REF: bowtie2

q2_types/__init__.py

@@ -23,7 +23,6 @@
 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/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 +29,4 @@
 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')

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/*',