[med-svn] [Git][med-team/mapdamage][master] 7 commits: New upstream version 2.2.2+dfsg
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Aug 25 17:39:23 BST 2024
Étienne Mollier pushed to branch master at Debian Med / mapdamage
Commits:
863fdd7d by Étienne Mollier at 2024-08-25T18:34:06+02:00
New upstream version 2.2.2+dfsg
- - - - -
a4e8c197 by Étienne Mollier at 2024-08-25T18:34:06+02:00
Update upstream source from tag 'upstream/2.2.2+dfsg'
Update to upstream version '2.2.2+dfsg'
with Debian dir fd83d1e38536344a9a69075840eb51039f335880
- - - - -
19eaec41 by Étienne Mollier at 2024-08-25T18:35:02+02:00
use_debian_packaged_seqtk.patch: unfuzz.
- - - - -
ff9af9dc by Étienne Mollier at 2024-08-25T18:35:44+02:00
d/control: add myself to uploaders.
- - - - -
c42dfe40 by Étienne Mollier at 2024-08-25T18:36:11+02:00
d/control: declare compliance to standards version 4.7.0.
- - - - -
fe927879 by Étienne Mollier at 2024-08-25T18:37:12+02:00
use_debian_packaged_seqtk.patch: declare forwarding not-needed.
- - - - -
20b433b8 by Étienne Mollier at 2024-08-25T18:38:06+02:00
Ready for upload to unstable.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/use_debian_packaged_seqtk.patch
- mapdamage/Rscripts/mapDamage.R
- mapdamage/version.py
- setup.py
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+mapdamage (2.2.2+dfsg-1) unstable; urgency=medium
+
+ * New upstream version 2.2.2+dfsg
+ * use_debian_packaged_seqtk.patch: unfuzz.
+ * d/control: add myself to uploaders.
+ * d/control: declare compliance to standards version 4.7.0.
+ * use_debian_packaged_seqtk.patch: declare forwarding not-needed.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 25 Aug 2024 18:37:56 +0200
+
mapdamage (2.2.1+dfsg-3) unstable; urgency=medium
* Fix watch file
=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
Source: mapdamage
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -13,7 +14,7 @@ Build-Depends: debhelper-compat (= 13),
r-cran-gam <!nocheck>,
r-cran-ggplot2 <!nocheck>,
r-cran-inline <!nocheck>
-Standards-Version: 4.6.1
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/mapdamage
Vcs-Git: https://salsa.debian.org/med-team/mapdamage.git
Homepage: https://ginolhac.github.io/mapDamage/
=====================================
debian/patches/use_debian_packaged_seqtk.patch
=====================================
@@ -2,10 +2,11 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Thu, 28 Jul 2016 15:13:14 +0200
Bug-Debian: https://bugs.debian.org/859090
Description: Use Debian packaged seqtk
+Forwarded: not-needed
---- a/setup.py
-+++ b/setup.py
-@@ -11,21 +11,6 @@ if sys.version_info < (3, 5):
+--- mapdamage.orig/setup.py
++++ mapdamage/setup.py
+@@ -11,21 +11,6 @@
print("At least Python 3.5 is required.\n", file=sys.stderr)
exit(1)
@@ -27,7 +28,7 @@ Description: Use Debian packaged seqtk
def setup_version():
if not os.path.exists(".git"):
# Release version, no .git folder
-@@ -45,17 +30,8 @@ class compileInstall(DistutilsInstall):
+@@ -45,17 +30,8 @@
def run(self):
self.record=""
setup_version()
@@ -45,8 +46,8 @@ Description: Use Debian packaged seqtk
setup(
cmdclass={'install': compileInstall},
-@@ -64,7 +40,7 @@ setup(
- author='Aurélien Ginolhac, Mikkel Schubert, Ãkon Jónsson',
+@@ -64,7 +40,7 @@
+ author='Aurélien Ginolhac, Mikkel Schubert, Hákon Jónsson',
author_email='MSchubert at snm.ku.dk, jonsson.hakon at gmail.com',
packages=['mapdamage'],
- package_data={'mapdamage': ['Rscripts/*.R','Rscripts/stats/*.R','tests/*','seqtk/seqtk']},
@@ -54,9 +55,9 @@ Description: Use Debian packaged seqtk
scripts=['bin/mapDamage'],
url='https://github.com/ginolhac/mapDamage',
license='LICENSE.txt',
---- a/bin/mapDamage
-+++ b/bin/mapDamage
-@@ -163,7 +163,7 @@ def main():
+--- mapdamage.orig/bin/mapDamage
++++ mapdamage/bin/mapDamage
+@@ -149,7 +149,7 @@
sys.path.insert(0,path_to_mm)
import mapdamage
@@ -65,9 +66,9 @@ Description: Use Debian packaged seqtk
if not (os.path.isfile(fpath_seqtk) and os.access(fpath_seqtk, os.X_OK)):
sys.stderr.write("Seqtk executable not accessible; mapDamage has not\n"
"been intalled properly or current user does not\n"
---- a/mapdamage/composition.py
-+++ b/mapdamage/composition.py
-@@ -33,7 +33,7 @@ def get_base_comp(filename,destination=F
+--- mapdamage.orig/mapdamage/composition.py
++++ mapdamage/mapdamage/composition.py
+@@ -33,7 +33,7 @@
Gets the basecomposition of all the sequences in filename
and returns the value to destination if given.
"""
=====================================
mapdamage/Rscripts/mapDamage.R
=====================================
@@ -43,7 +43,7 @@ plot.base.composition <- function(tbl, base, color, around, ylabels.at = c(), xl
plot.axis <- function(yaxis.at) {
axis(side = yaxis.at, labels = (yaxis.at == ylabels.at), line = 0, las = 2, cex.axis = 0.8)
- if ((yaxis.at == 2) && (yaxis.at == ylabels.at)) {
+ if ((yaxis.at == 2) && any(yaxis.at == ylabels.at)) {
mtext("Frequency", side = 2, line = 2.5, cex = 0.6)
}
=====================================
mapdamage/version.py
=====================================
@@ -2,4 +2,4 @@
try:
from mapdamage._version import __version__
except ImportError:
- __version__ = "2.2.1"
+ __version__ = "2.2.2"
=====================================
setup.py
=====================================
@@ -60,8 +60,8 @@ class compileInstall(DistutilsInstall):
setup(
cmdclass={'install': compileInstall},
name='mapdamage',
- version='2.2.0',
- author='Aurélien Ginolhac, Mikkel Schubert, Ãkon Jónsson',
+ version='2.2.2',
+ author='Aurélien Ginolhac, Mikkel Schubert, Hákon Jónsson',
author_email='MSchubert at snm.ku.dk, jonsson.hakon at gmail.com',
packages=['mapdamage'],
package_data={'mapdamage': ['Rscripts/*.R','Rscripts/stats/*.R','tests/*','seqtk/seqtk']},
View it on GitLab: https://salsa.debian.org/med-team/mapdamage/-/compare/956a213cdf8dface42da50f4dd1e45f0dddb7f8b...20b433b86de5e9b196ac7a3e3525ba14cd374014
--
View it on GitLab: https://salsa.debian.org/med-team/mapdamage/-/compare/956a213cdf8dface42da50f4dd1e45f0dddb7f8b...20b433b86de5e9b196ac7a3e3525ba14cd374014
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