaries)
     "D205",
-    # do not use bare except, specify exception instead
-    "E722",
     "F811",
-
-
-    # TODO: These bugbear issues are to be resolved
-    "B011", # Do not `assert False`
-    "B016", # Cannot raise a literal. Did you intend to return it or raise an Exception?
-    "B904", # Within an `except` clause, raise exceptions
 ]
 
 [tool.ruff.lint.pydocstyle]