set --log always to true

bokulich-lab · Jan 11, 2024 · cf83dba · cf83dba
1 parent 69156c6
commit cf83dba
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Showing 3 changed files with 3 additions and 8 deletions.
diff --git a/q2_moshpit/eggnog/_dbs.py b/q2_moshpit/eggnog/_dbs.py
@@ -43,7 +43,6 @@ def build_custom_diamond_db(
         seqs: ProteinSequencesDirectoryFormat,
         taxonomy: NCBITaxonomyDirFmt = None,
         threads: int = 1,
-        log: bool = False,
         file_buffer_size: int = 67108864,
         ignore_warnings: bool = False,
         no_parse_seqids: bool = False
@@ -77,7 +76,7 @@ def build_custom_diamond_db(
     # Run diamond makedb
     cmd = [
         "diamond", "makedb",
-        "--verbose",
+        "--verbose", "--log",
         "--in", f"{os.path.join(str(seqs), 'protein-sequences.fasta')}",
         "--db", f"{os.path.join(str(diamond_db), 'ref_db.dmnd')}",
         *parsed_args

diff --git a/q2_moshpit/eggnog/tests/test_dbs.py b/q2_moshpit/eggnog/tests/test_dbs.py
@@ -49,7 +49,7 @@ def test_build_custom_diamond_db_simple(self, subp_run):
         # Check that command was called in the expected way
         cmd = [
             "diamond", "makedb",
-            "--verbose",
+            "--verbose", "--log",
             "--in", f"{path_in}",
             "--db", f"{path_out}",
             "--threads", "1",
@@ -81,7 +81,7 @@ def test_build_custom_diamond_db_with_taxonomy(self, subp_run):
         # Check that command was called in the expected way
         cmd = [
             "diamond", "makedb",
-            "--verbose",
+            "--verbose", "--log",
             "--in", f"{path_in}",
             "--db", f"{path_out}",
             "--threads", "1",

diff --git a/q2_moshpit/plugin_setup.py b/q2_moshpit/plugin_setup.py
@@ -506,16 +506,12 @@
     },
     parameters={
         "threads": Int % Range(1, None),
-        "log": Bool,
         "file_buffer_size": Int % Range(1, None),
         "ignore_warnings": Bool,
         "no_parse_seqids": Bool
     },
     parameter_descriptions={
         "threads": "Number of CPU threads.",
-        "log": "Enable even more verbose terminal output, which is also "
-               "written to a file named diamond.log is the current working "
-               "directory.",
         "file_buffer_size": "File buffer size in bytes.",
         "ignore_warnings": "Ignore warnings.",
         "no_parse_seqids": "Print raw seqids without parsing."