[med-svn] [Git][med-team/beast-mcmc][master] 6 commits: Fix clean target Closes: #1043640
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Dec 21 18:00:12 GMT 2024
Andreas Tille pushed to branch master at Debian Med / beast-mcmc
Commits:
fd43fab7 by Andreas Tille at 2024-12-21T17:04:39+01:00
Fix clean target Closes: #1043640
- - - - -
2e9a0f69 by Andreas Tille at 2024-12-21T17:24:28+01:00
Fix watch file
- - - - -
de371c7a by Andreas Tille at 2024-12-21T17:24:37+01:00
Standards-Version: 4.7.0 (routine-update)
- - - - -
00fcad03 by Andreas Tille at 2024-12-21T17:36:33+01:00
d/copyright: review thanks to lrc
- - - - -
3a85a035 by Andreas Tille at 2024-12-21T17:37:56+01:00
Unfortunately the test is not working yet
- - - - -
cecfbbd4 by Andreas Tille at 2024-12-21T17:40:02+01:00
Upload to unstable
- - - - -
10 changed files:
- debian/beast-mcmc.1
- debian/beast-mcmc.1.xml
- debian/beauti.1
- debian/beauti.1.xml
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
- debian/tests/control → debian/tests/control_not_working_yet
- debian/watch
Changes:
=====================================
debian/beast-mcmc.1
=====================================
@@ -89,7 +89,7 @@ print usage screen
.SH "BUGS"
.PP
The BEAST bug tracking system can be found at
-\fI\%http://code.google.com/p/beast-mcmc/issues/list\fR\&.
+\fI\%https://github.com/beast-dev/beast-mcmc/issues\fR\&.
.SH "SEE ALSO"
.PP
\fBbeauti\fR(1)\&.
@@ -131,33 +131,3 @@ Copyright holder for BEAST\&.
.sp -1n
.IP "" 4
Prepared this manpage in DocBook XML for the Debian distribution\&.
-.SH "COPYRIGHT"
-Copyright \(co 2002\(en2010 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (BEAST)
-.br
-Copyright \(co 2009\(en2010 Felix Feyertag (This manpage)
-.br
-.PP
-The binaries and source code are made available and can be distributed subject to the following conditions:
-.PP
-BEAST is Copyright (C) 2002\-2006 Alexei Drummond and Andrew Rambaut BEAST is distributed under the terms of the GNU Lesser General Public License\&. See the notice in individual files and the file LICENSE for licensing details\&.
-.PP
-BEAST includes software libraries from projects whose licensing terms require that the following notices be included when they are distributed in binary form and that the recipient be given a copy of their respective licenses\&.
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'This product includes software developed by the JDOM Project (http://www\&.jdom\&.org/)
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'This product includes software developed by The Apache Software Foundation (http://www\&.apache\&.org/)
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'The license for JDOM can be read in the LICENSE\&.txt file in the source distribution available at http://www\&.jdom\&.org/
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'The license for the Commons Math library can be read at http://www\&.apache\&.org/licenses/LICENSE\-2\&.0 or in the LICENSE\&.txt file in the source distribution available at http://jakarta\&.apache\&.org/commons/math/
-.RE
-.PP
-This manual page and its XML source can be used, modified, and redistributed as if it were in public domain\&.
-.sp
=====================================
debian/beast-mcmc.1.xml
=====================================
@@ -285,7 +285,7 @@ measurably evolving populations (ancient DNA or time-stamped viral sequence data
<refsect1 id="bugs">
<!-- Or use this section to tell about upstream BTS. -->
<title>BUGS</title>
- <para>The &dhproduct; bug tracking system can be found at <ulink url="http://code.google.com/p/beast-mcmc/issues/list"/>.</para>
+ <para>The &dhproduct; bug tracking system can be found at <ulink url="https://github.com/beast-dev/beast-mcmc/issues"/>.</para>
</refsect1>
<refsect1 id="see_also">
@@ -297,29 +297,4 @@ measurably evolving populations (ancient DNA or time-stamped viral sequence data
</citerefentry>.</para>
</refsect1>
- <refsect1 id="references">
- <title>REFERENCES</title>
- <itemizedlist>
- <listitem>
- <para>
- Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7:214.
- </para>
- </listitem>
- <listitem>
- <para>
- Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88.
- </para>
- </listitem>
- <listitem>
- <para>
- Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185-1192.
- </para>
- </listitem>
- <listitem>
- <para>
- Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320.
- </para>
- </listitem>
- </itemizedlist>
- </refsect1>
</refentry>
=====================================
debian/beauti.1
=====================================
@@ -63,33 +63,3 @@ Copyright holder for BEAUti\&.
.sp -1n
.IP "" 4
Prepared this manpage in DocBook XML for the Debian distribution\&.
-.SH "COPYRIGHT"
-Copyright \(co 2002\(en2009 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (BEAUti)
-.br
-Copyright \(co 2002\(en2009 Felix Feyertag (This manpage)
-.br
-.PP
-The binaries and source code are made available and can be distributed subject to the following conditions:
-.PP
-BEAST is Copyright (C) 2002\-2006 Alexei Drummond and Andrew Rambaut BEAST is distributed under the terms of the GNU Lesser General Public License\&. See the notice in individual files and the file LICENSE for licensing details\&.
-.PP
-BEAST includes software libraries from projects whose licensing terms require that the following notices be included when they are distributed in binary form and that the recipient be given a copy of their respective licenses\&.
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'This product includes software developed by the JDOM Project (http://www\&.jdom\&.org/)
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'This product includes software developed by The Apache Software Foundation (http://www\&.apache\&.org/)
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'The license for JDOM can be read in the LICENSE\&.txt file in the source distribution available at http://www\&.jdom\&.org/
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'The license for the Commons Math library can be read at http://www\&.apache\&.org/licenses/LICENSE\-2\&.0 or in the LICENSE\&.txt file in the source distribution available at http://jakarta\&.apache\&.org/commons/math/
-.RE
-.PP
-This manual page and its XML source can be used, modified, and redistributed as if it were in public domain\&.
-.sp
=====================================
debian/beauti.1.xml
=====================================
@@ -157,29 +157,4 @@ http://jakarta.apache.org/commons/math/
</citerefentry>.</para>
</refsect1>
- <refsect1 id="references">
- <title>REFERENCES</title>
- <itemizedlist>
- <listitem>
- <para>
- Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7:214.
- </para>
- </listitem>
- <listitem>
- <para>
- Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88.
- </para>
- </listitem>
- <listitem>
- <para>
- Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185-1192.
- </para>
- </listitem>
- <listitem>
- <para>
- Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320.
- </para>
- </listitem>
- </itemizedlist>
- </refsect1>
</refentry>
=====================================
debian/changelog
=====================================
@@ -1,9 +1,12 @@
-beast-mcmc (1.10.4+dfsg-6) UNRELEASED; urgency=medium
+beast-mcmc (1.10.4+dfsg-6) unstable; urgency=medium
- * Add autopkgtest
- Closes: #1025424
+ * Fix clean target
+ Closes: #1043640
+ * Fix watch file
+ * Standards-Version: 4.7.0 (routine-update)
+ * d/copyright: review thanks to lrc
- -- Andreas Tille <tille at debian.org> Sun, 04 Dec 2022 18:16:16 +0100
+ -- Andreas Tille <tille at debian.org> Sat, 21 Dec 2024 17:38:11 +0100
beast-mcmc (1.10.4+dfsg-5) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -24,7 +24,7 @@ Build-Depends: debhelper-compat (= 13),
libitext1-java,
libejml-java (>= 0.41),
libjlapack-java
-Standards-Version: 4.6.1
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/beast-mcmc
Vcs-Git: https://salsa.debian.org/med-team/beast-mcmc.git
Homepage: http://beast.bio.ed.ac.uk/
=====================================
debian/copyright
=====================================
@@ -13,34 +13,27 @@ Files-Excluded: *.jar
Files: *
Copyright: 2002-2015 Alexei Drummond and Andrew Rambaut
-License: LGPL-3+
+License: LGPL-2+
Files: src/dr/math/matrixAlgebra/RobustSingularValueDecomposition.java
Copyright: 1999 CERN - European Organization for Nuclear Research
1999 Marc A. Suchard
-License: Colt-License-Agreement
- Permission to use, copy, modify, distribute and sell this software and its
- documentation for any purpose is hereby granted without fee, provided that
- the above copyright notice appear in all copies and that both that
- copyright notice and this permission notice appear in supporting
- documentation. CERN makes no representations about the suitability of this
- software for any purpose. It is provided "as is" without expressed or
- implied warranty.
+License: LGPL-2+
Files: src/dr/math/iterations/NewtonZeroFinder.java
src/dr/math/iterations/BisectionZeroFinder.java
src/dr/math/functionEval/DrMath.java
Copyright: 1999 Didier BESSET
-License: LGPL-3+
+License: LGPL-2+
Files: debian/*
Copyright: 2011-2015 Andreas Tille <tille at debian.org>
-License: LGPL-3+
+License: LGPL-2+
-License: LGPL-3+
+License: LGPL-2+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
+ the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
.
This program is distributed in the hope that it will be useful,
@@ -51,7 +44,7 @@ License: LGPL-3+
You should have received a copy of the GNU Lesser General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
.
- On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included
- in the file ‘/usr/share/common-licenses/LGPL-3’, and the GNU GPL license
- version 3 is included in the file ‘/usr/share/common-licenses/GPL-3’.
+ On a Debian GNU/Linux system, the GNU Lesser GPL license version 2 is included
+ in the file ‘/usr/share/common-licenses/LGPL-2’, and the GNU GPL license
+ version 2 is included in the file ‘/usr/share/common-licenses/GPL-2’.
=====================================
debian/rules
=====================================
@@ -26,6 +26,7 @@ ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true
override_dh_auto_clean:
rm -f native/*\.o native/*\.so native/*\.so\.*
+ rm -rf release/Linux/B*
ifeq ($(HASTEXDOC),yes)
for cleantex in \
Practical_BEAST \
=====================================
debian/tests/control → debian/tests/control_not_working_yet
=====================================
=====================================
debian/watch
=====================================
@@ -1,3 +1,5 @@
version=4
-opts="uversionmangle=s/_/./g,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/beast-dev/beast-mcmc/tags .*/[a-z_]*(\d[\d._]+)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
+
+opts="repacksuffix=+dfsg,dversionmangle=auto,searchmode=plain" \
+ https://api.github.com/repos/beast-dev/@PACKAGE@/releases \
+ https://github.com/beast-dev/@PACKAGE@/releases/download/v\d[\d.-]+/BEAST[^v]*v(\d[\d.-]+)\.tgz
View it on GitLab: https://salsa.debian.org/med-team/beast-mcmc/-/compare/1d484f04ca529f9c36a314f535559c9fae739f09...cecfbbd48c20d2317c955ba701d362ae02070702
--
View it on GitLab: https://salsa.debian.org/med-team/beast-mcmc/-/compare/1d484f04ca529f9c36a314f535559c9fae739f09...cecfbbd48c20d2317c955ba701d362ae02070702
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