Merge branch 'main' into partition_seqs_iss_126

ci/recipe/meta.yaml

@@ -27,7 +27,7 @@ requirements:
     - kraken2
     - metabat2
     - qiime2 {{ qiime2_epoch }}.*
-    - q2-types-genomics {{ qiime2_epoch }}.*
+    - q2-types {{ qiime2_epoch }}.*
     - q2templates {{ qiime2_epoch }}.*
     - q2-assembly {{ qiime2_epoch }}.*
     - eggnog-mapper >=2.1.10

q2_moshpit/busco/busco.py

@@ -15,7 +15,7 @@
     _render_html,
 )
 from q2_moshpit._utils import _process_common_input_params
-from q2_types_genomics.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_genomics.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_genomics.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_genomics.per_sample_data._format import MultiMAGSequencesDirFmt
+from q2_types.per_sample_sequences._format import MultiMAGSequencesDirFmt
 
 
 arguments_with_hyphens = {

q2_moshpit/dereplication/derep.py

@@ -14,8 +14,8 @@
 from q2_types.feature_data import DNAFASTAFormat
 from scipy.cluster.hierarchy import ward, fcluster
 
-from q2_types_genomics.feature_data import MAGSequencesDirFmt
-from q2_types_genomics.per_sample_data import MultiMAGSequencesDirFmt
+from q2_types.feature_data_mag import MAGSequencesDirFmt
+from q2_types.per_sample_sequences import MultiMAGSequencesDirFmt
 
 
 # def find_similar_bins(

q2_moshpit/dereplication/tests/test_dereplication.py

@@ -18,8 +18,8 @@
     _reassign_bins_to_samples, _write_unique_bins, _generate_pa_table,
     dereplicate_mags
 )
-from q2_types_genomics.feature_data import MAGSequencesDirFmt
-from q2_types_genomics.per_sample_data._format import MultiMAGSequencesDirFmt
+from q2_types.feature_data_mag import MAGSequencesDirFmt
+from q2_types.per_sample_sequences._format import MultiMAGSequencesDirFmt
 
 from qiime2.plugin.testing import TestPluginBase
 

q2_moshpit/eggnog/_dbs.py

@@ -10,7 +10,7 @@
 import pandas as pd
 from qiime2.core.exceptions import ValidationError
 from q2_types.feature_data import ProteinSequencesDirectoryFormat
-from q2_types_genomics.reference_db import (
+from q2_types.reference_db import (
     EggnogRefDirFmt, DiamondDatabaseDirFmt, NCBITaxonomyDirFmt,
     EggnogProteinSequencesDirFmt
 )

q2_moshpit/eggnog/_method.py

@@ -12,13 +12,13 @@
 import qiime2.util
 import pandas as pd
 from typing import Union
-from q2_types_genomics.per_sample_data import ContigSequencesDirFmt
-from q2_types_genomics.genome_data import SeedOrthologDirFmt, OrthologFileFmt
-from q2_types_genomics.reference_db import (
+from q2_types.per_sample_sequences import ContigSequencesDirFmt
+from q2_types.genome_data import SeedOrthologDirFmt, OrthologFileFmt
+from q2_types.reference_db import (
     EggnogRefDirFmt, DiamondDatabaseDirFmt
 )
 from q2_types.feature_data import DNAFASTAFormat
-from q2_types_genomics.feature_data import (
+from q2_types.feature_data_mag import (
     OrthologAnnotationDirFmt, MAGSequencesDirFmt
 )
 

q2_moshpit/eggnog/tests/test_dbs.py

@@ -15,7 +15,7 @@
     _validate_taxon_id, _collect_and_compare_md5
 )
 from q2_types.feature_data import ProteinSequencesDirectoryFormat
-from q2_types_genomics.reference_db import (
+from q2_types.reference_db import (
     NCBITaxonomyDirFmt, EggnogProteinSequencesDirFmt
 )
 

q2_moshpit/eggnog/tests/test_method.py

@@ -9,13 +9,13 @@
 import pandas as pd
 import pandas.testing as pdt
 from qiime2.plugin.testing import TestPluginBase
-from q2_types_genomics.feature_data import MAGSequencesDirFmt
+from q2_types.feature_data_mag import MAGSequencesDirFmt
 from .._method import eggnog_diamond_search, eggnog_annotate
-from q2_types_genomics.reference_db import (
+from q2_types.reference_db import (
     DiamondDatabaseDirFmt, EggnogRefDirFmt
 )
-from q2_types_genomics.per_sample_data import ContigSequencesDirFmt
-from q2_types_genomics.genome_data import SeedOrthologDirFmt, OrthologFileFmt
+from q2_types.per_sample_sequences import ContigSequencesDirFmt
+from q2_types.genome_data import SeedOrthologDirFmt, OrthologFileFmt
 
 
 class TestDiamond(TestPluginBase):

q2_moshpit/kaiju/classification.py

@@ -20,7 +20,7 @@
 )
 
 from q2_moshpit._utils import run_command
-from q2_types_genomics.kaiju import KaijuDBDirectoryFormat
+from q2_types.kaiju import KaijuDBDirectoryFormat
 
 DEFAULT_PREFIXES = ["d__", "p__", "c__", "o__", "f__", "g__", "s__", "ssp__"]
 

q2_moshpit/kaiju/database.py

@@ -11,7 +11,7 @@
 
 from tqdm import tqdm
 
-from q2_types_genomics.kaiju import KaijuDBDirectoryFormat
+from q2_types.kaiju import KaijuDBDirectoryFormat
 
 
 from bs4 import BeautifulSoup

q2_moshpit/kaiju/tests/test_database.py

@@ -20,7 +20,7 @@
 )
 from requests.exceptions import ConnectionError, RequestException
 
-from q2_types_genomics.kaiju import KaijuDBDirectoryFormat
+from q2_types.kaiju import KaijuDBDirectoryFormat
 
 
 class TestDatabaseFunctions(TestPluginBase):

q2_moshpit/kraken2/bracken.py

@@ -14,7 +14,7 @@
 
 from q2_moshpit._utils import run_command
 from q2_moshpit.kraken2.select import kraken2_to_features
-from q2_types_genomics.kraken2 import (
+from q2_types.kraken2 import (
     Kraken2ReportDirectoryFormat,
     BrackenDBDirectoryFormat,
 )

q2_moshpit/kraken2/classification.py

@@ -15,15 +15,15 @@
     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_genomics.feature_data import MAGSequencesDirFmt, MAG
-from q2_types_genomics.per_sample_data import ContigSequencesDirFmt, Contigs
-from q2_types_genomics.kraken2 import (
+from q2_types.feature_data_mag import MAGSequencesDirFmt, MAG
+from q2_types.kraken2 import (
     Kraken2ReportDirectoryFormat,
     Kraken2OutputDirectoryFormat,
     Kraken2DBDirectoryFormat,

q2_moshpit/kraken2/database.py

@@ -21,7 +21,7 @@
 from tqdm import tqdm
 
 from q2_moshpit._utils import _process_common_input_params, run_command
-from q2_types_genomics.kraken2 import (
+from q2_types.kraken2 import (
     Kraken2DBDirectoryFormat, BrackenDBDirectoryFormat,
     Kraken2DBReportDirectoryFormat
 )

q2_moshpit/kraken2/helpers.py

@@ -10,7 +10,7 @@
 
 import pandas as pd
 
-from q2_types_genomics.kraken2 import (
+from q2_types.kraken2 import (
     Kraken2ReportDirectoryFormat,
     Kraken2OutputDirectoryFormat
 )

q2_moshpit/kraken2/select.py

@@ -13,7 +13,7 @@
 from q2_moshpit.kraken2.utils import (
     _find_lca, _taxon_to_list, _join_ranks
 )
-from q2_types_genomics.kraken2 import (
+from q2_types.kraken2 import (
     Kraken2ReportDirectoryFormat, Kraken2OutputDirectoryFormat
 )
 

q2_moshpit/kraken2/tests/test_bracken.py

@@ -18,8 +18,8 @@
 
 from q2_moshpit.kraken2.bracken import (
     _assert_read_lens_available, _run_bracken_one_sample, _estimate_bracken)
-from q2_types_genomics.kraken2 import (BrackenDBDirectoryFormat,
-                                       Kraken2ReportDirectoryFormat)
+from q2_types.kraken2 import (BrackenDBDirectoryFormat,
+                              Kraken2ReportDirectoryFormat)
 
 
 class MockTempDir(tempfile.TemporaryDirectory):

q2_moshpit/kraken2/tests/test_classification.py

@@ -16,10 +16,10 @@
 from q2_types.per_sample_sequences import (
     SingleLanePerSampleSingleEndFastqDirFmt,
     SingleLanePerSamplePairedEndFastqDirFmt,
+    ContigSequencesDirFmt
 )
-from q2_types_genomics.feature_data import MAGSequencesDirFmt
-from q2_types_genomics.per_sample_data import ContigSequencesDirFmt
-from q2_types_genomics.kraken2 import (
+from q2_types.feature_data_mag import MAGSequencesDirFmt
+from q2_types.kraken2 import (
     Kraken2ReportDirectoryFormat,
     Kraken2OutputDirectoryFormat, Kraken2DBDirectoryFormat,
 )

q2_moshpit/kraken2/tests/test_database.py

@@ -30,7 +30,7 @@
     _find_latest_db, _fetch_db_collection, S3_COLLECTIONS_URL,
     _build_dbs_from_seqs, _fetch_prebuilt_dbs, inspect_kraken2_db
 )
-from q2_types_genomics.kraken2 import (
+from q2_types.kraken2 import (
     Kraken2DBDirectoryFormat, BrackenDBDirectoryFormat,
     Kraken2DBReportFormat, Kraken2DBReportDirectoryFormat
 )

q2_moshpit/kraken2/tests/test_selection.py

@@ -17,7 +17,7 @@
 from q2_moshpit.kraken2.select import _kraken_to_ncbi_tree, _find_lcas
 from qiime2.plugin.testing import TestPluginBase
 
-from q2_types_genomics.kraken2 import (
+from q2_types.kraken2 import (
     Kraken2ReportDirectoryFormat,  # Kraken2OutputDirectoryFormat,
 )
 

q2_moshpit/metabat2/metabat2.py

@@ -18,8 +18,8 @@
 import skbio.io
 from q2_types.feature_data import DNAIterator
 
-from q2_types_genomics.per_sample_data import ContigSequencesDirFmt, BAMDirFmt
-from q2_types_genomics.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_genomics.per_sample_data import ContigSequencesDirFmt, BAMDirFmt
-from q2_types_genomics.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
@@ -24,18 +24,17 @@
 from qiime2.plugin import (Plugin, Citations)
 import q2_moshpit._examples as ex
 import q2_moshpit
-from q2_types_genomics.feature_data import NOG, MAG
-from q2_types_genomics.genome_data import (
+from q2_types.feature_data_mag import NOG, MAG
+from q2_types.genome_data import (
     BLAST6, GenomeData, Loci, Genes, Proteins
 )
-from q2_types_genomics.kaiju import KaijuDB
-from q2_types_genomics.kraken2 import (
+from q2_types.kaiju import KaijuDB
+from q2_types.kraken2 import (
     Kraken2Reports, Kraken2Outputs, Kraken2DB, Kraken2DBReport
 )
-from q2_types_genomics.kraken2._type import BrackenDB
-from q2_types_genomics.per_sample_data import MAGs, Contigs
-from q2_types_genomics.per_sample_data._type import AlignmentMap
-from q2_types_genomics.reference_db import (
+from q2_types.kraken2._type import BrackenDB
+from q2_types.per_sample_sequences._type import AlignmentMap
+from q2_types.reference_db import (
     ReferenceDB, Diamond, Eggnog, NCBITaxonomy, EggnogProteinSequences
 )
 

q2_moshpit/prodigal/prodigal.py

@@ -8,8 +8,8 @@
 import os
 import copy as cp
 from .._utils import run_command
-from q2_types_genomics.feature_data import MAGSequencesDirFmt
-from q2_types_genomics.genome_data import (
+from q2_types.feature_data_mag import MAGSequencesDirFmt
+from q2_types.genome_data import (
     LociDirectoryFormat, GenesDirectoryFormat, ProteinsDirectoryFormat,
 )
 

q2_moshpit/prodigal/tests/test_prodigal.py

@@ -9,9 +9,9 @@
 import os
 from q2_moshpit.prodigal.prodigal import predict_genes_prodigal
 from qiime2.plugin.testing import TestPluginBase
-from q2_types_genomics.feature_data import MAGSequencesDirFmt
+from q2_types.feature_data_mag import MAGSequencesDirFmt
 from unittest.mock import patch, call
-from q2_types_genomics.genome_data import (
+from q2_types.genome_data import (
     LociDirectoryFormat, GenesDirectoryFormat, ProteinsDirectoryFormat,
 )