Fix flake8 warnings

.flake8

@@ -1,2 +1,3 @@
 [flake8]
-max-line-length = 120
+max-line-length = 120
+ignore = E266, W503

.github/workflows/python-app.yml → .github/workflows/python-package.yml

@@ -36,4 +36,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with unittest
       run: |
-        unittest discover
+        python -m unittest discover .

lcls_tools/common/beam_calcs/sol_calc/sol_calc.py

@@ -24,8 +24,8 @@
 
 
 class SolCalc(object):
-    def __init__(self, l, e_gun, d):
-        self._l = l  # Leff
+    def __init__(self, l_eff, e_gun, d):
+        self._l = l_eff  # Leff
         self._e_gun = e_gun  # MeV
         self._d = d  # distance from sol exit and bpm
         self._K = None
@@ -189,6 +189,5 @@ def gen_y_arr(self):
 
     def calc_offsets(self):
         """Solve the problem"""
-        r = np.array(self._x_vals + self._y_vals)
         self._results = pinv(np.vstack((self._x_arrays, self._y_arrays)))
         return self._results

lcls_tools/common/controls/pyepics/utils.py

@@ -105,6 +105,6 @@ def put(
             callback_data=callback_data,
         )
 
-        if retry and (status is not 1):
+        if retry and (status != 1):
             print(f"{self} put not successful, using caput")
             self.caput(value)

lcls_tools/common/data_analysis/fitting/fit_gaussian.py

@@ -11,15 +11,15 @@
 from numpy import argsort, power, exp, zeros
 from scipy.optimize import curve_fit
 from operator import itemgetter
-from time import time
+
 
 NUM_BUCKS = 10
 DEBUG = False
 
 
 # An unfortunate consequence of defining step as max/numbucks is that the
 # maximum point is in its own bucket (bucket 10), which would break a lot of
-# shit, so it necessitates the error checking
+# stuff, so it necessitates the error checking
 def get_bucket(val, step):
     bucket = int(floor(val / step))
     return bucket if bucket < 10 else 9  # TODO: should this use NUM_BUCKS?
@@ -80,7 +80,7 @@ def get_slope(x1, y1, x2, y2):
 # Idea to add a line instead of a really short, fat gaussian was all Ahemd.
 # Thanks, yo. You're great.
 def find_line(zero_runs, runs, xdata, ydata):
-    x1, y1, x2, y2, m, b = (0, 0, 0, 0, 0, 0)
+    x1, y1, x2, y2, m, _ = (0, 0, 0, 0, 0, 0)
 
     # This condition should only be possible if there are peaks on one or both
     # extremes, or if there is no peak
@@ -198,7 +198,6 @@ def get_runs(data, step):
 # A whole rigmarole to collapse multiple pedestals.
 # It assumes that the pedestal is the bucket with the most elements
 def adjust_data(data, step):
-    start = time()
     normalized_adjustment = 0
 
     bucket_count = zeros(NUM_BUCKS)

lcls_tools/common/devices/profile_monitor/profile_monitor.py

@@ -2,11 +2,10 @@
 
 from epics import PV
 import lcls_tools.common.devices.profile_monitor.profmon_constants as pc
-from inspect import getmembers
 from time import sleep
 from threading import Thread
 from numpy import array_equal
-from functools import partial
+
 
 # Implementation needs to be thought out, just a POC
 

lcls_tools/common/image_processing/image_processing.py

@@ -1,10 +1,8 @@
 import numpy as np
 import scipy.ndimage as snd
-from scipy.optimize import curve_fit
 from scipy import asarray
 import matplotlib.pyplot as plt
 import lcls_tools.common.data_analysis.fitting.fit_gaussian as fg
-from time import time
 
 
 def fliplr(image):

lcls_tools/common/logger/__init__.py

@@ -1 +0,0 @@
-from .logger import custom_logger

lcls_tools/common/matlab2py/cor_plot/cor_plot_mat_scan.py

@@ -1,6 +1,5 @@
 import os
 import scipy.io as sio
-import numpy as np
 
 FIT = [
     "Gaussian",
@@ -211,10 +210,9 @@ def _unpack_prof(self, data):
 
         idx = self._fields.index(PROF)
         prof = data[idx]
-        names = prof.dtype.names
         prof_pvs = dict()
         for pv in prof:
-            if isinstance(pv[0][0][0], unicode):  # one sample
+            if isinstance(pv[0][0][0], bytes):  # one sample
                 prof_pvs[str(pv[0][0][0])] = pv
             else:  # Multiple samples
                 prof_pvs[str(pv[0][0][0][0])] = pv

lcls_tools/common/matlab2py/emit_scan/mat_emit_scan.py

@@ -1,5 +1,4 @@
 import scipy.io as sio
-import numpy as np
 import os
 
 VAL = "val"
@@ -301,7 +300,7 @@ def _unpack_twiss_pv(self, data):
             temp2 = dict()
             for i, name in enumerate(names):
                 if name != UNITS:
-                    if isinstance(val[0][i][0], unicode):
+                    if isinstance(val[0][i][0], bytes):
                         temp2[name] = str(val[0][i][0])
                     else:
                         temp2[name] = val[0][i][0]

lcls_tools/common/matlab2py/image/mat_image.py

@@ -1,4 +1,3 @@
-import scipy.ndimage as snd
 from numpy import ndarray
 import numpy as np
 import scipy.io as sio

lcls_tools/superconducting/scLinac.py

@@ -1696,7 +1696,7 @@ def __init__(
         stepper_class=StepperTuner,
         piezo_class=Piezo,
     ):
-        # type: (str, Linac, Type[Cavity], Type[Magnet], Type[Rack], bool, Type[SSA], Type[StepperTuner], Type[Piezo]) -> None
+        # type: (str, Linac, Type[Cavity], Type[Magnet], Type[Rack], bool, Type[SSA], Type[StepperTuner], Type[Piezo],) -> None # noqa: E501
         """
         Parameters
         ----------

requirements.txt

@@ -3,3 +3,5 @@ numpy
 scipy
 matplotlib
 pyepics
+pyyaml
+requests

tests/unit_tests/lcls_tools/common/data_analysis/test_archiver.py

@@ -2,7 +2,6 @@
 from lcls_tools.common.data_analysis.archiver import (
     Archiver,
     ArchiverData,
-    ARCHIVER_URL_FORMATTER,
 )
 from datetime import datetime, timedelta
 import requests

tests/unit_tests/lcls_tools/common/devices/profile_monitor/test_profile_monitor.py

@@ -1,5 +1,4 @@
 # Built in
-import sys
 import unittest
 import inspect
 

tests/unit_tests/lcls_tools/common/devices/test_device.py

@@ -126,9 +126,15 @@ def mock_callback(message: str) -> None:
             print(f"callback: {message}")
 
         # Add different callbacks to Device
-        first_callback = lambda: mock_callback("first")
-        second_callback = lambda: mock_callback("second")
-        third_callback = lambda: mock_callback("third")
+        def first_callback():
+            mock_callback("first")
+
+        def second_callback():
+            mock_callback("second")
+
+        def third_callback():
+            mock_callback("third")
+
         self.device.add_callback_to_pv(
             "bact",
             first_callback,

tests/unit_tests/lcls_tools/common/image_processing/test_image_processing.py

@@ -1,4 +1,3 @@
-import sys
 import unittest
 import os
 import numpy as np

tests/unit_tests/lcls_tools/common/matlab2py/cor_plot/test_cor_plot_mat_scan.py

@@ -1,6 +1,5 @@
 import os
 import unittest
-import numpy as np
 from lcls_tools.common.matlab2py.cor_plot.cor_plot_mat_scan import (
     CorPlotMatScan as CPMS,
 )

tests/unit_tests/lcls_tools/common/matlab2py/emit_scan/test_mat_emit_scan.py

@@ -1,6 +1,5 @@
 import os
 import unittest
-import numpy as np
 from lcls_tools.common.matlab2py.emit_scan.mat_emit_scan import MatEmitScan as MES