[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/pgmcompiler.py

@@ -28,7 +28,6 @@
 
 @dataclasses.dataclass(repr=False)
 class PGMCompiler:
-
     filename: str  #: File name of the PGM file.
     laser: str = 'PHAROS'  #: Name of the laser source.
     export_dir: str = ''  #: Directory in which the G-Code files will be exported.
@@ -745,7 +744,7 @@ 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.
 
@@ -81,7 +78,6 @@ def get_path(key, d, path=None, prev_k=None):
         nothing = True
         if hasattr(d, 'items'):
             for k, v in d.items():
-
                 if k == key:
                     prev_k.append(k)
                     path.append(' '.join(prev_k))
@@ -113,7 +109,7 @@ 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 +131,10 @@ 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 +199,10 @@ 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:
@@ -223,7 +217,6 @@ def __post_init__(
 
         ac = generate_all_cols_data()
         if self.new_columns:
-
             for elem in self.new_columns:
                 tns = ac['tagname']
                 if elem[0] in tns:
@@ -370,7 +363,7 @@ 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}')
@@ -412,10 +405,7 @@ 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)
 
         if str_list is None:
@@ -514,11 +504,9 @@ def _build_struct_list(
         table_lines = np.zeros(n_structures, dtype=dtype)
 
         for i, ent in enumerate(structures):
-
             sline = []
 
             for t in tagnames:
-
                 if t in 'yin yout':
                     item = coords(ent)[type(ent)][t]
                 else:
@@ -536,7 +524,6 @@ def _build_struct_list(
         ignored_fields = []
 
         for i, t in enumerate(tagnames):
-
             if t.lower() == 'name':
                 # the name of the structure is always present
                 keep.append(i)
@@ -546,7 +533,7 @@ 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 +557,8 @@ 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
@@ -594,7 +579,6 @@ def _prepare_columns(self, columns=None) -> None:
             self.columns_data = columns
 
         for i, col in enumerate(columns):
-
             fmt = col['format']
             w = col['width']
 
@@ -643,7 +627,6 @@ def _create_numerical_format(self, fmt_string) -> None:
         self.formats[fmt_string] = wb.add_format({'align': 'center', 'valign': 'vcenter', 'num_format': fmt_string})
 
     def _fill_spreadsheet(self):
-
         self.struct_data = self.struct_data[self.columns_data['tagname']]
 
         self.ws.set_row(7, 50)
@@ -654,7 +637,6 @@ def _fill_spreadsheet(self):
         self._add_line((7, 5), titles, fmt='title')
 
         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)))
@@ -669,7 +651,6 @@ def _fill_spreadsheet(self):
             )
 
     def _write_header(self) -> None:
-
         ws = self.ws
 
         ws.set_column(1, 1, 15)
@@ -686,7 +667,6 @@ def _write_header(self) -> None:
         ws.merge_range(2, 3, 2, nc_f + 4, self.description, self.formats['parval'])
 
     def _write_preamble(self) -> None:
-
         ws = self.ws
 
         row = 8
@@ -703,7 +683,6 @@ def _write_preamble(self) -> None:
 
         for sg, parameters in self.preamble.dict.items():
             for tname, p in parameters.items():
-
                 if np.any(p.sz):
                     ws.merge_range(*p.loc, *(p.loc + p.sz), '', self.formats['parname'])
 
@@ -768,7 +747,6 @@ def _add_line(
 
 
 def main() -> None:
-
     import numpy as np
     from itertools import product
     from femto.device import Device
@@ -809,7 +787,6 @@ def main() -> None:
     all_fabb = Device(**PARS_GC)
 
     for i_guide, (p, v, ns) in enumerate(product(powers, speeds, scans)):
-
         start_pt = [LS, 2 + i_guide * 0.08, PARS_WG.depth]
         wg = Waveguide(**PARS_WG, speed=v, scan=ns)
         # wg.power = p  # Can NOT be added inside of the arguments of Waveguide

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/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:
@@ -810,7 +810,6 @@ def _export_trench_column(self, column: UTrenchColumn, column_path: pathlib.Path
 
         # Bed script
         for i, bed_block in enumerate(column.trenchbed):
-
             x_bed_block = np.array([])
             y_bed_block = np.array([])
             f_decel = np.array([])

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)
@@ -292,7 +292,6 @@ def test_plot3d_save_true(device, list_wg, list_mk, list_tcol) -> None:
 
 
 def test_device_pgm(device, list_wg, list_mk) -> None:
-
     device.extend(list_wg)
     device.extend(list_mk)
     device.pgm()