A little Ruff around the edges

.github/workflows/ruff.yml

@@ -0,0 +1,40 @@
+name: Ruff Check
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  # Get all commits
+
+      - name: Get changed files
+        id: changed-files
+        uses: tj-actions/changed-files@v35
+        with:
+          files: '**/*.py'  # Adjust pattern for your file types
+
+      - name: Setup Python environment
+        uses: actions/setup-python@v3
+
+      - name: Install Ruff
+        run: pip install ruff
+
+      - name: Run Ruff on changed files
+        env:
+            ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }}
+        run: |
+            - run: |
+              if [ -n "${ALL_CHANGED_FILES}" ]; then
+                # for file in ${ALL_CHANGED_FILES}; do
+                # echo "$file was changed"
+                # done
+                ruff check ${ALL_CHANGED_FILES}
+              else
+                echo "No files changed"
+              fi
+

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ repos:
     hooks:
       - id: black
         language_version: python3.9
-  - repo: https://github.com/pycqa/flake8
-    rev: '6.1.0'  
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.0
     hooks:
-      - id: flake8
+      - id: ruff

py4DSTEM/__init__.py

@@ -1,7 +1,6 @@
 from py4DSTEM.version import __version__
 from emdfile import tqdmnd
 
-
 ### io
 
 # substructure

ruff.toml

@@ -0,0 +1,51 @@
+required-version = ">=0.5.0"
+target-version = "py311"
+[lint]
+# From Flake8 config
+# select = [
+#     # "F402", # module level import not at top of file
+#     # "F404", # future import not at top of file
+#     # # "F812", # list comprehension redefines name from outer scope
+#     # "F823", # local variable name referenced before assignment
+#     # # "F831", # duplicate argument name in function definition
+#     # "F821", # undefined name
+#     # "F822", # undefined name in __all__
+#     # "E112", # expected an indented block
+#     # "E902", # IOError
+#     # # "E999", # SyntaxError deprecated since
+# ]
+
+ignore = [
+    "E501", # line-too-long
+    "F401", # unused import
+
+    # exisiting errors in code base
+    # "E721", # do not compare types, use 'isinstance()'
+    # "F841", # local variable is assigned to but never used
+    # "E741", # ambiguous variable name
+    # "F541", # f-string is missing placeholders
+    # "E731", # do not assign a lambda expression, use a def
+    # "E714", # test for object identity should be 'is not'
+    # "F811", # redefinition of unused name
+    # "E722", # do not use bare except
+    # "F405", # name may be undefined, or defined from star imports
+    # "F523", # string-dot-format-extra-positional-argument
+    # "F403", # unable to detect undefined names
+    # "F524", # string-dot-format-missing-arguments
+    # "E402", # module level import not at top of file
+    # "E713", # test for membership should be 'not in'
+    # "E743", # ambiguous function name
+    # "E712", # true-false-comparison
+
+]
+
+exclude = ["test/**/*.py"] # ignore test files
+
+[lint.per-file-ignores]
+# Ignore specific lint errors for __init__.py files
+"**/__init__.py" = [
+    "F401", # Unspecified import
+    "F403", # Unable to detect undefined names
+    "E402"  # Module level import not at top of file
+]
+# "./test/**/*.py" = ["E501", "F401", "E402"] # line-too-long, unused import, import not at top of file