[med-svn] [khmer] 10/10: new upstream release

Michael Crusoe misterc-guest at moszumanska.debian.org
Sun Jun 25 16:46:39 UTC 2017 

This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a commit to branch master
in repository khmer.

commit a5cdb20d8179f0dd0981a307f15334571044f825
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Fri Jun 23 05:57:33 2017 -0700

    new upstream release
---
 debian/changelog                        | 11 +++++++++--
 debian/clean                            |  4 ++--
 debian/control                          |  6 +++---
 debian/patches/amend-skip               | 20 +-------------------
 debian/patches/disable_google_analytics |  2 +-
 debian/patches/get_version              |  6 +++---
 debian/patches/older-setuptools         |  2 +-
 debian/patches/series                   |  1 +
 debian/patches/setup.py-py3             | 23 +++++++++++++++++++++++
 debian/patches/update-manifest          |  6 +++---
 debian/rules                            |  7 ++++---
 11 files changed, 51 insertions(+), 37 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 3e5aabc..a52c4f9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,13 +1,20 @@
-khmer (2.0~pre2.1-20170216-b2ab51575c2fa4c6bff078387ed8b67c4299df12-1) experimental; urgency=medium
+khmer (2.1.1+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]
   * Remove empty field
 
   [ Michael R. Crusoe ]
-  * New upstream version 2.0~pre2.1-20170216-b2ab51575c2fa4c6bff078387ed8b67c4299df12
+  * New upstream version 2.1.1
+  * Incorporate patch from Ubuntu, thank you Michael Hudson-Doyle. Closes: #862380
 
  -- Michael R. Crusoe <michael.crusoe at gmail.com>  Mon, 20 Feb 2017 01:50:56 -0800
 
+khmer (2.0+dfsg-10ubuntu1) artful; urgency=medium
+
+  * Fix build with Python 3.6.
+
+ -- Michael Hudson-Doyle <michael.hudson at ubuntu.com>  Fri, 12 May 2017 13:15:00 +1200
+
 khmer (2.0+dfsg-10) unstable; urgency=medium
 
   * Team upload.
diff --git a/debian/clean b/debian/clean
index 0efb6f1..fe4e972 100644
--- a/debian/clean
+++ b/debian/clean
@@ -1,2 +1,2 @@
-.pybuild
-fakehome
+.pybuild/
+fakehome/
diff --git a/debian/control b/debian/control
index 832b46e..9c7ae9f 100644
--- a/debian/control
+++ b/debian/control
@@ -7,15 +7,15 @@ Priority: optional
 Build-Depends: debhelper (>= 9),
                dh-python,
                dh-exec,
+               python3-guzzle-sphinx-theme,
                python3 (>= 3.3),
                python3-dev (>= 3.3),
                python3-all-dev (>= 3.3),
                python3-setuptools (>= 3.3),
-               python3-screed,
-               python3-sphinx,
-               python3-sphinxcontrib.autoprogram,
+               python3-screed (>= 1.0),
                python3-pytest,
                python3-pytest-runner,
+               python3-sphinx,
                zlib1g-dev,
                libbz2-dev,
                asciidoctor
diff --git a/debian/patches/amend-skip b/debian/patches/amend-skip
index 25a34ec..52f4736 100644
--- a/debian/patches/amend-skip
+++ b/debian/patches/amend-skip
@@ -1,26 +1,8 @@
 From: Michael R. Crusoe <michael.crusoe at gmail.com>
 Subject: Fix fatal pytest.skip usage
---- khmer.orig/tests/test_sandbox_scripts.py
-+++ khmer/tests/test_sandbox_scripts.py
-@@ -61,11 +61,12 @@
- def teardown():
-     utils.cleanup()
- 
--
-+ at pytest.mark.skipif(not os.path.exists(os.path.join(os.path.dirname(__file__),
-+    "../sandbox")))
- def _sandbox_scripts():
-     sandbox_path = os.path.join(os.path.dirname(__file__), "../sandbox")
--    if not os.path.exists(sandbox_path):
--        pytest.skip("sandbox scripts are only tested in a repository")
-+    #if not os.path.exists(sandbox_path):
-+    #    pytest.skip("sandbox scripts are only tested in a repository")
- 
-     path = os.path.join(sandbox_path, "*.py")
-     return [os.path.normpath(s) for s in glob.glob(path)]
 --- khmer.orig/tests/khmer_tst_utils.py
 +++ khmer/tests/khmer_tst_utils.py
-@@ -186,7 +186,7 @@
+@@ -187,7 +187,7 @@
              status = _runscript(scriptname, sandbox=sandbox)
          except SystemExit as err:
              status = err.code
diff --git a/debian/patches/disable_google_analytics b/debian/patches/disable_google_analytics
index 6351539..a6c3417 100644
--- a/debian/patches/disable_google_analytics
+++ b/debian/patches/disable_google_analytics
@@ -3,7 +3,7 @@ Author: Michael R. Crusoe <michael.crusoe at gmail.com>
 
 --- khmer.orig/doc/conf.py
 +++ khmer/doc/conf.py
-@@ -184,7 +184,7 @@
+@@ -186,7 +186,7 @@
  # Various settings to pass to templates:
  
  html_context = {
diff --git a/debian/patches/get_version b/debian/patches/get_version
index 93208f2..c04d91b 100644
--- a/debian/patches/get_version
+++ b/debian/patches/get_version
@@ -7,9 +7,9 @@ Description: Use debian package version instead of git version
  import os
 +import subprocess
  
- # If extensions (or modules to document with autodoc) are in another directory,
- # add these directories to sys.path here. If the directory is relative to the
-@@ -57,9 +58,12 @@
+ import guzzle_sphinx_theme
+ 
+@@ -56,9 +57,12 @@
  
  # The full version, including alpha/beta/rc tags.
  
diff --git a/debian/patches/older-setuptools b/debian/patches/older-setuptools
index c7ee1b6..a986fe4 100644
--- a/debian/patches/older-setuptools
+++ b/debian/patches/older-setuptools
@@ -12,7 +12,7 @@ Author: Michael R. Crusoe <michael.crusoe at gmail.com>
  import os
  import sys
  from os import listdir as os_listdir
-@@ -55,7 +53,6 @@
+@@ -56,7 +54,6 @@
  from distutils.errors import DistutilsPlatformError
  
  import versioneer
diff --git a/debian/patches/series b/debian/patches/series
index cad6753..0b16d07 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -8,3 +8,4 @@ install-prefix
 cpython-bug-empty-exceptions
 #silence-mt-bug
 amend-skip
+setup.py-py3
diff --git a/debian/patches/setup.py-py3 b/debian/patches/setup.py-py3
new file mode 100644
index 0000000..ee2fcf2
--- /dev/null
+++ b/debian/patches/setup.py-py3
@@ -0,0 +1,23 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Date:   Fri Jun 23 06:19:31 2017 -0700
+Forwarded: https://github.com/dib-lab/khmer/pull/1333
+Subject: fix py3 compat for setup.py
+
+diff --git a/setup.py b/setup.py
+index ef9b6c12..46fba6fa 100755
+--- a/setup.py
++++ b/setup.py
+@@ -244,7 +244,11 @@ else:
+ #     correctly for the citation information, but this requires a non-standard
+ #     library that we don't want to add as a dependency for `setup.py`.
+ #     -- Daniel Standage, 2017-05-21
+-with open('authors.csv', 'r') as csvin:
++if sys.version_info[0] == 2:
++    author_opts = {}
++else:
++    author_opts = { "newline": '', "encoding": 'utf-8'}
++with open('authors.csv', 'r', **author_opts) as csvin:
+     authors = csv.reader(csvin)
+     authorstr = ', '.join([row[0] for row in authors])
+     authorstr = 'Daniel Standage, ' + authorstr + ', C. Titus Brown'
+
diff --git a/debian/patches/update-manifest b/debian/patches/update-manifest
index 182fddf..364e7de 100644
--- a/debian/patches/update-manifest
+++ b/debian/patches/update-manifest
@@ -3,9 +3,9 @@ Subject: CONTRIBUTING.md has moved and isn't installed anymore
 --- khmer.orig/MANIFEST.in
 +++ khmer/MANIFEST.in
 @@ -1,5 +1,5 @@
- include ChangeLog ez_setup.py IDEAS Makefile README.rst setup.cfg
+ include ChangeLog ez_setup.py IDEAS Makefile README.md setup.cfg
 -include versioneer.py MANIFEST.in CITATION CONTRIBUTING.md Doxyfile.in
 +include versioneer.py MANIFEST.in CITATION Doxyfile.in
- include LICENSE TODO .ycm_extra_conf.py
+ include LICENSE TODO .ycm_extra_conf.py authors.csv
  recursive-include lib *.hh *.cc [Mm]akefile* get_version.py
- recursive-include third-party *.cc *.1 *.xsl README* sample* words* *.sh *.c
+ recursive-include khmer *.hh
diff --git a/debian/rules b/debian/rules
index e24d02b..8a96cfc 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,8 +8,6 @@ export PYBUILD_DESTDIR_python3=debian/khmer
 export USE_SYSTEM_ZLIB=true
 export USE_SYSTEM_LIBBZ2=true
 
-export PACKAGE_VERSION := $(shell dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ')
-
 export HOME=$(shell echo $$PWD"/fakehome")
 
 %:
@@ -26,7 +24,7 @@ override_dh_auto_test:
 	dh_auto_install
 	PYBUILD_SYSTEM=custom \
 	    PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$$PATH ; \
-	    cd {build_dir}; {interpreter} -m pytest \
+	    cd {build_dir}; export PYTHONPATH=$$(pwd); {interpreter} -m pytest \
 	    -m 'not known_failing and not jenkins and not huge'" dh_auto_test
 
 
@@ -42,5 +40,8 @@ override_dh_install:
 	dh_install
 	find debian/khmer -name .gitignore -delete
 
+override_dh_sphinxdoc:
+	dh_sphinxdoc -X jquery.js
+
 get-orig-source:
 	uscan --verbose --force-download --repack --compression xz

-- 
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