style: fix ruff settings

cancervariants · Dec 12, 2023 · c1d87ac · c1d87ac
1 parent c747340
commit c1d87ac
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Showing 30 changed files with 2,782 additions and 2,786 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,5 +10,6 @@ repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   rev: v0.1.2
   hooks:
-    - id: ruff
     - id: ruff-format
+    - id: ruff
+      args: [ --fix, --exit-non-zero-on-fix ]
diff --git a/docs/scripts/generate_normalize_figure.py b/docs/scripts/generate_normalize_figure.py
@@ -18,9 +18,9 @@
 from gene.schemas import UnmergedNormalizationService
 
 COLORS = [
-    "#F8766D",
-    "#00BA38",
-    "#00B9E3",
+    '#F8766D',
+    '#00BA38',
+    '#00B9E3',
 ]
 
 
@@ -30,50 +30,50 @@ def create_gjgf(result: UnmergedNormalizationService) -> Dict:
     :param result: result from Unmerged Normalization search
     """
     graph = {
-        "graph": {
-            "label": "tmp",
-            "nodes": {},
-            "edges": [],
-            "metadata": {
-                "arrow_size": 15,
-                "node_size": 15,
-                "node_label_size": 20,
-                "edge_size": 2,
+        'graph': {
+            'label': 'tmp',
+            'nodes': {},
+            'edges': [],
+            'metadata': {
+                'arrow_size': 15,
+                'node_size': 15,
+                'node_label_size': 20,
+                'edge_size': 2,
             },
         }
     }
 
-    for i, (source, matches) in enumerate(result.source_matches.items()):
+    for i, (_, matches) in enumerate(result.source_matches.items()):
         for match in matches.records:
-            graph["graph"]["nodes"][match.concept_id] = {
-                "metadata": {
-                    "color": COLORS[i],
-                    "hover": f"{match.concept_id}\n{match.symbol}\n<i>{match.label}</i>",  # noqa: E501
-                    "click": f"<p color='black'>{json.dumps(match.model_dump(), indent=2)}</p>",  # noqa: E501
+            graph['graph']['nodes'][match.concept_id] = {
+                'metadata': {
+                    'color': COLORS[i],
+                    'hover': f'{match.concept_id}\n{match.symbol}\n<i>{match.label}</i>',
+                    'click': f"<p color='black'>{json.dumps(match.model_dump(), indent=2)}</p>",
                 }
             }
             for xref in match.xrefs:
-                graph["graph"]["edges"].append(
-                    {"source": match.concept_id, "target": xref}
+                graph['graph']['edges'].append(
+                    {'source': match.concept_id, 'target': xref}
                 )
 
     included_edges = []
-    for edge in graph["graph"]["edges"]:
+    for edge in graph['graph']['edges']:
         if (
-            edge["target"] in graph["graph"]["nodes"]
-            and edge["source"] in graph["graph"]["nodes"]
+            edge['target'] in graph['graph']['nodes']
+            and edge['source'] in graph['graph']['nodes']
         ):
             included_edges.append(edge)
-    graph["graph"]["edges"] = included_edges
+    graph['graph']['edges'] = included_edges
 
-    included_nodes = {k["source"] for k in graph["graph"]["edges"]}.union(
-        {k["target"] for k in graph["graph"]["edges"]}
+    included_nodes = {k['source'] for k in graph['graph']['edges']}.union(
+        {k['target'] for k in graph['graph']['edges']}
     )
     new_nodes = {}
-    for key, value in graph["graph"]["nodes"].items():
+    for key, value in graph['graph']['nodes'].items():
         if key in included_nodes:
             new_nodes[key] = value
-    graph["graph"]["nodes"] = new_nodes
+    graph['graph']['nodes'] = new_nodes
 
     return graph
 
@@ -82,45 +82,45 @@ def gen_norm_figure() -> None:
     """Generate normalized graph figure for docs."""
     q = QueryHandler(create_db())
 
-    otx2p1 = "OTX2P1"
-    otx2p2 = "OTX2P2"
+    otx2p1 = 'OTX2P1'
+    otx2p2 = 'OTX2P2'
 
     otx2p1_result = q.normalize_unmerged(otx2p1)
     otx2p2_result = q.normalize_unmerged(otx2p2)
 
     otx2p1_graph = create_gjgf(otx2p1_result)
     otx2p2_graph = create_gjgf(otx2p2_result)
 
-    nodes = otx2p1_graph["graph"]["nodes"]
-    nodes.update(otx2p2_graph["graph"]["nodes"])
+    nodes = otx2p1_graph['graph']['nodes']
+    nodes.update(otx2p2_graph['graph']['nodes'])
 
     graph = {
-        "graph": {
-            "label": f"Reference network for {otx2p1} and {otx2p2}",
-            "metadata": otx2p1_graph["graph"]["metadata"],
-            "nodes": nodes,
-            "edges": otx2p1_graph["graph"]["edges"] + otx2p2_graph["graph"]["edges"],
+        'graph': {
+            'label': f'Reference network for {otx2p1} and {otx2p2}',
+            'metadata': otx2p1_graph['graph']['metadata'],
+            'nodes': nodes,
+            'edges': otx2p1_graph['graph']['edges'] + otx2p2_graph['graph']['edges'],
         }
     }
 
     fig = gv.d3(
         data=graph,
         graph_height=250,
         node_hover_neighborhood=True,
-        node_label_font="arial",
+        node_label_font='arial',
     )
     fig.export_html(
         (
             APP_ROOT.parents[0]
-            / "docs"
-            / "source"
-            / "_static"
-            / "html"
-            / "normalize_example.html"
+            / 'docs'
+            / 'source'
+            / '_static'
+            / 'html'
+            / 'normalize_example.html'
         ).absolute(),
         overwrite=True,
     )
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     gen_norm_figure()
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -57,14 +57,14 @@
     ],
 }
 # -- autodoc things ----------------------------------------------------------
-import os  # noqa: E402
-import sys  # noqa: E402
+import os
+import sys
 
 sys.path.insert(0, os.path.abspath("../../gene"))
 autodoc_preserve_defaults = True
 
 # -- get version -------------------------------------------------------------
-from gene import __version__  # noqa: E402
+from gene import __version__
 
 version = __version__
 release = version
@@ -77,7 +77,7 @@ def linkcode_resolve(domain, info):
     if not info["module"]:
         return None
     filename = info["module"].replace(".", "/")
-    return f"https://github.com/cancervariants/gene-normalization/blob/main/{filename}.py"  # noqa: E501
+    return f"https://github.com/cancervariants/gene-normalization/blob/main/{filename}.py"
 
 
 # -- code block style --------------------------------------------------------

diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
@@ -48,7 +48,7 @@ When running the web server, enable hot-reloading on new code changes: ::
 Style
 -----
 
-Code style is managed by `Ruff <https://github.com/astral-sh/ruff>`_ and `Black <https://github.com/psf/black>`_, and should be checked via pre-commit hook before commits. Final QC is applied with GitHub Actions to every pull request.
+Code style is managed by `Ruff <https://github.com/astral-sh/ruff>`_, and should be checked via pre-commit hook before commits. Final QC is applied with GitHub Actions to every pull request.
 
 Tests
 -----

diff --git a/pyproject.toml b/pyproject.toml
@@ -92,38 +92,44 @@ exclude = ["docs/source/conf.py"]
 # pycodestyle (E, W)
 # Pyflakes (F)
 # flake8-annotations (ANN)
-# flake8-quotes (Q)
 # pydocstyle (D)
 # pep8-naming (N)
 # isort (I)
-select = ["E", "W", "F", "ANN", "Q", "D", "N", "I"]
-
+select = ["E", "W", "F", "ANN", "D", "N", "I"]
 fixable = ["I", "F401"]
 
 # D203 - one-blank-line-before-class
 # D205 - blank-line-after-summary
+# D206 - indent-with-spaces*
 # D213 - multi-line-summary-second-line
+# D300 - triple-single-quotes
 # D400 - ends-in-period
 # D415 - ends-in-punctuation
 # ANN101 - missing-type-self
 # ANN003 - missing-type-kwargs
-# E501 - line-too-long
-ignore = ["D203", "D205", "D213", "D400", "D415", "ANN101", "ANN003", "E501"]
+# E111 - indentation-with-invalid-multiple*
+# E114 - indentation-with-invalid-multiple-comment*
+# E117 - over-indented*
+# E501 - line-too-long*
+# W191 - tab-indentation*
+# *ignored for compatibility with formatter
+ignore = [
+    "D203", "D205", "D206", "D213", "D300", "D400", "D415",
+    "ANN101", "ANN003",
+    "E111", "E114", "E117", "E501",
+    "W191"
+]
 
-[tool.ruff.flake8-quotes]
-docstring-quotes = "double"
+[tool.ruff.format]
+quote-style = "single"
 
 [tool.ruff.per-file-ignores]
 # ANN001 - missing-type-function-argument
+# ANN102 - missing-type-cls
 # ANN2 - missing-return-type
 # ANN201 - Missing type annotation
-# ANN102 - missing-type-cls
-# D103 - Missing docstring in public function
-# F821 - undefined-name
-# F401 - unused-import
-# I001 - Import block unsorted or unformatted
+# D301 - escape-sequence-in-docstring
 # N805 - invalid-first-argument-name-for-method
 "tests/*" = ["ANN001", "ANN102", "ANN2"]
-"*__init__.py" = ["F401"]
-"gene/schemas.py" = ["ANN001", "ANN201", "N805"]
-"docs/source/conf.py" = ["D100", "I001", "D103", "ANN201", "ANN001"]
+"src/gene/schemas.py" = ["ANN001", "ANN201", "N805"]
+"src/gene/cli.py" = ["D301"]
diff --git a/src/gene/__init__.py b/src/gene/__init__.py
@@ -3,27 +3,25 @@
 from os import environ
 from pathlib import Path
 
-from .version import __version__  # noqa: F401
-
 APP_ROOT = Path(__file__).resolve().parent
 
 logging.basicConfig(
-    filename="gene.log", format="[%(asctime)s] - %(name)s - %(levelname)s : %(message)s"
+    filename='gene.log', format='[%(asctime)s] - %(name)s - %(levelname)s : %(message)s'
 )
-logger = logging.getLogger("gene")
+logger = logging.getLogger('gene')
 logger.setLevel(logging.DEBUG)
 logger.handlers = []
 
-logging.getLogger("boto3").setLevel(logging.INFO)
-logging.getLogger("botocore").setLevel(logging.INFO)
-logging.getLogger("urllib3").setLevel(logging.INFO)
-logging.getLogger("python_jsonschema_objects").setLevel(logging.INFO)
-logging.getLogger("biocommons.seqrepo.seqaliasdb.seqaliasdb").setLevel(logging.INFO)
-logging.getLogger("biocommons.seqrepo.fastadir.fastadir").setLevel(logging.INFO)
+logging.getLogger('boto3').setLevel(logging.INFO)
+logging.getLogger('botocore').setLevel(logging.INFO)
+logging.getLogger('urllib3').setLevel(logging.INFO)
+logging.getLogger('python_jsonschema_objects').setLevel(logging.INFO)
+logging.getLogger('biocommons.seqrepo.seqaliasdb.seqaliasdb').setLevel(logging.INFO)
+logging.getLogger('biocommons.seqrepo.fastadir.fastadir').setLevel(logging.INFO)
 
 
 SEQREPO_ROOT_DIR = Path(
-    environ.get("SEQREPO_ROOT_DIR", "/usr/local/share/seqrepo/latest")
+    environ.get('SEQREPO_ROOT_DIR', '/usr/local/share/seqrepo/latest')
 )
 
 
@@ -61,5 +59,5 @@ class DownloadException(Exception):  # noqa: N818
 NAMESPACE_LOOKUP = {
     v.value.lower(): NamespacePrefix[k].value
     for k, v in SourceIDAfterNamespace.__members__.items()
-    if v.value != ""
+    if v.value != ''
 }
-Original file line number
+Diff line change
@@ Expand Up @@
     Style
     -----
-    Code style is managed by `Ruff <https://github.com/astral-sh/ruff>`_ and `Black <https://github.com/psf/black>`_, and should be checked via pre-commit hook before commits. Final QC is applied with GitHub Actions to every pull request.
+    Code style is managed by `Ruff <https://github.com/astral-sh/ruff>`_, and should be checked via pre-commit hook before commits. Final QC is applied with GitHub Actions to every pull request.
     Tests
     -----
@@ Expand Down @@