Merge pull request #27 from sot/ruff

Ruff

.github/workflows/python-formatting.yml

@@ -0,0 +1,10 @@
+name: check format using ruff
+on: [push]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: format --check

.github/workflows/python-linting.yml

@@ -0,0 +1,8 @@
+name: lint code using ruff
+on: [push]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1

.pre-commit-config.yaml

@@ -0,0 +1,9 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.8.3
+  hooks:
+    # Run the linter.
+    - id: ruff
+    # Run the formatter.
+    - id: ruff-format

ruff-base.toml

@@ -0,0 +1,61 @@
+# Copied originally from pandas. This config requires ruff >= 0.2.
+target-version = "py311"
+
+# fix = true
+lint.unfixable = []
+
+lint.select = [
+  "I", # isort
+  "F", # pyflakes
+  "E", "W", # pycodestyle
+  "YTT", # flake8-2020
+  "B", # flake8-bugbear
+  "Q", # flake8-quotes
+  "T10", # flake8-debugger
+  "INT", # flake8-gettext
+  "PLC", "PLE", "PLR", "PLW", # pylint
+  "PIE", # misc lints
+  "PYI", # flake8-pyi
+  "TID", # tidy imports
+  "ISC", # implicit string concatenation
+  "TCH", # type-checking imports
+  "C4", # comprehensions
+  "PGH" # pygrep-hooks
+]
+
+# Some additional rules that are useful
+lint.extend-select = [
+"UP009",  # UTF-8 encoding declaration is unnecessary
+"SIM118",  # Use `key in dict` instead of `key in dict.keys()`
+"D205",  # One blank line required between summary line and description
+"ARG001",  # Unused function argument
+"RSE102",  # Unnecessary parentheses on raised exception
+"PERF401",  # Use a list comprehension to create a transformed list
+"S101",  # Use of `assert` detected
+]
+
+lint.ignore = [
+  "ISC001", # Disable this for compatibility with ruff format
+  "E402", # module level import not at top of file
+  "E731", # do not assign a lambda expression, use a def
+  "PLR2004", # Magic number
+  "B028", # No explicit `stacklevel` keyword argument found
+  "PLR0913", # Too many arguments to function call
+  "PLR1730", # Checks for if statements that can be replaced with min() or max() calls
+]
+
+extend-exclude = [
+  "docs",
+]
+
+[lint.pycodestyle]
+max-line-length = 100 # E501 reports lines that exceed the length of 100.
+
+[lint.extend-per-file-ignores]
+"__init__.py" = ["E402", "F401", "F403"]
+# For tests:
+# - D205: Don't worry about test docstrings
+# - ARG001: Unused function argument false positives for some fixtures
+# - E501: Line-too-long
+# - S101: Do not use assert
+"**/tests/test_*.py" = ["D205", "ARG001", "E501", "S101"]

ruff.toml

@@ -0,0 +1,25 @@
+extend = "ruff-base.toml"
+
+# These are files to exclude for this project.
+extend-exclude = [
+  # "**/*.ipynb",  # commonly not ruff-compliant
+]
+
+# These are rules that commonly cause many ruff warnings. Code will be improved by
+# incrementally fixing code to adhere to these rules, but for practical purposes they
+# can be ignored by uncommenting each one. You can also add to this list as needed.
+lint.extend-ignore = [
+  # "B905", # `zip()` without an explicit `strict=` parameter
+  # "PLC1901", # compare-to-empty-string
+  # "PLR0911", # Too many returns
+  # "PLR0912", # Too many branches
+  # "PLR0915", # Too many statements
+  # "PGH004", # Use specific rule codes when using `noqa`
+  # "C401", # Unnecessary generator (rewrite as a `set` comprehension)
+  # "C402", # Unnecessary generator (rewrite as a dict comprehension)
+  # "C405", # Unnecessary `list` literal (rewrite as a `set` literal)
+  # "C408", # Unnecessary `dict` call (rewrite as a literal)
+  # "C416", # Unnecessary `dict` comprehension (rewrite using `dict()`)
+  # "G010", # warn is deprecated in favor of warning
+  # "PYI056", # Calling `.append()` on `__all__` may not be supported by all type checkers
+]

setup.py

@@ -1,29 +1,30 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 from setuptools import setup
-from testr.setup_helper import cmdclass
 from ska_helpers.setup_helper import duplicate_package_info
+from testr.setup_helper import cmdclass
 
 name = "ska_dbi"
 namespace = "Ska.DBI"
 
 packages = ["ska_dbi", "ska_dbi.tests"]
 package_dir = {name: name}
-package_data = {'ska_dbi.tests': ['ska_dbi_test_table.sql']}
+package_data = {"ska_dbi.tests": ["ska_dbi_test_table.sql"]}
 
 duplicate_package_info(packages, name, namespace)
 duplicate_package_info(package_dir, name, namespace)
 duplicate_package_info(package_data, name, namespace)
 
-setup(name=name,
-      author='Tom Aldcroft',
-      description='Database interface utilities',
-      author_email='taldcroft@cfa.harvard.edu',
-      use_scm_version=True,
-      setup_requires=['setuptools_scm', 'setuptools_scm_git_archive'],
-      zip_safe=False,
-      package_dir=package_dir,
-      packages=packages,
-      package_data=package_data,
-      tests_require=['pytest'],
-      cmdclass=cmdclass,
-      )
+setup(
+    name=name,
+    author="Tom Aldcroft",
+    description="Database interface utilities",
+    author_email="taldcroft@cfa.harvard.edu",
+    use_scm_version=True,
+    setup_requires=["setuptools_scm", "setuptools_scm_git_archive"],
+    zip_safe=False,
+    package_dir=package_dir,
+    packages=packages,
+    package_data=package_data,
+    tests_require=["pytest"],
+    cmdclass=cmdclass,
+)

ska_dbi/DBI.py

@@ -1,25 +1,28 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 """
 ska_dbi provides simple methods for database access and data insertion.
+
 Features:
 
 - Sqlite connections are supported.
 - Integration with numpy record arrays.
 - Verbose mode to show transaction information.
 """
-import os
-import sys
+
 import sqlite3 as dbapi2
-from ska_dbi.common import DEFAULT_CONFIG, NoPasswordError
+
+from ska_dbi.common import DEFAULT_CONFIG
 
 
 def _denumpy(x):
     """
+    Convert from numpy type to native python type.
+
     Try using the numpy.tolist() to convert to native python type.
     DBI's can't typically handle numpy vals."""
     try:
         return x.tolist()
-    except:
+    except Exception:
         return x
 
 
@@ -41,22 +44,29 @@ class DBI(object):
 
     :rtype: DBI object
     """
-    def __init__(self, dbi=None, server=None,
-                 numpy=True, autocommit=True, verbose=False,
-                 **kwargs):
 
-
-        if dbi != 'sqlite':
-            raise ValueError(f'ska_dbi.DBI only supports sqlite at this time.  Got {dbi}.')
+    def __init__(
+        self,
+        dbi=None,
+        server=None,
+        numpy=True,
+        autocommit=True,
+        verbose=False,
+        **kwargs,
+    ):
+        if dbi != "sqlite":
+            raise ValueError(
+                f"ska_dbi.DBI only supports sqlite at this time.  Got {dbi}."
+            )
 
         self.dbi = dbi
-        self.server = server or DEFAULT_CONFIG[dbi].get('server')
+        self.server = server or DEFAULT_CONFIG[dbi].get("server")
         self.numpy = numpy
         self.autocommit = autocommit
         self.verbose = verbose
 
         if self.verbose:
-            print('Connecting to', self.dbi, 'server', self.server)
+            print("Connecting to", self.dbi, "server", self.server)
 
         self.conn = dbapi2.connect(self.server)
         self.Error = dbapi2.Error
@@ -95,20 +105,24 @@ def execute(self, expr, vals=None, commit=None):
         # Get a new cursor (implicitly closing any previous cursor)
         self.cursor = self.conn.cursor()
 
-        for subexpr in expr.split(';\n'):
+        for subexpr in expr.split(";\n"):
             if vals is not None:
                 args = (subexpr, vals)
             else:
                 args = (subexpr,)
 
             if self.verbose:
-                print('Running:', args)
+                print("Running:", args)
             self.cursor.execute(*args)
 
         if (commit is None and self.autocommit) or commit:
             self.commit()
 
-    def fetch(self, expr, vals=None,):
+    def fetch(
+        self,
+        expr,
+        vals=None,
+    ):
         """
         Return a generator that will fetch one row at a time after executing with args.
 
@@ -127,15 +141,22 @@ def fetch(self, expr, vals=None,):
         while True:
             vals = self.cursor.fetchone()
             if vals:
-                yield dict(zip(cols, vals))
+                yield dict(zip(cols, vals, strict=False))
             else:
                 if self.autocommit:
                     self.commit()
                 self.cursor.close()
                 break
 
-    def fetchone(self, expr, vals=None,):
-        """Fetch one row after executing args.  This always gets the first row of the
+    def fetchone(
+        self,
+        expr,
+        vals=None,
+    ):
+        """
+        Fetch one row.
+
+        Fetch one row after executing args.  This always gets the first row of the
         SQL query.  Use ska_dbi.fetch() to get multiple rows one at a time.
 
         Example usage::
@@ -179,11 +200,12 @@ def fetchall(self, expr, vals=None):
 
         if self.numpy and vals:
             import numpy
+
             # Would be good to set dtype explicitly from database info instead of
             # having numpy auto-determine types
             return numpy.rec.fromrecords(vals, names=cols)
         else:
-            return [dict(zip(cols, x)) for x in vals]
+            return [dict(zip(cols, x, strict=False)) for x in vals]
 
     def insert(self, row, tablename, replace=False, commit=None):
         """Insert data row into table tablename.
@@ -210,13 +232,11 @@ def insert(self, row, tablename, replace=False, commit=None):
 
         # Create the insert command depending on dbi.  Start with the column
         # value replacement strings
-        colrepls = ('?',) * len(cols)
+        colrepls = ("?",) * len(cols)
 
         insert_str = "INSERT %s INTO %s (%s) VALUES (%s)"
-        replace_str = replace and 'OR REPLACE' or ''
-        cmd = insert_str % (replace_str, tablename,
-                            ','.join(cols),
-                            ','.join(colrepls))
+        replace_str = replace and "OR REPLACE" or ""
+        cmd = insert_str % (replace_str, tablename, ",".join(cols), ",".join(colrepls))
 
         # Finally run the insert command
         self.execute(cmd, vals, commit=commit)

ska_dbi/__init__.py

@@ -3,12 +3,13 @@
 
 from .DBI import *
 
-__version__ = ska_helpers.get_version('ska_dbi')
+__version__ = ska_helpers.get_version("ska_dbi")
 
 
 def test(*args, **kwargs):
-    '''
+    """
     Run py.test unit tests.
-    '''
+    """
     import testr
+
     return testr.test(*args, **kwargs)

ska_dbi/common.py

@@ -1,12 +1,10 @@
-DEFAULT_CONFIG = {'sqlite': {'server': 'db.sql3'},
-                  'sybase': {'server': 'sqlsao',
-                             'user': 'aca_ops',
-                             'database': 'axafapstat'}}
+DEFAULT_CONFIG = {
+    "sqlite": {"server": "db.sql3"},
+    "sybase": {"server": "sqlsao", "user": "aca_ops", "database": "axafapstat"},
+}
 
 
 class NoPasswordError(Exception):
     """
-    Special Error for the case when password is neither supplied nor available
-    from a file.
+    Error when password is neither supplied nor available from a file.
     """
-    pass