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 <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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