[med-svn] [Git][med-team/python-pybedtools][master] 2 commits: d/patches/fix-doctest-imports.py: Add patch from upstream to use

[Emmanuel Arias (@eamanu)]

Emmanuel Arias pushed to branch master at Debian Med / python-pybedtools


Commits:
5bbdbb43 by Emmanuel Arias at 2024-12-24T19:26:33-03:00
d/patches/fix-doctest-imports.py: Add patch from upstream to use
  explicit namespace in docstrings of long_range_interaction file (Closes:
  #1090283).

- - - - -
12be1cca by Emmanuel Arias at 2024-12-24T19:26:54-03:00
prepare for upload

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/fix-doctest-imports.py
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+python-pybedtools (0.10.0-3) unstable; urgency=medium
+
+  * Team Upload.
+  * d/patches/fix-doctest-imports.py: Add patch from upstream to use
+    explicit namespace in docstrings of long_range_interaction file (Closes:
+    #1090283).
+
+ -- Emmanuel Arias <eamanu at debian.org>  Tue, 24 Dec 2024 19:24:47 -0300
+
 python-pybedtools (0.10.0-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/fix-doctest-imports.py
=====================================
@@ -0,0 +1,43 @@
+From df144d1b335c82dcc02252a0274e150363b69165 Mon Sep 17 00:00:00 2001
+From: Ryan Dale <ryan.dale at nih.gov>
+Date: Tue, 5 Nov 2024 13:31:53 -0500
+Subject: [PATCH] use explicit namespace in docstrings of
+ long_range_interaction
+
+---
+ pybedtools/contrib/long_range_interaction.py | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/pybedtools/contrib/long_range_interaction.py b/pybedtools/contrib/long_range_interaction.py
+index 8baffe74..a3555a5c 100644
+--- a/pybedtools/contrib/long_range_interaction.py
++++ b/pybedtools/contrib/long_range_interaction.py
+@@ -120,7 +120,7 @@ def tag_bedpe(bedpe, queries, verbose=False):
+     >>> queries = OrderedDict()
+     >>> queries['tss'] = tsses
+     >>> queries['pk'] = peaks
+-    >>> iterator, n, extra = tag_bedpe(bedpe, queries)
++    >>> iterator, n, extra = pybedtools.contrib.long_range_interaction.tag_bedpe(bedpe, queries)
+     >>> print(n)
+     2
+     >>> print(extra)
+@@ -280,7 +280,7 @@ def cis_trans_interactions(iterator, n, extra, verbose=True):
+     >>> queries = OrderedDict()
+     >>> queries['tss'] = tsses
+     >>> queries['pk'] = peaks
+-    >>> iterator, n, extra = tag_bedpe(bedpe, queries)
++    >>> iterator, n, extra = pybedtools.contrib.long_range_interaction.tag_bedpe(bedpe, queries)
+     >>> for (label, group1, group2) in iterator:
+     ...    group1 = sorted(group1, key=lambda x: str(x))
+     ...    group2 = sorted(group2, key=lambda x: str(x))
+@@ -303,8 +303,8 @@ def cis_trans_interactions(iterator, n, extra, verbose=True):
+     and that they are also connected to gene3:
+ 
+     >>> import pandas; pandas.set_option('display.max_columns', 10)
+-    >>> iterator, n, extra = tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks})
+-    >>> df =  cis_trans_interactions(iterator, n, extra)
++    >>> iterator, n, extra = pybedtools.contrib.long_range_interaction.tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks})
++    >>> df =  pybedtools.contrib.long_range_interaction.cis_trans_interactions(iterator, n, extra)
+     >>> print(df.sort_values(list(df.columns)).reset_index(drop=True))
+       target_label target_name cis_label cis_name distal_label distal_name  label
+     0           pk       peak1       tss    gene1            .           .  pair2


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ remove_badges_from_documentation.patch
 add_missing_shebang.patch
 yaml_safe_load.patch
 416.patch
+fix-doctest-imports.py



View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/a63b21265eb3609c14e213d8ef721bedfef6e2f7...12be1cca9a242dd97e15deed361a67d06788e92c

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/a63b21265eb3609c14e213d8ef721bedfef6e2f7...12be1cca9a242dd97e15deed361a67d06788e92c
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