[med-svn] [Git][med-team/emperor][master] 2 commits: Add patch to fix FTBFS with pandas 2.0 (Closes: #1050144)

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / emperor


Commits:
276f8ee0 by Nilesh Patra at 2024-02-04T16:18:26+05:30
Add patch to fix FTBFS with pandas 2.0 (Closes: #1050144)

- - - - -
eac70e95 by Nilesh Patra at 2024-02-04T16:18:43+05:30
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/pandas-2.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+emperor (1.0.3+ds-9) unstable; urgency=medium
+
+  * Team Upload.
+  * Add patch to fix FTBFS with pandas 2.0 (Closes: #1050144)
+
+ -- Nilesh Patra <nilesh at debian.org>  Sun, 04 Feb 2024 16:18:31 +0530
+
 emperor (1.0.3+ds-8) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/pandas-2.patch
=====================================
@@ -0,0 +1,80 @@
+Description: Replace pd.util.testing with pd.testing as the former has been pruned in pandas2.x
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2024-02-04
+--- a/tests/test_core.py
++++ b/tests/test_core.py
+@@ -202,7 +202,7 @@
+         feature_mf['Second'] = ['No', 'Yes', 'Noes', 'Noooo', 'Yep']
+ 
+         # it is redundant, but the mapping file should remain untouched
+-        pd.util.testing.assert_frame_equal(feature_mf, emp.feature_mf,
++        pd.testing.assert_frame_equal(feature_mf, emp.feature_mf,
+                                            check_names=False)
+ 
+         self.assertEqual(emp.base_url, 'https://cdn.rawgit.com/biocore/emperor'
+@@ -223,7 +223,7 @@
+                                        'f.PC.481', 'f.PC.354'])
+         empty_mf['all'] = 'All elements'
+ 
+-        pd.util.testing.assert_frame_equal(empty_mf, emp.feature_mf,
++        pd.testing.assert_frame_equal(empty_mf, emp.feature_mf,
+                                            check_names=False)
+ 
+         self.assertEqual(emp.base_url, 'https://cdn.rawgit.com/biocore/emperor'
+@@ -291,7 +291,7 @@
+ 
+             expected.loc['PC.634'] = ['This element has no metadata'] * 3
+ 
+-            pd.util.testing.assert_frame_equal(expected.sort_index(),
++            pd.testing.assert_frame_equal(expected.sort_index(),
+                                                emp.mf.sort_index(),
+                                                check_names=False)
+ 
+@@ -313,7 +313,7 @@
+ 
+             expected.loc['f.PC.636'] = ['This element has no metadata'] * 2
+ 
+-            pd.util.testing.assert_frame_equal(expected.sort_index(),
++            pd.testing.assert_frame_equal(expected.sort_index(),
+                                                emp.feature_mf.sort_index(),
+                                                check_names=False)
+ 
+--- a/tests/test_pandas.py
++++ b/tests/test_pandas.py
+@@ -66,9 +66,9 @@
+         self.assertTrue(isinstance(emp, Emperor))
+         self.assertEqual(emp.dimensions, 4)
+ 
+-        pd.util.testing.assert_frame_equal(self.df, emp.mf)
++        pd.testing.assert_frame_equal(self.df, emp.mf)
+ 
+-        pd.util.testing.assert_frame_equal(emp.ordination.samples,
++        pd.testing.assert_frame_equal(emp.ordination.samples,
+                                            self.samples)
+ 
+     def test_scatterplot_reordered(self):
+@@ -80,11 +80,11 @@
+         self.assertEqual(emp.base_url, 'https://cdn.rawgit.com/biocore/'
+                          'emperor/new-api/emperor/support_files')
+ 
+-        pd.util.testing.assert_frame_equal(self.df, emp.mf)
++        pd.testing.assert_frame_equal(self.df, emp.mf)
+ 
+         reordered = self.samples[['num_3', 'num_2', 'num_1', 'num_4']].copy()
+ 
+-        pd.util.testing.assert_frame_equal(emp.ordination.samples,
++        pd.testing.assert_frame_equal(emp.ordination.samples,
+                                            reordered)
+ 
+     def test_bad_column_names(self):
+--- a/tests/test_util.py
++++ b/tests/test_util.py
+@@ -282,7 +282,7 @@
+         mf = pd.DataFrame(data=MAPPING_FILE_DATA, columns=columns)
+         obs = validate_and_process_custom_axes(mf, ['DOB'])
+         exp = pd.DataFrame(data=MAPPING_FILE_DATA_CONVERTED, columns=columns)
+-        pd.util.testing.assert_frame_equal(obs, exp)
++        pd.testing.assert_frame_equal(obs, exp)
+ 
+     def test_custom_axes_non_existent_names(self):
+         columns = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ EditSectionTitle.patch
 8b803cd81586b832550eaa2428fa2d0dd581d35f.patch
 no_future_dependency.patch
 python3.12,patch
+pandas-2.patch



View it on GitLab: https://salsa.debian.org/med-team/emperor/-/compare/4a4c3aa4cad762974555feb99dd979a77519332b...eac70e95bb2b95d8b897acfef1c3468cf940bb15

-- 
View it on GitLab: https://salsa.debian.org/med-team/emperor/-/compare/4a4c3aa4cad762974555feb99dd979a77519332b...eac70e95bb2b95d8b897acfef1c3468cf940bb15
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