F811, F523/F524, F841, F741 - Corrections in crystal.py

.flake8

@@ -0,0 +1,23 @@
+[flake8]
+extend-ignore =
+    E114,
+    E115,
+    E116,
+    E201,
+    E202,
+    E203,
+    E204,
+    E231,
+    E265,
+    E266,
+    E303,
+    E402,
+    E501,
+exclude =
+    ; __init__.py # totally ignore __init__.py files
+    setup.py # ignore setup.py file
+    docs/
+#F401 ignore unused imports in __init__.py files
+#F403 ignore unable to detect undefined names from import *
+per-file-ignores =
+    __init__.py:F401,F403

.github/workflows/linter.yml

@@ -1,4 +1,4 @@
-name: Check for errors with flake8
+name: Lint with super-linter@v5-slim
 
 on:
   push:
@@ -17,9 +17,14 @@ jobs:
           fetch-depth: 0
 
       - name: Lint Code Base
-        uses: github/super-linter@v4
+        uses: super-linter/super-linter/slim@v5 # updated to latest slim as quicker to download 
         env:
-          VALIDATE_ALL_CODEBASE: false
-          VALIDATE_PYTHON_FLAKE8: true
-          DEFAULT_BRANCH: "dev"
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          VALIDATE_ALL_CODEBASE: false # only check changes
+          VALIDATE_PYTHON_FLAKE8: true # lint with flake8
+          DEFAULT_BRANCH: "dev" # set default branch to dev
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # for github things
+          # FILTER_REGEX_EXCLUDE: .*test/.* # exclude test dirs
+          FILTER_REGEX_EXCLUDE: .*__init__.py/.* # exclude test dirs
+          FILTER_REGEX_INCLUDE: .*py4DSTEM/.* # only look for py4DSTEM
+          LINTER_RULES_PATH: / # set toplevel dir as the path to look for rules
+          PYTHON_FLAKE8_CONFIG_FILE: .flake8 # set specific config file

py4DSTEM/process/diffraction/crystal.py

@@ -34,7 +34,6 @@ class Crystal:
         save_ang_file,
         symmetry_reduce_directions,
         orientation_map_to_orix_CrystalMap,
-        save_ang_file,
     )
 
     from py4DSTEM.process.diffraction.crystal_viz import (
@@ -433,41 +432,31 @@ def from_unitcell_parameters(
         elif lattice_type == "hexagonal":
             assert (
                 len(latt_params) == 2
-            ), "2 lattice parametere are expected for hexagonal: a, c, but given {len(latt_params)}".format(
-                len(latt_params)
-            )
+            ), f"2 lattice parametere are expected for hexagonal: a, c, but given {len(latt_params)}"
             lattice = mg.core.Lattice.hexagonal(latt_params[0], latt_params[1])
         elif lattice_type == "tetragonal":
             assert (
                 len(latt_params) == 2
-            ), "2 lattice parametere are expected for tetragonal: a, c, but given {len(latt_params)}".format(
-                len(latt_params)
-            )
+            ), f"2 lattice parametere are expected for tetragonal: a, c, but given {len(latt_params)}"
             lattice = mg.core.Lattice.tetragonal(latt_params[0], latt_params[1])
         elif lattice_type == "orthorhombic":
             assert (
                 len(latt_params) == 3
-            ), "3 lattice parametere are expected for orthorhombic: a, b, c, but given {len(latt_params)}".format(
-                len(latt_params)
-            )
+            ), f"3 lattice parametere are expected for orthorhombic: a, b, c, but given {len(latt_params)}"
             lattice = mg.core.Lattice.orthorhombic(
                 latt_params[0], latt_params[1], latt_params[2]
             )
         elif lattice_type == "monoclinic":
             assert (
                 len(latt_params) == 4
-            ), "4 lattice parametere are expected for monoclinic: a, b, c, beta,  but given {len(latt_params)}".format(
-                len(latt_params)
-            )
+            ), f"4 lattice parametere are expected for monoclinic: a, b, c, beta,  but given {len(latt_params)}"
             lattice = mg.core.Lattice.monoclinic(
                 latt_params[0], latt_params[1], latt_params[2], latt_params[3]
             )
         else:
             assert (
                 len(latt_params) == 6
-            ), "all 6 lattice parametere are expected: a, b, c, alpha, beta, gamma, but given {len(latt_params)}".format(
-                len(latt_params)
-            )
+            ), f"all 6 lattice parametere are expected: a, b, c, alpha, beta, gamma, but given {len(latt_params)}"
             lattice = mg.core.Lattice.from_parameters(
                 latt_params[0],
                 latt_params[1],
@@ -659,9 +648,6 @@ def generate_diffraction_pattern(
             print("Accelerating voltage not set. Assuming 300 keV!")
             self.setup_diffraction(300e3)
 
-        # Tolerance for angular tests
-        tol = 1e-6
-
         # Parse orientation inputs
         if orientation is not None:
             if ind_orientation is None:
@@ -720,9 +706,9 @@ def generate_diffraction_pattern(
         gy_proj = g_diff[1, keep_int]
 
         # Diffracted peak labels
-        h = hkl[0, keep_int]
-        k = hkl[1, keep_int]
-        l = hkl[2, keep_int]
+        h = hkl[0, keep_int]  # noqa: E741
+        k = hkl[1, keep_int]  # noqa: E741
+        l = hkl[2, keep_int]  # noqa: E741
 
         # Output as PointList
         if keep_qz:
@@ -815,9 +801,7 @@ def generate_ring_pattern(
             )
 
         # check accelerating voltage
-        if hasattr(self, "accel_voltage"):
-            accelerating_voltage = self.accel_voltage
-        else:
+        if not hasattr(self, "accel_voltage"):
             self.accel_voltage = 300e3
             print("Accelerating voltage not set. Assuming 300 keV!")