Update ruff rules

pyproject.toml

@@ -8,7 +8,6 @@ reportUnknownArgumentType = "warning"
 
 [tool.ruff]
 output-format="concise"
-line-length = 90
 exclude = ["node_modules", "__pycache__"]
 lint.select = [
     "F",  # Pyflakes
@@ -19,11 +18,19 @@ lint.select = [
     "R",  # Ruff-specific
     "N",  # Naming
     "I",  # Import conventions
+    "SIM",  # flake8-simplify
+    "UP",  # pyupgrade
+    "RUF",  # ruff-specific rules
+    "ARG",  # flake8-unused-arguments
+    "TRY",  # tryceratops
+    "PLR0402", # import a.b as b -> from a import b
 ]
 
 lint.ignore = [
     "E501",  # Example: Ignore line length warnings
     "D",     # Ignore all docstring-related warnings
+    "ARG002",# Ignore unused-argument in method > problematic eg when required by parent class / interface
+    "TRY003",# Allow to write exception messages in place instead of subclassing
 ]
 
 [tool.ruff.format]

tests/ci/lint.sh

@@ -1,28 +1,45 @@
-#!/bin/bash
 #===============================================================================
 # Description: Runs ruff either on all Python files or only on changed files
-#             compared to master branch using a specified Singularity container
+# compared to master branch using a specified Singularity container
 #
 # Arguments:
-#   $1 - Path to Singularity (.sif) container
-#   $2 - Optional: "--all" to run on all files, otherwise runs only on changed files
+# $1 - Path to Singularity (.sif) container
+# $2 - Optional: "--all" to run on all files, otherwise runs only on changed files
+# $3+ - Optional: Additional arguments passed directly to ruff
 #
 # Usage:
-#   tests/ci/lint.sh container.sif         # Lint only changed Python files
-#   tests/ci/lint.sh container.sif --all   # Lint all Python files
-#   (run from top level directory!)
+# tests/ci/lint.sh container.sif # Lint only changed Python files
+# tests/ci/lint.sh container.sif --all # Lint all Python files
+# tests/ci/lint.sh container.sif --all --select E501,F401 # Lint all files with specific rules
+# tests/ci/lint.sh container.sif "" --fix # Fix changed files
+# (run from top level directory!)
 #
 # Dependencies:
-#   - Singularity/Apptainer + container
-#   - Container must have ruff installed
+# - Singularity/Apptainer + container
+# - Container must have ruff installed
 #===============================================================================
 
-if [ "$2" = "--all" ]; then
-    apptainer exec "$1" ruff check .
+# Store the container path
+CONTAINER="$1"
+shift
+
+# Check if --all flag is present
+if [ "$1" = "--all" ]; then
+    # Remove --all from arguments
+    shift
+    # Run ruff on all files with any remaining arguments
+    apptainer exec "$CONTAINER" ruff check . "$@"
 else
+    # If first arg isn't --all, put it back in the argument list
+    if [ -n "$1" ]; then
+        set -- "$1" "$@"
+    fi
+
+    # Get changed Python files
     changed_files=$(git diff --name-only origin/master...HEAD -- '*.py')
     if [ -n "$changed_files" ]; then
-        apptainer exec "$1" ruff check $(git diff --name-only origin/master...HEAD -- '*.py')
+        # Run ruff on changed files with any remaining arguments
+        apptainer exec "$CONTAINER" ruff check $(git diff --name-only origin/master...HEAD -- '*.py') "$@"
     else
         echo "No .py files changed"
     fi