[med-svn] [Git][med-team/bali-phy][master] 4 commits: Move single test scripts into single script and fix the new location of examples

2018-03-10 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / bali-phy


Commits:
ff28db02 by Andreas Tille at 2018-03-11T07:46:27+01:00
Move single test scripts into single script and fix the new location of examples

- - - - -
eb4c937c by Andreas Tille at 2018-03-11T07:47:43+01:00
Install autopkgtest script into usr/share/doc to enable users reproducing the 
tests on their local machine

- - - - -
b0663953 by Andreas Tille at 2018-03-11T07:51:29+01:00
Users are not permitted to write to /usr/share/doc - move examples to temporary 
dir to let the script work under all circumstances

- - - - -
c7ca5c91 by Andreas Tille at 2018-03-11T08:15:33+01:00
Upload to unstable

- - - - -


11 changed files:

- + debian/README.test
- debian/changelog
- + debian/docs
- debian/tests/control
- − debian/tests/help
- + debian/tests/run-unit-test
- − debian/tests/small-A
- − debian/tests/small-analysis
- − debian/tests/small-no-A
- − debian/tests/small-test
- − debian/tests/version


Changes:

=
debian/README.test
=
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+
+
+This package can be tested by executing
+
+sh run-unit-test
+
+in order to confirm its integrity.


=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-bali-phy (3.0.2+dfsg-1) UNRELEASED; urgency=medium
+bali-phy (3.0.2+dfsg-1) unstable; urgency=medium
 
   * Initial release (Closes: #891971).
 
- -- Benjamin Redelings   Tue, 06 Mar 2018 
22:01:35 -0500
+ -- Benjamin Redelings   Sun, 11 Mar 2018 
07:28:17 +0100


=
debian/docs
=
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+debian/README.test
+debian/tests/run-unit-test


=
debian/tests/control
=
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -1 +1,3 @@
-Tests: version, help, small-test, small-A, small-no-A, small-analysis
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=
debian/tests/help deleted
=
--- a/debian/tests/help
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-bali-phy --help
-


=
debian/tests/run-unit-test
=
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,23 @@
+#!/bin/sh
+
+set -e
+
+pkg=bali-phy
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+
+bali-phy --version
+bali-phy --help
+
+bali-phy sequences/5S-rRNA/5d.fasta --test --seed=0
+bali-phy sequences/5S-rRNA/5d.fasta --iter=50 --seed=0
+bali-phy sequences/5S-rRNA/5d.fasta --iter=200 -Inone --seed=0
+bali-phy sequences/5S-rRNA/5d.fasta --iter=100
+bp-analyze 5d-1


=
debian/tests/small-A deleted
=
--- a/debian/tests/small-A
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-bali-phy /usr/share/bali-phy/examples/sequences/5S-rRNA/5d.fasta --iter=50 
--seed=0
\ No newline at end of file


=
debian/tests/small-analysis deleted
=
--- a/debian/tests/small-analysis
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-bali-phy /usr/share/bali-phy/examples/sequences/5S-rRNA/5d.fasta --iter=100
-bp-analyze 5d-1


=
debian/tests/small-no-A deleted
=
--- a/debian/tests/small-no-A
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-bali-phy /usr/share/bali-phy/examples/sequences/5S-rRNA/5d.fasta --iter=200 
-Inone --seed=0
\ No newline at end of file


=
debian/tests/small-test deleted
=
--- a/debian/tests/small-test
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-bali-phy /usr/share/bali-phy/examples/sequences/5S-rRNA/5d.fasta --test 
--seed=0
\ No newline at end of file


=
debian/tests/version deleted
=
--- a/debian/tests/version
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/bin/sh
-bali-phy --version



View it on GitLab: 
https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f

---
View it on GitLab: 
https://salsa.debian.org/med-team/bali-phy/compare/c0638bd4f901995849294281af91e79eaad964cc...c7ca5c91ecb55344e15ebece3a8fba806be6f23f
You're receiving this email because of your account on salsa.debian.org.

[med-svn] [Git][med-team/bali-phy] Pushed new tag upstream/3.0.2+dfsg

2018-03-10 Thread Andreas Tille 
Andreas Tille pushed new tag upstream/3.0.2+dfsg at Debian Med / bali-phy

---
View it on GitLab: 
https://salsa.debian.org/med-team/bali-phy/tree/upstream/3.0.2+dfsg
You're receiving this email because of your account on salsa.debian.org.
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit

[med-svn] [Git][med-team/bali-phy][upstream] New upstream version 3.0.2+dfsg

2018-03-10 Thread Andreas Tille 
Andreas Tille pushed to branch upstream at Debian Med / bali-phy


Commits:
d23f72a9 by Andreas Tille at 2018-03-11T07:27:10+01:00
New upstream version 3.0.2+dfsg
- - - - -


30 changed files:

- doc/README.html
- doc/README.itex.xml
- doc/README.pdf
- doc/README.xhtml
- functions/Mixture.json
- functions/Rates/Gamma.json
- help/Codons.txt
- help/Triplets.txt
- help/commands/Rao-Blackwellize.txt
- help/commands/align.txt
- help/commands/alphabet.txt
- help/commands/branch-lengths.txt
- help/commands/config.txt
- help/commands/disable.txt
- help/commands/enable.txt
- help/commands/imodel.txt
- help/commands/initial-value.txt
- help/commands/iterations.txt
- help/commands/link.txt
- help/commands/model.txt
- help/commands/name.txt
- help/commands/package-path.txt
- help/commands/pre-burnin.txt
- help/commands/scale.txt
- help/commands/seed.txt
- help/commands/set.txt
- help/commands/smodel.txt
- help/commands/subsample.txt
- help/commands/test.txt
- help/commands/tree.txt


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/bali-phy/commit/d23f72a9956605b8a60f1d4665f57440dec3dfe6

---
View it on GitLab: 
https://salsa.debian.org/med-team/bali-phy/commit/d23f72a9956605b8a60f1d4665f57440dec3dfe6
You're receiving this email because of your account on salsa.debian.org.
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit

[med-svn] [Git][med-team/bali-phy][pristine-tar] pristine-tar data for bali-phy_3.0.2+dfsg.orig.tar.xz

2018-03-10 Thread Andreas Tille 
Andreas Tille pushed to branch pristine-tar at Debian Med / bali-phy


Commits:
5fc8f415 by Andreas Tille at 2018-03-11T07:27:13+01:00
pristine-tar data for bali-phy_3.0.2+dfsg.orig.tar.xz

- - - - -


2 changed files:

- + bali-phy_3.0.2+dfsg.orig.tar.xz.delta
- + bali-phy_3.0.2+dfsg.orig.tar.xz.id


Changes:

=
bali-phy_3.0.2+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/bali-phy_3.0.2+dfsg.orig.tar.xz.delta differ


=
bali-phy_3.0.2+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/bali-phy_3.0.2+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+8468acd355afd7d4822feb5e644e7185a15dd903



View it on GitLab: 
https://salsa.debian.org/med-team/bali-phy/commit/5fc8f41555200452ef8b373cecfa557bd9e42797

---
View it on GitLab: 
https://salsa.debian.org/med-team/bali-phy/commit/5fc8f41555200452ef8b373cecfa557bd9e42797
You're receiving this email because of your account on salsa.debian.org.
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit

[med-svn] [Git][med-team/bali-phy][master] 3 commits: New upstream version 3.0.2+dfsg

2018-03-10 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / bali-phy


Commits:
d23f72a9 by Andreas Tille at 2018-03-11T07:27:10+01:00
New upstream version 3.0.2+dfsg
- - - - -
b10f6276 by Andreas Tille at 2018-03-11T07:27:13+01:00
Update upstream source from tag upstream/3.0.2+dfsg

Update to upstream version 3.0.2+dfsg
with Debian dir 602b5b678356e7ce4702bf03452c11f8e94d96e9
- - - - -
c0638bd4 by Andreas Tille at 2018-03-11T07:27:54+01:00
Patch applied in new upstream version

- - - - -


30 changed files:

- debian/changelog
- − debian/patches/series
- − debian/patches/spelling.patch
- doc/README.html
- doc/README.itex.xml
- doc/README.pdf
- doc/README.xhtml
- functions/Mixture.json
- functions/Rates/Gamma.json
- help/Codons.txt
- help/Triplets.txt
- help/commands/Rao-Blackwellize.txt
- help/commands/align.txt
- help/commands/alphabet.txt
- help/commands/branch-lengths.txt
- help/commands/config.txt
- help/commands/disable.txt
- help/commands/enable.txt
- help/commands/imodel.txt
- help/commands/initial-value.txt
- help/commands/iterations.txt
- help/commands/link.txt
- help/commands/model.txt
- help/commands/name.txt
- help/commands/package-path.txt
- help/commands/pre-burnin.txt
- help/commands/scale.txt
- help/commands/seed.txt
- help/commands/set.txt
- help/commands/smodel.txt


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/bali-phy/compare/53682e09b2da81c8201d555ac7d3d7992cf7623d...c0638bd4f901995849294281af91e79eaad964cc

---
View it on GitLab: 
https://salsa.debian.org/med-team/bali-phy/compare/53682e09b2da81c8201d555ac7d3d7992cf7623d...c0638bd4f901995849294281af91e79eaad964cc
You're receiving this email because of your account on salsa.debian.org.
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit

[med-svn] [Git][med-team/canu][upstream] 2 commits: New upstream version 1.7+dfsg

2018-03-10 Thread Afif Elghraoui 
Afif Elghraoui pushed to branch upstream at Debian Med / canu


Commits:
243aa28b by Afif Elghraoui at 2018-03-10T17:09:47-05:00
New upstream version 1.7+dfsg
- - - - -
6f15624a by Afif Elghraoui at 2018-03-10T18:53:46-05:00
New upstream version 1.7+dfsg
- - - - -


30 changed files:

- README.md
- addCopyrights-BuildData.pl
- addCopyrights.dat
- addCopyrights.pl
- documentation/reST-markup-hints
- documentation/source/conf.py
- documentation/source/faq.rst
- documentation/source/parameter-reference.rst
- documentation/source/quick-start.rst
- documentation/source/tutorial.rst
- src/AS_UTL/AS_UTL_alloc.H
- src/AS_UTL/AS_UTL_fasta.C
- src/AS_UTL/AS_UTL_fasta.H
- src/AS_UTL/AS_UTL_fileIO.C
- src/AS_UTL/AS_UTL_fileIO.H
- src/AS_UTL/AS_UTL_reverseComplement.C
- src/AS_UTL/AS_UTL_reverseComplement.H
- src/AS_UTL/AS_UTL_stackTrace.C
- src/AS_UTL/bitPackedArray.C
- src/AS_UTL/bitPackedFile.C
- src/AS_UTL/bitPackedFile.H
- src/AS_UTL/bitPacking.H
- src/AS_UTL/dnaAlphabets.H
- src/AS_UTL/intervalList.H
- src/AS_UTL/intervalListTest.C
- + src/AS_UTL/memoryMappedFile.C
- src/AS_UTL/memoryMappedFile.H
- src/AS_UTL/mt19937ar.C
- src/AS_UTL/mt19937ar.H
- src/AS_UTL/readBuffer.C


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/canu/compare/3dbd24eb7ac4a7479ac4f8bfba75146f5a8908ff...6f15624ae2bb3dcc6f0a2a19679e5957131f78b8

---
View it on GitLab: 
https://salsa.debian.org/med-team/canu/compare/3dbd24eb7ac4a7479ac4f8bfba75146f5a8908ff...6f15624ae2bb3dcc6f0a2a19679e5957131f78b8
You're receiving this email because of your account on salsa.debian.org.
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit

[med-svn] [Git][med-team/canu][master] 14 commits: New upstream version 1.7+dfsg

2018-03-10 Thread Afif Elghraoui 
Afif Elghraoui pushed to branch master at Debian Med / canu


Commits:
243aa28b by Afif Elghraoui at 2018-03-10T17:09:47-05:00
New upstream version 1.7+dfsg
- - - - -
72ffbdd9 by Afif Elghraoui at 2018-03-10T17:09:51-05:00
Merge tag upstream/1.7+dfsg

Upstream version 1.7+dfsg

- - - - -
df269544 by Afif Elghraoui at 2018-03-10T18:51:20-05:00
Update handling of MHAP copy

The jar file is bundled rather than its source code.
The patches to exclude the build directory arent needed,
but Files-Excluded needed to be changed.

- - - - -
aba64962 by Afif Elghraoui at 2018-03-10T18:52:20-05:00
Refresh patches

- - - - -
ceb7a203 by Afif Elghraoui at 2018-03-10T18:52:20-05:00
use a wrapper script and leave /usr/lib/canu/ as undisturbed as possible

Rather than patching paths, let the canu main program live where
it expects to be, just using a wrapper script in /usr/bin.

- - - - -
6f15624a by Afif Elghraoui at 2018-03-10T18:53:46-05:00
New upstream version 1.7+dfsg
- - - - -
24d6be52 by Afif Elghraoui at 2018-03-10T18:53:50-05:00
Merge tag upstream/1.7+dfsg

Upstream version 1.7+dfsg

- - - - -
5419d316 by Afif Elghraoui at 2018-03-10T19:08:53-05:00
Remove build system dependency on bundled MHAP

- - - - -
0ce0b35d by Afif Elghraoui at 2018-03-10T19:25:44-05:00
fix typo in patch

- - - - -
2454ffa4 by Afif Elghraoui at 2018-03-10T19:48:01-05:00
fix path to mhap jar

- - - - -
d8b271be by Afif Elghraoui at 2018-03-10T19:48:21-05:00
move gnuplot to Depends

- - - - -
ae4c2a99 by Afif Elghraoui at 2018-03-10T20:16:24-05:00
Bump mhap minimum version

- - - - -
b673b3d8 by Afif Elghraoui at 2018-03-10T20:17:39-05:00
Bump Standards-Version to 4.1.3

- - - - -
4eafc31f by Afif Elghraoui at 2018-03-10T23:45:30-05:00
Update changelog (need update to mhap package)

- - - - -


30 changed files:

- README.md
- addCopyrights-BuildData.pl
- addCopyrights.dat
- addCopyrights.pl
- + debian/bin/canu
- debian/changelog
- debian/control
- debian/copyright
- debian/install
- − debian/links
- − debian/patches/external-deps.patch
- + debian/patches/external-mhap.patch
- debian/patches/gcc-7_format-security.patch
- − debian/patches/relative-paths.patch
- debian/patches/series
- debian/patches/use-debian-mhap-at-runtime.patch
- debian/rules
- documentation/reST-markup-hints
- documentation/source/conf.py
- documentation/source/faq.rst
- documentation/source/parameter-reference.rst
- documentation/source/quick-start.rst
- documentation/source/tutorial.rst
- src/AS_UTL/AS_UTL_alloc.H
- src/AS_UTL/AS_UTL_fasta.C
- src/AS_UTL/AS_UTL_fasta.H
- src/AS_UTL/AS_UTL_fileIO.C
- src/AS_UTL/AS_UTL_fileIO.H
- src/AS_UTL/AS_UTL_reverseComplement.C
- src/AS_UTL/AS_UTL_reverseComplement.H


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/canu/compare/5bffe33302bbe0f1210c01a75d6b0ca04b026ffa...4eafc31fe7e77b532289eb68cff4b3e81970b033

---
View it on GitLab: 
https://salsa.debian.org/med-team/canu/compare/5bffe33302bbe0f1210c01a75d6b0ca04b026ffa...4eafc31fe7e77b532289eb68cff4b3e81970b033
You're receiving this email because of your account on salsa.debian.org.
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit

[med-svn] [Git][med-team/canu][pristine-tar] 2 commits: pristine-tar data for canu_1.7+dfsg.orig.tar.gz

2018-03-10 Thread Afif Elghraoui 
Afif Elghraoui pushed to branch pristine-tar at Debian Med / canu


Commits:
61b48daf by Afif Elghraoui at 2018-03-10T17:09:51-05:00
pristine-tar data for canu_1.7+dfsg.orig.tar.gz

- - - - -
5efd6a26 by Afif Elghraoui at 2018-03-10T18:53:50-05:00
pristine-tar data for canu_1.7+dfsg.orig.tar.gz

- - - - -


2 changed files:

- + canu_1.7+dfsg.orig.tar.gz.delta
- + canu_1.7+dfsg.orig.tar.gz.id


Changes:

=
canu_1.7+dfsg.orig.tar.gz.delta
=
Binary files /dev/null and b/canu_1.7+dfsg.orig.tar.gz.delta differ


=
canu_1.7+dfsg.orig.tar.gz.id
=
--- /dev/null
+++ b/canu_1.7+dfsg.orig.tar.gz.id
@@ -0,0 +1 @@
+bb979e6c97d628c3430795a0f490ea76f8e71716



View it on GitLab: 
https://salsa.debian.org/med-team/canu/compare/af98a57aca17a8bd9c313b2ea089311fa2680274...5efd6a2600c09cd70f653d28c3c0aa7cf30a47d1

---
View it on GitLab: 
https://salsa.debian.org/med-team/canu/compare/af98a57aca17a8bd9c313b2ea089311fa2680274...5efd6a2600c09cd70f653d28c3c0aa7cf30a47d1
You're receiving this email because of your account on salsa.debian.org.
___
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit