TST: fixing test failures from python 3.9 update

bokulich-lab · Jun 4, 2024 · d112353 · d112353
2 parents 0b5c3db + 84b4ab1
commit d112353
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Showing 8 changed files with 10 additions and 10 deletions.
diff --git a/rescript/cross_validate.py b/rescript/cross_validate.py
@@ -31,7 +31,7 @@ def evaluate_fit_classifier(ctx,
     # Validate inputs
     start = timeit.default_timer()
     taxa, seq_ids = _validate_cross_validate_inputs(taxonomy, sequences)
-    taxa = taxa.loc[seq_ids]
+    taxa = taxa.loc[list(seq_ids)]
     taxonomy = q2.Artifact.import_data('FeatureData[Taxonomy]', taxa)
     new_time = _check_time(start, 'Validation')
 

diff --git a/rescript/evaluate.py b/rescript/evaluate.py
@@ -260,7 +260,7 @@ def _plot_eval_seqs(results, lengths, palette):
 
 def _visualize(output_dir, results, plot):
 
-    pd.set_option('display.max_colwidth', -1)
+    pd.set_option('display.max_colwidth', None)
 
     # save results
     results.to_csv(join(output_dir, 'evaluate_seqs_results.tsv'), sep='\t')

diff --git a/rescript/tests/test_cross_validate.py b/rescript/tests/test_cross_validate.py
@@ -12,7 +12,7 @@
 from qiime2.plugins import rescript
 import qiime2
 import pandas as pd
-import pandas.util.testing as pdt
+import pandas.testing as pdt
 
 from rescript import cross_validate
 
@@ -28,8 +28,8 @@ def setUp(self):
 
         # drop feature C1b because it is missing species level
         self.taxa_series = pd.read_csv(
-            self.get_data_path('derep-taxa.tsv'), sep='\t', index_col=0,
-            squeeze=True).drop('C1b')
+            self.get_data_path('derep-taxa.tsv'),
+            sep='\t', index_col=0).squeeze('columns').drop('C1b')
         self.taxa = import_data('FeatureData[Taxonomy]', self.taxa_series)
         seqs = import_data(
             'FeatureData[Sequence]', self.get_data_path('derep-test.fasta'))

diff --git a/rescript/tests/test_derep.py b/rescript/tests/test_derep.py
@@ -10,7 +10,7 @@
 from qiime2.plugins import rescript
 import qiime2
 import pandas as pd
-import pandas.util.testing as pdt
+import pandas.testing as pdt
 
 from rescript.dereplicate import _backfill_taxonomy
 from rescript._utilities import _return_stripped_taxon_rank_list

diff --git a/rescript/tests/test_evaluate.py b/rescript/tests/test_evaluate.py
@@ -11,7 +11,7 @@
 import qiime2
 import pandas as pd
 import numpy as np
-import pandas.util.testing as pdt
+import pandas.testing as pdt
 from q2_types.feature_data import DNAIterator
 
 from rescript import evaluate

diff --git a/rescript/tests/test_filter_length.py b/rescript/tests/test_filter_length.py
@@ -9,7 +9,7 @@
 
 import pandas as pd
 import qiime2
-import pandas.util.testing as pdt
+import pandas.testing as pdt
 from qiime2.plugin.testing import TestPluginBase
 from q2_types.feature_data import DNAIterator
 from qiime2.plugins import rescript

diff --git a/rescript/tests/test_merge.py b/rescript/tests/test_merge.py
@@ -11,7 +11,7 @@
 import qiime2
 import pandas as pd
 import numpy as np
-import pandas.util.testing as pdt
+import pandas.testing as pdt
 
 
 import_data = qiime2.Artifact.import_data

diff --git a/rescript/types/tests/test_types_formats_transformers.py b/rescript/types/tests/test_types_formats_transformers.py
@@ -7,7 +7,7 @@
 # ----------------------------------------------------------------------------
 import os
 import pandas as pd
-import pandas.util.testing as pdt
+import pandas.testing as pdt
 import numpy as np
 import tempfile
 import pkg_resources