Merge branch 'trs/merge/no-sqliterc'

nextstrain · Aug 28, 2024 · 47c83e0 · 47c83e0
2 parents d662698 + d2589af
commit 47c83e0
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diff --git a/CHANGES.md b/CHANGES.md
@@ -5,8 +5,10 @@
 ### Bug Fixes
 
 * filter: Improved warning and error messages in the case of missing columns. [#1604] (@victorlin)
+* merge: Any user-customized `~/.sqliterc` file is now ignored so it doesn't break `augur merge`'s internal use of SQLite. [#1608][] (@tsibley)
 
 [#1604]: https://github.com/nextstrain/augur/pull/1604
+[#1608]: https://github.com/nextstrain/augur/pull/1608
 
 ## 25.3.0 (22 August 2024)
 

diff --git a/augur/merge.py b/augur/merge.py
@@ -258,7 +258,7 @@ def sqlite3(*args, **kwargs):
             Nextstrain runtime.
             """))
 
-    argv = [sqlite3, "-batch", *args]
+    argv = [sqlite3, "-init", os.devnull, "-batch", *args]
 
     print_debug(f"running {argv!r}")
     proc = subprocess.run(argv, encoding="utf-8", text=True, **kwargs)