Refactor q2-types to avoid circular imports

q2_types/__init__.py

@@ -19,11 +19,9 @@
 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')
-importlib.import_module('q2_types.bowtie2')
 importlib.import_module('q2_types.metadata')
 importlib.import_module('q2_types.multiplexed_sequences')
 importlib.import_module('q2_types.kraken2')

q2_types/bowtie2/__init__.py

@@ -9,9 +9,4 @@
 from ._formats import (Bowtie2IndexFileFormat, Bowtie2IndexDirFmt)
 from ._types import Bowtie2Index
 
-from ..plugin_setup import plugin, citations
-
-plugin.register_views(Bowtie2IndexDirFmt,
-                      citations=[citations['langmead2012fast']])
-
 __all__ = ['Bowtie2IndexFileFormat', 'Bowtie2IndexDirFmt', 'Bowtie2Index']

q2_types/bowtie2/_deferred_setup/__init__.py

@@ -0,0 +1,26 @@
+# ----------------------------------------------------------------------------
+# 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 Citations
+
+from .. import Bowtie2IndexDirFmt
+from .. import Bowtie2Index
+
+from ...plugin_setup import plugin
+
+citations = Citations.load('citations.bib', package='q2_types.bowtie2')
+plugin.register_views(Bowtie2IndexDirFmt,
+                      citations=[citations['langmead2012fast']])
+
+plugin.register_semantic_types(Bowtie2Index)
+
+plugin.register_artifact_class(
+    Bowtie2Index,
+    directory_format=Bowtie2IndexDirFmt,
+    description='An index of sequences for Bowtie 2 to search against.'
+)

q2_types/bowtie2/_types.py

@@ -7,14 +7,9 @@
 # ----------------------------------------------------------------------------
 
 from qiime2.plugin import SemanticType
-from . import Bowtie2IndexDirFmt
-from ..plugin_setup import plugin
 
 
 # Technically there is a bit more to this, for instance the ref sequences may
 # or may not be present in an index, or may be the only thing in an index,
 # but let's not worry about that just yet.
 Bowtie2Index = SemanticType('Bowtie2Index')
-
-plugin.register_semantic_types(Bowtie2Index)
-plugin.register_artifact_class(Bowtie2Index, Bowtie2IndexDirFmt)

q2_types/bowtie2/citations.bib

@@ -0,0 +1,10 @@
+@article{langmead2012fast,
+  title={Fast gapped-read alignment with Bowtie 2},
+  author={Langmead, Ben and Salzberg, Steven L},
+  journal={Nature methods},
+  volume={9},
+  number={4},
+  pages={357},
+  year={2012},
+  publisher={Nature Publishing Group}
+}

q2_types/citations.bib

@@ -18,14 +18,3 @@ @InProceedings{ mckinney-proc-scipy-2010
   year      = { 2010 },
   editor    = { St{\'e}fan van der Walt and Jarrod Millman }
 }
-
-@article{langmead2012fast,
-  title={Fast gapped-read alignment with Bowtie 2},
-  author={Langmead, Ben and Salzberg, Steven L},
-  journal={Nature methods},
-  volume={9},
-  number={4},
-  pages={357},
-  year={2012},
-  publisher={Nature Publishing Group}
-}

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')

q2_types/distance_matrix/_type.py → q2_types/distance_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__)

q2_types/distance_matrix/_transformer.py → q2_types/distance_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

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)

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')

q2_types/plugin_setup.py

@@ -6,7 +6,10 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
+import importlib
+
 import pandas as pd
+
 import qiime2.plugin
 import qiime2.sdk
 
@@ -26,4 +29,5 @@
 plugin.register_views(pd.Series, pd.DataFrame,
                       citations=[citations['mckinney-proc-scipy-2010']])
 
-# __init__.py loads first and imports all of the subpackages.
+importlib.import_module('q2_types.bowtie2._deferred_setup')
+importlib.import_module('q2_types.distance_matrix._deferred_setup')

setup.py

@@ -27,6 +27,7 @@
     package_data={
         'q2_types': ['citations.bib'],
         'q2_types.tests': ['data/*'],
+        'q2_types.bowtie2': ['citations.bib'],
         'q2_types.distance_matrix.tests': ['data/*'],
         'q2_types.feature_data.tests': ['data/*',
                                         'data/taxonomy/*',