downgrade sqlite to 3.39.4

due to query plan regression in 3.40.0: https://sqlite.org/forum/forumpost/07b36e3899a9ae21

Author: mlin

Dockerfile

@@ -4,7 +4,7 @@
 FROM centos:7 as builder
 
 ARG CMAKE_VERSION=3.17.3
-ARG SQLITE_VERSION=3400000
+ARG SQLITE_VERSION=3390400
 ARG ZSTD_VERSION=1.5.2
 ARG CPU_ARCH=ivybridge
 ENV CFLAGS="-march=${CPU_ARCH} -O3"

test/genomicsqlite_smoke_test.py

@@ -129,6 +129,10 @@ def main():
             results == control_results
         ), "discrepancy between genomic_range_rowids_sql() and control results"
 
+        for expl in dbconn.execute("EXPLAIN " + query):
+            if expl[1] in {"OpenRead", "OpenPseudo", "Column"}:
+                print("  " + str(expl))
+
         if gri_constraints != 3:
             print("GRI query opcodes:")
             for expl in dbconn.execute("EXPLAIN " + query):

test/test_gri.py

@@ -56,9 +56,9 @@ def test_indexing():
 
     # The query should be covered by the index except for one final fetch of exons.id
     opcodes = list(con.execute("EXPLAIN " + query, ("chr17", 43044294, 43048294)))
-    # for expl in opcodes:
-    #    if expl[1] in {"OpenRead", "OpenPseudo", "Column"}:
-    #        print(expl)
+    for expl in opcodes:
+       if expl[1] in {"OpenRead", "OpenPseudo", "Column"}:
+           print(expl)
     accessed_cursors = list(opcode[2] for opcode in opcodes if opcode[1] == "Column")
     table_rootpages = set(
         row[0] for row in con.execute("SELECT rootpage FROM sqlite_master WHERE type='table'")