Updates to support using ruff for linting/formatting

.github/workflows/test-package.yml

@@ -29,12 +29,12 @@ jobs:
         pip install flake8 pytest pytest-astropy pytest-cov sphinx-astropy codecov
         # install package and requirements
         pip install ".[all]"
-    - name: Lint with flake8
+    - name: Lint with ruff
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        ruff check astrodbkit2 --select=E9,F63,F7,F82 --statistics
+        # exit-zero treats all errors as warnings.
+        ruff check astrodbkit2 --config=pyproject.toml --exit-zero
     - name: Test with pytest
       run: |
         pytest --cov --cov-config=setup.cfg --cov-report=term --cov-report=xml:coverage.xml

.pre-commit-config.yaml

@@ -7,4 +7,9 @@ repos:
 - repo: https://github.com/akaihola/darker
   rev: 1.7.2
   hooks:
-    - id: darker
+    - id: darker
+      args:
+        - --lint
+        - ruff check
+      additional_dependencies:
+          - ruff==0.3.7

astrodbkit2/astrodb.py

@@ -2,24 +2,25 @@
 
 __all__ = ["__version__", "Database", "or_", "and_", "create_database"]
 
-import os
 import json
+import os
 import sqlite3
+
 import numpy as np
 import pandas as pd
+import sqlalchemy.types as sqlalchemy_types
+from astropy.coordinates import SkyCoord
 from astropy.table import Table as AstropyTable
 from astropy.units.quantity import Quantity
-from astropy.coordinates import SkyCoord
-from sqlalchemy.orm import sessionmaker, declarative_base
-from sqlalchemy.orm.query import Query
+from sqlalchemy import Table, and_, create_engine, event, or_, text
 from sqlalchemy.engine import Engine
-import sqlalchemy.types as sqlalchemy_types
-from sqlalchemy import event, create_engine, Table
-from sqlalchemy import or_, and_, text
+from sqlalchemy.orm import declarative_base, sessionmaker
+from sqlalchemy.orm.query import Query
 from tqdm import tqdm
-from . import REFERENCE_TABLES, PRIMARY_TABLE, PRIMARY_TABLE_KEY, FOREIGN_KEY
-from .utils import json_serializer, get_simbad_names, deprecated_alias, datetime_json_parser
+
+from . import FOREIGN_KEY, PRIMARY_TABLE, PRIMARY_TABLE_KEY, REFERENCE_TABLES
 from .spectra import load_spectrum
+from .utils import datetime_json_parser, deprecated_alias, get_simbad_names, json_serializer
 
 try:
     from .version import version as __version__

astrodbkit2/schema_example.py

@@ -3,9 +3,11 @@
 # pylint: disable=unused-argument, unused-import
 
 import enum
+
 import sqlalchemy as sa
-from sqlalchemy import Boolean, Column, Float, ForeignKey, Integer, String, BigInteger, Enum, Date, DateTime
+from sqlalchemy import Boolean, Column, Enum, Float, ForeignKey, String
 from sqlalchemy.orm import validates
+
 from astrodbkit2.astrodb import Base
 from astrodbkit2.views import view
 

astrodbkit2/spectra.py

@@ -1,15 +1,16 @@
 """Functions to handle loading of spectrum objects"""
 
 import os
-import numpy as np
+
 import astropy.units as u
-from astropy.wcs import WCS
+import numpy as np
 from astropy.io import fits
 from astropy.nddata import StdDevUncertainty
 from astropy.units import Unit
+from astropy.wcs import WCS
 from specutils import Spectrum1D
-from specutils.io.registers import data_loader
 from specutils.io.parsing_utils import read_fileobj_or_hdulist
+from specutils.io.registers import data_loader
 
 # pylint: disable=no-member, unused-argument
 

astrodbkit2/tests/test_astrodb.py

@@ -1,19 +1,22 @@
 # Testing for astrodb
 
-import os
-import json
-import pytest
 import io
+import json
+import os
+
 import pandas as pd
+import pytest
 import sqlalchemy as sa
-from sqlalchemy.exc import IntegrityError
-from astropy.table import Table
 from astropy.coordinates import SkyCoord
-from astropy.units.quantity import Quantity
 from astropy.io import ascii
-from astrodbkit2.astrodb import Database, create_database, Base, copy_database_schema
-from astrodbkit2.views import view
+from astropy.table import Table
+from astropy.units.quantity import Quantity
+from sqlalchemy.exc import IntegrityError
+
+from astrodbkit2.astrodb import Database, copy_database_schema, create_database
 from astrodbkit2.schema_example import *
+from astrodbkit2.views import view
+
 try:
     import mock
 except ImportError:
@@ -26,7 +29,7 @@
 def test_nodatabase():
     connection_string = 'sqlite:///:memory:'
     with pytest.raises(RuntimeError, match='Create database'):
-        db = Database(connection_string)
+        _ = Database(connection_string)
 
 
 @pytest.fixture(scope="module")
@@ -144,9 +147,9 @@ def test_orm_use(db):
 
     # Adding a source with problematic ra/dec to test validation
     with pytest.raises(ValueError):
-        s2 = Sources(source="V4046 Sgr", ra=9999, dec=-32.79, reference="Schm10")
+        _ = Sources(source="V4046 Sgr", ra=9999, dec=-32.79, reference="Schm10")
     with pytest.raises(ValueError):
-        s2 = Sources(source="V4046 Sgr", ra=273.54, dec=-9999, reference="Schm10")
+        _ = Sources(source="V4046 Sgr", ra=273.54, dec=-9999, reference="Schm10")
 
 
 def test_add_table_data(db):

astrodbkit2/tests/test_spectra.py

@@ -1,15 +1,16 @@
 # Tests for spectra functions
 
-import pytest
 import numpy as np
+import pytest
 from astropy.io import fits
 from astropy.units import Unit
+
 from astrodbkit2.spectra import (
-    identify_spex_prism,
     _identify_spex,
+    identify_spex_prism,
+    identify_wcs1d_multispec,
     load_spectrum,
     spex_prism_loader,
-    identify_wcs1d_multispec,
     wcs1d_multispec_loader,
 )
 

astrodbkit2/tests/test_utils.py

@@ -1,12 +1,15 @@
 # Testing for utils
 
-import pytest
 import json
 from datetime import datetime
 from decimal import Decimal
 from io import StringIO
+
+import pytest
 from astropy.table import Table
-from astrodbkit2.utils import json_serializer, get_simbad_names, _name_formatter, datetime_json_parser
+
+from astrodbkit2.utils import _name_formatter, datetime_json_parser, get_simbad_names, json_serializer
+
 try:
     import mock
 except ImportError:

astrodbkit2/tests/test_views.py

@@ -2,8 +2,8 @@
 # Adapted from https://github.com/sqlalchemy/sqlalchemy/wiki/Views
 
 import sqlalchemy as sa
-from sqlalchemy.orm import declarative_base
-from sqlalchemy.orm import Session
+from sqlalchemy.orm import Session, declarative_base
+
 from astrodbkit2.views import *
 
 

astrodbkit2/utils.py

@@ -1,10 +1,11 @@
 """Utility functions for Astrodbkit2"""
 
-import re
 import functools
+import re
 import warnings
 from datetime import datetime
 from decimal import Decimal
+
 from astroquery.simbad import Simbad
 
 __all__ = ["json_serializer", "get_simbad_names"]

pyproject.toml

@@ -9,6 +9,29 @@ requires = ["setuptools",
 
 build-backend = 'setuptools.build_meta'
 
+[tool.ruff.lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+# See https://docs.astral.sh/ruff/rules/
+select = ["E4", "E7", "E9", "F", "I", "PL", "C901", "RUF010"]
+#select = ["ALL"]
+ignore = ["PLR",  # pylint refactor
+          "F403", # star imports used
+          "F405", # referring to import from star imports
+          ]  
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+[tool.ruff]
+line-length = 120
+
+[tool.ruff.lint.mccabe]
+# Flag errors (`C901`) whenever the complexity level exceeds 15.
+max-complexity = 15
+
 [tool.darker]
 line-length = 120
 

setup.cfg

@@ -39,6 +39,7 @@ test =
     darker==1.7.2
     black==23.9.1
     pre-commit==3.4.0
+    ruff==0.3.7
 docs =
     sphinx-astropy