[med-svn] [Git][med-team/community/helper-scripts][master] automatic update
Andreas Tille pushed to branch master at Debian Med / community / helper-scripts Commits: 68db6516 by Andreas Tille at 2023-01-03T01:43:29+00:00 automatic update - - - - - 4 changed files: - debian-med-tests.txt - debian-science-tests.txt - outdated_med-packages.txt - python-team-tests.txt Changes: = debian-med-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Mon, 02 Jan 2023 13:42:04 + +Last-Update: Tue, 03 Jan 2023 01:42:04 + Source| Vote | Tasks | Tags ---++-+-- = debian-science-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Mon, 02 Jan 2023 13:42:06 + +Last-Update: Tue, 03 Jan 2023 01:42:04 + Source | Vote | Tasks |Tags -+++ = outdated_med-packages.txt = The diff for this file was not included because it is too large. = python-team-tests.txt = @@ -1,4 +1,4 @@ -Last-Update: Mon, 02 Jan 2023 13:42:06 + +Last-Update: Tue, 03 Jan 2023 01:42:05 + Source | Vote | Tags --++ View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/68db651678ab431680c8290602dc1abe1cc6fc79 -- View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/68db651678ab431680c8290602dc1abe1cc6fc79 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-pybedtools] Pushed new tag debian/0.9.0-4
Étienne Mollier pushed new tag debian/0.9.0-4 at Debian Med / python-pybedtools -- View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/tree/debian/0.9.0-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-pybedtools][master] ready for Team upload.
Étienne Mollier pushed to branch master at Debian Med / python-pybedtools Commits: 5bbfcf77 by Étienne Mollier at 2023-01-02T21:56:05+01:00 ready for Team upload. - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,5 +1,6 @@ python-pybedtools (0.9.0-4) unstable; urgency=medium + * Team upload. * d/control: restore python3 all versions support now that pysam supports python3.11. Thanks to Andreas Beckmann for the reminder. (Closes: #1025116) View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/commit/5bbfcf7715c2b57d78d39d981ca4eb3685a6507f -- View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/commit/5bbfcf7715c2b57d78d39d981ca4eb3685a6507f You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-pybedtools][master] 4 commits: d/control: restore python3 all versions support.
Étienne Mollier pushed to branch master at Debian Med / python-pybedtools Commits: 0f2590b7 by Étienne Mollier at 2023-01-02T21:46:56+01:00 d/control: restore python3 all versions support. This is doable now that #1024425 affecting python-pysam is resolved. Closes: #1025116 Thanks: Andreas Beckmann for the reminder. - - - - - f8623b05 by Étienne Mollier at 2023-01-02T21:48:09+01:00 d/copyright: update copyright year. - - - - - 78f535f3 by Étienne Mollier at 2023-01-02T21:48:49+01:00 d/control: declare compliance to standards version 4.6.2. - - - - - c4ef9e1f by Étienne Mollier at 2023-01-02T21:50:35+01:00 ready to upload to unstable. - - - - - 3 changed files: - debian/changelog - debian/control - debian/copyright Changes: = debian/changelog = @@ -1,3 +1,13 @@ +python-pybedtools (0.9.0-4) unstable; urgency=medium + + * d/control: restore python3 all versions support now that pysam supports +python3.11. +Thanks to Andreas Beckmann for the reminder. (Closes: #1025116) + * d/copyright: update copyright year. + * d/control: declare compliance to standards version 4.6.2. + + -- Étienne Mollier Mon, 02 Jan 2023 21:49:24 +0100 + python-pybedtools (0.9.0-3) unstable; urgency=medium * Team Upload. = debian/control = @@ -9,8 +9,7 @@ Build-Depends: debhelper-compat (= 13), dh-python, bedtools, cython3, -# FIXME: restore python3-all-dev when #1024425 is resolved. - python3-dev, + python3-all-dev, python3-setuptools, python3-pysam, python3-matplotlib, @@ -25,13 +24,11 @@ Build-Depends: debhelper-compat (= 13), python3-sphinx, r-base-core, zlib1g-dev -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/python-pybedtools Vcs-Git: https://salsa.debian.org/med-team/python-pybedtools.git Homepage: https://daler.github.io/pybedtools/ Rules-Requires-Root: no -# FIXME: remove the below when #1024425 is resolved. -X-Python3-Version: 3.10 Package: pybedtools-bin Architecture: all = debian/copyright = @@ -62,6 +62,7 @@ License: LGPL-2.1+ Files: debian/* Copyright: © 2017 Michael R. Crusoe + 2022-2023 Étienne Mollier License: GPL-2+ License: GPL-2+ View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/bfee1c1bc232b3b1f078f198a51d9e5bdfa16733...c4ef9e1f67dcbe4d5b95f16b0b2c4972cdf29a14 -- View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/bfee1c1bc232b3b1f078f198a51d9e5bdfa16733...c4ef9e1f67dcbe4d5b95f16b0b2c4972cdf29a14 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/biobambam2] Pushed new tag debian/2.0.185+ds-1
Étienne Mollier pushed new tag debian/2.0.185+ds-1 at Debian Med / biobambam2 -- View it on GitLab: https://salsa.debian.org/med-team/biobambam2/-/tree/debian/2.0.185+ds-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/pairtools][master] 3 commits: Add B+R on "python3-pairtools (<< 1.0.2)" (Closes: #1027701)
Nilesh Patra pushed to branch master at Debian Med / pairtools
Commits:
de3a0e81 by Nilesh Patra at 2023-01-03T00:30:10+05:30
Add B+R on python3-pairtools ( 1.0.2) (Closes: #1027701)
- - - - -
808505e3 by Nilesh Patra at 2023-01-03T00:37:36+05:30
B-D on python3-exceptiongroup at least temporarily to fix FTBFS
- - - - -
0df1b002 by Nilesh Patra at 2023-01-03T00:38:11+05:30
Upload to unstable
- - - - -
2 changed files:
- debian/changelog
- debian/control
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+pairtools (1.0.2-2) unstable; urgency=medium
+
+ * Team Upload.
+ * Add B+R on "python3-pairtools (<< 1.0.2)" (Closes: #1027701)
+ * B-D on python3-exceptiongroup at least temporarily to fix FTBFS
+
+ -- Nilesh Patra Tue, 03 Jan 2023 00:30:28 +0530
+
pairtools (1.0.2-1) unstable; urgency=medium
[ Nilesh Patra ]
=
debian/control
=
@@ -10,6 +10,7 @@ Build-Depends: debhelper-compat (= 13),
python3-setuptools,
python3-bioframe,
python3-click,
+ python3-exceptiongroup,
python3-numpy,
python3-pandas,
python3-pysam (>= 0.20.0+ds-3~),
@@ -27,7 +28,8 @@ Package: python3-pairtools
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- ${python3:Depends},
+ ${python3:Depends}
+Suggests: python3-pairtools-examples (>= 1.0.2)
Description: Framework to process sequencing data from a Hi-C experiment
Simple and fast command-line framework to process sequencing data from a Hi-C
experiment.
@@ -47,6 +49,8 @@ Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
Enhances: python3-pairtools
+Breaks: python3-pairtools (<< 1.0.2)
+Replaces: python3-pairtools (<< 1.0.2)
Multi-Arch: same
Description: Process sequencing data from a Hi-C experiment (examples)
Simple and fast command-line framework to process sequencing data from a Hi-C
View it on GitLab:
https://salsa.debian.org/med-team/pairtools/-/compare/c1bcd84ea92880889248754f03c4270c1cd7c0ca...0df1b0022edcc92cc0ae025bd8d8a7f9301e0cee
--
View it on GitLab:
https://salsa.debian.org/med-team/pairtools/-/compare/c1bcd84ea92880889248754f03c4270c1cd7c0ca...0df1b0022edcc92cc0ae025bd8d8a7f9301e0cee
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[med-svn] [Git][med-team/pairtools] Pushed new tag debian/1.0.2-2
Nilesh Patra pushed new tag debian/1.0.2-2 at Debian Med / pairtools -- View it on GitLab: https://salsa.debian.org/med-team/pairtools/-/tree/debian/1.0.2-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/dssp][master] 4 commits: New upstream version 4.2.0a
Maarten L. Hekkelman pushed to branch master at Debian Med / dssp
Commits:
fb26b565 by Maarten L. Hekkelman at 2022-12-31T10:25:40+01:00
New upstream version 4.2.0a
- - - - -
4e304399 by Maarten L. Hekkelman at 2022-12-31T10:29:31+01:00
new version
- - - - -
e1b4016e by Maarten L. Hekkelman at 2023-01-02T09:52:51+01:00
New upstream version 4.2.1
- - - - -
02087582 by Maarten L. Hekkelman at 2023-01-02T09:53:29+01:00
Update upstream source from tag upstream/4.2.1
Update to upstream version 4.2.1
with Debian dir 7adf734a515204ae9b8e4d5459317c4ac94adbe0
- - - - -
5 changed files:
- CMakeLists.txt
- changelog
- debian/changelog
- src/mkdssp.cpp
- test/unit-test-dssp.cpp
Changes:
=
CMakeLists.txt
=
@@ -25,7 +25,7 @@
cmake_minimum_required(VERSION 3.15)
# set the project name
-project(mkdssp VERSION 4.2.0 LANGUAGES CXX)
+project(mkdssp VERSION 4.2.1 LANGUAGES CXX)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
=
changelog
=
@@ -1,3 +1,7 @@
+Version 4.2.1
+- The previous version was a bit overly strict
+- Introduce a --quiet flag.
+
Version 4.2.0
- Changes for packaging
- New mmCIF DSSP output, added several categories
=
debian/changelog
=
@@ -1,3 +1,15 @@
+dssp (4.2.1-1) unstable; urgency=medium
+
+ * New upstream.
+
+ -- Maarten L. Hekkelman Mon, 02 Jan 2023 09:53:03
+0100
+
+dssp (4.2.0a-1) unstable; urgency=medium
+
+ * Now with new source...
+
+ -- Maarten L. Hekkelman Sat, 31 Dec 2022 10:29:08
+0100
+
dssp (4.2.0-3) unstable; urgency=medium
* Pushing.
=
src/mkdssp.cpp
=
@@ -81,6 +81,7 @@ int d_main(int argc, const char *argv[])
mcfp::make_option("help,h", "Display help message"),
mcfp::make_option("version", "Print version"),
mcfp::make_option("verbose,v", "verbose output"),
+ mcfp::make_option("quiet", "Reduce verbose output to a
minimum"),
mcfp::make_hidden_option("debug,d", "Debug level (for even
more verbose output)"));
@@ -112,7 +113,10 @@ int d_main(int argc, const char *argv[])
exit(1);
}
- cif::VERBOSE = config.count("verbose");
+ if (config.count("quiet"))
+ cif::VERBOSE = -1;
+ else
+ cif::VERBOSE = config.count("verbose");
//
@@ -138,11 +142,8 @@ int d_main(int argc, const char *argv[])
}
cif::file f = cif::pdb::read(in);
- if (not f.is_valid())
- {
- std::cerr << "Could not validate file" << std::endl;
- exit(1);
- }
+ if (cif::VERBOSE >= 0 and not f.is_valid())
+ std::cerr << "Warning, the input file is not valid. Run with
--verbose to see why." << std::endl;
//
=
test/unit-test-dssp.cpp
=
@@ -134,7 +134,7 @@ BOOST_AUTO_TEST_CASE(ut_mmcif_2)
std::stringstream test;
- annotateDSSP(f.front(), dssp, true, test);
+ annotateDSSP(f.front(), dssp, true, false, test);
cif::file rf(gTestDir / "1cbs-dssp.cif");
View it on GitLab:
https://salsa.debian.org/med-team/dssp/-/compare/4703d039ac86aa36011eb2c9b772f5f2da63a88a...020875829eed7dc92570a39966545037c7711193
--
View it on GitLab:
https://salsa.debian.org/med-team/dssp/-/compare/4703d039ac86aa36011eb2c9b772f5f2da63a88a...020875829eed7dc92570a39966545037c7711193
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[med-svn] [Git][med-team/unifrac-tools] Pushed new tag upstream/1.2
Andreas Tille pushed new tag upstream/1.2 at Debian Med / unifrac-tools -- View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/tree/upstream/1.2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gdcm] Pushed new tag debian/3.0.17-5
Mathieu Malaterre pushed new tag debian/3.0.17-5 at Debian Med / gdcm -- View it on GitLab: https://salsa.debian.org/med-team/gdcm/-/tree/debian/3.0.17-5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
