MAINT: Changed all imports from types-genomics to types

README.md

@@ -13,9 +13,9 @@ To install _q2-amr_, follow the steps described below.
 
 ```shell
 mamba create -yn q2-amr \
-  -c conda-forge -c bioconda -c qiime2 -c defaults \
-  -c https://packages.qiime2.org/qiime2/2023.9/shotgun/released/ \
-  qiime2 q2cli q2templates q2-types q2-types-genomics rgi
+  -c conda-forge -c bioconda -c defaults \
+  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ -c qiime2\
+  qiime2 q2cli q2templates q2-types rgi
 
 conda activate q2-amr
 
@@ -36,9 +36,9 @@ qiime info
 
 ```shell
 CONDA_SUBDIR=osx-64 mamba create -yn q2-amr \
-  -c conda-forge -c bioconda -c qiime2 -c defaults \
-  -c https://packages.qiime2.org/qiime2/2023.9/shotgun/released/ \
-  qiime2 q2cli q2templates q2-types q2-types-genomics rgi
+  -c conda-forge -c bioconda -c defaults \
+  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ -c qiime2\
+  qiime2 q2cli q2templates q2-types rgi
 
 conda activate q2-amr
 conda config --env --set subdir osx-64

ci/recipe/meta.yaml

@@ -19,7 +19,6 @@ requirements:
   run:
     - python {{ python }}
     - qiime2 {{ qiime2_epoch }}.*
-    - q2-types-genomics {{ qiime2_epoch }}.*
     - q2-types {{ qiime2_epoch }}.*
     - q2templates {{ qiime2_epoch }}.*
     - q2cli {{ qiime2_epoch }}.*

q2_amr/card/mags.py

@@ -4,7 +4,7 @@
 import tempfile
 
 import pandas as pd
-from q2_types_genomics.per_sample_data import MultiMAGSequencesDirFmt
+from q2_types.per_sample_sequences import MultiMAGSequencesDirFmt
 
 from q2_amr.card.utils import create_count_table, load_card_db, read_in_txt, run_command
 from q2_amr.types import CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat

q2_amr/card/tests/test_mags.py

@@ -3,7 +3,7 @@
 import subprocess
 from unittest.mock import MagicMock, patch
 
-from q2_types_genomics.per_sample_data import MultiMAGSequencesDirFmt
+from q2_types.per_sample_sequences import MultiMAGSequencesDirFmt
 from qiime2.plugin.testing import TestPluginBase
 
 from q2_amr.card.mags import annotate_mags_card, run_rgi_main

q2_amr/plugin_setup.py

@@ -9,11 +9,11 @@
 
 from q2_types.feature_table import FeatureTable, Frequency
 from q2_types.per_sample_sequences import (
+    MAGs,
     PairedEndSequencesWithQuality,
     SequencesWithQuality,
 )
 from q2_types.sample_data import SampleData
-from q2_types_genomics.per_sample_data import MAGs
 from qiime2.core.type import Bool, Choices, Int, Properties, Range, Str, TypeMap
 from qiime2.plugin import Citations, Plugin
 

q2_amr/types/_format.py

@@ -12,7 +12,7 @@
 import pandas as pd
 import qiime2.plugin.model as model
 from q2_types.feature_data._format import DNAFASTAFormat
-from q2_types_genomics.per_sample_data._format import BAMFormat, MultiDirValidationMixin
+from q2_types.per_sample_sequences._format import BAMFormat, MultiDirValidationMixin
 from qiime2.plugin import ValidationError
 
 

q2_amr/types/_transformer.py

@@ -14,7 +14,7 @@
 import skbio
 from q2_types.feature_data import DNAFASTAFormat, DNAIterator, ProteinFASTAFormat
 from q2_types.feature_data._transformer import ProteinIterator
-from q2_types_genomics.genome_data import GenesDirectoryFormat, ProteinsDirectoryFormat
+from q2_types.genome_data import GenesDirectoryFormat, ProteinsDirectoryFormat
 from skbio import DNA, Protein
 
 from q2_amr.types import CARDAnnotationDirectoryFormat

q2_amr/types/tests/test_types_formats_transformers.py

@@ -20,7 +20,7 @@
     ProteinFASTAFormat,
     ProteinIterator,
 )
-from q2_types_genomics.genome_data import GenesDirectoryFormat, ProteinsDirectoryFormat
+from q2_types.genome_data import GenesDirectoryFormat, ProteinsDirectoryFormat
 from qiime2.plugin.testing import TestPluginBase
 from skbio import DNA, Protein