Issue between ete3 3.1.3 and sqlite3 3.49.1

[ArnaudBelcour]

There is an incompatibility between ete3 and sqlite3 producing errors like this one:

sqlite3.OperationalError: no such column: "XXX" - should this be a string literal in single-quotes?

I have encountered this issue with sqlite3 version 3.49.1 (version checked with python3 -c "import sqlite3; print(sqlite3.sqlite_version)").

It has been identified (and fix) in a PR in the GitHub repository of ete3: etetoolkit/ete#770

A temporary workaround (if sqlite3 has been installed with conda/mamba) is to downgrade to another version, with command like:

mamba install libsqlite==3.46.1

[conchoecia]

I ran into the same issue, this is the relevant section of the traceback from a simple query:

    taxid2name = ncbi.get_taxid_translator([9606, 9443])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/path/to/lib/python3.12/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 268, in get_taxid_translator
    result = self.db.execute(cmd)
             ^^^^^^^^^^^^^^^^^^^^
sqlite3.OperationalError: no such column: "9443" - should this be a string literal in single-quotes?

This is my sqlite version:

conda list sqlite

# Name                    Version                   Build  Channel
libsqlite                 3.49.1               hee588c1_1    conda-forge