Merge branch 'main' into remove-pipfile

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.14
+    rev: v0.2.0
     hooks:
       - id: ruff-format
       - id: ruff

pyproject.toml

@@ -37,7 +37,7 @@ dynamic = ["version"]
 [project.optional-dependencies]
 etl = ["disease-normalizer[etl]~=0.4.0.dev0", "owlready2", "rdflib", "wikibaseintegrator>=0.12.0", "wags-tails"]
 test = ["pytest", "pytest-cov", "pytest-mock"]
-dev = ["pre-commit", "ruff>=0.1.14", "lxml", "xmlformatter", "mypy", "types-pyyaml"]
+dev = ["pre-commit", "ruff==0.2.0", "lxml", "xmlformatter", "mypy", "types-pyyaml"]
 
 [project.urls]
 Homepage = "https://github.com/cancervariants/therapy-normalization"
@@ -76,6 +76,8 @@ ignore_missing_imports = true
 
 [tool.ruff]
 src = ["src"]
+
+[tool.ruff.lint]
 select = [
     "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
     "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
@@ -132,26 +134,27 @@ fixable = [
 # E114 - indentation-with-invalid-multiple-comment*
 # E117 - over-indented*
 # E501 - line-too-long*
-# W191 - tab-indentation*
 # PGH003 - blanket-type-ignore
+# W191 - tab-indentation*
+# S321 - suspicious-ftp-lib-usage
 # *ignored for compatibility with formatter
 ignore = [
     "ANN101", "ANN003",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
-    "W191",
     "PGH003",
+    "W191",
+    "S321",
 ]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # ANN001 - missing-type-function-argument
 # ANN2 - missing-return-type
-# ANN201 - Missing type annotation
 # ANN102 - missing-type-cls
-# N805 - invalid-first-argument-name-for-method
 # S101 - assert
 # B011 - assert-false
+# N805 - invalid-first-argument-name-for-method
 # RUF001 - ambiguous-unicode-character-string
-"tests/*" = ["ANN001", "ANN102", "ANN2", "S101", "B011"]
+"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011"]
 "tests/unit/test_emit_warnings.py" = ["RUF001"]
 "src/therapy/schemas.py" = ["ANN001", "ANN201", "N805"]

src/therapy/etl/rxnorm.py

@@ -273,7 +273,7 @@ def _add_term(params: Dict, term: str, label_type: str) -> None:
         :param Str term: The term to be added
         :param Str label_type: The type of term
         """
-        if label_type in params and params[label_type]:
+        if params.get(label_type):
             if term not in params[label_type]:
                 params[label_type].append(term)
         else: