Merge branch 'main' into improve-graph-app

.github/workflows/checks.yaml

@@ -42,10 +42,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        hook:
-          - "end-of-file-fixer"
-          - "trailing-whitespace"
-          - "mixed-line-ending"
+        - cmd: "end-of-file-fixer"
+        - cmd: "trailing-whitespace"
+        - cmd: "mixed-line-ending"
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.12

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
       - id: mixed-line-ending
         args: [ --fix=lf ]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0  # ruff version
+    rev: v0.8.6  # ruff version
     hooks:
       - id: ruff-format
       - id: ruff

pyproject.toml

@@ -40,7 +40,10 @@ tests = [
     "pytest-benchmark",
     "requests_mock",
 ]
-dev = ["pre-commit>=3.7.1", "ruff==0.5.0"]
+dev = [
+    "pre-commit>=3.7.1",
+    "ruff==0.8.6",
+]
 docs = [
     "sphinx==6.1.3",
     "sphinx-autodoc-typehints==1.22.0",
@@ -80,7 +83,9 @@ branch = true
 
 [tool.ruff]
 src = ["src"]
-exclude = ["docs/source/conf.py"]
+exclude = [
+    "docs/source/conf.py",
+]
 lint.select = [
     "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
     "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
@@ -107,10 +112,14 @@ lint.select = [
     "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
     "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
     "SLF",  # https://docs.astral.sh/ruff/rules/#flake8-self-slf
+    "SLOT",  # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
     "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
     "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
     "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
     "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "PLC",  # https://docs.astral.sh/ruff/rules/#convention-c
+    "PLE",  # https://docs.astral.sh/ruff/rules/#error-e_1
+    "TRY",  # https://docs.astral.sh/ruff/rules/#tryceratops-try
     "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
     "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
     "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
@@ -129,14 +138,15 @@ lint.fixable = [
     "PT",
     "RSE",
     "SIM",
+    "PLC",
+    "PLE",
+    "TRY",
     "PERF",
     "FURB",
     "RUF"
 ]
 
 # ANN003 - missing-type-kwargs
-# ANN101 - missing-type-self
-# ANN102 - missing-type-cls
 # D203 - one-blank-line-before-class
 # D205 - blank-line-after-summary
 # D206 - indent-with-spaces*
@@ -149,18 +159,19 @@ lint.fixable = [
 # E117 - over-indented*
 # E501 - line-too-long*
 # W191 - tab-indentation*
+# PLC0206 - dict-index-missing-items
 # *ignored for compatibility with formatter
 lint.ignore = [
-    "ANN003", "ANN101", "ANN102",
+    "ANN003",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
     "W191",
-    "E722"
+    "E722",
+    "PLC0206",
 ]
 
 [tool.ruff.lint.per-file-ignores]
 # ANN001 - missing-type-function-argument
-# ANN102 - missing-type-cls
 # ANN2 - missing-return-type
 # D100 - undocumented-public-module
 # D101 - undocumented-public-class
@@ -171,7 +182,6 @@ lint.ignore = [
 # INP001 - implicit-namespace-package
 "tests/*" = [
     "ANN001",
-    "ANN102",
     "ANN2",
     "S101",
     "B011",

src/dgipy/__init__.py

@@ -14,15 +14,15 @@
 from .network_graph import create_network, generate_cytoscape
 
 __all__ = [
+    "SourceType",
+    "generate_app",
+    "get_all_genes",
+    "get_categories",
+    "get_drug_applications",
     "get_drugs",
     "get_genes",
     "get_interactions",
-    "get_categories",
     "get_sources",
-    "SourceType",
-    "get_all_genes",
-    "get_drug_applications",
-    "generate_app",
     "create_network",
     "generate_cytoscape",
 ]

src/dgipy/dgidb.py

@@ -153,6 +153,7 @@ def get_interactions(
     :param approved: filter option for approved interactions
     :param api_url: API endpoint for GraphQL request
     :return: interaction results for terms
+    :raise ValueError: if invalid `search` arg used
     """
     params: dict[str, str | int | bool | list[str]] = {"names": terms}
     if immunotherapy is not None:
@@ -179,7 +180,7 @@ def get_interactions(
         results = raw_results["drugs"]["nodes"]
     else:
         msg = "Search type must be specified using: search='drugs' or search='genes'"
-        raise Exception(msg)
+        raise ValueError(msg)
     output = {
         "gene_name": [],
         "gene_concept_id": [],

src/dgipy/queries/__init__.py

@@ -41,8 +41,8 @@ def query(self) -> DocumentNode:
 
 
 __all__ = [
-    "get_all_genes",
     "get_all_drugs",
+    "get_all_genes",
     "get_drug_applications",
     "get_drugs",
     "get_gene_categories",

src/dgipy/vcf.py

@@ -52,10 +52,11 @@ def annotate(filepath: Path, contig: str) -> pd.DataFrame:
     :param filepath: link to a valid VCF file
     :param contig: specified chromosome (i.e. chr7)
     :return: Dataframe of drug-gene interactions
+    :raise TypeError: if filepath arg is not of type ``Path``
     """
     if not isinstance(filepath, Path):
         msg = "Filepath argument must be a valid pathlib.Path object"
-        raise ValueError(msg)
+        raise TypeError(msg)
 
     # Open VCF file
     records = _process_vcf(filepath, contig)

tests/test_dgidb.py

@@ -217,7 +217,7 @@ def test_get_drug_applications(fixtures_dir, set_up_graphql_mock: Callable):
         assert results["drug_dosage_form"][0] == ProductDosageForm.TABLET
 
 
-@pytest.mark.performance()
+@pytest.mark.performance
 def test_get_interactions_benchmark(benchmark):
     """Skipped by default -- call pytest with `--performance` flag to run.