Add pre-commit And poetry For Demonstration

[O957]

This PR covers adding poetry and pre-commit to PyStarshade for @xiaziyna to determine their utility.

[O957]

By default, I have, for ruff, "--ignore=E741", "--ignore=E731".

I am flagging below there are decent number of ruff issues:

• E402 Module level import not at top of file
• F841 Local variable bit_x is assigned to but never used
• E711 Comparison to None should be cond is None
• F821 Undefined name four_chunked_zoom_fft
• F601 Dictionary key literal "dist_ss_t" repeated
• F405 FresnelSingle may be undefined, or defined from star imports

For now, I am going to ignore all of them. If the author of PyStarshade wants to un-ignore them at some point in the future, fixing them so pre-commit runs successfully, this is their choice.

[O957]

In settings, one can creation a Branch protection for main that makes it required for status checks to pass before a PR can be merged.

[O957]

Updated Workflow:

Clone the repository:

git clone https://github.com/xiaziyna/PyStarshade.git
cd PyStarshade

Install dependencies using Poetry:

poetry install

(Optional) If you need to work with pre-computed data, use Git LFS to pull the necessary files:

git lfs pull

Activate the virtual environment created by Poetry:

poetry shell

[O957]

This PR is about ready for review.

Idea: Close with comment and then re-open once you better desire and or understand what is occurring with pre-commit and poetry.

Hope this helps and or is interesting, @xiaziyna; any comments are appreciated!

[O957]

Actually, one more thing. Here is the original output from running pre-commit run --all-files the first time:

Details

AFg6K7h4fhy2@Trevors-MacBook-Air PyStarshade % pre-commit install
pre-commit installed at .git/hooks/pre-commit
AFg6K7h4fhy2@Trevors-MacBook-Air PyStarshade % pre-commit run --all-files
check for added large files..............................................Passed
check python ast.........................................................Failed
- hook id: check-ast
- exit code: 1

tests/test_circle.py: failed parsing with CPython 3.12.5:

    Traceback (most recent call last):
      File "/Users/AFg6K7h4fhy2/.cache/pre-commit/reporx39rhbl/py_env-python3.12/lib/python3.12/site-packages/pre_commit_hooks/check_ast.py", line 21, in main
        ast.parse(f.read(), filename=filename)
      File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/ast.py", line 52, in parse
        return compile(source, filename, mode, flags,
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "tests/test_circle.py", line 9
        from from pystarshade.apodization.apodize import *
             ^^^^
    SyntaxError: invalid syntax

check for case conflicts.................................................Passed
check docstring is first.................................................Passed
check yaml...............................................................Passed
check toml...........................................(no files to check)Skipped
fix end of files.........................................................Failed
- hook id: end-of-file-fixer
- exit code: 1
- files were modified by this hook

Fixing docs/content/usage.rst
Fixing pystarshade/data/masks/grey_mask.py
Fixing pystarshade/__init__.py
Fixing setup.py
Fixing docs/index.rst
Fixing pystarshade/apodization/__init__.py
Fixing pystarshade/diffraction/__init__.py

mixed line ending........................................................Passed
python tests naming......................................................Passed
pretty format json...................................(no files to check)Skipped
trim trailing whitespace.................................................Failed
- hook id: trailing-whitespace
- exit code: 1
- files were modified by this hook

Fixing docs/content/usage.rst
Fixing pystarshade/propagator.py
Fixing pystarshade/diffraction/util.py
Fixing pystarshade/data/masks/mp_gen_mask.py
Fixing docs/content/test.rst
Fixing pystarshade/diffraction/bluestein_fft.py
Fixing pystarshade/data/masks/README
Fixing tests/test_chunk_fft.py
Fixing examples/visualize_throughput.py
Fixing docs/index.rst
Fixing pystarshade/diffraction/field.py
Fixing README.md
Fixing examples/exovista_sim.py
Fixing tests/test_circle.py
Fixing pystarshade/apodization/apodize.py
Fixing pystarshade/data/drm.py
Fixing tests/test_bluestein_fft.py
Fixing docs/paper/paper.md
Fixing pystarshade/diffraction/diffract.py
Fixing pystarshade/data/masks/make_memmap.py
Fixing pystarshade/simulate_field.py

check that executables have shebangs.................(no files to check)Skipped
detect private key.......................................................Passed
black....................................................................Failed
- hook id: black
- exit code: 123
- files were modified by this hook

reformatted docs/conf.py
reformatted examples/simple_point_source.py
reformatted examples/download_exovista.py
reformatted examples/star_exo.py
reformatted pystarshade/data/masks/grey_mask.py
reformatted pystarshade/apodization/pupil.py
reformatted pystarshade/data/masks/make_memmap.py
reformatted pystarshade/data/drm.py
reformatted examples/exovista_sim.py
reformatted pystarshade/data/masks/mp_gen_mask.py
reformatted pystarshade/apodization/apodize.py
reformatted setup.py
reformatted examples/visualize_throughput.py
reformatted pystarshade/diffraction/field.py
error: cannot format tests/test_circle.py: Cannot parse: 9:5: from from pystarshade.apodization.apodize import *
reformatted pystarshade/diffraction/util.py
reformatted tests/test_chunk_fft.py
reformatted pystarshade/simulate_field.py
reformatted pystarshade/diffraction/diffract.py
reformatted pystarshade/propagator.py
reformatted tests/test_bluestein_fft.py
reformatted pystarshade/diffraction/bluestein_fft.py

Oh no! 💥 💔 💥
21 files reformatted, 13 files left unchanged, 1 file failed to reformat.

isort....................................................................Failed
- hook id: isort
- files were modified by this hook

Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/docs/conf.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/examples/exovista_sim.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/examples/simple_point_source.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/examples/star_exo.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/examples/visualize_throughput.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/pystarshade/apodization/apodize.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/pystarshade/apodization/pupil.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/pystarshade/data/masks/grey_mask.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/pystarshade/data/masks/mp_gen_mask.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/pystarshade/diffraction/bluestein_fft.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/pystarshade/diffraction/diffract.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/pystarshade/diffraction/field.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/pystarshade/diffraction/util.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/pystarshade/propagator.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/pystarshade/simulate_field.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/setup.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/tests/test_bluestein_fft.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/tests/test_chunk_fft.py
Fixing /Users/AFg6K7h4fhy2/Documents/GitHub/Repositories/PyStarshade/tests/test_circle.py

ruff.....................................................................Failed
- hook id: ruff
- exit code: 1
- files were modified by this hook

docs/conf.py:17:1: E402 Module level import not at top of file
   |
15 | # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
16 | 
17 | import os
   | ^^^^^^^^^ E402
18 | 
19 | # paths from conf.py
   |

docs/conf.py:20:1: E402 Module level import not at top of file
   |
19 | # paths from conf.py
20 | import sys
   | ^^^^^^^^^^ E402
21 | 
22 | sys.path.insert(
   |

examples/exovista_sim.py:15:1: E402 Module level import not at top of file
   |
14 | download_exovista.exovista_scenes_file()
15 | import os
   | ^^^^^^^^^ E402
16 | 
17 | import matplotlib.pyplot as plt
   |

examples/exovista_sim.py:17:1: E402 Module level import not at top of file
   |
15 | import os
16 | 
17 | import matplotlib.pyplot as plt
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E402
18 | from matplotlib.colors import LogNorm
   |

examples/exovista_sim.py:18:1: E402 Module level import not at top of file
   |
17 | import matplotlib.pyplot as plt
18 | from matplotlib.colors import LogNorm
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E402
19 | 
20 | from pystarshade.data.scenes.Scene import *
   |

examples/exovista_sim.py:20:1: E402 Module level import not at top of file
   |
18 | from matplotlib.colors import LogNorm
19 | 
20 | from pystarshade.data.scenes.Scene import *
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E402
21 | from pystarshade.diffraction.util import (
22 |     au_to_meter,
   |

examples/exovista_sim.py:20:1: F403 `from pystarshade.data.scenes.Scene import *` used; unable to detect undefined names
   |
18 | from matplotlib.colors import LogNorm
19 | 
20 | from pystarshade.data.scenes.Scene import *
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F403
21 | from pystarshade.diffraction.util import (
22 |     au_to_meter,
   |

examples/exovista_sim.py:21:1: E402 Module level import not at top of file
   |
20 |   from pystarshade.data.scenes.Scene import *
21 | / from pystarshade.diffraction.util import (
22 | |     au_to_meter,
23 | |     data_file_path,
24 | |     mas_to_rad,
25 | |     pc_to_meter,
26 | | )
   | |_^ E402
27 |   from pystarshade.propagator import StarshadeProp
   |

examples/exovista_sim.py:27:1: E402 Module level import not at top of file
   |
25 |     pc_to_meter,
26 | )
27 | from pystarshade.propagator import StarshadeProp
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E402
28 | 
29 | fname = "1215-HIP_16537-TYC_-mv_3.72-L_0.35-d_3.20-Teff_5048.07.fits"
   |

examples/exovista_sim.py:39:9: F405 `Scene` may be undefined, or defined from star imports
   |
38 | t = 0  # timestep
39 | scene = Scene(file_path)
   |         ^^^^^ F405
40 | bg_scene = scene.getDiskImage()
41 | star_xy = scene.getXYstar()
   |

examples/exovista_sim.py:55:10: F405 `np` may be undefined, or defined from star imports
   |
54 | N_wl = len(wl_range)
55 | N_dust = np.shape(bg_scene)[1]
   |          ^^ F405
56 | N_dust_half = N_dust // 2
   |

examples/exovista_sim.py:59:18: F405 `np` may be undefined, or defined from star imports
   |
58 | N_s = 1001
59 | extended_field = np.zeros((N_wl, N_s, N_s), dtype=np.complex128)
   |                  ^^ F405
60 | half_N = N_s // 2
61 | half_in_N = N_dust // 2
   |

examples/exovista_sim.py:59:51: F405 `np` may be undefined, or defined from star imports
   |
58 | N_s = 1001
59 | extended_field = np.zeros((N_wl, N_s, N_s), dtype=np.complex128)
   |                                                   ^^ F405
60 | half_N = N_s // 2
61 | half_in_N = N_dust // 2
   |

examples/exovista_sim.py:71:8: F405 `np` may be undefined, or defined from star imports
   |
69 | n_planet = 0
70 | for i in range(1, scene.nplanets):
71 |     if np.all(planet_xy[i] - N_dust_half + half_N <= N_s - 1) and np.all(
   |        ^^ F405
72 |         planet_xy[i] - N_dust_half + half_N >= 0
73 |     ):
   |

examples/exovista_sim.py:71:67: F405 `np` may be undefined, or defined from star imports
   |
69 | n_planet = 0
70 | for i in range(1, scene.nplanets):
71 |     if np.all(planet_xy[i] - N_dust_half + half_N <= N_s - 1) and np.all(
   |                                                                   ^^ F405
72 |         planet_xy[i] - N_dust_half + half_N >= 0
73 |     ):
   |

examples/exovista_sim.py:95:7: F405 `np` may be undefined, or defined from star imports
   |
93 |     "Semi major axis[au]: ",
94 |     ds_au
95 |     * np.hypot(planet_xy[1:, 0] - N_dust_half, planet_xy[1:, 1] - N_dust_half),
   |       ^^ F405
96 | )
97 | print("wavelength [m]", wl)
   |

examples/exovista_sim.py:110:37: F405 `np` may be undefined, or defined from star imports
    |
108 | hwo_starshade.gen_psf_basis(pupil_type=pupil_type, pupil_symmetry=True)
109 | focal_intensity = hwo_starshade.gen_scene(
110 |     pupil_type, source_field.astype(np.float32), 500e-9, pupil_symmetry=True
    |                                     ^^ F405
111 | )
    |

examples/exovista_sim.py:122:1: F405 `np` may be undefined, or defined from star imports
    |
120 | )
121 | print(save_path)
122 | np.savez_compressed(save_path, field=focal_intensity)
    | ^^ F405
    |

examples/simple_point_source.py:6:14: F821 Undefined name `np`
  |
4 | hwo_starshade.gen_pupil_field()
5 | hwo_starshade.gen_psf_basis("hex")
6 | test_field = np.zeros((1001, 1001))
  |              ^^ F821
7 | test_field[500, 500] = 1e11
8 | test_field[800, 760] = 1
  |

examples/simple_point_source.py:10:1: F821 Undefined name `np`
   |
 8 | test_field[800, 760] = 1
 9 | out = hwo_starshade.gen_scene("hex", test_field, 500e-9)
10 | np.savez_compressed("test_field.npz", field=out)
   | ^^ F821
   |

examples/visualize_throughput.py:24:48: F821 Undefined name `fname`
   |
22 |     os.path.join(script_dir, "..", "pystarshade", "data")
23 | )
24 | file_path_on = os.path.join(data_dir, "pupil", fname)
   |                                                ^^^^^ F821
25 | file_path_off = os.path.join(data_dir, "pupil", fname)
   |

examples/visualize_throughput.py:25:49: F821 Undefined name `fname`
   |
23 | )
24 | file_path_on = os.path.join(data_dir, "pupil", fname)
25 | file_path_off = os.path.join(data_dir, "pupil", fname)
   |                                                 ^^^^^ F821
26 | 
27 | data = np.load(file_path_on)
   |

pystarshade/apodization/pupil.py:2:1: F403 `from hcipy import *` used; unable to detect undefined names
  |
1 | import numpy as np
2 | from hcipy import *
  | ^^^^^^^^^^^^^^^^^^^ F403
  |

pystarshade/apodization/pupil.py:13:12: F405 `make_hexagonal_segmented_aperture` may be undefined, or defined from star imports
   |
11 |         pupil_diameter - (2 * num_rings + 1) * gap_size
12 |     ) / (2 * num_rings + 1)
13 |     return make_hexagonal_segmented_aperture(
   |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F405
14 |         num_rings, segment_flat_to_flat, gap_size
15 |     )
   |

pystarshade/apodization/pupil.py:19:13: F405 `make_circular_aperture` may be undefined, or defined from star imports
   |
18 | aperture_funcs = {
19 |     "circ": make_circular_aperture,
   |             ^^^^^^^^^^^^^^^^^^^^^^ F405
20 |     "ELT": make_elt_aperture,
21 |     "GMT": make_gmt_aperture,
   |

pystarshade/apodization/pupil.py:20:12: F405 `make_elt_aperture` may be undefined, or defined from star imports
   |
18 | aperture_funcs = {
19 |     "circ": make_circular_aperture,
20 |     "ELT": make_elt_aperture,
   |            ^^^^^^^^^^^^^^^^^ F405
21 |     "GMT": make_gmt_aperture,
22 |     "TMT": make_tmt_aperture,
   |

pystarshade/apodization/pupil.py:21:12: F405 `make_gmt_aperture` may be undefined, or defined from star imports
   |
19 |     "circ": make_circular_aperture,
20 |     "ELT": make_elt_aperture,
21 |     "GMT": make_gmt_aperture,
   |            ^^^^^^^^^^^^^^^^^ F405
22 |     "TMT": make_tmt_aperture,
23 |     "Hale": make_hale_aperture,
   |

pystarshade/apodization/pupil.py:22:12: F405 `make_tmt_aperture` may be undefined, or defined from star imports
   |
20 |     "ELT": make_elt_aperture,
21 |     "GMT": make_gmt_aperture,
22 |     "TMT": make_tmt_aperture,
   |            ^^^^^^^^^^^^^^^^^ F405
23 |     "Hale": make_hale_aperture,
24 |     "LUVOIR-A": make_luvoir_a_aperture,
   |

pystarshade/apodization/pupil.py:23:13: F405 `make_hale_aperture` may be undefined, or defined from star imports
   |
21 |     "GMT": make_gmt_aperture,
22 |     "TMT": make_tmt_aperture,
23 |     "Hale": make_hale_aperture,
   |             ^^^^^^^^^^^^^^^^^^ F405
24 |     "LUVOIR-A": make_luvoir_a_aperture,
25 |     "LUVOIR-B": make_luvoir_b_aperture,
   |

pystarshade/apodization/pupil.py:24:17: F405 `make_luvoir_a_aperture` may be undefined, or defined from star imports
   |
22 |     "TMT": make_tmt_aperture,
23 |     "Hale": make_hale_aperture,
24 |     "LUVOIR-A": make_luvoir_a_aperture,
   |                 ^^^^^^^^^^^^^^^^^^^^^^ F405
25 |     "LUVOIR-B": make_luvoir_b_aperture,
26 |     "Magellan": make_magellan_aperture,
   |

pystarshade/apodization/pupil.py:25:17: F405 `make_luvoir_b_aperture` may be undefined, or defined from star imports
   |
23 |     "Hale": make_hale_aperture,
24 |     "LUVOIR-A": make_luvoir_a_aperture,
25 |     "LUVOIR-B": make_luvoir_b_aperture,
   |                 ^^^^^^^^^^^^^^^^^^^^^^ F405
26 |     "Magellan": make_magellan_aperture,
27 |     "VLT": make_vlt_aperture,
   |

pystarshade/apodization/pupil.py:26:17: F405 `make_magellan_aperture` may be undefined, or defined from star imports
   |
24 |     "LUVOIR-A": make_luvoir_a_aperture,
25 |     "LUVOIR-B": make_luvoir_b_aperture,
26 |     "Magellan": make_magellan_aperture,
   |                 ^^^^^^^^^^^^^^^^^^^^^^ F405
27 |     "VLT": make_vlt_aperture,
28 |     "HiCAT": make_hicat_aperture,
   |

pystarshade/apodization/pupil.py:27:12: F405 `make_vlt_aperture` may be undefined, or defined from star imports
   |
25 |     "LUVOIR-B": make_luvoir_b_aperture,
26 |     "Magellan": make_magellan_aperture,
27 |     "VLT": make_vlt_aperture,
   |            ^^^^^^^^^^^^^^^^^ F405
28 |     "HiCAT": make_hicat_aperture,
29 |     "HabEx": make_habex_aperture,
   |

pystarshade/apodization/pupil.py:28:14: F405 `make_hicat_aperture` may be undefined, or defined from star imports
   |
26 |     "Magellan": make_magellan_aperture,
27 |     "VLT": make_vlt_aperture,
28 |     "HiCAT": make_hicat_aperture,
   |              ^^^^^^^^^^^^^^^^^^^ F405
29 |     "HabEx": make_habex_aperture,
30 |     "HST": make_hst_aperture,
   |

pystarshade/apodization/pupil.py:29:14: F405 `make_habex_aperture` may be undefined, or defined from star imports
   |
27 |     "VLT": make_vlt_aperture,
28 |     "HiCAT": make_hicat_aperture,
29 |     "HabEx": make_habex_aperture,
   |              ^^^^^^^^^^^^^^^^^^^ F405
30 |     "HST": make_hst_aperture,
31 |     "JWST": make_jwst_aperture,
   |

pystarshade/apodization/pupil.py:30:12: F405 `make_hst_aperture` may be undefined, or defined from star imports
   |
28 |     "HiCAT": make_hicat_aperture,
29 |     "HabEx": make_habex_aperture,
30 |     "HST": make_hst_aperture,
   |            ^^^^^^^^^^^^^^^^^ F405
31 |     "JWST": make_jwst_aperture,
32 |     "Keck": make_keck_aperture,
   |

pystarshade/apodization/pupil.py:31:13: F405 `make_jwst_aperture` may be undefined, or defined from star imports
   |
29 |     "HabEx": make_habex_aperture,
30 |     "HST": make_hst_aperture,
31 |     "JWST": make_jwst_aperture,
   |             ^^^^^^^^^^^^^^^^^^ F405
32 |     "Keck": make_keck_aperture,
33 |     "hex": custom_hex,
   |

pystarshade/apodization/pupil.py:32:13: F405 `make_keck_aperture` may be undefined, or defined from star imports
   |
30 |     "HST": make_hst_aperture,
31 |     "JWST": make_jwst_aperture,
32 |     "Keck": make_keck_aperture,
   |             ^^^^^^^^^^^^^^^^^^ F405
33 |     "hex": custom_hex,
34 | }
   |

pystarshade/apodization/pupil.py:63:18: F405 `make_pupil_grid` may be undefined, or defined from star imports
   |
61 |     - The pupil data is reshaped into a 2D array of size `(N_t, N_t)` before saving.
62 |     """
63 |     pupil_grid = make_pupil_grid(N_t)
   |                  ^^^^^^^^^^^^^^^ F405
64 |     pupil = evaluate_supersampled(
65 |         call_aperture_function(pupil_type, normalized=True), pupil_grid, 8
   |

pystarshade/apodization/pupil.py:64:13: F405 `evaluate_supersampled` may be undefined, or defined from star imports
   |
62 |     """
63 |     pupil_grid = make_pupil_grid(N_t)
64 |     pupil = evaluate_supersampled(
   |             ^^^^^^^^^^^^^^^^^^^^^ F405
65 |         call_aperture_function(pupil_type, normalized=True), pupil_grid, 8
66 |     )
   |

pystarshade/data/drm.py:21:9: F601 Dictionary key literal `"dist_ss_t"` repeated
   |
19 |         "dx_": [0.01, 0.005, 0.002, 0.001, 0.0005],
20 |         "wl_bands": wfirst_wl_bands,
21 |         "dist_ss_t": 3.724225668350351e07
   |         ^^^^^^^^^^^ F601
22 |         * np.sum(wfirst_wl_bands[0])
23 |         / np.sum(wfirst_wl_bands, axis=1),
   |
   = help: Remove repeated key literal `"dist_ss_t"`

pystarshade/data/masks/mp_gen_mask.py:104:13: F821 Undefined name `convolve`
    |
103 | mask = mask.astype(np.float64)
104 | grey_mask = convolve(mask, np.ones((up_sample, up_sample)))[
    |             ^^^^^^^^ F821
105 |     ::up_sample, ::up_sample
106 | ].astype(np.float64)
    |

pystarshade/data/masks/mp_gen_mask.py:109:43: F821 Undefined name `final_dx_str`
    |
107 | grey_mask /= up_sample**2
108 | np.savez_compressed(
109 |     "starshade_masks/grey_hwo_24_mask_" + final_dx_str + "m_qu.npz",
    |                                           ^^^^^^^^^^^^ F821
110 |     grey_mask=grey_mask,
111 | )
    |

pystarshade/diffraction/bluestein_fft.py:44:5: F841 Local variable `bit_x` is assigned to but never used
   |
42 |     N_chirp = N_x + N_out - 1
43 | 
44 |     bit_x = N_x % 2
   |     ^^^^^ F841
45 |     bit_chirp = N_chirp % 2
46 |     bit_out = N_out % 2
   |
   = help: Remove assignment to unused variable `bit_x`

pystarshade/diffraction/bluestein_fft.py:425:5: F841 Local variable `bit_x` is assigned to but never used
    |
423 | def single_chunked_zoom_fft_mod(x, N_x, N_out, N_X, i=0):
424 |     # For computing the FFT over a single input chunk i = 0...3, and deciding which one
425 |     bit_x = N_x % 2
    |     ^^^^^ F841
426 |     sec_N_x = (
427 |         N_x // 2 + 1
    |
    = help: Remove assignment to unused variable `bit_x`

pystarshade/diffraction/diffract.py:8:1: F403 `from pystarshade.diffraction.util import *` used; unable to detect undefined names
  |
6 |     zoom_fft_2d_mod,
7 | )
8 | from pystarshade.diffraction.util import *
  | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F403
  |

pystarshade/diffraction/diffract.py:124:17: F405 `grid_points` may be undefined, or defined from star imports
    |
122 |         """
123 |         Ny, Nx = field.shape
124 |         in_xy = grid_points(Nx, Ny, dx=self.d_x)
    |                 ^^^^^^^^^^^ F405
125 |         field *= np.exp(
126 |             1j * (np.pi / self.wl_z) * (in_xy[0] ** 2 + in_xy[1] ** 2)
    |

pystarshade/diffraction/diffract.py:134:18: F405 `grid_points` may be undefined, or defined from star imports
    |
132 |         #        output_field = zoom_fft_2d_mod(field, self.N_in, N_out, Z_pad=self.ZP) * (self.d_x**2)
133 |         #        df = (self.max_freq*self.wl_z / (self.ZP*self.N_in + 1))
134 |         out_xy = grid_points(N_out, N_out, dx=df)
    |                  ^^^^^^^^^^^ F405
135 |         quad_out_fac = (
136 |             np.exp(1j * self.k * self.z)
    |

pystarshade/diffraction/diffract.py:173:18: F405 `grid_points` may be undefined, or defined from star imports
    |
171 |         ) * (self.d_x**2)
172 |         df = self.max_freq * self.wl_z / self.N_X
173 |         out_xy = grid_points(N_out, N_out, dx=df)
    |                  ^^^^^^^^^^^ F405
174 |         quad_out_fac = (
175 |             np.exp(1j * self.k * self.z)
    |

pystarshade/diffraction/diffract.py:216:43: F405 `wl_z` may be undefined, or defined from star imports
    |
214 |                 x_trunc[
215 |                     : self.N_in // 2 + bit_x, : self.N_in // 2 + bit_x
216 |                 ] *= np.exp(1j * (np.pi / wl_z) * (xx**2 + yy**2)).astype(
    |                                           ^^^^ F405
217 |                     np.complex128
218 |                 )
    |

pystarshade/diffraction/diffract.py:227:43: F405 `wl_z` may be undefined, or defined from star imports
    |
225 |                 x_trunc[
226 |                     : self.N_in // 2 + bit_x, self.N_in // 2 + bit_x :
227 |                 ] *= np.exp(1j * (np.pi / wl_z) * (xx**2 + yy**2)).astype(
    |                                           ^^^^ F405
228 |                     np.complex128
229 |                 )
    |

pystarshade/diffraction/diffract.py:241:43: F405 `wl_z` may be undefined, or defined from star imports
    |
239 |                 x_trunc[
240 |                     self.N_in // 2 + bit_x :, self.N_in // 2 + bit_x :
241 |                 ] *= np.exp(1j * (np.pi / wl_z) * (xx**2 + yy**2)).astype(
    |                                           ^^^^ F405
242 |                     np.complex128
243 |                 )
    |

pystarshade/diffraction/diffract.py:252:43: F405 `wl_z` may be undefined, or defined from star imports
    |
250 |                 x_trunc[
251 |                     self.N_in // 2 + bit_x :, : self.N_in // 2 + bit_x
252 |                 ] *= np.exp(1j * (np.pi / wl_z) * (xx**2 + yy**2)).astype(
    |                                           ^^^^ F405
253 |                     np.complex128
254 |                 )
    |

pystarshade/diffraction/diffract.py:256:24: F405 `four_chunked_zoom_fft_mod` may be undefined, or defined from star imports
    |
254 |                 )
255 |             x_trunc.flush()
256 |         output_field = four_chunked_zoom_fft_mod(
    |                        ^^^^^^^^^^^^^^^^^^^^^^^^^ F405
257 |             x_file, self.N_in, N_out, self.N_X
258 |         ) * (self.d_x**2)
    |

pystarshade/diffraction/diffract.py:260:18: F405 `grid_points` may be undefined, or defined from star imports
    |
258 |         ) * (self.d_x**2)
259 |         df = self.max_freq * self.wl_z / self.N_X
260 |         out_xy = grid_points(N_out, N_out, dx=df)
    |                  ^^^^^^^^^^^ F405
261 |         quad_out_fac = (
262 |             np.exp(1j * self.k * self.z)
    |

pystarshade/diffraction/diffract.py:309:17: F405 `single_chunked_zoom_fft_mod` may be undefined, or defined from star imports
    |
307 |             y = np.arange(-(self.N_in // 2), 1)[np.newaxis, :] * self.d_x
308 |         field *= np.exp(1j * (np.pi / self.wl_z) * (x**2 + y**2))
309 |         field = single_chunked_zoom_fft_mod(
    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ F405
310 |             field, self.N_in, N_out, self.N_X, i=chunk
311 |         ) * (self.d_x**2)
    |

pystarshade/diffraction/diffract.py:313:18: F405 `grid_points` may be undefined, or defined from star imports
    |
311 |         ) * (self.d_x**2)
312 |         df = self.max_freq * self.wl_z / self.N_X
313 |         out_xy = grid_points(N_out, N_out, dx=df)
    |                  ^^^^^^^^^^^ F405
314 |         quad_out_fac = (
315 |             np.exp(1j * k * self.z)
    |

pystarshade/diffraction/diffract.py:370:19: F405 `grid_points` may be undefined, or defined from star imports
    |
368 |         Ny, Nx = field_copy.shape
369 |         df = self.max_freq / Nx
370 |         freq_xy = grid_points(Nx, Ny, dx=df)
    |                   ^^^^^^^^^^^ F405
371 |         spectral_field = (
372 |             np.fft.fft2(field_copy)
    |

pystarshade/diffraction/diffract.py:486:18: F405 `grid_points` may be undefined, or defined from star imports
    |
484 |         ) * (self.d_x**2)
485 |         df = self.max_freq * self.wl_z / self.N_X
486 |         out_xy = grid_points(N_out, N_out, dx=df)
    |                  ^^^^^^^^^^^ F405
487 |         out_fac = np.exp(
488 |             (1j * k / (2 * self.z)) * (out_xy[0] ** 2 + out_xy[1] ** 2)
    |

pystarshade/diffraction/field.py:4:1: F403 `from pystarshade.diffraction.util import *` used; unable to detect undefined names
  |
3 | from pystarshade.diffraction.bluestein_fft import zoom_fft_2d_mod
4 | from pystarshade.diffraction.util import *
  | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F403
  |

pystarshade/diffraction/util.py:31:5: F841 Local variable `script_dir` is assigned to but never used
   |
29 |     """
30 |     package_path = pkg_resources.resource_filename("pystarshade", "")
31 |     script_dir = os.path.dirname(os.path.abspath(__file__))
   |     ^^^^^^^^^^ F841
32 |     os.environ["BASE_PATH"] = os.path.abspath(
33 |         os.path.join(package_path, "data")
   |
   = help: Remove assignment to unused variable `script_dir`

pystarshade/diffraction/util.py:206:19: E711 Comparison to `None` should be `cond is None`
    |
204 |         The padded 2D array with zeros, centered around the original array.
205 |     """
206 |     if N_out_y == None:
    |                   ^^^^ E711
207 |         N_out_y = N_out_x
208 |     zp_arr = np.zeros(
    |
    = help: Replace with `cond is None`

pystarshade/simulate_field.py:3:1: F403 `from pystarshade.apodization.apodize import *` used; unable to detect undefined names
  |
1 | import numpy as np
2 | 
3 | from pystarshade.apodization.apodize import *
  | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F403
4 | from pystarshade.diffraction.diffract import *
5 | from pystarshade.diffraction.field import *
  |

pystarshade/simulate_field.py:4:1: F403 `from pystarshade.diffraction.diffract import *` used; unable to detect undefined names
  |
3 | from pystarshade.apodization.apodize import *
4 | from pystarshade.diffraction.diffract import *
  | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F403
5 | from pystarshade.diffraction.field import *
6 | from pystarshade.diffraction.util import *
  |

pystarshade/simulate_field.py:5:1: F403 `from pystarshade.diffraction.field import *` used; unable to detect undefined names
  |
3 | from pystarshade.apodization.apodize import *
4 | from pystarshade.diffraction.diffract import *
5 | from pystarshade.diffraction.field import *
  | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F403
6 | from pystarshade.diffraction.util import *
  |

pystarshade/simulate_field.py:6:1: F403 `from pystarshade.diffraction.util import *` used; unable to detect undefined names
  |
4 | from pystarshade.diffraction.diffract import *
5 | from pystarshade.diffraction.field import *
6 | from pystarshade.diffraction.util import *
  | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F403
  |

pystarshade/simulate_field.py:31:25: F405 `bluestein_pad` may be undefined, or defined from star imports
   |
29 |         Field in the focal plane.
30 |     """
31 |     field_aperture_ss = bluestein_pad(pupil_field * pupil_mask, N_t, N_pix)
   |                         ^^^^^^^^^^^^^ F405
32 |     fraunhofer = Fraunhofer(dt, dp, N_t, focal_length_lens, wl)
33 |     out_field_ss, dp = fraunhofer.zoom_fraunhofer(field_aperture_ss, N_pix)
   |

pystarshade/simulate_field.py:32:18: F405 `Fraunhofer` may be undefined, or defined from star imports
   |
30 |     """
31 |     field_aperture_ss = bluestein_pad(pupil_field * pupil_mask, N_t, N_pix)
32 |     fraunhofer = Fraunhofer(dt, dp, N_t, focal_length_lens, wl)
   |                  ^^^^^^^^^^ F405
33 |     out_field_ss, dp = fraunhofer.zoom_fraunhofer(field_aperture_ss, N_pix)
34 |     return out_field_ss
   |

pystarshade/simulate_field.py:76:17: F405 `au_to_meter` may be undefined, or defined from star imports
   |
74 |         raise ValueError("starshade mask must be a memmap file")
75 |     N_s = 11
76 |     ds = 0.04 * au_to_meter
   |                 ^^^^^^^^^^^ F405
77 |     source_field = np.zeros((N_s, N_s))
78 |     source_field[N_s // 2, N_s // 2] = 1
   |

pystarshade/simulate_field.py:79:23: F405 `pc_to_meter` may be undefined, or defined from star imports
   |
77 |     source_field = np.zeros((N_s, N_s))
78 |     source_field[N_s // 2, N_s // 2] = 1
79 |     dist_xo_ss = 10 * pc_to_meter
   |                       ^^^^^^^^^^^ F405
80 |     source_prop = SourceField(ds, N_s, wl, dist_xo_ss, source_field)
81 |     field_free_prop = source_prop.farfield(dt, N_t, dist_ss_t)
   |

pystarshade/simulate_field.py:80:19: F405 `SourceField` may be undefined, or defined from star imports
   |
78 |     source_field[N_s // 2, N_s // 2] = 1
79 |     dist_xo_ss = 10 * pc_to_meter
80 |     source_prop = SourceField(ds, N_s, wl, dist_xo_ss, source_field)
   |                   ^^^^^^^^^^^ F405
81 |     field_free_prop = source_prop.farfield(dt, N_t, dist_ss_t)
   |

pystarshade/simulate_field.py:84:15: F405 `FresnelSingle` may be undefined, or defined from star imports
   |
83 |     field_incident_telescope_compl = np.zeros((N_t, N_t), dtype=np.complex128)
84 |     fresnel = FresnelSingle(dx, dt, N_x, dist_ss_t, wl)
   |               ^^^^^^^^^^^^^ F405
85 |     if chunk:
86 |         field_incident_telescope_compl, dt = (
   |

pystarshade/simulate_field.py:93:21: F405 `qu_mask_to_full` may be undefined, or defined from star imports
   |
91 |     else:
92 |         starshade_qu = np.load(ss_mask_fname)
93 |         starshade = qu_mask_to_full(starshade_qu)
   |                     ^^^^^^^^^^^^^^^ F405
94 |         field_incident_telescope_compl, dt = fresnel.zoom_fresnel_single_fft(
95 |             starshade, field_after_ss, N_t
   |

pystarshade/simulate_field.py:95:24: F405 `field_after_ss` may be undefined, or defined from star imports
   |
93 |         starshade = qu_mask_to_full(starshade_qu)
94 |         field_incident_telescope_compl, dt = fresnel.zoom_fresnel_single_fft(
95 |             starshade, field_after_ss, N_t
   |                        ^^^^^^^^^^^^^^ F405
96 |         )
   |

pystarshade/simulate_field.py:112:14: F405 `au_to_meter` may be undefined, or defined from star imports
    |
110 |     N_x=6401,
111 |     N_t=1001,
112 |     ds=0.1 * au_to_meter,
    |              ^^^^^^^^^^^ F405
113 |     dx=0.01,
114 |     dt=0.03,
    |

pystarshade/simulate_field.py:119:10: F405 `PointSource` may be undefined, or defined from star imports
    |
117 |     !!!!!!!! I need checking, likely replace with chunky crazy, along wiht functions in fresnel and fft
118 |     """
119 |     ps = PointSource(dx, N_x, wl, 0, 0, dist_xo_ss, 1)
    |          ^^^^^^^^^^^ F405
120 |     k_vals = ps.wave_numbers()
121 |     field_incident_telescope_compl = np.zeros((N_t, N_t), dtype=np.complex128)
    |

pystarshade/simulate_field.py:120:5: F841 Local variable `k_vals` is assigned to but never used
    |
118 |     """
119 |     ps = PointSource(dx, N_x, wl, 0, 0, dist_xo_ss, 1)
120 |     k_vals = ps.wave_numbers()
    |     ^^^^^^ F841
121 |     field_incident_telescope_compl = np.zeros((N_t, N_t), dtype=np.complex128)
122 |     source_prop = SourceField(ds, N_s, wl, dist_xo_ss, source_field)
    |
    = help: Remove assignment to unused variable `k_vals`

pystarshade/simulate_field.py:122:19: F405 `SourceField` may be undefined, or defined from star imports
    |
120 |     k_vals = ps.wave_numbers()
121 |     field_incident_telescope_compl = np.zeros((N_t, N_t), dtype=np.complex128)
122 |     source_prop = SourceField(ds, N_s, wl, dist_xo_ss, source_field)
    |                   ^^^^^^^^^^^ F405
123 |     #    test_plane = ps.plane_wave(k_vals, 0)
124 |     for chunk in range(4):
    |

pystarshade/simulate_field.py:139:19: F405 `FresnelSingle` may be undefined, or defined from star imports
    |
137 |         elif chunk == 3:
138 |             field_after_ss = np.fliplr(field_after_ss[1:,])
139 |         fresnel = FresnelSingle(dx, dt, N_x, dist_ss_t, wl)
    |                   ^^^^^^^^^^^^^ F405
140 |         field_incident_telescope_compl_quad, dt = (
141 |             fresnel.one_chunk_zoom_fresnel_single_fft(
    |

pystarshade/simulate_field.py:142:17: F405 `self` may be undefined, or defined from star imports
    |
140 |         field_incident_telescope_compl_quad, dt = (
141 |             fresnel.one_chunk_zoom_fresnel_single_fft(
142 |                 self, field, N_out, chunk=0
    |                 ^^^^ F405
143 |             )(field_after_ss, N_t, chunk=chunk)
144 |         )
    |

pystarshade/simulate_field.py:142:23: F405 `field` may be undefined, or defined from star imports
    |
140 |         field_incident_telescope_compl_quad, dt = (
141 |             fresnel.one_chunk_zoom_fresnel_single_fft(
142 |                 self, field, N_out, chunk=0
    |                       ^^^^^ F405
143 |             )(field_after_ss, N_t, chunk=chunk)
144 |         )
    |

pystarshade/simulate_field.py:142:30: F405 `N_out` may be undefined, or defined from star imports
    |
140 |         field_incident_telescope_compl_quad, dt = (
141 |             fresnel.one_chunk_zoom_fresnel_single_fft(
142 |                 self, field, N_out, chunk=0
    |                              ^^^^^ F405
143 |             )(field_after_ss, N_t, chunk=chunk)
144 |         )
    |

pystarshade/simulate_field.py:167:20: F405 `au_to_meter` may be undefined, or defined from star imports
    |
165 |     N_t=1001,
166 |     N_pix=4001,
167 |     ds=10 * 0.03 * au_to_meter,
    |                    ^^^^^^^^^^^ F405
168 |     dx=0.01,
169 |     dt=0.0116,
    |

pystarshade/simulate_field.py:215:19: F405 `SourceField` may be undefined, or defined from star imports
    |
213 |     """
214 | 
215 |     source_prop = SourceField(ds, N_s, wl, dist_xo_ss, source_field)
    |                   ^^^^^^^^^^^ F405
216 |     field_incident_ss = source_prop.farfield(dx, N_x, 0)
    |

pystarshade/simulate_field.py:218:25: F405 `eval_hypergauss` may be undefined, or defined from star imports
    |
216 |     field_incident_ss = source_prop.farfield(dx, N_x, 0)
217 | 
218 |     ss_complement = 1 - eval_hypergauss(N_x, dx)
    |                         ^^^^^^^^^^^^^^^ F405
219 | 
220 |     field_after_ss = field_incident_ss * ss_complement
    |

pystarshade/simulate_field.py:221:22: F405 `bluestein_pad` may be undefined, or defined from star imports
    |
220 |     field_after_ss = field_incident_ss * ss_complement
221 |     field_after_ss = bluestein_pad(field_after_ss, N_x, N_t)
    |                      ^^^^^^^^^^^^^ F405
222 | 
223 |     fresnel = FresnelSingle(dx, dt, N_x, dist_ss_t, wl)
    |

pystarshade/simulate_field.py:223:15: F405 `FresnelSingle` may be undefined, or defined from star imports
    |
221 |     field_after_ss = bluestein_pad(field_after_ss, N_x, N_t)
222 | 
223 |     fresnel = FresnelSingle(dx, dt, N_x, dist_ss_t, wl)
    |               ^^^^^^^^^^^^^ F405
224 |     test_new, dt = fresnel.zoom_fresnel_single_fft(field_after_ss, N_t)
    |

pystarshade/simulate_field.py:228:18: F405 `grey_pupil_func` may be undefined, or defined from star imports
    |
226 |     field_free_prop = source_prop.farfield(dt, N_t, dist_ss_t)
227 | 
228 |     pupil_mask = grey_pupil_func(N_t, dx=dt, r=radius_lens)
    |                  ^^^^^^^^^^^^^^^ F405
229 |     N_xt, N_yt = N_in_2d(
230 |         pupil_mask
    |

pystarshade/simulate_field.py:229:18: F405 `N_in_2d` may be undefined, or defined from star imports
    |
228 |     pupil_mask = grey_pupil_func(N_t, dx=dt, r=radius_lens)
229 |     N_xt, N_yt = N_in_2d(
    |                  ^^^^^^^ F405
230 |         pupil_mask
231 |     )  # Number of non-zero samples in telescope pupil
    |

pystarshade/simulate_field.py:233:29: F405 `bluestein_pad` may be undefined, or defined from star imports
    |
231 |     )  # Number of non-zero samples in telescope pupil
232 | 
233 |     field_aperture_freesp = bluestein_pad(
    |                             ^^^^^^^^^^^^^ F405
234 |         field_free_prop * pupil_mask, N_xt, N_pix
235 |     )
    |

pystarshade/simulate_field.py:236:25: F405 `bluestein_pad` may be undefined, or defined from star imports
    |
234 |         field_free_prop * pupil_mask, N_xt, N_pix
235 |     )
236 |     field_aperture_ss = bluestein_pad(test_new * pupil_mask, N_xt, N_pix)
    |                         ^^^^^^^^^^^^^ F405
237 | 
238 |     fraunhofer = Fraunhofer(dt, dp, N_xt, focal_length_lens, wl)
    |

pystarshade/simulate_field.py:238:18: F405 `Fraunhofer` may be undefined, or defined from star imports
    |
236 |     field_aperture_ss = bluestein_pad(test_new * pupil_mask, N_xt, N_pix)
237 | 
238 |     fraunhofer = Fraunhofer(dt, dp, N_xt, focal_length_lens, wl)
    |                  ^^^^^^^^^^ F405
239 |     out_field_free_space, dp = fraunhofer.zoom_fraunhofer(
240 |         field_aperture_freesp, N_pix
    |

pystarshade/simulate_field.py:314:14: F405 `PointSource` may be undefined, or defined from star imports
    |
312 |     field_incident_ss = np.zeros((N_X, N_X), dtype="complex128")
313 |     for i in range(no_sources):
314 |         ps = PointSource(dx, N_X, wl, *loc_s[i], mag_s[i])
    |              ^^^^^^^^^^^ F405
315 |         pointsource_list.append(ps)
316 |         k_list.append(ps.wave_numbers())
    |

pystarshade/simulate_field.py:324:25: F405 `eval_hypergauss` may be undefined, or defined from star imports
    |
322 |     #    field_incident_ss += gs.far_field_gaussian(gs_A, gs_inv_sigma, 0)
323 | 
324 |     ss_complement = 1 - eval_hypergauss(
    |                         ^^^^^^^^^^^^^^^ F405
325 |         N_X, dx
326 |     )  # Complement of starshade aperture
    |

pystarshade/simulate_field.py:330:15: F405 `FresnelSingle` may be undefined, or defined from star imports
    |
328 |     field_after_ss = field_incident_ss * ss_complement
329 | 
330 |     fresnel = FresnelSingle(dx, dt, N_x, dist_ss_t, wl)
    |               ^^^^^^^^^^^^^ F405
331 |     field_ss_prop, dt = fresnel.zoom_fresnel_single_fft(field_after_ss, N_t)
    |

pystarshade/simulate_field.py:333:18: F405 `grey_pupil_func` may be undefined, or defined from star imports
    |
331 |     field_ss_prop, dt = fresnel.zoom_fresnel_single_fft(field_after_ss, N_t)
332 | 
333 |     pupil_mask = grey_pupil_func(N_t, dx=dt, r=radius_lens)
    |                  ^^^^^^^^^^^^^^^ F405
334 | 
335 |     field_free_prop = np.zeros((N_t, N_t), dtype="complex128")
    |

pystarshade/simulate_field.py:343:18: F405 `N_in_2d` may be undefined, or defined from star imports
    |
341 |     #    field_free_prop += gs.far_field_gaussian(gs_A, gs_inv_sigma, dist_ss_t)
342 | 
343 |     N_xt, N_yt = N_in_2d(
    |                  ^^^^^^^ F405
344 |         pupil_mask
345 |     )  # Number of non-zero samples in telescope pupil
    |

pystarshade/simulate_field.py:347:29: F405 `bluestein_pad` may be undefined, or defined from star imports
    |
345 |     )  # Number of non-zero samples in telescope pupil
346 | 
347 |     field_aperture_freesp = bluestein_pad(
    |                             ^^^^^^^^^^^^^ F405
348 |         field_free_prop * pupil_mask, N_xt, N_pix
349 |     )
    |

pystarshade/simulate_field.py:350:25: F405 `bluestein_pad` may be undefined, or defined from star imports
    |
348 |         field_free_prop * pupil_mask, N_xt, N_pix
349 |     )
350 |     field_aperture_ss = bluestein_pad(field_ss_prop * pupil_mask, N_xt, N_pix)
    |                         ^^^^^^^^^^^^^ F405
351 | 
352 |     fraunhofer = Fraunhofer(dt, dp, N_xt, focal_length_lens, wl)
    |

pystarshade/simulate_field.py:352:18: F405 `Fraunhofer` may be undefined, or defined from star imports
    |
350 |     field_aperture_ss = bluestein_pad(field_ss_prop * pupil_mask, N_xt, N_pix)
351 | 
352 |     fraunhofer = Fraunhofer(dt, dp, N_xt, focal_length_lens, wl)
    |                  ^^^^^^^^^^ F405
353 |     out_field_free_space, dp = fraunhofer.zoom_fraunhofer(
354 |         field_aperture_freesp, N_pix
    |

tests/test_bluestein_fft.py:134:23: F821 Undefined name `four_chunked_zoom_fft`
    |
132 |     x_memmap[:] = x_trunc[:]
133 |     x_memmap.flush()
134 |     test_chunked_bs = four_chunked_zoom_fft("mm_data.dat", N_x, N_out, N_X)
    |                       ^^^^^^^^^^^^^^^^^^^^^ F821
135 |     os.remove("mm_data.dat")
136 |     real_ft_x = np.fft.fftshift(np.fft.fft2(x))[
    |

tests/test_bluestein_fft.py:191:5: F841 Local variable `N_y_seg` is assigned to but never used
    |
190 |     N_x_seg = in_N_X // 2 + bit_x
191 |     N_y_seg = in_N_Y // 2 + bit_y
    |     ^^^^^^^ F841
192 |     shift_seg = N_x_seg // 2 - N_x // 4
    |
    = help: Remove assignment to unused variable `N_y_seg`

tests/test_bluestein_fft.py:192:5: F841 Local variable `shift_seg` is assigned to but never used
    |
190 |     N_x_seg = in_N_X // 2 + bit_x
191 |     N_y_seg = in_N_Y // 2 + bit_y
192 |     shift_seg = N_x_seg // 2 - N_x // 4
    |     ^^^^^^^^^ F841
193 | 
194 |     N_x_1 = max(N_in_2d(x_1))
    |
    = help: Remove assignment to unused variable `shift_seg`

tests/test_bluestein_fft.py:284:23: F821 Undefined name `four_chunked_zoom_fft`
    |
282 |     x_memmap[:] = x_trunc[:]
283 |     x_memmap.flush()
284 |     test_chunked_bs = four_chunked_zoom_fft("mm_data.dat", N_x, N_out, N_X)
    |                       ^^^^^^^^^^^^^^^^^^^^^ F821
285 |     os.remove("mm_data.dat")
    |

tests/test_circle.py:9:1: F403 `from frompystarshade.apodization.apodize import *` used; unable to detect undefined names
   |
 7 | import numpy as np
 8 | import pytest
 9 | from frompystarshade.apodization.apodize import *
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F403
10 | from frompystarshade.diffraction.diffract import *
11 | from frompystarshade.diffraction.field import *
   |

tests/test_circle.py:10:1: F403 `from frompystarshade.diffraction.diffract import *` used; unable to detect undefined names
   |
 8 | import pytest
 9 | from frompystarshade.apodization.apodize import *
10 | from frompystarshade.diffraction.diffract import *
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F403
11 | from frompystarshade.diffraction.field import *
12 | from frompystarshade.diffraction.util import *
   |

tests/test_circle.py:11:1: F403 `from frompystarshade.diffraction.field import *` used; unable to detect undefined names
   |
 9 | from frompystarshade.apodization.apodize import *
10 | from frompystarshade.diffraction.diffract import *
11 | from frompystarshade.diffraction.field import *
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F403
12 | from frompystarshade.diffraction.util import *
13 | from scipy.special import jn
   |

tests/test_circle.py:12:1: F403 `from frompystarshade.diffraction.util import *` used; unable to detect undefined names
   |
10 | from frompystarshade.diffraction.diffract import *
11 | from frompystarshade.diffraction.field import *
12 | from frompystarshade.diffraction.util import *
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ F403
13 | from scipy.special import jn
   |

tests/test_circle.py:20:17: F405 `pc_to_meter` may be undefined, or defined from star imports
   |
18 | R_lens = 2.4
19 | R_ss = 30
20 | dist_xo_ss = 10*pc_to_meter
   |                 ^^^^^^^^^^^ F405
21 | dist_ss_t = 63942090. # distance for hypergaussian mask
22 | N_t = 257
   |

tests/test_circle.py:116:10: F405 `PointSource` may be undefined, or defined from star imports
    |
114 |     """ Fresnel diffraction via PyStarshade for comparison to analytic circle mask diffraction"""
115 | 
116 |     ps = PointSource(dx, N_x, wl, 0, 0, dist_xo_ss, 1)
    |          ^^^^^^^^^^^ F405
117 |     k_vals = ps.wave_numbers()
118 |     field_incident_ss = ps.plane_wave(k_vals, 0)
    |

tests/test_circle.py:120:21: F405 `grey_pupil_func` may be undefined, or defined from star imports
    |
118 |     field_incident_ss = ps.plane_wave(k_vals, 0)
119 | 
120 |     ss_complement = grey_pupil_func(N_x, dx, R_ss)
    |                     ^^^^^^^^^^^^^^^ F405
121 |     field_after_ss = field_incident_ss * ss_complement
    |

tests/test_circle.py:123:15: F405 `FresnelSingle` may be undefined, or defined from star imports
    |
121 |     field_after_ss = field_incident_ss * ss_complement
122 | 
123 |     fresnel = FresnelSingle(dx, dt, N_x, dist_ss_t, wl)
    |               ^^^^^^^^^^^^^ F405
124 |     field_aperture, dt = fresnel.zoom_fresnel_single_fft(field_after_ss, N_t)
    |

Found 126 errors (14 fixed, 112 remaining).
No fixes available (7 hidden fixes can be enabled with the `--unsafe-fixes` option).

mypy.....................................................................Failed
- hook id: mypy
- exit code: 1

tests/test_circle.py:20: error: Name "pc_to_meter" is not defined  [name-defined]
pystarshade/diffraction/util.py:4: error: Library stubs not installed for "pkg_resources"  [import-untyped]
pystarshade/diffraction/util.py:4: note: Hint: "python3 -m pip install types-setuptools"
pystarshade/diffraction/util.py:4: note: (or run "mypy --install-types" to install all missing stub packages)
pystarshade/diffraction/util.py:4: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
pystarshade/apodization/pupil.py:19: error: Name "make_circular_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:20: error: Name "make_elt_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:21: error: Name "make_gmt_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:22: error: Name "make_tmt_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:23: error: Name "make_hale_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:24: error: Name "make_luvoir_a_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:25: error: Name "make_luvoir_b_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:26: error: Name "make_magellan_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:27: error: Name "make_vlt_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:28: error: Name "make_hicat_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:29: error: Name "make_habex_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:30: error: Name "make_hst_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:31: error: Name "make_jwst_aperture" is not defined  [name-defined]
pystarshade/apodization/pupil.py:32: error: Name "make_keck_aperture" is not defined  [name-defined]
examples/visualize_throughput.py:24: error: Name "fname" is not defined  [name-defined]
examples/visualize_throughput.py:25: error: Name "fname" is not defined  [name-defined]
examples/simple_point_source.py:6: error: Name "np" is not defined  [name-defined]
examples/simple_point_source.py:10: error: Name "np" is not defined  [name-defined]
pystarshade/data/masks/mp_gen_mask.py:104: error: Name "convolve" is not defined  [name-defined]
pystarshade/data/masks/mp_gen_mask.py:109: error: Name "final_dx_str" is not defined  [name-defined]
examples/exovista_sim.py:39: error: Name "Scene" is not defined  [name-defined]
examples/exovista_sim.py:55: error: Name "np" is not defined  [name-defined]
examples/exovista_sim.py:59: error: Name "np" is not defined  [name-defined]
examples/exovista_sim.py:71: error: Name "np" is not defined  [name-defined]
examples/exovista_sim.py:95: error: Name "np" is not defined  [name-defined]
examples/exovista_sim.py:110: error: Name "np" is not defined  [name-defined]
examples/exovista_sim.py:122: error: Name "np" is not defined  [name-defined]
Found 29 errors in 7 files (checked 35 source files)

typos....................................................................Failed
- hook id: typos
- exit code: 2

error: `paramters` should be `parameters`
  --> pystarshade/propagator.py:53:70
   |
53 |                 "Design reference mission not set. Insert instrument paramters into data/telescope_drm.py"
   |                                                                      ^^^^^^^^^
   |
error: `multipled` should be `multiplied`
  --> docs/content/fft.rst:4:442
  |
4 | When a starshade is aligned with a star, starlight is diffracted by the starshade :math:`s(\mathbf{x})` onto a telescope aperture. For a starshade mask :math:`s(u, v)` which is zero inside the mask and unity outside, at a wavelength :math:`\lambda` and starshade-telescope distance :math:`z`, the field at the telescope aperture is :math:`f_{\lambda}(x, y)` (Eq :eq:`bluestein`) and is related to the Fourier transform of the starshade mask multipled by a highly oscillatory chirp term.
  |                                                                                                                                                                                                                                                                                                                                                                                                                                                          ^^^^^^^^^
  |
error: `Sebastiaan` should be `Sebastian`
  --> docs/paper/paper.bib:58:49
   |
58 |        author = {{Por}, Emiel H. and {Haffert}, Sebastiaan Y. and {Radhakrishnan}, Vikram M. and {Doelman}, David S. and {van Kooten}, Maaike and {Bos}, Steven P.},
   |                                                 ^^^^^^^^^^
   |
error: `wiht` should be `with`
  --> pystarshade/simulate_field.py:117:71
    |
117 |     !!!!!!!! I need checking, likely replace with chunky crazy, along wiht functions in fresnel and fft
    |                                                                       ^^^^
    |