Merge pull request #162 from tataratat/update-pre-commit

Update pre commit

.pre-commit-config.yaml

@@ -6,7 +6,7 @@
 
 # use default options for ci
 ci:
-  autoupdate_schedule: "monthly"
+  autoupdate_schedule: "weekly"
   submodules: false
 
 repos:
@@ -26,25 +26,29 @@ repos:
   - id: requirements-txt-fixer
   - id: trailing-whitespace
 
-- repo: https://github.com/asottile/pyupgrade
-  rev: "v3.14.0"
-  hooks:
-  - id: pyupgrade
-    args: [--py36-plus]
-
-- repo: https://github.com/PyCQA/isort
-  rev: "5.12.0"
-  hooks:
-  - id: isort
-
 - repo: https://github.com/psf/black
   rev: "23.9.1"
   hooks:
   - id: black
     args: [--line-length=79]
 
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.0.291
+  hooks:
+    - id: ruff
+      args: [
+        --fix,
+        --exit-non-zero-on-fix,
+      ]
+
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.5
+  hooks:
+  - id: codespell
+    args: [-w]
+
+- repo: https://github.com/keewis/blackdoc
+  rev: v0.3.8
   hooks:
-  - id: flake8
-    args: [--extend-ignore=E203]
+  - id: blackdoc
+    args: [--line-length=75]

docs/source/handle_markdown.py

@@ -100,9 +100,7 @@ def process_file(
     links = get_markdown_links(content)
 
     for item in links:
-        if item[1].startswith(
-            tuple(["http", "#"])
-        ):  # skip http links and anchors
+        if item[1].startswith(("http", "#")):  # skip http links and anchors
             content = content.replace(
                 f"[{item[0]}]({item[1]})",
                 f"<a href='{item[1]}'>{item[0]}</a>",

examples/load_sample_file.py

@@ -30,5 +30,5 @@ def load_sample_file(filename: str, force_reload: bool = False) -> bool:
             f.write(response.content)
         return True
     else:
-        print(f"Cant load {url}, status code: {response.status_code}.")
+        print(f"Can't load {url}, status code: {response.status_code}.")
         return False

examples/run_all_examples.py

@@ -9,11 +9,15 @@
     files_not_completed = []
 
     for file in glob.glob(str(pathlib.Path(__file__).parent) + "/*.py"):
-        if file.split("/")[-1] == "run_all_examples.py":
+        if file.split("/")[-1] in [
+            "run_all_examples.py",
+            "load_sample_file.py",
+        ]:
             continue
         print(f"Calling {file}")
-        proc_return = subprocess.run([sys.executable, file])
-        if proc_return.returncode != 0:
+        try:
+            proc_return = subprocess.run([sys.executable, file], check=True)
+        except subprocess.CalledProcessError:
             files_not_completed.append(file)
     if len(files_not_completed) > 0:
         print(

gustaf/create/edges.py

@@ -84,12 +84,10 @@ def from_data(gus_obj, data, scale=None, data_norm=None):
     if scale is None:
         if isinstance(data, str):
             norm = gus_obj.vertex_data.as_scalar(data, None, True)
+        elif data_norm is None:
+            norm = np.linalg.norm(increment, axis=1)
         else:
-            # compute
-            if data_norm is None:
-                norm = np.linalg.norm(increment, axis=1)
-            else:
-                norm = np.asanyarray(data_norm)
+            norm = np.asanyarray(data_norm)
 
         max_data_norm = norm.max()
         aabb_diagonal_norm = gus_obj.bounds_diagonal_norm()

gustaf/create/faces.py

@@ -8,9 +8,7 @@
 from gustaf.faces import Faces
 
 
-def box(
-    bounds=[[0, 0], [1, 1]], resolutions=[2, 2], simplex=False, backslash=False
-):
+def box(bounds=None, resolutions=None, simplex=False, backslash=False):
     """Create structured quadrangle or triangle block mesh.
 
     Parameters
@@ -27,6 +25,10 @@ def box(
     face_mesh: Volumes
     """
 
+    if resolutions is None:
+        resolutions = [2, 2]
+    if bounds is None:
+        bounds = [[0, 0], [1, 1]]
     if np.array(bounds).shape != (2, 2):
         raise ValueError("Bounds must have a dimension of (2, 2).")
     if len(resolutions) != 2:
@@ -56,7 +58,7 @@ def to_simplex(quad, alternate=False):
     vice versa. Will return a tri-mesh, if input is triangular.
     Default diagonalization looks like this:
 
-    .. code-block::
+    .. code-block:: text
 
         (3) *---* (2)
             |  /|
@@ -66,7 +68,7 @@ def to_simplex(quad, alternate=False):
 
     resembling 'slash'.
 
-    .. code-block::
+    .. code-block:: text
 
         (3) *---* (2)
             |\\  |
@@ -136,7 +138,8 @@ def to_quad(tri):
         each triangle face. Warning: mesh quality could be bad!
 
         ``(new) Quad Face``
-        .. code-block::
+
+        .. code-block:: text
 
             Ref: (node_ind), face_ind
 

gustaf/create/vertices.py

@@ -35,7 +35,7 @@ def raster(
     if len(resolutions) != len(bounds[0]) == len(bounds[1]):
         raise ValueError("Length of resolutions and bounds should match.")
 
-    slices = list()
+    slices = []
     for b0, b1, r in zip(bounds[0], bounds[1], resolutions):
         slices.append(slice(b0, b1, int(r) * 1j))
 

gustaf/create/volumes.py

@@ -8,7 +8,7 @@
 from gustaf.volumes import Volumes
 
 
-def box(bounds=[[0.0, 0.0, 0.0], [1.0, 1.0, 1.0]], resolutions=[2, 2, 2]):
+def box(bounds=None, resolutions=None):
     """Create structured hexahedron block mesh.
 
     Parameters
@@ -23,6 +23,10 @@ def box(bounds=[[0.0, 0.0, 0.0], [1.0, 1.0, 1.0]], resolutions=[2, 2, 2]):
     volume_mesh: Volumes
     """
 
+    if resolutions is None:
+        resolutions = [2, 2, 2]
+    if bounds is None:
+        bounds = [[0.0, 0.0, 0.0], [1.0, 1.0, 1.0]]
     if np.array(bounds).shape != (2, 3):
         raise ValueError("Bounds must have a dimension of (2, 3).")
     if len(resolutions) != 3:

gustaf/edges.py

@@ -365,7 +365,7 @@ def dashed(self, spacing=None):
 
         ``dashed edges``
 
-        .. code-block::
+        .. code-block:: text
 
              o--------o    o--------o    o--------o
              |<------>|             |<-->|

gustaf/faces.py

@@ -114,7 +114,7 @@ def __init__(
         elif elements is not None:
             self.faces = elements
 
-        self.BC = dict()
+        self.BC = {}
 
     @helpers.data.ComputedMeshData.depends_on(["elements"])
     def edges(self):

gustaf/helpers/data.py

@@ -31,7 +31,7 @@ def __array_finalize__(self, obj):
         """Sets default flags for any arrays that maybe generated based on
         tracked array."""
         self._modified = True
-        self._source = int(0)
+        self._source = 0
 
         if isinstance(obj, type(self)):
             if isinstance(obj._source, int):
@@ -53,7 +53,7 @@ def _set_modified(self):
         if isinstance(self._source, type(self)):
             self._source._modified = True
 
-    def copy(self, *args, **kwargs):
+    def copy(self, *_args, **_kwargs):
         """copy gives np.ndarray.
 
         no more tracking.
@@ -170,10 +170,11 @@ def make_tracked_array(array, dtype=None, copy=True):
         array = []
     # make sure it is contiguous then view it as our subclass
     tracked = np.ascontiguousarray(array, dtype=dtype)
-    if copy:
-        tracked = tracked.copy().view(TrackedArray)
-    else:
-        tracked = tracked.view(TrackedArray)
+    tracked = (
+        tracked.copy().view(TrackedArray)
+        if copy
+        else tracked.view(TrackedArray)
+    )
 
     # should always be contiguous here
     assert tracked.flags["C_CONTIGUOUS"]
@@ -196,7 +197,7 @@ def __init__(self, helpee):
           GustafBase objects would probably make the most sense here.
         """
         self._helpee = helpee
-        self._saved = dict()
+        self._saved = {}
 
     def __setitem__(self, key, value):
         """Raise Error to disable direct value setting.
@@ -222,7 +223,7 @@ def __getitem__(self, key):
         --------
         value: object
         """
-        if key in self._saved.keys():
+        if key in self._saved:
             return self._saved[key]
 
         else:
@@ -247,7 +248,7 @@ def clear(self):
         """
         Clears saved data by reassigning new dict
         """
-        self._saved = dict()
+        self._saved = {}
 
     def get(self, key, default_values=None):
         """Returns stored item if the key exists. Else, given default value. If
@@ -263,7 +264,7 @@ def get(self, key, default_values=None):
         --------
         value: object
         """
-        if key in self._saved.keys():
+        if key in self._saved:
             return self._saved[key]
         else:
             return default_values
@@ -302,7 +303,7 @@ class ComputedData(DataHolder):
 
     __slots__ = ()
 
-    def __init__(self, helpee, **kwargs):
+    def __init__(self, helpee, **_kwargs):
         """Stores last computed values.
 
         Keys are expected to be the same as helpee's function that computes the
@@ -334,26 +335,26 @@ def depends_on(cls, var_names, make_property=False):
         """
 
         def inner(func):
-            # followings are done once while modules are loaded
+            # following are done once while modules are loaded
             # just subclass this class to make a special helper
             # for each helpee class.
             assert isinstance(var_names, list), "var_names should be a list"
             # initialize property
             # _depends is dict(str: list)
             if cls._depends is None:
-                cls._depends = dict()
+                cls._depends = {}
             if cls._depends.get(func.__name__, None) is None:
-                cls._depends[func.__name__] = list()
+                cls._depends[func.__name__] = []
             # add dependency info
             cls._depends[func.__name__].extend(var_names)
 
             # _inv_depends is dict(str: list)
             if cls._inv_depends is None:
-                cls._inv_depends = dict()
+                cls._inv_depends = {}
             # add inverse dependency
             for vn in var_names:
                 if cls._inv_depends.get(vn, None) is None:
-                    cls._inv_depends[vn] = list()
+                    cls._inv_depends[vn] = []
 
                 cls._inv_depends[vn].append(func.__name__)
 
@@ -373,7 +374,7 @@ def compute_or_return_saved(*args, **kwargs):
                     recompute = kwargs.get("recompute", True)
 
                 # computed arrays are called _computed.
-                # loop over dependees and check if they are modified
+                # loop over dependencies and check if they are modified
                 for dependee_str in cls._depends[func.__name__]:
                     dependee = getattr(self, dependee_str)
                     # is modified?