[med-svn] [Git][med-team/python-biom-format][master] 2 commits: Pull upstream patch to fix FTBFS (Closes: #1044074)

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / python-biom-format


Commits:
c11f2d26 by Nilesh Patra at 2024-02-05T00:46:28+05:30
Pull upstream patch to fix FTBFS (Closes: #1044074)

- - - - -
cdecfc8e by Nilesh Patra at 2024-02-05T00:46:46+05:30
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/adjust-pd-df-interaction-with-greater-than.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-biom-format (2.1.15.2-3) unstable; urgency=medium
+
+  * Team Upload.
+  * Pull upstream patch to fix FTBFS (Closes: #1044074)
+
+ -- Nilesh Patra <nilesh at debian.org>  Mon, 05 Feb 2024 00:46:33 +0530
+
 python-biom-format (2.1.15.2-2) unstable; urgency=medium
 
   * Drop python3-future from Build-Depends


=====================================
debian/patches/adjust-pd-df-interaction-with-greater-than.patch
=====================================
@@ -0,0 +1,45 @@
+From 5d1c921ca2cde5d7332508503ce990a7209d1fdc Mon Sep 17 00:00:00 2001
+From: Daniel McDonald <danielmcdonald at ucsd.edu>
+Date: Tue, 7 Nov 2023 16:36:07 -0800
+Subject: [PATCH] MAINT: adjust to change in pd.DataFrame interaction with >
+ (#940)
+
+* MAINT: adjust to change in pd.DataFrame interaction with >
+
+* STY: adjust for flake8
+---
+ biom/tests/test_table.py | 2 +-
+ biom/util.py             | 4 ++--
+ 2 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/biom/tests/test_table.py b/biom/tests/test_table.py
+index 28d187e5..75675847 100644
+--- a/biom/tests/test_table.py
++++ b/biom/tests/test_table.py
+@@ -1593,7 +1593,7 @@ def test_to_dataframe_is_sparse(self):
+         df = example_table.to_dataframe()
+         density = (float(example_table.matrix_data.getnnz()) /
+                    np.prod(example_table.shape))
+-        df_density = (df > 0).sum().sum() / np.prod(df.shape)
++        df_density = (df.values > 0).sum().sum() / np.prod(df.shape)
+         assert np.allclose(df_density, density)
+ 
+     def test_to_dataframe_dense(self):
+diff --git a/biom/util.py b/biom/util.py
+index 879779dc..12700839 100644
+--- a/biom/util.py
++++ b/biom/util.py
+@@ -441,11 +441,11 @@ def biom_open(fp, permission='r'):
+         opener = h5py.File
+ 
+     if mode in ['U', 'r', 'rb'] and is_gzip(fp):
+-        def opener(fp, mode):
++        def opener(fp, mode):  # noqa
+             return codecs.getreader('utf-8')(gzip_open(fp, mode))
+         mode = 'rb' if permission in ['U', 'r'] else permission
+     elif mode in ['w', 'wb'] and str(fp).endswith('.gz'):
+-        def opener(fp, mode):
++        def opener(fp, mode):  # noqa
+             codecs.getwriter('utf-8')(gzip_open(fp, mode))
+ 
+     f = opener(fp, mode)


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ no-web-adds.patch
 fix_future_import.patch
 sphinx_1.6.patch
 posix_shell.patch
+adjust-pd-df-interaction-with-greater-than.patch



View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/-/compare/7de41b27960ac73ede32397f30f5e897ef2c12e0...cdecfc8e4f0ddec9e28ddcd28a17a62cb7e9a933

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/-/compare/7de41b27960ac73ede32397f30f5e897ef2c12e0...cdecfc8e4f0ddec9e28ddcd28a17a62cb7e9a933
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