Phase-2 modernization: SQLite 3.54.1 pin, ruff migration, JDBC plugin hygiene

.github/workflows/build.yml

@@ -19,7 +19,7 @@ jobs:
         sudo apt-get -qq update
         sudo apt-get install -y clang-format cppcheck python3-pip python3-venv
         python3 -m venv "$HOME/.lint-venv"
-        "$HOME/.lint-venv/bin/pip" install pre-commit $PIP_DEPS black flake8 pylint
+        "$HOME/.lint-venv/bin/pip" install pre-commit $PIP_DEPS ruff
         echo "$HOME/.lint-venv/bin" >> "$GITHUB_PATH"
     - name: pre-commit
       run: pre-commit run --all-files

.pre-commit-config.yaml

@@ -17,26 +17,12 @@ repos:
     verbose: true
     entry: cppcheck
     args: [-q,--std=c++11]
-  - id: black
-    name: black
-    language: system
-    files: \.py$
-    verbose: true
-    entry: black
-    args: [-l,'100']
-  - id: flake8
-    name: flake8
-    language: system
-    files: \.py$
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.17.1
+  hooks:
+  - id: ruff-check
+    name: ruff-check
     verbose: true
-    entry: flake8
-    args: [--max-line-length, "100", "--ignore=E501,W503,E722"]
-  - id: pylint
-    name: pylint
-    language: system
-    files: \.py$
-    exclude: version\.py
+  - id: ruff-format
+    name: ruff-format
     verbose: true
-    entry: env PYTHONPATH=bindings/python pylint
-    args: [-d, "global-statement,missing-docstring,missing-module-docstring,line-too-long,too-many-arguments,too-many-positional-arguments,duplicate-code,redefined-outer-name,too-many-locals,bare-except,broad-except,import-outside-toplevel,protected-access,too-many-statements,too-many-branches,unspecified-encoding"]
-# CI re-run trigger 2026-10-19 (run 39294337754 lost its macOS runner to GitHub capacity)

Dockerfile

@@ -4,7 +4,7 @@
 FROM almalinux:8 as builder
 
 ARG CMAKE_VERSION=3.17.3
-ARG SQLITE_VERSION=3410200
+ARG SQLITE_VERSION=3540100
 ARG ZSTD_VERSION=1.5.5
 ARG CPU_ARCH=ivybridge
 ENV CFLAGS="-march=${CPU_ARCH} -O3"
@@ -34,7 +34,7 @@ RUN mkdir -p /work/GenomicSQLite
 
 # SQLite
 WORKDIR /work
-RUN wget -nv http://www.sqlite.org/2023/sqlite-amalgamation-${SQLITE_VERSION}.zip \
+RUN wget -nv http://www.sqlite.org/2026/sqlite-amalgamation-${SQLITE_VERSION}.zip \
         && unzip -o sqlite-amalgamation-${SQLITE_VERSION}.zip
 WORKDIR /work/sqlite-amalgamation-${SQLITE_VERSION}
 RUN bash -c "gcc -shared -o libsqlite3.so.0 -fPIC -shared -Wl,-soname,libsqlite3.so.0 -g ${CFLAGS} ${SQLITE_CFLAGS} sqlite3.c & pid=$? \

README.md

@@ -54,7 +54,7 @@ cmake --build build -j 4 --target genomicsqlite
 
 * htslib ≥ 1.9, samtools, and tabix
 * pigz
-* Python ≥ 3.6 and packages: pytest pytest-xdist pre-commit black pylint flake8 
+* Python ≥ 3.6 and packages: pytest pytest-xdist pre-commit ruff
 * JDK, mvn, rust
 * clang-format & cppcheck
 

bindings/jdbc/genomicsqlite-jdbc/pom.xml

@@ -61,7 +61,7 @@
     <dependency>
       <groupId>junit</groupId>
       <artifactId>junit</artifactId>
-      <version>4.13.1</version>
+      <version>4.13.2</version>
       <scope>test</scope>
     </dependency>
   </dependencies>
@@ -72,44 +72,44 @@
         <!-- clean lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#clean_Lifecycle -->
         <plugin>
           <artifactId>maven-clean-plugin</artifactId>
-          <version>3.1.0</version>
+          <version>3.5.0</version>
         </plugin>
         <!-- default lifecycle, jar packaging: see https://maven.apache.org/ref/current/maven-core/default-bindings.html#Plugin_bindings_for_jar_packaging -->
         <plugin>
           <artifactId>maven-resources-plugin</artifactId>
-          <version>3.0.2</version>
+          <version>3.5.0</version>
         </plugin>
         <plugin>
           <artifactId>maven-compiler-plugin</artifactId>
-          <version>3.8.0</version>
+          <version>3.16.0</version>
         </plugin>
         <plugin>
           <artifactId>maven-surefire-plugin</artifactId>
-          <version>2.22.2</version>
+          <version>3.6.0</version>
           <configuration>
             <trimStackTrace>false</trimStackTrace>
           </configuration>
         </plugin>
         <plugin>
           <artifactId>maven-jar-plugin</artifactId>
-          <version>3.0.2</version>
+          <version>3.5.1</version>
         </plugin>
         <plugin>
           <artifactId>maven-install-plugin</artifactId>
-          <version>2.5.2</version>
+          <version>3.2.0</version>
         </plugin>
         <plugin>
           <artifactId>maven-deploy-plugin</artifactId>
-          <version>2.8.2</version>
+          <version>3.2.0</version>
         </plugin>
         <!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
         <plugin>
           <artifactId>maven-site-plugin</artifactId>
-          <version>3.7.1</version>
+          <version>3.22.0</version>
         </plugin>
         <plugin>
           <artifactId>maven-project-info-reports-plugin</artifactId>
-          <version>3.0.0</version>
+          <version>3.9.0</version>
         </plugin>
         <plugin>
           <groupId>com.diffplug.spotless</groupId>

bindings/python/genomicsqlite/__init__.py

@@ -3,12 +3,12 @@
 GenomicSQLite Python binding
 """
 
+import json
 import os
-import sys
 import platform
-import json
 import sqlite3
-from typing import Optional, NamedTuple, Dict, Any
+import sys
+from typing import Any, Dict, NamedTuple, Optional
 
 _HERE = os.path.dirname(__file__)
 _YES = ("1", "true", "t", "yes", "y")
@@ -182,9 +182,9 @@ def get_reference_sequences_by_rid(
         params = (assembly,)
     ans = {}
     for row in con.execute(sql, params):
-        assert (
-            isinstance(row[0], int) and row[0] not in ans
-        ), "genomicsqlite: invalid or duplicate reference sequence rid"
+        assert isinstance(row[0], int) and row[0] not in ans, (
+            "genomicsqlite: invalid or duplicate reference sequence rid"
+        )
         ans[row[0]] = ReferenceSequence(
             rid=row[0],
             name=row[1],
@@ -200,7 +200,7 @@ def get_reference_sequences_by_name(
     con: sqlite3.Connection, assembly: Optional[str] = None, schema: Optional[str] = None
 ) -> Dict[str, ReferenceSequence]:
     ans = {}
-    for _, item in get_reference_sequences_by_rid(con, assembly, schema).items():
+    for item in get_reference_sequences_by_rid(con, assembly, schema).values():
         assert item.name not in ans, "genomicsqlite: non-unique reference sequence names"
         ans[item.name] = item
     return ans
@@ -333,12 +333,10 @@ def _cli(argv=None):
             print(
                 " ".join(
                     (
-                        (
-                            (arg if " " not in arg else f"'{arg}'")
-                            + (" \\\n    " if len(arg) > 50 else "")
-                        )
-                        for arg in cmd
+                        (arg if " " not in arg else f"'{arg}'")
+                        + (" \\\n    " if len(arg) > 50 else "")
                     )
+                    for arg in cmd
                 )
             )
         os.execvp("sqlite3", cmd)
@@ -403,7 +401,7 @@ def _compact(dbfilename, argv):
 
     # sniff whether input db is currently compressed with zstd_vfs or not
     con = None
-    web = dbfilename.startswith("http:") or dbfilename.startswith("https:")
+    web = dbfilename.startswith(("http:", "https:"))
     if not web:
         con = sqlite3.connect(f"file:{urllib.parse.quote(dbfilename)}?mode=ro", uri=True)
         if next(con.execute("PRAGMA application_id"))[0] != 0x7A737464:

bindings/python/genomicsqlite/__main__.py

@@ -1,4 +1,5 @@
 import sys
+
 from . import _cli
 
 if __name__ == "__main__":

bindings/python/setup.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 from os import path
-from setuptools import setup, find_packages  # pylint: disable=import-error
+
+from setuptools import find_packages, setup  # pylint: disable=import-error
 from version import get_version
 
 HERE = path.abspath(path.dirname(__file__))

bindings/python/version.py

@@ -76,7 +76,7 @@ def read_git_version():
         return None
     match = re.search(_GIT_DESCRIPTION_RE, ver)
     if not match:
-        sys.stderr.write("version: git description (%s) is invalid, " "ignoring\n" % ver)
+        sys.stderr.write("version: git description (%s) is invalid, ignoring\n" % ver)
         return None
 
     commits = int(match.group("commits"))
@@ -90,9 +90,7 @@ def read_release_version():
         with open(RELEASE_VERSION_FILE) as infile:
             ver = infile.readline().strip()
         if not re.search(_PEP386_VERSION_RE, ver):
-            sys.stderr.write(
-                "version: release version (%s) is invalid, " "will use it anyway\n" % ver
-            )
+            sys.stderr.write("version: release version (%s) is invalid, will use it anyway\n" % ver)
         return ver
     except:
         return None

docs/guide_db.md

@@ -94,9 +94,9 @@ First complete the [installation instructions](index.md).
 === "Python"
     ``` python3
     dbconn = genomicsqlite.connect(
-      db_filename,
-      read_only=False,
-      **kwargs  #  genomicsqlite + sqlite3.connect() arguments
+        db_filename,
+        read_only=False,
+        **kwargs,  #  genomicsqlite + sqlite3.connect() arguments
     )
     assert isinstance(dbconn, sqlite3.Connection)
     ```

docs/guide_gri.md

@@ -21,11 +21,7 @@ The extension provides routines to populate a small `_gri_refseq` table describi
 === "Python"
     ``` python3
     create_gri_sql = genomicsqlite.create_genomic_range_index_sql(
-      dbconn,
-      'tableName',
-      'chromosome',
-      'beginPosition',
-      'endPosition'
+        dbconn, "tableName", "chromosome", "beginPosition", "endPosition"
     )
     dbconn.executescript(create_gri_sql)
     ```
@@ -229,9 +225,7 @@ The following routines support the aforementioned, recommended convention for st
 
 === "Python"
     ``` python3
-    refseq_sql = genomicsqlite.put_reference_assembly_sql(
-      dbconn, 'GRCh38_no_alt_analysis_set'
-    )
+    refseq_sql = genomicsqlite.put_reference_assembly_sql(dbconn, "GRCh38_no_alt_analysis_set")
     dbconn.executescript(refseq_sql)
     ```
 
@@ -307,8 +301,10 @@ Available assemblies:
 === "Python"
     ``` python3
     refseq_sql = genomicsqlite.put_reference_sequence_sql(
-      dbconn, 'chr17', 83257441
-      # optional: assembly, refget_id, meta (dict), rid
+        dbconn,
+        "chr17",
+        83257441,
+        # optional: assembly, refget_id, meta (dict), rid
     )
     dbconn.executescript(refseq_sql)
     ```
@@ -407,12 +403,13 @@ If the `rid` argument is omitted or -1 then it will be assigned automatically up
 === "Python"
     ``` python3
     class ReferenceSequence(NamedTuple):
-      rid: int
-      name: str
-      length: int
-      assembly: Optional[str]
-      refget_id: Optional[str]
-      meta: Dict[str, Any]
+        rid: int
+        name: str
+        length: int
+        assembly: Optional[str]
+        refget_id: Optional[str]
+        meta: Dict[str, Any]
+
 
     refseq_by_rid = genomicsqlite.get_reference_sequences_by_rid(dbconn)
     # refseq_by_rid: Dict[int, ReferenceSequence]
@@ -492,12 +489,13 @@ The optional `assembly` argument restricts the retrieved sequences to those with
 === "Python"
     ``` python3
     class ReferenceSequence(NamedTuple):
-      rid: int
-      name: str
-      length: int
-      assembly: Optional[str]
-      refget_id: Optional[str]
-      meta: Dict[str, Any]
+        rid: int
+        name: str
+        length: int
+        assembly: Optional[str]
+        refget_id: Optional[str]
+        meta: Dict[str, Any]
+
 
     refseq_by_name = genomicsqlite.get_reference_sequences_by_name(dbconn)
     # refseq_by_name: Dict[str, ReferenceSequence]

docs/guide_helpers.md

@@ -88,8 +88,8 @@ The [UINT collating sequence](https://www.sqlite.org/uintcseq.html) is also bund
 
 === "Python"
     ``` python3
-    dbconn = sqlite3.connect('any.db', uri=True)
-    attach_sql = genomicsqlite.attach_sql(dbconn, 'compressed.db', 'db2')
+    dbconn = sqlite3.connect("any.db", uri=True)
+    attach_sql = genomicsqlite.attach_sql(dbconn, "compressed.db", "db2")
     # attach_sql() also takes configuration keyword arguments like
     # genomicsqlite.connect()
     dbconn.executescript(attach_sql)
@@ -190,13 +190,13 @@ The [UINT collating sequence](https://www.sqlite.org/uintcseq.html) is also bund
 
 === "Python"
     ``` python3
-    dbconn = sqlite3.connect('existing.db', uri=True)
-    vacuum_sql = genomicsqlite.vacuum_into_sql(dbconn, 'compressed.db')
+    dbconn = sqlite3.connect("existing.db", uri=True)
+    vacuum_sql = genomicsqlite.vacuum_into_sql(dbconn, "compressed.db")
     # vacuum_into_sql() also takes configuration keyword arguments like
     # genomicsqlite.connect() to control compression level & page sizes
 
     dbconn.executescript(vacuum_sql)
-    dbconn2 = genomicsqlite.connect('compressed.db')
+    dbconn2 = genomicsqlite.connect("compressed.db")
     ```
 
 === "Java"

docs/internals.md

@@ -70,13 +70,19 @@ The extension also exposes the routine to generate the SQL subquery, which you c
 === "Python"
     ``` python3
     query = (
-      'SELECT * FROM tableName WHERE tableName._rowid_ IN ' +
-      genomicsqlite.genomic_range_rowids_sql(dbconn, 'tableName',
-                                             # defaults:
-                                             qrid='?1', qbeg='?2', qend='?3',
-                                             ceiling=-1, floor=-1)
+        "SELECT * FROM tableName WHERE tableName._rowid_ IN "
+        + genomicsqlite.genomic_range_rowids_sql(
+            dbconn,
+            "tableName",
+            # defaults:
+            qrid="?1",
+            qbeg="?2",
+            qend="?3",
+            ceiling=-1,
+            floor=-1,
+        )
     )
-    cursor = dbconn.execute(query, ('chr12',111803912,111804012))
+    cursor = dbconn.execute(query, ("chr12", 111803912, 111804012))
     ```
 
 === "SQLiteCpp"

ruff.toml

@@ -0,0 +1,16 @@
+# Ruff: run on ruff's own defaults (project lint policy, 2026-10-20).
+# Opt out of specific rules only where warranted; each opt-out is documented
+# inline. No rule sets are selected or opted into.
+line-length = 100 # exception to the ruff default (88): matches this codebase's black -l 100 formatting; avoids a whole-tree reformat
+
+[lint]
+ignore = [
+    "E722", # bare except: deliberate bare-except uses in this codebase, carried from the flake8 era
+    "UP006", # non-pep585-annotation: binding annotations are evaluated at runtime; package declares python_requires>=3.6
+    "UP045", # non-pep604-annotation-optional: same runtime-annotation / python>=3.6 constraint as UP006
+    "UP035", # deprecated-import: typing.Dict/Optional etc. retained for the same python>=3.6 annotation constraint
+    "UP031", # printf-string-formatting: fires only in vendored bindings/python/version.py (third-party, public domain), not hand-edited
+    "UP009", # utf8-encoding-declaration: fires only in vendored bindings/python/version.py, not hand-edited
+    "PLE0605", # invalid-all-format: fires only in vendored bindings/python/version.py, not hand-edited
+    "BLE001", # blind-except: smoke-test harness deliberately catches broad exceptions to degrade gracefully
+]