added new ignores for previously unchanged files

Author: Reece Hart

docs/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # eutils documentation build configuration file, created by
 # sphinx-quickstart on Tue Aug 11 10:03:31 2015.
@@ -12,12 +11,10 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
-import os
 
 import sphinx_rtd_theme
 
-import biocommons.eutils as eutils
+from biocommons import eutils
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -55,7 +52,7 @@
 
 # General information about the project.
 project = "eutils"
-copyright = "2018, eutils Committers"
+copyright = "2018, eutils Committers"  # noqa: A001
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

pyproject.toml

@@ -130,7 +130,7 @@ testpaths = ["src", "tests"]
 [tool.ruff]
 line-length = 100
 src = ["src", "tests"]
-target-version = "py314"
+target-version = "py313"
 
 [tool.ruff.format]
 docstring-code-format = true
@@ -198,22 +198,37 @@ select = [
 # These warnings became visible with the adoption of ruff. They
 # should be addressed in separate issues.
 "src/**/*.py" = [
+  # "C416", # Unnecessary list comprehension (rewrite using `list()`)
+  "A001", # Variable `id` is shadowing a Python builtin
+  "A002", # Function argument `id` is shadowing a Python builtin
+  "B006", # Do not use mutable data structures for argument defaults
   "C416", # Unnecessary list comprehension (rewrite using `list()`)
   "E741", # Ambiguous variable name: `l`
   "EM101", # Exception must not use a string literal, assign to variable first
+  "EM102", # Exception must not use an f-string literal, assign to variable first
   "F522", # `.format` call has unused named argument(s): n
   "F524", # `.format` call is missing argument(s) for placeholder(s): n=n
   "F821", # Undefined name `pas`
+  "G003", # Logging statement uses `+`
+  "G004", # Logging statement uses f-string
   "PTH118", # `os.path.join()` should be replaced by `Path` with `/` operator
   "PTH120", # `os.path.dirname()` should be replaced by `Path.parent`
   "RET504", # Unnecessary assignment to `nodes` before `return` statement
   "S101", # Use of `assert` detected
+  "S108", # Probable insecure usage of temporary file or directory: "/tmp/SQLiteCache-test.db"
+  "S301", # `pickle` and modules that wrap it can be unsafe when used to deserialize untrusted data, possible security issue
+  "SIM101", # Multiple `isinstance` calls for `xml`, merge into a single call
   "TRY003", # Avoid specifying long messages outside the exception class
   "UP008", # Use `super()` instead of `super(__class__, self)`
 ]
 "tests/**/*.py" = [
   "C405", # Unnecessary list literal (rewrite as a set literal)
+  "N801", # Class name (various) should use CapWords convention
+  "N802", # Function name (various) should be lowercase
+  "PLR2004", # Magic value used in comparison
+  "PTH107", # `os.remove()` should be replaced by `Path.unlink()`
   "S101", # Use of `assert` detected
+  "UP008", # Use `super()` instead of `super(__class__, self)`
 ]
 
 [tool.setuptools]

src/biocommons/eutils/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 from importlib.metadata import PackageNotFoundError, version
 
 from ._internal.client import Client

src/biocommons/eutils/_internal/client.py

@@ -1,7 +1,4 @@
-# -*- coding: utf-8 -*-
-
 import logging
-import os
 
 import lxml.etree as le
 
@@ -15,11 +12,10 @@
 from .xmlfacades.pubmedarticleset import PubmedArticleSet
 from .xmlfacades.pubmedcentralarticleset import PubmedCentralArticleSet
 
-
 logger = logging.getLogger(__name__)
 
 
-class Client(object):
+class Client:
     """class-based access to NCBI E-Utilities, returning Python classes
     with rich data accessors
 
@@ -69,8 +65,8 @@ def esearch(self, db, term):
         esr = ESearchResult(self._qs.esearch({"db": db, "term": term}))
         if esr.count > esr.retmax:
             logger.warning(
-                "NCBI found {esr.count} results, but we truncated the reply at {esr.retmax}"
-                " results; see https://github.com/biocommons/eutils/issues/124/".format(esr=esr)
+                f"NCBI found {esr.count} results, but we truncated the reply at {esr.retmax}"
+                " results; see https://github.com/biocommons/eutils/issues/124/"
             )
         return esr
 
@@ -90,7 +86,7 @@ def efetch(self, db, id):
             return ExchangeSet(xml)
         if db in ["pmc"]:
             return PubmedCentralArticleSet(doc)
-        raise EutilsError("database {db} is not currently supported by eutils".format(db=db))
+        raise EutilsError(f"database {db} is not currently supported by eutils")
 
 
 # <LICENSE>

src/biocommons/eutils/_internal/exceptions.py

@@ -1,41 +1,30 @@
-# -*- coding: utf-8 -*-
-
-
 class EutilsError(Exception):
     """Base class for all Eutils exceptions, and also used to raise
     general exception.
 
     """
 
-    pass
-
 
 class EutilsNCBIError(EutilsError):
     """Raised when NCBI returns data that appears to be incorrect or
     invalid.
 
     """
 
-    pass
-
 
 class EutilsNotFoundError(EutilsError):
     """Raised when the requested data is not available. (Used only by the
     :mod:`eutils.sketchy.clientx` interface currently.)
 
     """
 
-    pass
-
 
 class EutilsRequestError(EutilsError):
     """Raised when NCBI responds with an error, such as when a non-existent
     database is specified.
 
     """
 
-    pass
-
 
 # <LICENSE>
 # Copyright 2015 eutils Committers

src/biocommons/eutils/_internal/sqlitecache.py

@@ -1,12 +1,9 @@
-# -*- coding: utf-8 -*-
-
 """simple key-value cache with transparent payload compression and expiration
 
 Taken from http://bitbucket.org/reece/rcore/
 """
 
 import logging
-import os
 import pickle
 import sqlite3
 import zlib
@@ -29,7 +26,7 @@ def val_from(pobj, compress):
     return pickle.loads(zlib.decompress(pobj) if compress else pobj)
 
 
-class SQLiteCache(object):
+class SQLiteCache:
     ############################################################################
     ## Exposed methods
     def __init__(self, db_path, compress_values=True):
@@ -46,16 +43,14 @@ def expire(self, age):
         ## Special Python methods
 
     def __str__(self):
-        return "SQLiteCache(db_path={self._db_path},compress_values={self.compress_values})".format(
-            self=self
-        )
+        return f"SQLiteCache(db_path={self._db_path},compress_values={self.compress_values})"
 
     def __dir__(self):
         self._logger.debug("__dir__()")
         return [key_from(row[0]) for row in self._execute("SELECT key FROM cache", [])]
 
     def __getitem__(self, key):
-        self._logger.debug("__getitem__({key})".format(key=key))
+        self._logger.debug(f"__getitem__({key})")
         cur = self._execute("SELECT value,value_compressed FROM cache WHERE key = ?", [key_to(key)])
         row = cur.fetchone()
         if row is None:
@@ -64,20 +59,20 @@ def __getitem__(self, key):
 
     def __setitem__(self, key, value):
         db_val = val_to(value, self.compress_values)
-        self._logger.debug("__setitem__({key},({vlen} bytes))".format(key=key, vlen=len(db_val)))
+        self._logger.debug(f"__setitem__({key},({len(db_val)} bytes))")
         self._execute(
             "INSERT OR REPLACE INTO cache (key,value_compressed,value) VALUES (?,?,?)",
             [key_to(key), self.compress_values, db_val],
         )
 
     def __delitem__(self, key):
-        self._logger.debug("__delitem__({key})".format(key=key))
+        self._logger.debug(f"__delitem__({key})")
         cur = self._execute("DELETE FROM cache WHERE key = ?", [key_to(key)])
         if cur.rowcount == 0:
             raise KeyError(key)
 
     def __contains__(self, key):
-        self._logger.debug("__contains__({key})".format(key=key))
+        self._logger.debug(f"__contains__({key})")
         return self._fetch1v(
             "SELECT EXISTS(SELECT 1 FROM cache WHERE key=? LIMIT 1)", [key_to(key)]
         )
@@ -110,11 +105,7 @@ def _get_schema_version(self):
 
     def _execute(self, query, params=[]):
         cur = self._con.cursor()
-        self._logger.debug(
-            "executing query <{query}> with params <{nvars} vars>".format(
-                query=query, nvars=len(params)
-            )
-        )
+        self._logger.debug(f"executing query <{query}> with params <{len(params)} vars>")
         cur.execute(query, params)
         return cur
 

src/biocommons/eutils/_internal/utils.py

@@ -1,6 +1,3 @@
-# -*- coding: utf-8 -*-
-
-
 def xml_get1(node, xpath):
     return node.xpath(xpath)[0]
 

src/biocommons/eutils/_internal/xmlfacades/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """xmlfacades/__init__.py doc string"""
 
 # <LICENSE>

src/biocommons/eutils/_internal/xmlfacades/base.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 import logging
 
 import lxml.etree
@@ -9,7 +7,7 @@
 logger = logging.getLogger(__name__)
 
 
-class Base(object):
+class Base:
     """Root class for all xmlfacade classes.
 
     This class is instantiated only by subclasses.
@@ -33,12 +31,10 @@ def __init__(self, xml):
             raise EutilsError("Cannot create object from type " + type(xml).__name__)
 
         if self._root_tag is None:
-            raise EutilsError("_root_tag not defined for class {}".format(type(self).__name__))
-        elif self._root_tag != self._xml_root.tag:
+            raise EutilsError(f"_root_tag not defined for class {type(self).__name__}")
+        if self._root_tag != self._xml_root.tag:
             raise EutilsError(
-                "XML for {} object must be a {} element (got {})".format(
-                    type(self).__name__, self._root_tag, self._xml_root.tag
-                )
+                f"XML for {type(self).__name__} object must be a {self._root_tag} element (got {self._xml_root.tag})"
             )
 
 

src/biocommons/eutils/_internal/xmlfacades/dbinfo.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Provides support for parsing NCBI einfo queries as described here:
 
 http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EInfo