MAINT: port Bowtie2Index to q2-types (#16)

qiime2-graveyard · Jul 16, 2020 · edccba8 · edccba8
1 parent 8c6705f
commit edccba8
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Showing 6 changed files with 4 additions and 71 deletions.
diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml
@@ -19,6 +19,8 @@ requirements:
 
   run:
     - python {{ python }}
+    - qiime2 {{ release }}.*
+    - q2-types {{ release }}.*
     - SHOGUN
     - bowtie2
     - cytoolz

diff --git a/q2_shogun/__init__.py b/q2_shogun/__init__.py
@@ -7,11 +7,7 @@
 # ----------------------------------------------------------------------------
 
 from ._version import get_versions
-from ._formats import (Bowtie2IndexFileFormat, Bowtie2IndexDirFmt)
-from ._types import Bowtie2Index
 
 
 __version__ = get_versions()['version']
 del get_versions
-
-__all__ = ['Bowtie2IndexFileFormat', 'Bowtie2IndexDirFmt', 'Bowtie2Index']
diff --git a/q2_shogun/_formats.py b/q2_shogun/_formats.py
diff --git a/q2_shogun/_shogun.py b/q2_shogun/_shogun.py
@@ -17,7 +17,7 @@
 from qiime2.util import duplicate
 from q2_types.feature_data import DNAFASTAFormat
 
-from q2_shogun._formats import Bowtie2IndexDirFmt
+from q2_types.bowtie2 import Bowtie2IndexDirFmt
 
 
 def _run_command(cmd, verbose=True):

diff --git a/q2_shogun/_types.py b/q2_shogun/_types.py
diff --git a/q2_shogun/plugin_setup.py b/q2_shogun/plugin_setup.py
@@ -10,9 +10,8 @@
 
 from q2_types.feature_data import FeatureData, Sequence, Taxonomy
 from q2_types.feature_table import FeatureTable, Frequency
+from q2_types.bowtie2 import Bowtie2Index
 
-from ._formats import Bowtie2IndexDirFmt
-from ._types import Bowtie2Index
 from ._shogun import minipipe, nobunaga
 import q2_shogun
 
@@ -30,11 +29,6 @@
     citations=[citations['Hillmann320986']]
 )
 
-plugin.register_views(Bowtie2IndexDirFmt,
-                      citations=[citations['langmead2012fast']])
-plugin.register_semantic_types(Bowtie2Index)
-plugin.register_semantic_type_to_format(Bowtie2Index, Bowtie2IndexDirFmt)
-
 plugin.methods.register_function(
     function=nobunaga,
     inputs={'query': FeatureData[Sequence],