chore(python): format and lint with ruff

.editorconfig

@@ -7,8 +7,8 @@ end_of_line = lf
 charset = utf-8
 trim_leading_whitespace = true
 insert_final_newline = true
-max_line_length = 100
 
 [*.py]
 indent_style = space
 indent_size = 4
+max_line_length = 88

.github/workflows/build.yml

@@ -56,7 +56,6 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - '3.8'
           - '3.9'
           - '3.10'
           - '3.11'

cors_webserver.py

@@ -23,38 +23,33 @@
 can connect to the web server.
 """
 
-from __future__ import print_function, absolute_import
 
 import argparse
 import os
 import sys
-
-try:
-    # Python3 and Python2 with future package.
-    from http.server import SimpleHTTPRequestHandler, HTTPServer
-except ImportError:
-    from BaseHTTPServer import HTTPServer
-    from SimpleHTTPServer import SimpleHTTPRequestHandler
+from http.server import HTTPServer, SimpleHTTPRequestHandler
 
 
 class RequestHandler(SimpleHTTPRequestHandler):
     def end_headers(self):
-        self.send_header('Access-Control-Allow-Origin', '*')
+        self.send_header("Access-Control-Allow-Origin", "*")
         SimpleHTTPRequestHandler.end_headers(self)
 
 
 class Server(HTTPServer):
-    protocol_version = 'HTTP/1.1'
+    protocol_version = "HTTP/1.1"
 
     def __init__(self, server_address):
         HTTPServer.__init__(self, server_address, RequestHandler)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     ap = argparse.ArgumentParser()
-    ap.add_argument('-p', '--port', type=int, default=9000, help='TCP port to listen on')
-    ap.add_argument('-a', '--bind', default='127.0.0.1', help='Bind address')
-    ap.add_argument('-d', '--directory', default='.', help='Directory to serve')
+    ap.add_argument(
+        "-p", "--port", type=int, default=9000, help="TCP port to listen on"
+    )
+    ap.add_argument("-a", "--bind", default="127.0.0.1", help="Bind address")
+    ap.add_argument("-d", "--directory", default=".", help="Directory to serve")
 
     args = ap.parse_args()
     os.chdir(args.directory)

noxfile.py

@@ -0,0 +1,22 @@
+import nox
+
+nox.options.reuse_existing_virtualenvs = True
+nox.options.error_on_external_run = True
+
+
+@nox.session
+def lint(session):
+    session.install("-r", "python/requirements-lint.txt")
+    session.run("ruff", "check", ".")
+
+
+@nox.session
+def format(session):
+    session.install("-r", "python/requirements-lint.txt")
+    session.run("ruff", "format", ".")
+
+
+@nox.session
+def mypy(session):
+    session.install("-r", "python/requirements-mypy.txt")
+    session.run("mypy", ".")

pyproject.toml

@@ -1,2 +1,50 @@
 [build-system]
-requires = ["setuptools>=64", "wheel", "setuptools_scm", "oldest-supported-numpy"]
+requires = [
+    "setuptools>=64",
+    "wheel",
+    "setuptools_scm",
+    "oldest-supported-numpy",
+]
+
+[tool.ruff]
+target-version = "py39"
+select = [
+    "E", # pycodestyle
+    "W", # pycodestyle
+    "F", # pyflakes
+    "I", # isort
+    "UP", # pyupgrade
+    "NPY", # numpy
+]
+ignore = [
+    "E501",  # Line length regulated by ruff format
+]
+
+[tool.mypy]
+show_error_codes = true
+pretty = true
+exclude = [
+    "noxfile\\.py",
+    "^src/",
+    "/guide_video_recorder/",
+    "^docs/",
+]
+
+[[tool.mypy.overrides]]
+module = [
+    "apitools",
+    "apitools.*",
+    "numcodecs",
+    "google",
+    "google.*",
+    "zarr",
+    "zarrita",
+    "tensorstore",
+    "dask",
+    "dask.*",
+    "scipy",
+    "scipy.*",
+    "cloudvolume",
+    "trio",
+]
+ignore_missing_imports = true

python/build_tools/cibuildwheel.sh

@@ -1,17 +1,14 @@
 #!/bin/bash
 
 export CIBW_ARCHS_MACOS="x86_64 arm64"
-export CIBW_SKIP="cp27-* cp36-* pp* *_i686 *-win32"
+export CIBW_SKIP="cp27-* cp36-* cp37-* cp38-* pp* *_i686 *-win32 *-musllinux*"
 export CIBW_TEST_EXTRAS="test"
 export CIBW_TEST_COMMAND="python -m pytest {project}/python/tests -vv -s --skip-browser-tests"
 export CIBW_MANYLINUX_X86_64_IMAGE=manylinux2014
 export CIBW_ENVIRONMENT_PASS_LINUX="NEUROGLANCER_BUILD_BUNDLE_INPLACE"
 
 export NEUROGLANCER_BUILD_BUNDLE_INPLACE=1
 
-# Skip testing on musllinux due to pillow binary wheels not being available.
-export CIBW_TEST_SKIP="*-musllinux*"
-
 script_dir="$(dirname "$0")"
 root_dir="${script_dir}/../.."
 cd "${root_dir}"

python/copy_openmesh_deps.py

@@ -7,27 +7,43 @@
 import sys
 
 script_dir = os.path.dirname(sys.argv[0])
-src_dir = os.path.join(script_dir, 'ext/src')
-dest_openmesh_dir = os.path.join(script_dir, 'ext/third_party/openmesh/OpenMesh')
+src_dir = os.path.join(script_dir, "ext/src")
+dest_openmesh_dir = os.path.join(script_dir, "ext/third_party/openmesh/OpenMesh")
 
 ap = argparse.ArgumentParser()
-ap.add_argument('openmesh_directory', help='Path to OpenMesh root directory')
+ap.add_argument("openmesh_directory", help="Path to OpenMesh root directory")
 args = ap.parse_args()
 
 openmesh_dir = os.path.abspath(args.openmesh_directory)
 
 deps = subprocess.check_output(
-    ['gcc', '-pthread', '-I', os.path.join(openmesh_dir, 'src'), '-c', 'openmesh_dependencies.cc',
-     'on_demand_object_mesh_generator.cc', '-MM', '-MF', '/dev/stdout',
-     '-fopenmp', '-std=c++11'], cwd=src_dir).split()
-deps = [x[len(openmesh_dir)+1:] for x in deps if x.startswith(openmesh_dir + '/')] + ['LICENSE', 'VERSION']
+    [
+        "gcc",
+        "-pthread",
+        "-I",
+        os.path.join(openmesh_dir, "src"),
+        "-c",
+        "openmesh_dependencies.cc",
+        "on_demand_object_mesh_generator.cc",
+        "-MM",
+        "-MF",
+        "/dev/stdout",
+        "-fopenmp",
+        "-std=c++11",
+    ],
+    text=True,
+    cwd=src_dir,
+).split()
+deps = [
+    x[len(openmesh_dir) + 1 :] for x in deps if x.startswith(openmesh_dir + "/")
+] + ["LICENSE", "VERSION"]
 
 if os.path.exists(dest_openmesh_dir):
-  shutil.rmtree(dest_openmesh_dir)
+    shutil.rmtree(dest_openmesh_dir)
 
 for dep in deps:
-  dest_path = os.path.join(dest_openmesh_dir, dep)
-  dest_dir = os.path.dirname(dest_path)
-  if not os.path.exists(dest_dir):
-    os.makedirs(dest_dir)
-  shutil.copyfile(os.path.join(openmesh_dir, dep), dest_path)
+    dest_path = os.path.join(dest_openmesh_dir, dep)
+    dest_dir = os.path.dirname(dest_path)
+    if not os.path.exists(dest_dir):
+        os.makedirs(dest_dir)
+    shutil.copyfile(os.path.join(openmesh_dir, dep), dest_path)

python/examples/agglomeration_split_tool_csv_to_sqlite.py

@@ -1,56 +1,83 @@
-import pandas
+import argparse
 import sqlite3
+
 import neuroglancer.equivalence_map
-import argparse
 import numpy as np
+import pandas
+
 
 def load_edges2(path, include_agglo_id=False):
-  edges = []
-  dtype = {'segment_a': np.uint64, 'segment_b': np.uint64, 'score': np.float64, 'x': np.int64, 'y': np.int64, 'z': np.int64}
-  if include_agglo_id:
-    dtype['agglo_id'] = np.uint64
-  df = pandas.read_csv(path, sep=',', dtype=dtype)
-  return df
+    dtype = {
+        "segment_a": np.uint64,
+        "segment_b": np.uint64,
+        "score": np.float64,
+        "x": np.int64,
+        "y": np.int64,
+        "z": np.int64,
+    }
+    if include_agglo_id:
+        dtype["agglo_id"] = np.uint64
+    df = pandas.read_csv(path, sep=",", dtype=dtype)
+    return df
 
 
 def write_db(edges_csv_path, output_path, include_agglo_id=False):
+    print("Loading edges")
+    edges = load_edges2(edges_csv_path, include_agglo_id=include_agglo_id)
+
+    all_eqs = neuroglancer.equivalence_map.EquivalenceMap()
+    print("Creating equivalence map for agglomeration")
+    for a, b in edges[["segment_a", "segment_b"]].values:
+        all_eqs.union(a, b)
+
+    conn = sqlite3.connect(output_path)
+    c = conn.cursor()
+
+    c.execute("CREATE TABLE supervoxels (supervoxel_id INTEGER, agglo_id INTEGER)")
+    c.execute(
+        "CREATE INDEX supervoxels_by_supervoxel_id_index ON supervoxels (supervoxel_id)"
+    )
+    c.execute("CREATE INDEX supervoxels_by_agglo_id_index ON supervoxels (agglo_id)")
+    c.execute(
+        "CREATE TABLE edges (agglo_id INTEGER, segment_a INTEGER, segment_b INTEGER, score REAL, x INTEGER, y INTEGER, z INTEGER)"
+    )
+    c.execute("CREATE INDEX edges_by_agglo_id_index ON edges (agglo_id)")
+
+    print("Writing supervoxels table")
+    c.executemany(
+        "INSERT INTO supervoxels VALUES (?,?)",
+        ((int(x), int(all_eqs[x])) for x in all_eqs),
+    )
+
+    print("Writing edges table")
+    c.executemany(
+        "INSERT INTO edges VALUES (?, ?, ?, ?, ?, ?, ?)",
+        (
+            (
+                int(all_eqs[segment_a]),
+                int(segment_a),
+                int(segment_b),
+                float(score),
+                int(x),
+                int(y),
+                int(z),
+            )
+            for (segment_a, segment_b), score, (x, y, z) in zip(
+                edges[["segment_a", "segment_b"]].values,
+                edges["score"].values,
+                edges[["x", "y", "z"]].values,
+            )
+        ),
+    )
+    print("Committing")
+    conn.commit()
+    conn.close()
+
+
+if __name__ == "__main__":
+    ap = argparse.ArgumentParser()
+    ap.add_argument("csv", help="Path to CSV file specifying edges.")
+    ap.add_argument("db", help="Output path to sqlite3 db.")
+    args = ap.parse_args()
 
-  print('Loading edges')
-  edges = load_edges2(edges_csv_path, include_agglo_id=include_agglo_id)
-
-  all_eqs = neuroglancer.equivalence_map.EquivalenceMap()
-  print('Creating equivalence map for agglomeration')
-  for a, b in edges[['segment_a', 'segment_b']].values:
-    all_eqs.union(a, b)
-
-  conn = sqlite3.connect(output_path)
-  c = conn.cursor()
-
-  c.execute('CREATE TABLE supervoxels (supervoxel_id INTEGER, agglo_id INTEGER)')
-  c.execute('CREATE INDEX supervoxels_by_supervoxel_id_index ON supervoxels (supervoxel_id)')
-  c.execute('CREATE INDEX supervoxels_by_agglo_id_index ON supervoxels (agglo_id)')
-  c.execute('CREATE TABLE edges (agglo_id INTEGER, segment_a INTEGER, segment_b INTEGER, score REAL, x INTEGER, y INTEGER, z INTEGER)')
-  c.execute('CREATE INDEX edges_by_agglo_id_index ON edges (agglo_id)')
-
-  print('Writing supervoxels table')
-  c.executemany('INSERT INTO supervoxels VALUES (?,?)',
-                ((int(x), int(all_eqs[x])) for x in all_eqs.keys()))
-
-  print('Writing edges table')
-  c.executemany(
-      'INSERT INTO edges VALUES (?, ?, ?, ?, ?, ?, ?)',
-      ((int(all_eqs[segment_a]), int(segment_a), int(segment_b), float(score), int(x), int(y), int(z))
-       for (segment_a, segment_b), score,
-       (x, y, z) in zip(edges[['segment_a', 'segment_b']].values, edges['score']
-                        .values, edges[['x', 'y', 'z']].values)))
-  print('Committing')
-  conn.commit()
-  conn.close()
-
-if __name__ == '__main__':
-  ap = argparse.ArgumentParser()
-  ap.add_argument('csv', help='Path to CSV file specifying edges.')
-  ap.add_argument('db', help='Output path to sqlite3 db.')
-  args = ap.parse_args()
-
-  write_db(args.csv, args.db)
+    write_db(args.csv, args.db)