[med-svn] [Git][med-team/khmer][master] 5 commits: minor patch cleanup

Michael R. Crusoe (@crusoe) gitlab at salsa.debian.org
Mon Aug 22 10:59:22 BST 2022 


Michael R. Crusoe pushed to branch master at Debian Med / khmer


Commits:
63597242 by Michael R. Crusoe at 2022-08-22T11:42:23+02:00
minor patch cleanup

- - - - -
6a63ade9 by Michael R. Crusoe at 2022-08-22T11:42:55+02:00
Another fix for recent Python versions

- - - - -
378d04cf by Michael R. Crusoe at 2022-08-22T11:45:55+02:00
Fix license mismatch in AppStream metadata

- - - - -
5862bc87 by Michael R. Crusoe at 2022-08-22T11:53:31+02:00
routine-update: Standards-Version: 4.6.1

- - - - -
180eca41 by Michael R. Crusoe at 2022-08-22T11:57:09+02:00
routine-update: Ready to upload to unstable

- - - - -


15 changed files:

- debian/changelog
- debian/control
- debian/khmer.metainfo.xml
- debian/patches/amend-skip
- debian/patches/disable_google_analytics
- debian/patches/fix_liboxli_test
- debian/patches/get_version
- debian/patches/install-prefix
- debian/patches/local-libs
- debian/patches/older-setuptools
- debian/patches/python3
- debian/patches/setup.py-py3
- debian/patches/silence-mt-bug
- debian/patches/stringio-buffer.patch
- debian/patches/update-manifest


Changes:

=====================================
debian/changelog
=====================================
@@ -1,12 +1,17 @@
-khmer (2.1.2+dfsg-11) UNRELEASED; urgency=medium
-
-  * Team upload.
+khmer (2.1.2+dfsg-11) unstable; urgency=medium
 
   [ Stefano Rivera ]
   * Adapt to a change in Python3
     Closes: #1008402
 
- -- Andreas Tille <tille at debian.org>  Sun, 03 Apr 2022 08:34:16 +0200
+  [ Michael R. Crusoe ]
+  * debian/patches: some header cleanups.
+  * debian/patches/stringio-buffer.patch: another fix for recent Python
+    versions.
+  * Fix license mismatch in AppStream metadata
+  * Standards-Version: 4.6.1 (routine-update)
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Mon, 22 Aug 2022 11:53:48 +0200
 
 khmer (2.1.2+dfsg-10) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -22,7 +22,7 @@ Build-Depends: debhelper-compat (= 13),
                libbz2-dev,
                asciidoctor,
                rdfind
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/khmer
 Vcs-Git: https://salsa.debian.org/med-team/khmer.git
 Homepage: https://khmer.readthedocs.org


=====================================
debian/khmer.metainfo.xml
=====================================
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <component>
   <id>io.readthedocs.khmer</id>
-  <metadata_license>MIT</metadata_license>
+  <metadata_license>BSD-3-Clause</metadata_license>
   <name>khmer</name>
   <summary>in-memory DNA sequence kmer counting, filtering & graph traversal</summary>
   <description>


=====================================
debian/patches/amend-skip
=====================================
@@ -1,4 +1,4 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
+From: Michael R. Crusoe <crusoe at debian.org>
 Subject: Fix fatal pytest.skip usage
 --- khmer.orig/tests/khmer_tst_utils.py
 +++ khmer/tests/khmer_tst_utils.py


=====================================
debian/patches/disable_google_analytics
=====================================
@@ -1,6 +1,6 @@
 Description: Turn off Google analytics as per Lintian warning
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-
+Author: Michael R. Crusoe <crusoe at debian.org>
+Forwarded: not-needed
 --- khmer.orig/doc/conf.py
 +++ khmer/doc/conf.py
 @@ -186,7 +186,7 @@


=====================================
debian/patches/fix_liboxli_test
=====================================
@@ -1,4 +1,4 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
+From: Michael R. Crusoe <crusoe at debian.org>
 Subject: Fix liboxli sanity check test
 --- khmer.orig/src/oxli/test-compile.cc
 +++ khmer/src/oxli/test-compile.cc


=====================================
debian/patches/get_version
=====================================
@@ -1,4 +1,6 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
 Description: Use debian package version instead of git version
+Forwarded: not-needed
 --- khmer.orig/doc/conf.py
 +++ khmer/doc/conf.py
 @@ -13,6 +13,7 @@


=====================================
debian/patches/install-prefix
=====================================
@@ -1,3 +1,4 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
 Description: Use correct library version etc. (fixed by upstream #1240, remove for 2.0)
 --- khmer.orig/Makefile
 +++ khmer/Makefile


=====================================
debian/patches/local-libs
=====================================
@@ -1,5 +1,5 @@
 Description: Use Debian packaged libraries
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
 
 --- khmer.orig/setup.cfg
 +++ khmer/setup.cfg


=====================================
debian/patches/older-setuptools
=====================================
@@ -1,6 +1,6 @@
-Description: Fix version of setuptools
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-
+Description: Allow any version of setuptools
+Author: Michael R. Crusoe <crusoe at debian.org>
+Forwarded: not-needed
 --- khmer.orig/setup.py
 +++ khmer/setup.py
 @@ -36,7 +36,6 @@


=====================================
debian/patches/python3
=====================================
@@ -1,4 +1,4 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
 Description: s/python/python3/ as appropriate
 
 --- khmer.orig/Makefile


=====================================
debian/patches/setup.py-py3
=====================================
@@ -1,4 +1,4 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
 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


=====================================
debian/patches/silence-mt-bug
=====================================
@@ -1,5 +1,5 @@
 Description: silence a known inconsistency with multithreading
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Author: Michael R. Crusoe <crusoe at debian.org>
 --- khmer.orig/tests/test_scripts.py
 +++ khmer/tests/test_scripts.py
 @@ -1375,6 +1375,7 @@


=====================================
debian/patches/stringio-buffer.patch
=====================================
@@ -4,8 +4,8 @@ Bug-Debian: https://bugs.debian.org/1008402
 Description: The issue seems to be caused by a change in Python where
   https://bugs.python.org/issue14156 being fixed
 
---- a/tests/khmer_tst_utils.py
-+++ b/tests/khmer_tst_utils.py
+--- khmer.orig/tests/khmer_tst_utils.py
++++ khmer/tests/khmer_tst_utils.py
 @@ -44,18 +44,13 @@
  import sys
  import traceback
@@ -64,8 +64,8 @@ Description: The issue seems to be caused by a change in Python where
  
          if in_directory:
              os.chdir(in_directory)
---- a/khmer/khmer_args.py
-+++ b/khmer/khmer_args.py
+--- khmer.orig/khmer/khmer_args.py
++++ khmer/khmer/khmer_args.py
 @@ -158,14 +158,16 @@
  
  # Temporary fix to argparse FileType which ignores the
@@ -85,19 +85,23 @@ Description: The issue seems to be caused by a change in Python where
              if 'r' in self._mode:
                  fname = sys.stdin.fileno()
              elif 'w' in self._mode:
---- a/khmer/kfile.py
-+++ b/khmer/kfile.py
-@@ -209,6 +209,8 @@
+--- khmer.orig/khmer/kfile.py
++++ khmer/khmer/kfile.py
+@@ -209,6 +209,12 @@
      """Take in a file object and checks to see if it's a block or fifo."""
      if fthing is sys.stdout or fthing is sys.stdin:
          return True
++    if hasattr(fthing, "iastty") and fthing.isatty():
++        return True
 +    elif not hasattr(fthing, 'name'):
++        return True
++    if fthing.name == "<stdout>":
 +        return True
      else:
          mode = os.stat(fthing.name).st_mode
          return S_ISBLK(mode) or S_ISCHR(mode)
---- a/scripts/trim-low-abund.py
-+++ b/scripts/trim-low-abund.py
+--- khmer.orig/scripts/trim-low-abund.py
++++ khmer/scripts/trim-low-abund.py
 @@ -512,7 +512,7 @@
  
      if args.output is None:


=====================================
debian/patches/update-manifest
=====================================
@@ -1,4 +1,4 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
+From: Michael R. Crusoe <crusoe at debian.org>
 Subject: CONTRIBUTING.md has moved and isn't installed anymore
 --- khmer.orig/MANIFEST.in
 +++ khmer/MANIFEST.in



View it on GitLab: https://salsa.debian.org/med-team/khmer/-/compare/de92d8c3f7727b729a02c931131bfbe94682d5a2...180eca419fdf532ad0b15cf843bd93dfb2421236

-- 
View it on GitLab: https://salsa.debian.org/med-team/khmer/-/compare/de92d8c3f7727b729a02c931131bfbe94682d5a2...180eca419fdf532ad0b15cf843bd93dfb2421236
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