[med-svn] [khmer] 03/03: new upstream release

Fri Jun 23 13:36:27 UTC 2017

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misterc-guest pushed a commit to branch experimental-2.1
in repository khmer.

commit 4f0fab4be97d50f9bb7baa04c116cc089f3e93f5
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Fri Jun 23 05:57:33 2017 -0700

    new upstream release
---
 debian/changelog                        |  4 ++--
 debian/control                          |  2 +-
 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 +++---
 9 files changed, 36 insertions(+), 30 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 26c49d6..dd0715c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,10 @@
-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
 
  -- Michael R. Crusoe <michael.crusoe at gmail.com>  Mon, 20 Feb 2017 01:50:56 -0800
 
diff --git a/debian/control b/debian/control
index 165df68..d8c40b4 100644
--- a/debian/control
+++ b/debian/control
@@ -11,7 +11,7 @@ Build-Depends: debhelper (>= 9),
                python3-dev (>= 3.3),
                python3-all-dev (>= 3.3),
                python3-setuptools (>= 3.3),
-               python3-screed,
+               python3-screed (>= 1.0),
                python3-sphinx,
                python3-sphinxcontrib.autoprogram,
                python3-pytest,
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

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