per_sample_data -> per_sample_sequences

q2_moshpit/busco/busco.py

@@ -15,7 +15,7 @@
     _render_html,
 )
 from q2_moshpit._utils import _process_common_input_params
-from q2_types.per_sample_data._format import MultiMAGSequencesDirFmt
+from q2_types.per_sample_sequences._format import MultiMAGSequencesDirFmt
 
 
 def evaluate_busco(

q2_moshpit/busco/tests/test_busco.py

@@ -12,7 +12,7 @@
 from q2_moshpit.busco.busco import evaluate_busco
 from unittest.mock import patch, ANY
 from qiime2.plugin.testing import TestPluginBase
-from q2_types.per_sample_data._format import MultiMAGSequencesDirFmt
+from q2_types.per_sample_sequences._format import MultiMAGSequencesDirFmt
 
 
 class TestBUSCO(TestPluginBase):

q2_moshpit/busco/tests/test_utils.py

@@ -22,7 +22,7 @@
 )
 from unittest.mock import patch, call
 from qiime2.plugin.testing import TestPluginBase
-from q2_types.per_sample_data._format import MultiMAGSequencesDirFmt
+from q2_types.per_sample_sequences._format import MultiMAGSequencesDirFmt
 
 
 class TestBUSCO(TestPluginBase):

q2_moshpit/busco/utils.py

@@ -8,7 +8,7 @@
 from .._utils import run_command
 from copy import deepcopy
 from typing import List, Dict
-from q2_types.per_sample_data._format import MultiMAGSequencesDirFmt
+from q2_types.per_sample_sequences._format import MultiMAGSequencesDirFmt
 
 
 arguments_with_hyphens = {

q2_moshpit/dereplication/derep.py

@@ -15,7 +15,7 @@
 from scipy.cluster.hierarchy import ward, fcluster
 
 from q2_types.feature_data_mag import MAGSequencesDirFmt
-from q2_types.per_sample_data import MultiMAGSequencesDirFmt
+from q2_types.per_sample_sequences import MultiMAGSequencesDirFmt
 
 
 # def find_similar_bins(

q2_moshpit/dereplication/tests/test_dereplication.py

@@ -19,7 +19,7 @@
     dereplicate_mags
 )
 from q2_types.feature_data_mag import MAGSequencesDirFmt
-from q2_types.per_sample_data._format import MultiMAGSequencesDirFmt
+from q2_types.per_sample_sequences._format import MultiMAGSequencesDirFmt
 
 from qiime2.plugin.testing import TestPluginBase
 

q2_moshpit/eggnog/_method.py

@@ -12,7 +12,7 @@
 import qiime2.util
 import pandas as pd
 from typing import Union
-from q2_types.per_sample_data import ContigSequencesDirFmt
+from q2_types.per_sample_sequences import ContigSequencesDirFmt
 from q2_types.genome_data import SeedOrthologDirFmt, OrthologFileFmt
 from q2_types.reference_db import (
     EggnogRefDirFmt, DiamondDatabaseDirFmt

q2_moshpit/eggnog/tests/test_method.py

@@ -14,7 +14,7 @@
 from q2_types.reference_db import (
     DiamondDatabaseDirFmt, EggnogRefDirFmt
 )
-from q2_types.per_sample_data import ContigSequencesDirFmt
+from q2_types.per_sample_sequences import ContigSequencesDirFmt
 from q2_types.genome_data import SeedOrthologDirFmt, OrthologFileFmt
 
 

q2_moshpit/kraken2/classification.py

@@ -15,14 +15,14 @@
     SequencesWithQuality,
     PairedEndSequencesWithQuality,
     SingleLanePerSamplePairedEndFastqDirFmt,
-    SingleLanePerSampleSingleEndFastqDirFmt
+    SingleLanePerSampleSingleEndFastqDirFmt,
+    ContigSequencesDirFmt, Contigs
 )
 from q2_types.sample_data import SampleData
 from q2_types.feature_data import FeatureData
 from q2_moshpit._utils import run_command, _process_common_input_params
 from q2_moshpit.kraken2.utils import _process_kraken2_arg
 from q2_types.feature_data_mag import MAGSequencesDirFmt, MAG
-from q2_types.per_sample_data import ContigSequencesDirFmt, Contigs
 from q2_types.kraken2 import (
     Kraken2ReportDirectoryFormat,
     Kraken2OutputDirectoryFormat,

q2_moshpit/kraken2/tests/test_classification.py

@@ -16,9 +16,9 @@
 from q2_types.per_sample_sequences import (
     SingleLanePerSampleSingleEndFastqDirFmt,
     SingleLanePerSamplePairedEndFastqDirFmt,
+    ContigSequencesDirFmt
 )
 from q2_types.feature_data_mag import MAGSequencesDirFmt
-from q2_types.per_sample_data import ContigSequencesDirFmt
 from q2_types.kraken2 import (
     Kraken2ReportDirectoryFormat,
     Kraken2OutputDirectoryFormat, Kraken2DBDirectoryFormat,

q2_moshpit/metabat2/metabat2.py

@@ -18,8 +18,8 @@
 import skbio.io
 from q2_types.feature_data import DNAIterator
 
-from q2_types.per_sample_data import ContigSequencesDirFmt, BAMDirFmt
-from q2_types.per_sample_data._format import MultiFASTADirectoryFormat
+from q2_types.per_sample_sequences import ContigSequencesDirFmt, BAMDirFmt
+from q2_types.per_sample_sequences._format import MultiFASTADirectoryFormat
 
 from q2_moshpit._utils import run_command, _process_common_input_params
 from q2_moshpit.metabat2.utils import _process_metabat2_arg

q2_moshpit/metabat2/tests/test_metabat2.py

@@ -13,8 +13,8 @@
 from pathlib import Path
 import tempfile
 import unittest
-from q2_types.per_sample_data import ContigSequencesDirFmt, BAMDirFmt
-from q2_types.per_sample_data._format import MultiFASTADirectoryFormat
+from q2_types.per_sample_sequences import ContigSequencesDirFmt, BAMDirFmt
+from q2_types.per_sample_sequences._format import MultiFASTADirectoryFormat
 from unittest.mock import patch, ANY, call
 
 from qiime2.plugin.testing import TestPluginBase

q2_moshpit/plugin_setup.py

@@ -13,7 +13,7 @@
 )
 from q2_types.feature_table import FeatureTable, Frequency, PresenceAbsence
 from q2_types.per_sample_sequences import (
-    SequencesWithQuality, PairedEndSequencesWithQuality
+    SequencesWithQuality, PairedEndSequencesWithQuality, MAGs, Contigs
 )
 from q2_types.sample_data import SampleData
 from q2_types.feature_map import FeatureMap, MAGtoContigs
@@ -31,8 +31,7 @@
     Kraken2Reports, Kraken2Outputs, Kraken2DB, Kraken2DBReport
 )
 from q2_types.kraken2._type import BrackenDB
-from q2_types.per_sample_data import MAGs, Contigs
-from q2_types.per_sample_data._type import AlignmentMap
+from q2_types.per_sample_sequences._type import AlignmentMap
 from q2_types.reference_db import (
     ReferenceDB, Diamond, Eggnog, NCBITaxonomy, EggnogProteinSequences
 )