renamed to dirfmt

bokulich-lab · Jul 4, 2024 · 0bf7f20 · 0bf7f20
1 parent 317e5cb
commit 0bf7f20
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Showing 4 changed files with 8 additions and 10 deletions.
diff --git a/q2_amr/amrfinderplus/types/__init__.py b/q2_amr/amrfinderplus/types/__init__.py
@@ -6,13 +6,13 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 from q2_amr.amrfinderplus.types._format import (
-    AMRFinderPlusDatabaseDirectoryFormat,
+    AMRFinderPlusDatabaseDirFmt,
     BinaryFormat,
     TextFormat,
 )
 
 __all__ = [
-    "AMRFinderPlusDatabaseDirectoryFormat",
+    "AMRFinderPlusDatabaseDirFmt",
     "TextFormat",
     "BinaryFormat",
 ]
diff --git a/q2_amr/amrfinderplus/types/_format.py b/q2_amr/amrfinderplus/types/_format.py
@@ -19,7 +19,7 @@ def _validate_(self, level):
         pass
 
 
-class AMRFinderPlusDatabaseDirectoryFormat(model.DirectoryFormat):
+class AMRFinderPlusDatabaseDirFmt(model.DirectoryFormat):
     amr_lib = model.File("AMR.LIB", format=TextFormat)
     amr_lib_comp = model.FileCollection(r"^AMR\.LIB\.h3.$", format=BinaryFormat)
     amrprot = model.File("AMRProt", format=ProteinFASTAFormat)

diff --git a/q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py b/q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py
@@ -7,14 +7,12 @@
 # ----------------------------------------------------------------------------
 from qiime2.plugin.testing import TestPluginBase
 
-from q2_amr.amrfinderplus.types._format import AMRFinderPlusDatabaseDirectoryFormat
+from q2_amr.amrfinderplus.types._format import AMRFinderPlusDatabaseDirFmt
 
 
 class TestAMRFinderPlusDatabaseTypesAndFormats(TestPluginBase):
     package = "q2_amr.amrfinderplus.types.tests"
 
     def test_amrfinderplus_database_directory_format_validate_positive(self):
-        format = AMRFinderPlusDatabaseDirectoryFormat(
-            self.get_data_path("database"), mode="r"
-        )
+        format = AMRFinderPlusDatabaseDirFmt(self.get_data_path("database"), mode="r")
         format.validate()
diff --git a/q2_amr/plugin_setup.py b/q2_amr/plugin_setup.py
@@ -29,7 +29,7 @@
 
 from q2_amr import __version__
 from q2_amr.amrfinderplus.types._format import (
-    AMRFinderPlusDatabaseDirectoryFormat,
+    AMRFinderPlusDatabaseDirFmt,
     BinaryFormat,
     TextFormat,
 )
@@ -1116,7 +1116,7 @@
 )
 plugin.register_semantic_type_to_format(
     AMRFinderPlusDatabase,
-    artifact_format=AMRFinderPlusDatabaseDirectoryFormat,
+    artifact_format=AMRFinderPlusDatabaseDirFmt,
 )
 plugin.register_formats(
     CARDKmerDatabaseDirectoryFormat,
@@ -1142,7 +1142,7 @@
     CARDReadsKmerAnalysisJSONFormat,
     CARDReadsGeneKmerAnalysisDirectoryFormat,
     CARDReadsAlleleKmerAnalysisDirectoryFormat,
-    AMRFinderPlusDatabaseDirectoryFormat,
+    AMRFinderPlusDatabaseDirFmt,
     TextFormat,
     BinaryFormat,
 )