bump dependencies

Author: mlin

CMakeLists.txt

@@ -18,7 +18,7 @@ endif()
 FetchContent_Declare(
     sqlite_zstd_vfs
     GIT_REPOSITORY  https://github.com/mlin/sqlite_zstd_vfs.git
-    GIT_TAG         fe754eb
+    GIT_TAG         4ccc782
 )
 FetchContent_MakeAvailable(sqlite_zstd_vfs)
 FetchContent_MakeAvailable(sqlitecpp)

Dockerfile

@@ -4,8 +4,8 @@
 FROM centos:7 as builder
 
 ARG CMAKE_VERSION=3.17.3
-ARG SQLITE_VERSION=3360000
-ARG ZSTD_VERSION=1.5.0
+ARG SQLITE_VERSION=3380200
+ARG ZSTD_VERSION=1.5.2
 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/2021/sqlite-amalgamation-${SQLITE_VERSION}.zip \
+RUN wget -nv http://www.sqlite.org/2022/sqlite-amalgamation-${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} ${SQLITE_CFLAGS} sqlite3.c' & pid=$? \

src/genomicsqlite.cc

@@ -1763,13 +1763,15 @@ static int register_genomicsqlite_functions(sqlite3 *db, const char **pzErrMsg,
     }
     // other extensions may return SQLITE_BUSY if another version is already loaded; that is
     // tolerable.
-    rc = genomicsqliteJson1Register(db);
-    if (rc != SQLITE_OK && rc != SQLITE_BUSY) {
-        if (pzErrMsg) {
-            *pzErrMsg =
-                sqlite3_mprintf("Genomics Extension %s failed to register JSON1", GIT_REVISION);
+    if (sqlite3_libversion_number() < 3038000) { // JSON1 is bundled in SQLite 3.38.0 & above
+        rc = genomicsqliteJson1Register(db);
+        if (rc != SQLITE_OK && rc != SQLITE_BUSY) {
+            if (pzErrMsg) {
+                *pzErrMsg =
+                    sqlite3_mprintf("Genomics Extension %s failed to register JSON1", GIT_REVISION);
+            }
+            return rc;
         }
-        return rc;
     }
     rc = genomicsqlite_uint_init(db);
     if (rc != SQLITE_OK && rc != SQLITE_BUSY) {

test/test_gri.py

@@ -17,7 +17,7 @@ def test_gri_lvl():
     )
     for lvl in range(16):
         for ofs in (-2, -1, 0, 1):
-            featlen = 16 ** lvl + ofs
+            featlen = 16**lvl + ofs
             tup = (420, 420 + featlen, (0 - lvl if ofs < 1 else 0 - lvl - 1))
             con.execute("INSERT INTO features VALUES(42,?,?,?)", tup)
     con.executescript(
@@ -93,7 +93,7 @@ def test_abutment():
     pos0 = 10000000000
     for lvl in range(9):
         for ofs in (-1, 0, 1):
-            for tup in ((pos0 - 16 ** lvl, pos0 + ofs), (pos0 + 123 + ofs, pos0 + 123 + 16 ** 9)):
+            for tup in ((pos0 - 16**lvl, pos0 + ofs), (pos0 + 123 + ofs, pos0 + 123 + 16**9)):
                 con.execute("INSERT INTO features VALUES(42,?,?)", tup)
     con.executescript(
         genomicsqlite.create_genomic_range_index_sql(con, "features", "rid", "beg", "end")
@@ -431,7 +431,7 @@ def test_query_in_sql(tmp_path):
     results = list(
         con.execute("SELECT * FROM genomic_range_rowids('empty', 'chr17', 43044294, 43048294)")
     )
-    assert results == []
+    assert not results
 
 
 def _fill_exons(con, floor=None, table="exons", gri=True, len_gri=False):