merge 80

bokulich-lab · Jul 4, 2024 · 060f24d · 060f24d
2 parents 71a8da2 + 0bf7f20
commit 060f24d
Show file tree

Hide file tree

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
@@ -6,7 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 from q2_amr.amrfinderplus.types._format import (
-    AMRFinderPlusDatabaseDirectoryFormat,
+    AMRFinderPlusDatabaseDirFmt,
     ARMFinderPlusAnnotationDirFmt,
     ARMFinderPlusAnnotationFormat,
     ARMFinderPlusAnnotationsDirFmt,
@@ -15,7 +15,7 @@
 )
 
 __all__ = [
-    "AMRFinderPlusDatabaseDirectoryFormat",
+    "AMRFinderPlusDatabaseDirFmt",
     "ARMFinderPlusAnnotationFormat",
     "ARMFinderPlusAnnotationsDirFmt",
     "ARMFinderPlusAnnotationDirFmt",

diff --git a/q2_amr/amrfinderplus/types/_format.py b/q2_amr/amrfinderplus/types/_format.py
@@ -24,7 +24,7 @@ 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
@@ -11,7 +11,7 @@
 from qiime2.plugin.testing import TestPluginBase
 
 from q2_amr.amrfinderplus.types._format import (
-    AMRFinderPlusDatabaseDirectoryFormat,
+    AMRFinderPlusDatabaseDirFmt,
     ARMFinderPlusAnnotationDirFmt,
     ARMFinderPlusAnnotationFormat,
     ARMFinderPlusAnnotationsDirFmt,
@@ -22,9 +22,7 @@ class TestAMRFinderPlusTypesAndFormats(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()
 
     def test_amrfinderplus_annotation_format_validate_positive(self):

diff --git a/q2_amr/plugin_setup.py b/q2_amr/plugin_setup.py
@@ -30,7 +30,7 @@
 
 from q2_amr import __version__
 from q2_amr.amrfinderplus.types._format import (
-    AMRFinderPlusDatabaseDirectoryFormat,
+    AMRFinderPlusDatabaseDirFmt,
     ARMFinderPlusAnnotationDirFmt,
     ARMFinderPlusAnnotationFormat,
     ARMFinderPlusAnnotationsDirFmt,
@@ -1124,7 +1124,7 @@
 )
 plugin.register_semantic_type_to_format(
     AMRFinderPlusDatabase,
-    artifact_format=AMRFinderPlusDatabaseDirectoryFormat,
+    artifact_format=AMRFinderPlusDatabaseDirFmt,
 )
 plugin.register_semantic_type_to_format(
     SampleData[ARMFinderPlusAnnotations],
@@ -1158,7 +1158,7 @@
     CARDReadsKmerAnalysisJSONFormat,
     CARDReadsGeneKmerAnalysisDirectoryFormat,
     CARDReadsAlleleKmerAnalysisDirectoryFormat,
-    AMRFinderPlusDatabaseDirectoryFormat,
+    AMRFinderPlusDatabaseDirFmt,
     TextFormat,
     BinaryFormat,
     ARMFinderPlusAnnotationFormat,