MAINT: change imports from q2-types-genomics to q2-types. (#8)

* changed all imports from q2-types-genomics to q2-types

* typo in meta.yaml

* lint

ci/recipe/meta.yaml

@@ -27,7 +27,7 @@ requirements:
     - pysam
     - python {{ python }}
     - qiime2 {{ qiime2_epoch }}.*
-    - q2-types-genomics {{ qiime2_epoch }}.*
+    - q2-types {{ qiime2_epoch }}.*
     - q2templates {{ qiime2_epoch }}.*
 
 test:

q2_checkm/checkm.py

@@ -17,7 +17,7 @@
 import pandas as pd
 import pkg_resources
 import q2templates
-from q2_types_genomics.per_sample_data._format import MultiMAGSequencesDirFmt
+from q2_types.per_sample_sequences import MultiMAGSequencesDirFmt
 
 from q2_checkm.plots import _draw_detailed_plots, _draw_overview_plots
 from q2_checkm.utils import (

q2_checkm/plugin_setup.py

@@ -5,8 +5,8 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
+from q2_types.per_sample_sequences import MAGs
 from q2_types.sample_data import SampleData
-from q2_types_genomics.per_sample_data import MAGs
 from qiime2.core.type import Bool, Float, Int, Range, Str
 from qiime2.plugin import Citations, Plugin
 

q2_checkm/tests/test_checkm.py

@@ -16,7 +16,7 @@
 
 import pandas as pd
 from pandas._testing import assert_frame_equal
-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_checkm.checkm import (

q2_checkm/utils.py

@@ -53,7 +53,7 @@ def _process_common_input_params(processing_func, params: dict) -> List[str]:
     processed_args = []
     for arg_key, arg_val in params.items():
         # bool is a subclass of int so to only reject ints we need to do:
-        if type(arg_val) != int and not arg_val:
+        if type(arg_val) is not int and not arg_val:
             continue
         else:
             processed_args.extend(processing_func(arg_key, arg_val))