update SQLite & zstd

Author: mlin

.github/workflows/build.yml

@@ -3,7 +3,7 @@ on: [push, pull_request]
 
 env:
   APT_DEPS: libzstd-dev samtools tabix libhts-dev pigz python3-pip libcurl4-openssl-dev
-  BREW_DEPS: python@3.8 zstd samtools pigz coreutils
+  BREW_DEPS: python@3.8 zstd samtools pigz coreutils sqlite
   PIP_DEPS: pytest pytest-xdist
 
 jobs:
@@ -127,11 +127,6 @@ jobs:
           brew install $dep || brew upgrade $dep
         done
 
-        # FIXME 2022-12-27: pin sqlite 3.39.4 due to query plan regression in 3.40.0
-        #                   https://sqlite.org/forum/forumpost/07b36e3899a9ae21
-        wget https://raw.githubusercontent.com/Homebrew/homebrew-core/fc08979e0cc7c580a2feba5447d9a518dc518826/Formula/sqlite.rb
-        brew reinstall -s sqlite.rb
-
         /usr/local/bin/pip3 install $PIP_DEPS
     - name: rust toolchain
       uses: actions-rs/toolchain@v1

Dockerfile

@@ -4,8 +4,8 @@
 FROM centos:7 as builder
 
 ARG CMAKE_VERSION=3.17.3
-ARG SQLITE_VERSION=3390400
-ARG ZSTD_VERSION=1.5.2
+ARG SQLITE_VERSION=3410000
+ARG ZSTD_VERSION=1.5.4
 ARG CPU_ARCH=ivybridge
 ENV CFLAGS="-march=${CPU_ARCH} -O3"
 ENV CXXFLAGS=${CFLAGS}
@@ -35,7 +35,7 @@ RUN mkdir -p /work/GenomicSQLite
 
 # SQLite
 WORKDIR /work
-RUN wget -nv http://www.sqlite.org/2022/sqlite-amalgamation-${SQLITE_VERSION}.zip \
+RUN wget -nv http://www.sqlite.org/2023/sqlite-amalgamation-${SQLITE_VERSION}.zip \
         && unzip -o sqlite-amalgamation-${SQLITE_VERSION}.zip
 WORKDIR /work/sqlite-amalgamation-${SQLITE_VERSION}
 RUN bash -c "scl enable devtoolset-8 'gcc -shared -o libsqlite3.so.0 -fPIC -shared -Wl,-soname,libsqlite3.so.0 -g ${CFLAGS} ${SQLITE_CFLAGS} sqlite3.c' & pid=$? \

test/genomicsqlite_smoke_test.py

@@ -85,7 +85,7 @@ def main():
     print(f"\ntest database: {dbfile}")
     try:
         dbconn = genomicsqlite.connect(dbfile)
-        for (table, bed) in (("exons1", _EXONS1), ("exons2", _EXONS2)):
+        for table, bed in (("exons1", _EXONS1), ("exons2", _EXONS2)):
             dbconn.execute(
                 f"CREATE TABLE {table}(chrom TEXT, pos INTEGER, end INTEGER, id TEXT PRIMARY KEY)"
             )

test/test_parse_genomic_range.py

@@ -5,7 +5,7 @@
 
 def test_parse_genomic_range():
     con = genomicsqlite.connect(":memory:")
-    for (txt, chrom, begin_pos, end_pos) in [
+    for txt, chrom, begin_pos, end_pos in [
         ("chr1:2,345-06,789", "chr1", 2344, 6789),
         ("π:1-9,223,372,036,854,775,799", "π", 0, 9223372036854775799),
     ]: