REF: distance_matrix

qiime2 · Jul 22, 2024 · 040988e · 040988e
1 parent ccd25ff
commit 040988e
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Showing 10 changed files with 26 additions and 18 deletions.
diff --git a/q2_types/__init__.py b/q2_types/__init__.py
@@ -19,7 +19,6 @@
 importlib.import_module('q2_types.per_sample_sequences')
 importlib.import_module('q2_types.feature_map')
 importlib.import_module('q2_types.feature_table')
-importlib.import_module('q2_types.distance_matrix')
 importlib.import_module('q2_types.tree')
 importlib.import_module('q2_types.ordination')
 importlib.import_module('q2_types.sample_data')

diff --git a/q2_types/distance_matrix/__init__.py b/q2_types/distance_matrix/__init__.py
@@ -6,11 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-import importlib
-
-from ._format import LSMatFormat, DistanceMatrixDirectoryFormat
-from ._type import DistanceMatrix
+from ._formats import LSMatFormat, DistanceMatrixDirectoryFormat
+from ._types import DistanceMatrix
 
 __all__ = ['LSMatFormat', 'DistanceMatrixDirectoryFormat', 'DistanceMatrix']
-
-importlib.import_module('q2_types.distance_matrix._transformer')
diff --git a/q2_types/distance_matrix/_type.py → ...stance_matrix/_deferred_setup/__init__.py b/q2_types/distance_matrix/_type.py → ...stance_matrix/_deferred_setup/__init__.py
@@ -6,17 +6,21 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-from qiime2.plugin import SemanticType
+import importlib
 
-from ..plugin_setup import plugin
-from . import DistanceMatrixDirectoryFormat
+from .. import LSMatFormat, DistanceMatrixDirectoryFormat
+from .. import DistanceMatrix
 
+from ...plugin_setup import plugin
 
-DistanceMatrix = SemanticType('DistanceMatrix')
+plugin.register_formats(LSMatFormat, DistanceMatrixDirectoryFormat)
 
 plugin.register_semantic_types(DistanceMatrix)
+
 plugin.register_artifact_class(
     DistanceMatrix,
     directory_format=DistanceMatrixDirectoryFormat,
     description="A symmetric matrix representing distances between entities."
 )
+
+importlib.import_module('._transformers', __name__)
diff --git a/q2_types/distance_matrix/_transformer.py → ...e_matrix/_deferred_setup/_transformers.py b/q2_types/distance_matrix/_transformer.py → ...e_matrix/_deferred_setup/_transformers.py
@@ -8,8 +8,9 @@
 
 import skbio
 
-from ..plugin_setup import plugin
-from . import LSMatFormat
+from .. import LSMatFormat
+
+from ...plugin_setup import plugin
 
 
 @plugin.register_transformer

diff --git a/q2_types/distance_matrix/_format.py → q2_types/distance_matrix/_formats.py b/q2_types/distance_matrix/_format.py → q2_types/distance_matrix/_formats.py
@@ -9,8 +9,6 @@
 import skbio.io
 import qiime2.plugin.model as model
 
-from ..plugin_setup import plugin
-
 
 class LSMatFormat(model.TextFileFormat):
     def sniff(self):
@@ -20,6 +18,3 @@ def sniff(self):
 
 DistanceMatrixDirectoryFormat = model.SingleFileDirectoryFormat(
     'DistanceMatrixDirectoryFormat', 'distance-matrix.tsv', LSMatFormat)
-
-
-plugin.register_formats(LSMatFormat, DistanceMatrixDirectoryFormat)
diff --git a/q2_types/distance_matrix/_types.py b/q2_types/distance_matrix/_types.py
@@ -0,0 +1,12 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+from qiime2.plugin import SemanticType
+
+
+DistanceMatrix = SemanticType('DistanceMatrix')
diff --git a/...ypes/distance_matrix/tests/test_format.py → ...pes/distance_matrix/tests/test_formats.py b/...ypes/distance_matrix/tests/test_format.py → ...pes/distance_matrix/tests/test_formats.py
diff --git a/...distance_matrix/tests/test_transformer.py → ...istance_matrix/tests/test_transformers.py b/...distance_matrix/tests/test_transformer.py → ...istance_matrix/tests/test_transformers.py
diff --git a/q2_types/distance_matrix/tests/test_type.py → q2_types/distance_matrix/tests/test_types.py b/q2_types/distance_matrix/tests/test_type.py → q2_types/distance_matrix/tests/test_types.py
diff --git a/q2_types/plugin_setup.py b/q2_types/plugin_setup.py
@@ -30,3 +30,4 @@
                       citations=[citations['mckinney-proc-scipy-2010']])
 
 importlib.import_module('q2_types.bowtie2._deferred_setup')
+importlib.import_module('q2_types.distance_matrix._deferred_setup')
Original file line number	Diff line number	Diff line change
Expand Up		@@ -30,3 +30,4 @@
		citations=[citations['mckinney-proc-scipy-2010']])

		importlib.import_module('q2_types.bowtie2._deferred_setup')
		importlib.import_module('q2_types.distance_matrix._deferred_setup')