Use ruff for linting and autoformat code (#63)

* Use ruff and update pre-commit config
* Lint/autoformat code
* Remove flake8 test

.github/workflows/publish.yml

@@ -19,7 +19,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
         python setup.py sdist bdist_wheel
-    
+
     - name: Publish package
       uses: pypa/gh-action-pypi-publish@master
       with:

.github/workflows/test.yml

@@ -40,13 +40,6 @@ jobs:
       run: |
         python -m pip install -e .[develop]
 
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --ignore E501
-
     - name: Test with pytest
       run: |
         pytest tests

.pre-commit-config.yaml

@@ -17,40 +17,19 @@ repos:
     # -   id: check-json
     # -   id: check-added-large-files
 -   repo: https://github.com/myint/docformatter
-    rev: v1.5.1
+    rev: v1.6.0
     hooks:
     -   id: docformatter
--   repo: https://github.com/asottile/reorder_python_imports
-    rev: v3.9.0
-    hooks:
-    -   id: reorder-python-imports
-        args: [--py3-plus]
 -   repo: https://github.com/pre-commit/mirrors-autopep8
     rev: v2.0.2
     hooks:
     -   id: autopep8
         args: ['--in-place', '--ignore=E501,W504']
--   repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
-    hooks:
-    -   id: pyupgrade
-        args: ['--py36-plus']
--   repo: https://github.com/PyCQA/flake8
-    rev: '6.0.0'
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: 'v0.0.261'
     hooks:
-    -   id: flake8
-        args: ['--statistics', '--ignore=F401,F403,F405,F821,F841,E265,E501,A003']
-        additional_dependencies: [
-          'flake8-blind-except',
-          'flake8-commas',
-          'flake8-comprehensions',
-          'flake8-deprecated',
-          'flake8-mutable',
-          'flake8-quotes',
-          'flake8-tidy-imports',
-          # 'flake8-type-annotations',
-          'flake8-builtins',
-          ]
+    -   id: ruff
+        args: [--fix]
 -   repo: https://github.com/kynan/nbstripout
     rev: 0.6.1
     hooks:

MANIFEST.in

@@ -26,4 +26,4 @@ include instamatic/config/calibration/*.yaml
 include instamatic/config/camera/*.yaml
 include instamatic/config/microscope/*.yaml
 include instamatic/config/scripts/*.md
-include instamatic.neural_network/*.p
+include instamatic.neural_network/*.p

instamatic/TEMController/TEMController.py

@@ -5,17 +5,17 @@
 
 import numpy as np
 
-from .deflectors import *
-from .lenses import *
-from .microscope import Microscope
-from .stage import *
-from .states import *
 from instamatic import config
 from instamatic.camera import Camera
 from instamatic.exceptions import TEMControllerError
 from instamatic.formats import write_tiff
 from instamatic.image_utils import rotate_image
 
+from .deflectors import *
+from .lenses import *
+from .microscope import Microscope
+from .stage import *
+from .states import *
 
 _ctrl = None  # store reference of ctrl so it can be accessed without re-initializing
 
@@ -44,7 +44,6 @@ def initialize(tem_name: str = default_tem, cam_name: str = default_cam, stream:
     ctrl : `TEMController`
         Return TEM control object
     """
-
     print(f"Microscope: {tem_name}{' (server)' if use_tem_server else ''}")
     tem = Microscope(tem_name, use_server=use_tem_server)
 
@@ -267,7 +266,6 @@ def get_stagematrix(self, binning: int = None, mag: int = None, mode: int = None
         stagematrix : np.array[2, 2]
             Affine transformation matrix to convert from stage to pixel coordinates
         """
-
         if not mode:
             mode = self.mode.get()
         if not mag:
@@ -443,7 +441,6 @@ def to_dict(self, *keys) -> dict:
 
         self.to_dict('all') or self.to_dict() will return all properties
         """
-
         # Each of these costs about 40-60 ms per call on a JEOL 2100, stage is 265 ms per call
         funcs = {
             'FunctionMode': self.tem.getFunctionMode,
@@ -477,7 +474,6 @@ def to_dict(self, *keys) -> dict:
 
     def from_dict(self, dct: dict):
         """Restore microscope parameters from dict."""
-
         funcs = {
             # 'FunctionMode': self.tem.setFunctionMode,
             'GunShift': self.gunshift.set,

instamatic/TEMController/__init__.py

@@ -1,3 +1,2 @@
 from .microscope import Microscope
-from .TEMController import get_instance
-from .TEMController import initialize
+from .TEMController import get_instance, initialize

instamatic/TEMController/deflectors.py

@@ -1,7 +1,6 @@
 from collections import namedtuple
 from typing import Tuple
 
-
 DeflectorTuple = namedtuple('DeflectorTuple', ['x', 'y'])
 
 

instamatic/TEMController/fei_microscope.py

@@ -6,8 +6,8 @@
 from numpy import pi
 
 from instamatic import config
-from instamatic.exceptions import FEIValueError
-from instamatic.exceptions import TEMCommunicationError
+from instamatic.exceptions import FEIValueError, TEMCommunicationError
+
 logger = logging.getLogger(__name__)
 
 

instamatic/TEMController/fei_simu_microscope.py

@@ -6,8 +6,8 @@
 import comtypes.client
 
 from instamatic import config
-from instamatic.exceptions import FEIValueError
-from instamatic.exceptions import TEMCommunicationError
+from instamatic.exceptions import FEIValueError, TEMCommunicationError
+
 logger = logging.getLogger(__name__)
 
 

instamatic/TEMController/jeol_microscope.py

@@ -6,8 +6,8 @@
 import comtypes.client
 
 from instamatic import config
-from instamatic.exceptions import JEOLValueError
-from instamatic.exceptions import TEMCommunicationError
+from instamatic.exceptions import JEOLValueError, TEMCommunicationError
+
 logger = logging.getLogger(__name__)
 
 NTRLMAPPING = {

instamatic/TEMController/microscope.py

@@ -7,7 +7,6 @@
 
 def get_tem(interface: str):
     """Grab tem class with the specific 'interface'."""
-
     simulate = config.settings.simulate
 
     if config.settings.tem_require_admin:
@@ -39,7 +38,6 @@ def Microscope(name: str = None, use_server: bool = False):
 
     returns: TEM interface class
     """
-
     if name is None:
         interface = default_tem_interface
         name = interface

instamatic/TEMController/microscope_client.py

@@ -9,11 +9,8 @@
 from functools import wraps
 
 from instamatic import config
-from instamatic.exceptions import exception_list
-from instamatic.exceptions import TEMCommunicationError
-from instamatic.server.serializer import dumper
-from instamatic.server.serializer import loader
-
+from instamatic.exceptions import TEMCommunicationError, exception_list
+from instamatic.server.serializer import dumper, loader
 
 HOST = config.settings.tem_server_host
 PORT = config.settings.tem_server_port
@@ -78,7 +75,6 @@ def connect(self):
         print(f'Connected to TEM server ({HOST}:{PORT})')
 
     def __getattr__(self, func_name):
-
         try:
             wrapped = self._dct[func_name]
         except KeyError as e:
@@ -95,7 +91,6 @@ def wrapper(*args, **kwargs):
 
     def _eval_dct(self, dct):
         """Takes approximately 0.2-0.3 ms per call if HOST=='localhost'."""
-
         self.s.send(dumper(dct))
 
         response = self.s.recv(self._bufsize)

instamatic/TEMController/simu_microscope.py

@@ -5,7 +5,6 @@
 from instamatic import config
 from instamatic.exceptions import TEMValueError
 
-
 NTRLMAPPING = {
     'GUN1': 0,
     'GUN2': 1,

instamatic/TEMController/stage.py

@@ -5,7 +5,6 @@
 
 import numpy as np
 
-
 # namedtuples to store results from .get()
 StagePositionTuple = namedtuple('StagePositionTuple', ['x', 'y', 'z', 'a', 'b'])
 
@@ -110,8 +109,9 @@ def xy(self, values: Tuple[int, int]):
         self.set(x=x, y=y, wait=self._wait)
 
     def move_in_projection(self, delta_x: int, delta_y: int) -> None:
-        r"""y and z are always perpendicular to the sample stage. To achieve the movement
-        in the projection, x and yshould be broken down into the components z' and y'.
+        r"""y and z are always perpendicular to the sample stage. To achieve the
+        movement in the projection, x and yshould be broken down into the
+        components z' and y'.
 
         y = y' * cos(a)
         z = y' * sin(a)
@@ -262,7 +262,6 @@ def move_xy_with_backlash_correction(self, shift_x: int = None, shift_y: int = N
         wait: bool,
             block until stage movement is complete (JEOL only)
         """
-
         stage = self.get()
 
         if shift_x:

instamatic/acquire_at_items.py

@@ -66,7 +66,7 @@ def __init__(self, ctrl,
 
         if post_acquire:
             self._post_acquire = self.validate(post_acquire)
-            print(f'Post-acquire:', ', '.join([func.__name__ for func in self._post_acquire]))
+            print('Post-acquire:', ', '.join([func.__name__ for func in self._post_acquire]))
 
         self.backlash = backlash
 
@@ -139,8 +139,8 @@ def start(self, start_index: int = 0):
         start_index : int
             Start acquisition from this item.
         """
-        import time
         import msvcrt
+        import time
 
         ctrl = self.ctrl
         nav_items = self.nav_items[start_index:]

instamatic/browser.py

@@ -128,7 +128,7 @@ def onclick(self, event, double_click_delay=0.5):
             self.update_ax3(ind)
 
         if ind == self.current_ind and (t1 - self.t0 < double_click_delay):
-            print(f'Moving stage to:', self.coord)
+            print('Moving stage to:', self.coord)
             self.ctrl.stage.xy = self.coord
 
         self.t0 = time.perf_counter()

instamatic/calibrate/calibrate_beamshift.py

@@ -7,14 +7,14 @@
 import numpy as np
 from skimage.registration import phase_cross_correlation
 
-from .filenames import *
-from .fit import fit_affine_transformation
 from instamatic import config
-from instamatic.image_utils import autoscale
-from instamatic.image_utils import imgscale
+from instamatic.image_utils import autoscale, imgscale
 from instamatic.processing.find_holes import find_holes
-from instamatic.tools import find_beam_center
-from instamatic.tools import printer
+from instamatic.tools import find_beam_center, printer
+
+from .filenames import *
+from .fit import fit_affine_transformation
+
 logger = logging.getLogger(__name__)
 
 
@@ -133,7 +133,6 @@ def calibrate_beamshift_live(ctrl, gridsize=None, stepsize=None, save_images=Fal
     return:
         instance of Calibration class with conversion methods
     """
-
     exposure = kwargs.get('exposure', ctrl.cam.default_exposure)
     binsize = kwargs.get('binsize', ctrl.cam.default_binsize)
 
@@ -170,7 +169,7 @@ def calibrate_beamshift_live(ctrl, gridsize=None, stepsize=None, save_images=Fal
     for dx, dy in np.stack([x_grid, y_grid]).reshape(2, -1).T:
         ctrl.beamshift.set(x=x_cent + dx, y=y_cent + dy)
 
-        printer('Position: {}/{}: {}'.format(i + 1, tot, ctrl.beamshift))
+        printer(f'Position: {i + 1}/{tot}: {ctrl.beamshift}')
 
         outfile = os.path.join(outdir, 'calib_beamshift_{i:04d}') if save_images else None
 

instamatic/calibrate/calibrate_brightness.py

@@ -5,10 +5,12 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-from .filenames import *
 from instamatic.image_utils import autoscale
 from instamatic.processing.find_holes import find_holes
 from instamatic.tools import find_beam_center
+
+from .filenames import *
+
 logger = logging.getLogger(__name__)
 
 
@@ -88,7 +90,6 @@ def calibrate_brightness_live(ctrl, step=1000, save_images=False, **kwargs):
     return:
         instance of CalibBrightness class with conversion methods
     """
-
     raise NotImplementedError('calibrate_brightness_live function needs fixing...')
 
     exposure = kwargs.get('exposure', ctrl.cam.default_exposure)
@@ -140,7 +141,6 @@ def calibrate_brightness_from_image_fn(fns):
     return:
         instance of Calibration class with conversion methods
     """
-
     values = []
 
     for fn in fns:

instamatic/calibrate/calibrate_directbeam.py

@@ -7,12 +7,13 @@
 import numpy as np
 from skimage.registration import phase_cross_correlation
 
-from .filenames import *
-from .fit import fit_affine_transformation
 from instamatic import config
-from instamatic.image_utils import autoscale
-from instamatic.image_utils import imgscale
+from instamatic.image_utils import autoscale, imgscale
 from instamatic.tools import printer
+
+from .filenames import *
+from .fit import fit_affine_transformation
+
 logger = logging.getLogger(__name__)
 
 
@@ -195,7 +196,6 @@ def calibrate_directbeam_live(ctrl, key='DiffShift', gridsize=None, stepsize=Non
     return:
         instance of Calibration class with conversion methods
     """
-
     if ctrl.mode != 'diff':
         print(' >> Switching to diffraction mode')
         ctrl.mode.set('diff')

instamatic/calibrate/calibrate_imageshift12.py

@@ -5,11 +5,11 @@
 from tqdm.auto import tqdm
 
 from instamatic.calibrate.fit import fit_affine_transformation
+
 logger = logging.getLogger(__name__)
 
 
 def Calibrate_Imageshift(ctrl, diff_defocus, stepsize, logger, key='IS1'):
-
     if key != 'S':
         input(f"""Calibrate {key}
     -------------------