[med-svn] [Git][med-team/python-pybedtools][master] 11 commits: Rebuild against available architectures

Andreas Tille gitlab at salsa.debian.org
Wed May 13 09:16:40 BST 2020 


Andreas Tille pushed to branch master at Debian Med / python-pybedtools


Commits:
bcecf9a3 by Andreas Tille at 2020-05-13T08:55:50+02:00
Rebuild against available architectures

- - - - -
18297b49 by Andreas Tille at 2020-05-13T08:56:33+02:00
routine-update: Standards-Version: 4.5.0

- - - - -
c233707f by Andreas Tille at 2020-05-13T08:56:40+02:00
R-U: Trailing whitespace in debian/rules

- - - - -
b1f37009 by Andreas Tille at 2020-05-13T08:56:40+02:00
routine-update: Add salsa-ci file

- - - - -
93d78f9a by Andreas Tille at 2020-05-13T08:56:40+02:00
routine-update: Rules-Requires-Root: no

- - - - -
8084054a by Andreas Tille at 2020-05-13T08:56:48+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.

Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html


Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

- - - - -
e85142bc by Andreas Tille at 2020-05-13T09:08:07+02:00
Add missing shebang lines

- - - - -
d860ae79 by Andreas Tille at 2020-05-13T09:12:05+02:00
Move example script to examples

- - - - -
ebc34a08 by Andreas Tille at 2020-05-13T09:13:35+02:00
Fix permission of script

- - - - -
9c707c14 by Andreas Tille at 2020-05-13T09:14:30+02:00
There is obviously some reason to do manual cleaning

- - - - -
6e694bb0 by Andreas Tille at 2020-05-13T09:18:35+02:00
Upload to unstable

- - - - -


8 changed files:

- debian/changelog
- debian/control
- + debian/patches/add_missing_shebang.patch
- debian/patches/series
- debian/pybedtools-bin.lintian-overrides
- debian/rules
- + debian/salsa-ci.yml
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+python-pybedtools (0.8.0-4) unstable; urgency=medium
+
+  * Team upload.
+  * Rebuild against available architectures
+    Closes: #960411
+  * Standards-Version: 4.5.0 (routine-update)
+  * Remove trailing whitespace in debian/rules (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+  * Add missing shebang lines in scripts
+  * Move example script to examples
+  * Fix permission of script
+
+ -- Andreas Tille <tille at debian.org>  Wed, 13 May 2020 09:14:53 +0200
+
 python-pybedtools (0.8.0-3) unstable; urgency=medium
 
   * Mark the -doc package Multi-Arch: foreign


=====================================
debian/control
=====================================
@@ -24,10 +24,11 @@ Build-Depends: debhelper-compat (= 12),
                python3-sphinx,
                r-base-core,
                zlib1g-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/python-pybedtools
 Vcs-Git: https://salsa.debian.org/med-team/python-pybedtools.git
 Homepage: https://daler.github.io/pybedtools/
+Rules-Requires-Root: no
 
 Package: pybedtools-bin
 Architecture: all


=====================================
debian/patches/add_missing_shebang.patch
=====================================
@@ -0,0 +1,21 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 13 May 2020 08:56:48 +0200
+Description: Add missing shebang lines
+
+--- a/pybedtools/scripts/annotate.py
++++ b/pybedtools/scripts/annotate.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/python3
+ """
+ annotate a file with the neearest features in another.
+ 
+--- a/pybedtools/scripts/examples/pbt_plotting_example.py
++++ b/pybedtools/scripts/examples/pbt_plotting_example.py
+@@ -1,4 +1,6 @@
+-from __future__ import print_function
++#!/usr/bin/python3
++
++# from __future__ import print_function
+ import time
+ import os
+ import pybedtools


=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ spelling
 define_filenotfounderror_python2.patch
 remove_badges_from_documentation.patch
 parseDebianVersions.patch
+add_missing_shebang.patch


=====================================
debian/pybedtools-bin.lintian-overrides
=====================================
@@ -1,9 +1,9 @@
 # Better not messing with the community which expects these executables
 # just the ways these are.
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
 pybedtools-bin: script-with-language-extension usr/bin/annotate.py
 pybedtools-bin: script-with-language-extension usr/bin/intersection_matrix.py
 pybedtools-bin: script-with-language-extension usr/bin/intron_exon_reads.py
-pybedtools-bin: script-with-language-extension usr/bin/pbt_plotting_example.py
 pybedtools-bin: script-with-language-extension usr/bin/peak_pie.py
 pybedtools-bin: script-with-language-extension usr/bin/venn_gchart.py
 pybedtools-bin: script-with-language-extension usr/bin/venn_mpl.py


=====================================
debian/rules
=====================================
@@ -5,7 +5,7 @@ DH_VERBOSE := 1
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 export PYBUILD_NAME=pybedtools
 export MATPLOTLIBRC=$(CURDIR)/debian/
-#export PYBUILD_TEST_ARGS=--attr '!url' 
+#export PYBUILD_TEST_ARGS=--attr '!url'
 export PYBUILD_BEFORE_TEST=cp {dir}/debian/mpl-expected.png {build_dir}/pybedtools/test/ ; python3 {dir}/setup.py install --user ; export HOME=$(CURDIR)/fakehome
 export PYBUILD_TEST_ARGS=-v --doctest-modules
 export PYBUILD_AFTER_TEST=cd {dir}/docs ; make clean doctest
@@ -22,12 +22,13 @@ override_dh_auto_build:
 	python3 setup.py develop --user
 	python3 setup.py build_sphinx
 
-override_dh_auto_install:
-	dh_auto_install
+override_dh_install:
+	dh_install
 	rm -f debian/python3-pybedtools/usr/lib/python3*/dist-packages/pybedtools/test/prevent_open_file_regression
 	mkdir -p debian/pybedtools-bin/usr/bin
+	mkdir -p debian/pybedtools-bin/usr/share/doc/pybedtools-bin/examples
+	mv debian/python3-pybedtools/usr/bin/*example* debian/pybedtools-bin/usr/share/doc/pybedtools-bin/examples
 	mv debian/python3-pybedtools/usr/bin/* debian/pybedtools-bin/usr/bin/
-	rm -fr debian/python-pybedtools/usr/bin
 	rm -fr debian/python3-pybedtools/usr/bin
 
 override_dh_auto_clean:
@@ -41,4 +42,8 @@ override_dh_auto_clean:
 	rm -rf build
 	/bin/rm -rf pybedtools/cbedtools.cpp pybedtools/featurefuncs.cpp
 	find docs/source/autodocs/ -name "*.rst" | xargs -r /bin/rm
-	#dh_auto_clean
+	# dh_auto_clean
+
+override_dh_fixperms:
+	dh_fixperms
+	chmod -x debian/*/usr/lib/python3/dist-packages/pybedtools/scripts/pybedtools


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/daler/pybedtools/issues
+Bug-Submit: https://github.com/daler/pybedtools/issues/new
 Reference:
 - Author: R. K. Dale and B. S. Pedersen and A. R. Quinlan
   Title: "Pybedtools: a flexible Python library for manipulating genomic datasets\
@@ -21,4 +23,5 @@ Registry:
   Entry: OMICS_09508
 - Name: conda:bioconda
   Entry: pybedtools
-Repository: https://github.com/daler/pybedtools
+Repository: https://github.com/daler/pybedtools.git
+Repository-Browse: https://github.com/daler/pybedtools



View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/b920999b74040b9c96af14770b42e23a6a2e8b98...6e694bb007d6d21b38865304d638c49a12bf324f

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/b920999b74040b9c96af14770b42e23a6a2e8b98...6e694bb007d6d21b38865304d638c49a12bf324f
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