[med-svn] [Git][med-team/python-ete3][master] custom changes

[zhaofeng]

zhaofeng pushed to branch master at Debian Med / python-ete3


Commits:
f88563d5 by zhaofeng-shu33 at 2020-07-05T15:51:24+08:00
custom changes

- - - - -


8 changed files:

- debian/control
- debian/copyright
- + debian/missing-sources/examples/webplugin/jquery-1.4.2.js
- + debian/missing-sources/examples/webplugin/jquery-ui-1.8.4.custom.js
- debian/patches/series
- − debian/patches/skip_online_tests.patch
- + debian/python3-ete3.remove
- debian/rules


Changes:

=====================================
debian/control
=====================================
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
                python3-pyqt5,
                python3-scipy,
                python3-six,
-               python3-skbio
+               python3-pytest
 Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-ete3
 Vcs-Git: https://salsa.debian.org/med-team/python-ete3.git
@@ -24,6 +24,7 @@ Architecture: any
 Depends: ${misc:Depends},
          ${python3:Depends},
          ${shlibs:Depends}
+         python3-six
 Recommends: ${python3:Recommends}
 Suggests: ${python3:Suggests}
 Description: Python Environment for (phylogenetic) Tree Exploration - Python 3.X


=====================================
debian/copyright
=====================================
@@ -16,6 +16,11 @@ Files: ete3/tools/phylobuild_lib/validate.py
 Copyright: Copyright (C) 2005-2010 Michael Foord, Mark Andrews, Nicola Larosa
 License: GPL-3+
 
+Files: ete3/ncbi_taxonomy/SQLite-Levenshtein/*
+Copyright: Mateusz Adamowski <mateusz at adamowski.pl>
+License: public-domain
+ This program is in public-domain.
+
 Files: doc/*
 Copyright: Copyright 2015, The ETE Toolkit Team.
 License: GPL-3+


=====================================
debian/missing-sources/examples/webplugin/jquery-1.4.2.js
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/missing-sources/examples/webplugin/jquery-ui-1.8.4.custom.js
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/patches/series
=====================================
@@ -1,2 +1 @@
-skip_online_tests.patch
 syntax_fixes.patch


=====================================
debian/patches/skip_online_tests.patch deleted
=====================================
@@ -1,14 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 29 Oct 2018 14:47:53 +0100
-Description: Ignore test requiring online access
-
---- a/ete3/test/test_api.py
-+++ b/ete3/test/test_api.py
-@@ -6,7 +6,6 @@ from .test_tree import *
- from .test_interop import *
- from .test_seqgroup import *
- from .test_phylotree import *
--from .test_ncbiquery import *
- 
- from .test_arraytable import *
- from .test_clustertree import *


=====================================
debian/python3-ete3.remove
=====================================
@@ -0,0 +1,5 @@
+test.*
+ete3/ncbi_taxonomy/SQLite-Levenshtein/.gitignore
+ete3/test/*
+ete3/tools/*
+ete3/ncbi_taxonomy/SQLite-Levenshtein/*


=====================================
debian/rules
=====================================
@@ -7,12 +7,26 @@ export PYBUILD_NAME=ete3
 
 %:
 	dh $@ --with python3 --buildsystem=pybuild
+override_dh_auto_install:
+	dh_auto_install -O--buildsystem=pybuild
+	rm -r debian/python3-ete3/usr/bin
+	rm -r debian/python3-ete3/usr/ete3
+override_dh_fixperms:
+	dh_fixperms
+	find debian -name 'webapp.py' -exec chmod a-x {} +
+export PYBUILD_TEST_PYTEST = 1
+# external library missing
+EXCLUDE_TESTS = not test_ncbiquery and not test_skbio
+# no network skip
+EXCLUDE_TESTS += and not test_ncbi_compare and not test_get_topology
+EXCLUDE_TESTS += and not test_01tree_annotation and not test_00_update_database
+EXCLUDE_TESTS += and not test_renderer
+# test launch file used by upstream continuous integration
+export PYBUILD_TEST_ARGS_python3 = -k "$(EXCLUDE_TESTS)" ete3/test/test_api.py
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-	# Exclude tests requiring online access (no idea how to exclude these more elegantly
-	find .pybuild -name test_ncbiquery.py -delete
 	# link to examples
 	find .pybuild -name build -type d -exec ln -s $(CURDIR)/examples \{\} \;
-	dh_auto_test || true
+	dh_auto_test
 endif



View it on GitLab: https://salsa.debian.org/med-team/python-ete3/-/commit/f88563d55ceb53a88f884c88c16fd2260272e10c

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-ete3/-/commit/f88563d55ceb53a88f884c88c16fd2260272e10c
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