REF: tree

Author: ebolyen

q2_types/__init__.py

@@ -6,11 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-import importlib
-
 from ._version import get_versions
 
 __version__ = get_versions()['version']
 del get_versions
-
-importlib.import_module('q2_types.tree')

q2_types/plugin_setup.py

@@ -44,3 +44,4 @@
 importlib.import_module('q2_types.profile_hmms._deferred_setup')
 importlib.import_module('q2_types.reference_db._deferred_setup')
 importlib.import_module('q2_types.sample_data._deferred_setup')
+importlib.import_module('q2_types.tree._deferred_setup')

q2_types/tree/__init__.py

@@ -5,14 +5,9 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-
-import importlib
-
-from ._format import NewickFormat, NewickDirectoryFormat
-from ._type import Phylogeny, Rooted, Unrooted, Hierarchy
+from ._formats import NewickFormat, NewickDirectoryFormat
+from ._types import Phylogeny, Rooted, Unrooted, Hierarchy
 
 __all__ = [
     'NewickFormat', 'NewickDirectoryFormat', 'Phylogeny',
     'Rooted', 'Unrooted', 'Hierarchy']
-
-importlib.import_module('q2_types.tree._transformer')

q2_types/tree/_type.py q2_types/tree/_deferred_setup/__init__.py

@@ -6,23 +6,19 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
+import importlib
 from io import StringIO
 
 from skbio import TreeNode
 
-from qiime2.plugin import SemanticType
 from qiime2.plugin.util import transform
 
-from ..plugin_setup import plugin
-from . import NewickDirectoryFormat
+from .. import (NewickFormat, NewickDirectoryFormat,
+                Phylogeny, Rooted, Unrooted, Hierarchy)
 
-Phylogeny = SemanticType('Phylogeny', field_names=['type'])
+from ...plugin_setup import plugin
 
-Rooted = SemanticType('Rooted', variant_of=Phylogeny.field['type'])
-
-Unrooted = SemanticType('Unrooted', variant_of=Phylogeny.field['type'])
-
-Hierarchy = SemanticType('Hierarchy')
+plugin.register_formats(NewickFormat, NewickDirectoryFormat)
 
 plugin.register_semantic_types(Phylogeny, Rooted, Unrooted, Hierarchy)
 
@@ -57,3 +53,5 @@ def factory():
 
 plugin.register_artifact_class(Hierarchy,
                                directory_format=NewickDirectoryFormat)
+
+importlib.import_module('._transformers', __name__)

q2_types/tree/_transformer.py q2_types/tree/_deferred_setup/_transformers.py

@@ -8,8 +8,9 @@
 
 import skbio
 
-from ..plugin_setup import plugin
-from . import NewickFormat
+from .. import NewickFormat
+
+from ...plugin_setup import plugin
 
 
 @plugin.register_transformer

q2_types/tree/_format.py q2_types/tree/_formats.py

@@ -5,12 +5,9 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-
 import skbio.io
 import qiime2.plugin.model as model
 
-from ..plugin_setup import plugin
-
 
 class NewickFormat(model.TextFileFormat):
     def sniff(self):
@@ -20,6 +17,3 @@ def sniff(self):
 
 NewickDirectoryFormat = model.SingleFileDirectoryFormat(
     'NewickDirectoryFormat', 'tree.nwk', NewickFormat)
-
-
-plugin.register_formats(NewickFormat, NewickDirectoryFormat)

q2_types/tree/_types.py

@@ -0,0 +1,17 @@
+# ----------------------------------------------------------------------------
+# 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
+
+
+Phylogeny = SemanticType('Phylogeny', field_names=['type'])
+
+Rooted = SemanticType('Rooted', variant_of=Phylogeny.field['type'])
+
+Unrooted = SemanticType('Unrooted', variant_of=Phylogeny.field['type'])
+
+Hierarchy = SemanticType('Hierarchy')