style: pre-commit isort/black

.flake8

@@ -1,3 +1,3 @@
 [flake8]
 max-line-length = 88
-extend-ignore = E203
+extend-ignore = E203

.github/ISSUE_TEMPLATE/questions-.md

@@ -6,5 +6,3 @@ labels: ''
 assignees: ''
 
 ---
-
-

.github/workflows/pypi.yml

@@ -33,4 +33,4 @@ jobs:
           skip_existing: true
           verbose: true
           user: ${{ secrets.PYPI_USERNAME }}
-          password: ${{ secrets.PYPI_PASSWORD }}
+          password: ${{ secrets.PYPI_PASSWORD }}

.gitignore

@@ -135,4 +135,4 @@ docs/source/sg_execution_times.rst
 conda/index.html
 conda/channeldata.json
 conda/noarch
-conda/win-64
+conda/win-64

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 25.1.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/pycqa/isort
+    rev: 6.0.1
+    hooks:
+      - id: isort
+        name: isort (python)
+        args: ["--profile", "black"]

Dockerfile

@@ -88,4 +88,4 @@ WORKDIR ${HOME}/notebooks
 CMD ["jupyter", "lab", "--ip='0.0.0.0'", "--NotebookApp.token=''", "--no-browser" ]
 
 EXPOSE 8050
-EXPOSE 8080:8090
+EXPOSE 8080:8090

LoopStructural/__init__.py

@@ -8,8 +8,9 @@
 from logging.config import dictConfig
 
 __all__ = ["GeologicalModel"]
-import tempfile
 from pathlib import Path
+import tempfile
+
 from .version import __version__
 
 experimental = False
@@ -18,11 +19,11 @@
 ch.setFormatter(formatter)
 ch.setLevel(logging.WARNING)
 loggers = {}
-from .modelling.core.geological_model import GeologicalModel
-from .interpolators._api import LoopInterpolator
-from .interpolators import InterpolatorBuilder
 from .datatypes import BoundingBox
-from .utils import log_to_console, log_to_file, getLogger, rng, get_levels
+from .interpolators import InterpolatorBuilder
+from .interpolators._api import LoopInterpolator
+from .modelling.core.geological_model import GeologicalModel
+from .utils import get_levels, getLogger, log_to_console, log_to_file, rng
 
 logger = getLogger(__name__)
 logger.info("Imported LoopStructural")

LoopStructural/datasets/__init__.py

@@ -5,19 +5,21 @@
 Various datasets used for documentation and tutorials.
 """
 
-from ._base import load_claudius
-from ._base import load_grose2017
-from ._base import load_grose2018
-from ._base import load_grose2019
-from ._base import load_laurent2016
-from ._base import load_noddy_single_fold
-from ._base import load_intrusion
-from ._base import normal_vector_headers
-from ._base import strike_dip_headers
-from ._base import value_headers
-from ._base import load_unconformity
-from ._base import load_duplex
-from ._base import load_tabular_intrusion
-from ._base import load_geological_map_data
-from ._base import load_fault_trace
-from ._base import load_horizontal
+from ._base import (
+    load_claudius,
+    load_duplex,
+    load_fault_trace,
+    load_geological_map_data,
+    load_grose2017,
+    load_grose2018,
+    load_grose2019,
+    load_horizontal,
+    load_intrusion,
+    load_laurent2016,
+    load_noddy_single_fold,
+    load_tabular_intrusion,
+    load_unconformity,
+    normal_vector_headers,
+    strike_dip_headers,
+    value_headers,
+)

LoopStructural/datasets/_base.py

@@ -1,6 +1,7 @@
 from os.path import dirname, join
 from pathlib import Path
 from typing import Tuple
+
 import numpy as np
 import pandas as pd
 

LoopStructural/datasets/data/fault_trace/fault_trace.cpg

@@ -1 +1 @@
-UTF-8
+UTF-8

LoopStructural/datasets/data/fault_trace/fault_trace.prj

@@ -1 +1 @@
-PROJCS["GDA2020_MGA_Zone_53",GEOGCS["GCS_GDA2020",DATUM["GDA2020",SPHEROID["GRS_1980",6378137.0,298.257222101]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Transverse_Mercator"],PARAMETER["False_Easting",500000.0],PARAMETER["False_Northing",10000000.0],PARAMETER["Central_Meridian",135.0],PARAMETER["Scale_Factor",0.9996],PARAMETER["Latitude_Of_Origin",0.0],UNIT["Meter",1.0]]
+PROJCS["GDA2020_MGA_Zone_53",GEOGCS["GCS_GDA2020",DATUM["GDA2020",SPHEROID["GRS_1980",6378137.0,298.257222101]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Transverse_Mercator"],PARAMETER["False_Easting",500000.0],PARAMETER["False_Northing",10000000.0],PARAMETER["Central_Meridian",135.0],PARAMETER["Scale_Factor",0.9996],PARAMETER["Latitude_Of_Origin",0.0],UNIT["Meter",1.0]]

LoopStructural/datatypes/__init__.py

@@ -1,4 +1,4 @@
-from ._surface import Surface
 from ._bounding_box import BoundingBox
 from ._point import ValuePoints, VectorPoints
 from ._structured_grid import StructuredGrid
+from ._surface import Surface

LoopStructural/datatypes/_bounding_box.py

@@ -1,11 +1,13 @@
 from __future__ import annotations
-from typing import Optional, Union, Dict
-from LoopStructural.utils.exceptions import LoopValueError
-from LoopStructural.utils import rng
-from LoopStructural.datatypes._structured_grid import StructuredGrid
-import numpy as np
+
 import copy
+from typing import Dict, Optional, Union
 
+import numpy as np
+
+from LoopStructural.datatypes._structured_grid import StructuredGrid
+from LoopStructural.utils import rng
+from LoopStructural.utils.exceptions import LoopValueError
 from LoopStructural.utils.logging import getLogger
 
 logger = getLogger(__name__)

LoopStructural/datatypes/_point.py

@@ -1,8 +1,9 @@
 from dataclasses import dataclass, field
+import io
+from typing import Optional, Union
+
 import numpy as np
 
-from typing import Optional, Union
-import io
 from LoopStructural.utils import getLogger
 
 logger = getLogger(__name__)

LoopStructural/datatypes/_structured_grid.py

@@ -1,6 +1,8 @@
+from dataclasses import dataclass, field
 from typing import Dict
+
 import numpy as np
-from dataclasses import dataclass, field
+
 from LoopStructural.utils import getLogger
 
 logger = getLogger(__name__)

LoopStructural/datatypes/_surface.py

@@ -1,7 +1,9 @@
 from dataclasses import dataclass, field
+import io
 from typing import Optional, Union
+
 import numpy as np
-import io
+
 from LoopStructural.utils import getLogger
 
 logger = getLogger(__name__)

LoopStructural/export/exporters.py

@@ -3,14 +3,15 @@
 """
 
 import os
-from pyevtk.hl import unstructuredGridToVTK, pointsToVTK
-from pyevtk.vtk import VtkTriangle
+
 import numpy as np
+from pyevtk.hl import pointsToVTK, unstructuredGridToVTK
+from pyevtk.vtk import VtkTriangle
 from skimage.measure import marching_cubes
 
-from LoopStructural.utils.helper import create_box
-from LoopStructural.export.file_formats import FileFormat
 from LoopStructural.datatypes import Surface
+from LoopStructural.export.file_formats import FileFormat
+from LoopStructural.utils.helper import create_box
 
 from ..utils import getLogger
 

LoopStructural/export/geoh5.py

@@ -1,6 +1,7 @@
 import geoh5py
 import geoh5py.workspace
 import numpy as np
+
 from LoopStructural.datatypes import ValuePoints, VectorPoints
 
 

LoopStructural/export/omf_wrapper.py

@@ -5,10 +5,11 @@
         "You need to install the omf package to use this feature. "
         "You can install it with: pip install mira-omf"
     )
-import numpy as np
 import datetime
 import os
 
+import numpy as np
+
 
 def get_project(filename):
     if os.path.exists(filename):

LoopStructural/interpolators/__init__.py

@@ -54,31 +54,29 @@ class InterpolatorType(IntEnum):
     "DFI": InterpolatorType.DISCRETE_FOLD,
     'surfe': InterpolatorType.SURFE,
 }
-from ..interpolators._geological_interpolator import GeologicalInterpolator
-from ..interpolators._discrete_interpolator import DiscreteInterpolator
-from ..interpolators.supports import (
-    TetMesh,
-    StructuredGrid,
-    UnStructuredTetMesh,
-    P1Unstructured2d,
-    P2Unstructured2d,
-    StructuredGrid2D,
-    P2UnstructuredTetMesh,
-    SupportType,
+from ..interpolators._discrete_fold_interpolator import (
+    DiscreteFoldInterpolator,
 )
-
-
+from ..interpolators._discrete_interpolator import DiscreteInterpolator
 from ..interpolators._finite_difference_interpolator import (
     FiniteDifferenceInterpolator,
 )
+from ..interpolators._geological_interpolator import GeologicalInterpolator
 from ..interpolators._p1interpolator import (
+    P1Interpolator,
     P1Interpolator as PiecewiseLinearInterpolator,
 )
-from ..interpolators._discrete_fold_interpolator import (
-    DiscreteFoldInterpolator,
-)
 from ..interpolators._p2interpolator import P2Interpolator
-from ..interpolators._p1interpolator import P1Interpolator
+from ..interpolators.supports import (
+    P1Unstructured2d,
+    P2Unstructured2d,
+    P2UnstructuredTetMesh,
+    StructuredGrid,
+    StructuredGrid2D,
+    SupportType,
+    TetMesh,
+    UnStructuredTetMesh,
+)
 
 try:
     from ..interpolators._surfe_wrapper import SurfeRBFInterpolator
@@ -113,7 +111,7 @@ class InterpolatorType(IntEnum):
     },
 }
 
-from ._interpolator_factory import InterpolatorFactory
 from ._interpolator_builder import InterpolatorBuilder
+from ._interpolator_factory import InterpolatorFactory
 
 # from ._api import LoopInterpolator

LoopStructural/interpolators/_api.py

@@ -1,12 +1,13 @@
+from typing import Optional
+
 import numpy as np
 
-from typing import Optional
+from LoopStructural.datatypes import BoundingBox
 from LoopStructural.interpolators import (
     GeologicalInterpolator,
     InterpolatorFactory,
     InterpolatorType,
 )
-from LoopStructural.datatypes import BoundingBox
 from LoopStructural.utils import getLogger
 
 logger = getLogger(__name__)

LoopStructural/interpolators/_cython/dsi_helper.pyx

@@ -1,8 +1,12 @@
 import cython
 import numpy as np
 import numpy.linalg as la
+
 cimport numpy as np
+
 from math import *
+
+
 @cython.boundscheck(False)
 @cython.wraparound(False)
 #cython: language_level=3
@@ -306,4 +310,4 @@ def tetra_neighbours(long long [:,:] elements, long long [:,:] neighbours):
 #            pairs[face_n][1] = n
 #
 #            face_n+=1
-#    return pairs
+#    return pairs

LoopStructural/interpolators/_discrete_fold_interpolator.py

@@ -2,11 +2,11 @@
 Piecewise linear interpolator using folds
 """
 
-from typing import Optional, Callable
+from typing import Callable, Optional
 
 import numpy as np
 
-from ..interpolators import PiecewiseLinearInterpolator, InterpolatorType
+from ..interpolators import InterpolatorType, PiecewiseLinearInterpolator
 from ..modelling.features.fold import FoldEvent
 from ..utils import getLogger, rng
 

LoopStructural/interpolators/_discrete_interpolator.py

@@ -3,14 +3,13 @@
 """
 
 from abc import abstractmethod
-from typing import Callable, Optional, Union
 import logging
+from typing import Callable, Optional, Union
 
 import numpy as np
 from scipy import sparse  # import sparse.coo_matrix, sparse.bmat, sparse.eye
-from ..interpolators import InterpolatorType
 
-from ..interpolators import GeologicalInterpolator
+from ..interpolators import GeologicalInterpolator, InterpolatorType
 from ..utils import getLogger
 
 logger = getLogger(__name__)

LoopStructural/interpolators/_finite_difference_interpolator.py

@@ -3,12 +3,13 @@
 """
 
 import numpy as np
+from scipy.spatial import KDTree
+
+from LoopStructural.utils import getLogger
 
+from ..interpolators import InterpolatorType
 from ..utils import get_vectors
 from ._discrete_interpolator import DiscreteInterpolator
-from ..interpolators import InterpolatorType
-from scipy.spatial import KDTree
-from LoopStructural.utils import getLogger
 
 logger = getLogger(__name__)
 

LoopStructural/interpolators/_geological_interpolator.py

@@ -3,11 +3,13 @@
 """
 
 from abc import ABCMeta, abstractmethod
-from LoopStructural.utils.exceptions import LoopTypeError
-from ..interpolators import InterpolatorType
+from typing import Optional
+
 import numpy as np
 
-from typing import Optional
+from LoopStructural.utils.exceptions import LoopTypeError
+
+from ..interpolators import InterpolatorType
 from ..utils import getLogger
 
 logger = getLogger(__name__)