[pre-commit.ci] auto fixes from pre-commit.com hooks

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docs/guide/tutorial.rst

@@ -1,2 +1,2 @@
 Tutorial
-========
+========

requirements_dev.txt

@@ -1,8 +1,8 @@
+black>=22.10.0
 flake8>=3.9.2
-tox>=3.24.3
-pytest>=6.2.5
-pytest-cov>=2.12.1
 mypy>=0.910
-black>=22.10.0
-pre-commit>=2.1.0
 openpyxl>=3.0.10
+pre-commit>=2.1.0
+pytest>=6.2.5
+pytest-cov>=2.12.1
+tox>=3.24.3

setup.py

@@ -1,4 +1,6 @@
+from __future__ import annotations
+
 from setuptools import setup
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     setup()

src/femto/laserpath.py

@@ -374,9 +374,7 @@ def curvature_radius(self) -> npt.NDArray[np.float32]:
         norm_r1 = np.linalg.norm(r1, axis=1)
 
         # Return the local curvature radius, where cannot divide by 0 return inf
-        return np.divide(
-            norm_r1**3, norm_cross, out=np.full_like(norm_r1, fill_value=np.inf), where=~(norm_cross == 0)
-        )
+        return np.divide(norm_r1**3, norm_cross, out=np.full_like(norm_r1, fill_value=np.inf), where=~(norm_cross == 0))
 
     @property
     def cmd_rate(self) -> npt.NDArray[np.float32]:

src/femto/pgmcompiler.py

@@ -59,9 +59,9 @@ def __post_init__(self) -> None:
         self._loaded_files: list[str] = []
         self._dvars: list[str] = []
 
-        self.fwarp: Callable[
-            [npt.NDArray[np.float32], npt.NDArray[np.float32]], npt.NDArray[np.float32]
-        ] = self.warp_management(self.warp_flag)
+        self.fwarp: Callable[[npt.NDArray[np.float32], npt.NDArray[np.float32]], npt.NDArray[np.float32]] = (
+            self.warp_management(self.warp_flag)
+        )
 
         # Set rotation angle in radians for matrix rotations
         if self.rotation_angle:
@@ -745,7 +745,7 @@ def write(self, points: npt.NDArray[np.float32]) -> None:
 
         # Convert points if G-Code commands
         args = [self._format_args(x, y, z, f) for (x, y, z, f) in zip(x_gc, y_gc, z_gc, f_gc)]
-        for (arg, s) in itertools.zip_longest(args, s_gc):
+        for arg, s in itertools.zip_longest(args, s_gc):
             if s == 0 and self._shutter_on is True:
                 self.instruction('\n')
                 self.dwell(self.short_pause)

src/femto/spreadsheet.py

@@ -1,34 +1,31 @@
 from __future__ import annotations
 
 import time
-
-from xlsxwriter import Workbook
-
+from dataclasses import dataclass
 from pathlib import Path
-
-from femto import __file__ as fpath
-import numpy as np
-
 from types import TracebackType
-from femto.waveguide import Waveguide
-from femto.marker import Marker
-from femto.helpers import flatten
-from femto.writer import WaveguideWriter, MarkerWriter
-
+from typing import Any
 from typing import cast
 from typing import Union
-from typing import Any
-import nptyping as nptyp
-
-from dataclasses import dataclass
 
 import femto.device
+import nptyping as nptyp
+import numpy as np
+from femto import __file__ as fpath
+from femto.helpers import flatten
+from femto.marker import Marker
+from femto.waveguide import Waveguide
+from femto.writer import MarkerWriter
+from femto.writer import WaveguideWriter
+from xlsxwriter import Workbook
 
 
-def generate_all_cols_data() -> nptyp.NDArray[
-    Any,
-    nptyp.Structure["tagname: Str, fullname: Str, unit: Str, width: Int, format: Str"],
-]:
+def generate_all_cols_data() -> (
+    nptyp.NDArray[
+        Any,
+        nptyp.Structure[tagname:Str, fullname:Str, unit:Str, width:Int, format:Str],
+    ]
+):
     """
     Create the available columns array from a file.
 
@@ -113,7 +110,7 @@ class Parameter:
     """Class that handles preamble parameters."""
 
     n: str  # Full name
-    v: str = ""  # Value
+    v: str = ''  # Value
     loc: tuple[int, int] = (0, 0)  # Location (1-indexing)
     sz: tuple[int, int] = (0, 0)  # Size (for merged cells)
     fmt: str = 'parval'  # Format
@@ -135,10 +132,10 @@ class Spreadsheet:
     """Class representing the spreadsheet with all entities to fabricate."""
 
     device: femto.device.Device | None = None
-    columns_names: str = ""
-    book_name: str | Path = "my_fabrication.xlsx"
-    sheet_name: str = "Fabrication"
-    font_name: str = "DejaVu Sans Mono"
+    columns_names: str = ''
+    book_name: str | Path = 'my_fabrication.xlsx'
+    sheet_name: str = 'Fabrication'
+    font_name: str = 'DejaVu Sans Mono'
     font_size: int = 11
     suppr_redd_cols: bool = True
     static_preamble: bool = False
@@ -203,12 +200,10 @@ def __post_init__(
             self.columns_names = scn
             self.suppr_redd_cols = True
             print(
-                (
-                    'Columns_names not given in spreadsheet initialization.'
-                    f' Will proceed with standard columns names \'{scn}\' '
-                    'and activate the suppr_redd_cols flag to deal with '
-                    'reddundant columns.'
-                )
+                'Columns_names not given in spreadsheet initialization.'
+                f' Will proceed with standard columns names \'{scn}\' '
+                'and activate the suppr_redd_cols flag to deal with '
+                'reddundant columns.'
             )
 
         if 'name' not in self.columns_names:
@@ -370,7 +365,7 @@ def _write_saints_list(self, column: int = 156) -> None:
         None.
 
         """
-        with open(Path(fpath).parent / 'utils' / 'saints_data.txt', 'r') as f:
+        with open(Path(fpath).parent / 'utils' / 'saints_data.txt') as f:
             for i in range(367):
                 s = f.readline().strip('\n')
                 # print(f'writing day {i}\t{s}')
@@ -412,9 +407,7 @@ def _dtype(self, tagname):
 
         return dt
 
-    def _get_structure_list(
-        self, str_list: list[Union[Waveguide, Marker]] | None = None
-    ) -> list[Union[Waveguide, Marker]]:
+    def _get_structure_list(self, str_list: list[Waveguide | Marker] | None = None) -> list[Waveguide | Marker]:
 
         assert isinstance(self.device, femto.device.Device)
 
@@ -546,7 +539,7 @@ def _build_struct_list(
                 ignored_fields.append(t)
                 continue
 
-            if np.all(table_lines[t] == table_lines[t][0]) and suppr_redd_cols and table_lines[t][0] != "":
+            if np.all(table_lines[t] == table_lines[t][0]) and suppr_redd_cols and table_lines[t][0] != '':
                 # eliminate reddundancies if explicitly requested
                 ignored_fields.append(t)
 
@@ -570,10 +563,8 @@ def _build_struct_list(
         if ignored_fields and verbose:
             fields_left_out = ', '.join(ignored_fields)
             print(
-                (
-                    f'For all entities, the fields {fields_left_out} were not '
-                    'defined, so they will not be shown as table columns.'
-                )
+                f'For all entities, the fields {fields_left_out} were not '
+                'defined, so they will not be shown as table columns.'
             )
 
         self.keep = keep
@@ -656,9 +647,12 @@ def _fill_spreadsheet(self):
         for i, sdata in enumerate(self.struct_data):
 
             sdata = [
-                s
-                if (isinstance(s, (np.int64, np.float64)) and s < 1e5) or (not isinstance(s, (np.int64, np.float64)))
-                else ''
+                (
+                    s
+                    if (isinstance(s, (np.int64, np.float64)) and s < 1e5)
+                    or (not isinstance(s, (np.int64, np.float64)))
+                    else ''
+                )
                 for s in sdata
             ]
 

src/femto/trench.py

@@ -736,7 +736,7 @@ def main() -> None:
     # b = T._trench_list[0]
     # b = T.trenchbed[0]
     for tr in T._trench_list:
-        for (x, y) in tr.toolpath():
+        for x, y in tr.toolpath():
             plt.plot(x, y)
 
     plt.axis('equal')

src/femto/utils/spreadsheet_columns.txt

@@ -7,9 +7,9 @@ speed, Speed, mm/s, 6, 0.0
 scan, Scans, , 5, 0
 depth, Depth, mm, 8, 0.000
 radius, R, mm, 5, 0.00
-int_dist, Cdist, um, 8, 0.0000 
+int_dist, Cdist, um, 8, 0.0000
 wl, λ, um, 8, 0.000
-int_length, Clength, mm, 8, 0.000 
+int_length, Clength, mm, 8, 0.000
 arm_length, Alength, mm, 8, 0.000
 yin, Yin, mm, 8, 0.0000
 yout, Yout, mm, 8, 0.0000

src/femto/waveguide.py

@@ -410,9 +410,7 @@ def sin_bridge(
 
         x_sin = np.linspace(self._x[-1], self._x[-1] + dx, num)
         tmp_cos = np.cos(omega_y * np.pi / dx * (x_sin - self._x[-1]))
-        y_sin = self._y[-1] + 0.5 * dy * (
-            1 - np.sqrt((1 + flat_peaks**2) / (1 + flat_peaks**2 * tmp_cos**2)) * tmp_cos
-        )
+        y_sin = self._y[-1] + 0.5 * dy * (1 - np.sqrt((1 + flat_peaks**2) / (1 + flat_peaks**2 * tmp_cos**2)) * tmp_cos)
         z_sin = self._z[-1] + 0.5 * dzb * (1 - np.cos(omega_z * np.pi / dx * (x_sin - self._x[-1])))
         f_sin = np.repeat(f, num)
         s_sin = np.repeat(shutter, num)

src/femto/writer.py

@@ -535,7 +535,7 @@ def export_array2d(
         ]
 
         gcode_instr = []
-        for (line, dec) in itertools.zip_longest(instr, listcast(forced_deceleration)):
+        for line, dec in itertools.zip_longest(instr, listcast(forced_deceleration)):
             if bool(dec):
                 gcode_instr.append(f'G9 G1 {line}\n')
             else:

tests/device_test.py

@@ -53,7 +53,7 @@ def list_wg() -> list[Waveguide]:
 def list_mk() -> list[Marker]:
     PARAM_MK = dotdict(scan=1, speed=2, speed_pos=5, speed_closed=5, depth=0.000, lx=1, ly=1)
     markers = []
-    for (x, y) in zip(range(4, 8), range(3, 7)):
+    for x, y in zip(range(4, 8), range(3, 7)):
         m = Marker(**PARAM_MK)
         m.cross([x, y])
         markers.append(m)

tests/helpers_test.py

@@ -1,9 +1,10 @@
 from __future__ import annotations
 
+import pathlib
+
 import numpy as np
 import pytest
 import yaml
-import pathlib
 from femto.helpers import almost_equal
 from femto.helpers import dotdict
 from femto.helpers import flatten
@@ -296,7 +297,7 @@ def test_load_param_empty_default():
     PARAM_GC = dict(filename='UPP8.pgm', laser='PHAROS', aerotech_angle=0.0, rotation_angle=0.0)
     p_dicts = {'DEFAULT': {}, 'wg': PARAM_WG, 'mk': PARAM_MK, 'gc': PARAM_GC}
 
-    with open('test.yaml', "w") as f:
+    with open('test.yaml', 'w') as f:
         yaml.dump(p_dicts, f, sort_keys=False)
 
     pw, pm, pg = load_parameters('test.yaml')
@@ -340,7 +341,7 @@ def test_load_param_no_default():
     )
     p_dicts = {'wg': PARAM_WG, 'mk': PARAM_MK, 'gc': PARAM_GC}
 
-    with open('test.yaml', "w") as f:
+    with open('test.yaml', 'w') as f:
         yaml.dump(p_dicts, f, sort_keys=False)
 
     pw, pm, pg = load_parameters('test.yaml')
@@ -380,7 +381,7 @@ def test_load_param_pathlib():
     p_dicts = {'wg': PARAM_WG, 'mk': PARAM_MK, 'gc': PARAM_GC}
 
     fp = pathlib.Path('test.yaml')
-    with open(fp, "w") as f:
+    with open(fp, 'w') as f:
         yaml.dump(p_dicts, f, sort_keys=False)
 
     pw, pm, pg = load_parameters(fp)
@@ -393,7 +394,7 @@ def test_load_param_pathlib():
 def test_load_param_empty():
     p_dicts = {}
     fp = pathlib.Path('test.yaml')
-    with open(fp, "w") as f:
+    with open(fp, 'w') as f:
         yaml.dump(p_dicts, f, sort_keys=False)
 
     assert load_parameters(fp) == []

tests/spreadsheet_test.py

@@ -1,17 +1,18 @@
 from __future__ import annotations
-from femto import __file__ as fpath
+
+from contextlib import nullcontext as does_not_raise
+from itertools import product
+from pathlib import Path
 
 import numpy as np
+import openpyxl
 import pytest
+from femto import __file__ as fpath
 from femto.device import Device
 from femto.helpers import dotdict
 from femto.marker import Marker
 from femto.spreadsheet import Spreadsheet
-from itertools import product
 from femto.waveguide import Waveguide
-from pathlib import Path
-import openpyxl
-from contextlib import nullcontext as does_not_raise
 
 src_path = Path(fpath).parent
 dot_path = Path('.').cwd()
@@ -59,7 +60,7 @@ def list_wg() -> list[Waveguide]:
 def list_mk() -> list[Marker]:
     PARAM_MK = dotdict(scan=1, speed=2, speed_pos=5, speed_closed=5, depth=0.000, lx=1, ly=1)
     markers = []
-    for (x, y) in zip(range(4, 8), range(3, 7)):
+    for x, y in zip(range(4, 8), range(3, 7)):
         m = Marker(**PARAM_MK)
         m.cross([x, y])
         markers.append(m)

tests/trench_test.py

@@ -263,7 +263,7 @@ def test_buffer_polygon(p, offset, p_expected) -> None:
     tc = Trench(block=Polygon())
     buff_polygon = tc.buffer_polygon(p, offset)
 
-    for (p_calc, p_exp) in zip(buff_polygon, p_expected):
+    for p_calc, p_exp in zip(buff_polygon, p_expected):
         assert almost_equal(p_calc, p_exp)
 
 
@@ -439,7 +439,7 @@ def test_trenchcol_dig() -> None:
 
     tc._dig(coords)
 
-    for (t, c) in zip(tc._trench_list, comp_box):
+    for t, c in zip(tc._trench_list, comp_box):
         assert normalize_polygon(c).equals_exact(t.block, tolerance=1e-8)
         assert almost_equal(normalize_polygon(c), t.block)
 
@@ -461,7 +461,7 @@ def test_trenchcol_dig_remove() -> None:
 
     tc._dig(coords, remove=[1])
 
-    for (t, c) in zip(tc._trench_list, comp_box):
+    for t, c in zip(tc._trench_list, comp_box):
         assert normalize_polygon(c).equals_exact(t.block, tolerance=1e-8)
 
 
@@ -649,7 +649,7 @@ def test_u_dig() -> None:
 
     utc._dig(coords)
 
-    for (t, c) in zip(utc._trench_list, comp_box):
+    for t, c in zip(utc._trench_list, comp_box):
         assert normalize_polygon(c).equals_exact(t.block, tolerance=1e-8)
         assert almost_equal(normalize_polygon(c), t.block)
     assert utc.trenchbed is not []
@@ -675,7 +675,7 @@ def test_u_dig_no_pillars() -> None:
 
     utc._dig(coords)
 
-    for (t, c) in zip(utc._trench_list, comp_box):
+    for t, c in zip(utc._trench_list, comp_box):
         assert normalize_polygon(c).equals_exact(t.block, tolerance=1e-8)
         assert almost_equal(normalize_polygon(c), t.block)
     assert utc.trenchbed is not []

tests/writer_test.py

@@ -68,7 +68,7 @@ def list_ng() -> list[NasuWaveguide]:
 def list_mk() -> list[Marker]:
     PARAM_MK = dotdict(scan=1, speed=2, speed_pos=5, speed_closed=5, depth=0.000, lx=1, ly=1)
     markers = []
-    for (x, y) in zip(range(4, 8), range(3, 7)):
+    for x, y in zip(range(4, 8), range(3, 7)):
         m = Marker(**PARAM_MK)
         m.cross([x, y])
         markers.append(m)