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commit e0e41a443c0ff132db75be720c60c9ba60bf1e00
Author: Alba Crespi <crespialba+deb...@gmail.com>
Date: Sun Aug 13 02:47:33 2017 +0100
Initial Debian packaging
---
debian/NEWS | 246 +++++++++++++++
debian/changelog | 6 +
debian/compat | 1 +
debian/control | 65 ++++
debian/copyright | 706 ++++++++++++++++++++++++++++++++++++++++++++
debian/python-ete3.docs | 1 +
debian/python-ete3.examples | 1 +
debian/rules | 11 +
debian/source/format | 1 +
debian/source/options | 1 +
debian/upstream/metadata | 6 +
debian/watch | 4 +
12 files changed, 1049 insertions(+)
diff --git a/debian/NEWS b/debian/NEWS
new file mode 100644
index 0000000..39e52cf
--- /dev/null
+++ b/debian/NEWS
@@ -0,0 +1,246 @@
+MIME-Version: 1.0
+Received: by 10.100.179.79 with HTTP; Fri, 19 May 2017 09:46:20 -0700 (PDT)
+Date: Fri, 19 May 2017 17:46:20 +0100
+Delivered-To: crespia...@gmail.com
+Message-ID:
<cadq1ucl2gb3tfkkjdykfgd49gwt+vbcqo+72k1+0uwvoygb...@mail.gmail.com>
+Subject: ete toolkit copyright
+From: Alba Crespi <crespia...@gmail.com>
+To: Jaime Huerat-Cepas <jhce...@gmail.com>, "François Serra"
<serra.franc...@gmail.com>
+Content-Type: multipart/alternative; boundary="94eb2c13af7ece2b7d054fe342ad"
+
+--94eb2c13af7ece2b7d054fe342ad
+Content-Type: text/plain; charset="UTF-8"
+Content-Transfer-Encoding: quoted-printable
+
+Dear ete authors,
+
+I am a Debian contributor and I am currently creating packages for the ete
+toolkit.
+
+I was checking the copyright and I found only a couple of files with
+explicit copyright messages:
+
+./ete3/tools/ete_build_lib/validate.py:# Copyright (C) 2005-2010 Michael
+Foord, Mark Andrews, Nicola Larosa
+./ete3/tools/ete_build_lib/configobj.py:# Copyright (C) 2005-2010 Michael
+Foord, Nicola Larosa
+
+This seems to miss the main authors. Can you confirm what I should list?
+Perhaps something like this:
+
+Copyright (C) 2009-2017 Jaime Huerat-Cepas <jhce...@gmail.com>,
+Copyright (C) 2011-2017 Fran=C3=A7ois Serra <serra.franc...@gmail.com>
+
+(But I don't know if I am missing copyright holders, or if the copyright is
+held by EBI, for example, so please let me know.)
+
+Kind regards,
+Alba Crespi
+Debian Contributor
+
+--94eb2c13af7ece2b7d054fe342ad
+Content-Type: text/html; charset="UTF-8"
+Content-Transfer-Encoding: quoted-printable
+
+<div dir=3D"ltr"><div><div><div><div><div><div><div><div>Dear ete authors,<=
+br><br></div>I am a Debian contributor and I am currently creating packages=
+ for the ete toolkit. <br><br></div>I was checking the copyright and I foun=
+d only a couple of files with explicit copyright messages:<br><br>./ete3/to=
+ols/ete_build_lib/validate.py:# Copyright (C) 2005-2010 Michael Foord, Mark=
+ Andrews, Nicola Larosa<br>./ete3/tools/ete_build_lib/configobj.py:# Copyri=
+ght (C) 2005-2010 Michael Foord, Nicola Larosa<br><br></div><div>This seems=
+ to miss the main authors.=C2=A0 Can you confirm what I should list?=C2=A0 =
+Perhaps something like this:<br></div><br>Copyright (C) 2009-2017 Jaime Hue=
+rat-Cepas <<a href=3D"mailto:jhce...@gmail.com";>jhce...@gmail.com</a>>=
+;,<br></div>Copyright (C) 2011-2017 Fran=C3=A7ois Serra <<a href=3D"mail=
+to:serra.franc...@gmail.com">serra.franc...@gmail.com</a>><br><br></div>=
+<div>(But I don't know if I am missing copyright holders, or if the cop=
+yright is held by EBI, for example, so please let me know.)<br></div><br></=
+div>Kind regards,<br></div>Alba Crespi<br></div>Debian Contributor<br></div=
+>
+
+--94eb2c13af7ece2b7d054fe342ad--
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+In-Reply-To:
<cadq1ucl2gb3tfkkjdykfgd49gwt+vbcqo+72k1+0uwvoygb...@mail.gmail.com>
+References:
<cadq1ucl2gb3tfkkjdykfgd49gwt+vbcqo+72k1+0uwvoygb...@mail.gmail.com>
+From: Jaime Huerta Cepas <jhce...@gmail.com>
+Date: Mon, 29 May 2017 14:00:34 +0200
+Message-ID:
<CANU7+zEB=wwgn3x73ncrswqwr1qfnfhfw0rtf0jnedj4jek...@mail.gmail.com>
+Subject: Re: ete toolkit copyright
+To: Alba Crespi <crespia...@gmail.com>
+Cc: "François Serra" <serra.franc...@gmail.com>
+Content-Type: multipart/alternative; boundary="001a1149416807ef9b0550a87175"
+
+--001a1149416807ef9b0550a87175
+Content-Type: text/plain; charset="UTF-8"
+Content-Transfer-Encoding: quoted-printable
+
+Hi Alba,
+sorry for the long delay (and thanks for taking care of this!).
+
+The copyright statement in validate.py refers to a third-party module used
+by ETE.
+
+For ETE itself, there are contributions from several people to different
+parts of the code (and the license is already copylefted), so I would
+prefer to keep the copyright statement as general as possible. For
+instance,
+
+Copyright (C) 2007-2017 ETE Toolkit Developers
+
+and then credit every author specifically in the source code. This is how
+other python projects seem to do it
+<https://github.com/numpy/numpy/blob/c90d7c94fd2077d0beca48fa89a423da2b0bb6=
+63/doc/source/license.rst>
+.
+
+You can keep my concat information as current maintainer of the project.
+
+thanks again,
+looking forward to see ETE on debian :)
+-jaime
+
+
+
+On 19 May 2017 at 18:46, Alba Crespi <crespia...@gmail.com> wrote:
+
+> Dear ete authors,
+>
+> I am a Debian contributor and I am currently creating packages for the et=
+e
+> toolkit.
+>
+> I was checking the copyright and I found only a couple of files with
+> explicit copyright messages:
+>
+> ./ete3/tools/ete_build_lib/validate.py:# Copyright (C) 2005-2010 Michael
+> Foord, Mark Andrews, Nicola Larosa
+> ./ete3/tools/ete_build_lib/configobj.py:# Copyright (C) 2005-2010 Michael
+> Foord, Nicola Larosa
+>
+> This seems to miss the main authors. Can you confirm what I should list?
+> Perhaps something like this:
+>
+> Copyright (C) 2009-2017 Jaime Huerat-Cepas <jhce...@gmail.com>,
+> Copyright (C) 2011-2017 Fran=C3=A7ois Serra <serra.franc...@gmail.com>
+>
+> (But I don't know if I am missing copyright holders, or if the copyright
+> is held by EBI, for example, so please let me know.)
+>
+> Kind regards,
+> Alba Crespi
+> Debian Contributor
+>
+
+--001a1149416807ef9b0550a87175
+Content-Type: text/html; charset="UTF-8"
+Content-Transfer-Encoding: quoted-printable
+
+<div dir=3D"ltr">Hi Alba,=C2=A0<div>sorry for the long delay (and thanks fo=
+r taking care of this!).=C2=A0</div><div><br></div><div>The copyright state=
+ment in validate.py refers to a third-party module used by ETE.=C2=A0</div>=
+<div><br></div><div>For ETE itself, there are contributions from several pe=
+ople to different parts of the code (and the license is already copylefted)=
+, so I would prefer to keep the copyright statement as general as possible.=
+ For instance, =C2=A0</div><div><br></div><div style=3D"font-size:12.8px">C=
+opyright (C)=C2=A02007-2017 ETE Toolkit Developers<br></div><div style=3D"f=
+ont-size:12.8px"><br></div><div style=3D"font-size:12.8px">and then credit =
+every author specifically in the source code. This is how other python proj=
+ects <a href=3D"https://github.com/numpy/numpy/blob/c90d7c94fd2077d0beca48f=
+a89a423da2b0bb663/doc/source/license.rst">seem to do it</a>.</div><div styl=
+e=3D"font-size:12.8px"><br></div><div style=3D"font-size:12.8px">You can ke=
+ep my concat information as current maintainer of the project.=C2=A0</div><=
+div style=3D"font-size:12.8px"><br></div><div style=3D"font-size:12.8px">th=
+anks again,=C2=A0</div><div style=3D"font-size:12.8px">looking forward to s=
+ee ETE on debian :)</div><div style=3D"font-size:12.8px">-jaime</div><div s=
+tyle=3D"font-size:12.8px"><br></div><div style=3D"font-size:12.8px"><br></d=
+iv></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On 19 Ma=
+y 2017 at 18:46, Alba Crespi <span dir=3D"ltr"><<a href=3D"mailto:crespi=
+a...@gmail.com" target=3D"_blank">crespia...@gmail.com</a>></span> wrote=
+:<br><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-le=
+ft:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr"><div><div><div><div><d=
+iv><div><div><div>Dear ete authors,<br><br></div>I am a Debian contributor =
+and I am currently creating packages for the ete toolkit. <br><br></div>I w=
+as checking the copyright and I found only a couple of files with explicit =
+copyright messages:<br><br>./ete3/tools/ete_build_lib/<wbr>validate.py:# Co=
+pyright (C) 2005-2010 Michael Foord, Mark Andrews, Nicola Larosa<br>./ete3/=
+tools/ete_build_lib/<wbr>configobj.py:# Copyright (C) 2005-2010 Michael Foo=
+rd, Nicola Larosa<br><br></div><div>This seems to miss the main authors.=C2=
+=A0 Can you confirm what I should list?=C2=A0 Perhaps something like this:<=
+br></div><br>Copyright (C) 2009-2017 Jaime Huerat-Cepas <<a href=3D"mail=
+to:jhce...@gmail.com" target=3D"_blank">jhce...@gmail.com</a>>,<br></div=
+>Copyright (C) 2011-2017 Fran=C3=A7ois Serra <<a href=3D"mailto:serra.fr=
+anc...@gmail.com" target=3D"_blank">serra.franc...@gmail.com</a>><br><br=
+></div><div>(But I don't know if I am missing copyright holders, or if =
+the copyright is held by EBI, for example, so please let me know.)<br></div=
+><br></div>Kind regards,<br></div>Alba Crespi<br></div>Debian Contributor<b=
+r></div>
+</blockquote></div><br></div>
+
+--001a1149416807ef9b0550a87175--
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f8db665
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,6 @@
+python-ete3 (3.0.0b35-1) unstable; urgency=medium
+
+ * Initial release. (Closes: #861182)
+
+ -- Alba Crespi <crespialba+deb...@gmail.com> Sat, 12 Aug 2017 19:28:33 +0000
+
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..3f3753e
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,65 @@
+Source: python-ete3
+Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
+Uploaders: Alba Crespi <crespialba+deb...@gmail.com>
+Section: python
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ dh-python,
+ python-all-dev,
+ python-setuptools,
+ python3-all-dev,
+ python3-setuptools
+Standards-Version: 3.9.8
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-ete3.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/python-ete3.git
+Homepage: http://etetoolkit.org
+
+Package: python-ete3
+Architecture: any
+Depends: ${misc:Depends},
+ ${python:Depends},
+ ${shlibs:Depends}
+Recommends: ${python:Recommends}
+Suggests: ${python:Suggests}
+Description: Python Environment for (phylogenetic) Tree Exploration - Python
2.X
+ The Environment for Tree Exploration (ETE) is a Python programming
+ toolkit that assists in the recontruction, manipulation, analysis and
+ visualization of phylogenetic trees (although clustering trees or any
+ other tree-like data structure are also supported).
+ .
+ ETE is currently developed as a tool for researchers working in
+ phylogenetics and genomics. If you use ETE for a published work,
+ please cite:
+ .
+ ::
+ .
+ Jaime Huerta-Cepas, François Serra and Peer Bork. "ETE 3: Reconstruction,
+ analysis and visualization of phylogenomic data." Mol Biol Evol (2016)
doi:
+ 10.1093/molbev/msw046
+ .
+ Visit http://etetoolkit.org for more info.
+
+Package: python3-ete3
+Architecture: any
+Depends: ${misc:Depends},
+ ${python3:Depends},
+ ${shlibs:Depends}
+Recommends: ${python3:Recommends}
+Suggests: ${python3:Suggests}
+Description: Python Environment for (phylogenetic) Tree Exploration - Python
3.X
+ The Environment for Tree Exploration (ETE) is a Python programming
+ toolkit that assists in the recontruction, manipulation, analysis and
+ visualization of phylogenetic trees (although clustering trees or any
+ other tree-like data structure are also supported).
+ .
+ ETE is currently developed as a tool for researchers working in
+ phylogenetics and genomics. If you use ETE for a published work,
+ please cite:
+ .
+ ::
+ .
+ Jaime Huerta-Cepas, François Serra and Peer Bork. "ETE 3: Reconstruction,
+ analysis and visualization of phylogenomic data." Mol Biol Evol (2016)
doi:
+ 10.1093/molbev/msw046
+ .
+ Visit http://etetoolkit.org for more info.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..5660799
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,706 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ete3
+Upstream-Contact: Jaime Huerta-Cepas <hue...@embl.de>
+Source: http://etetoolkit.org
+Files-Excluded: doc/_static
+ examples/webplugin
+
+Files: *
+Copyright: Copyright (C) 2007-2017 ETE Toolkit Developers
+License: GPL-3
+Comment: Author confirmed by email.
+ The full text is in debian/NEWS
+
+Files: debian/*
+Copyright: 2017 © Alba Crespi <crespialba+deb...@gmail.com>
+License: GPL-3
+
+Files: ete3/tools/phylobuild_lib/validate.py
+ ete3/tools/phylobuild_lib/configobj.py
+Copyright: Copyright (C) 2005-2010 Michael Foord, Mark Andrews, Nicola Larosa
+License: GPL-3
+
+Files: examples/webplugin/jquery-1.4.2.min.js
+Copyright: Copyright 2010, John Resig
+License: Dual licensed under the MIT or GPL Version 2 licenses.
+
+Files: doc/*
+Copyright: Copyright 2015, The ETE Toolkit Team.
+License: GPL-3
+
+
+License: GPL-3
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+ .
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+ .
+ Preamble
+ .
+ The GNU General Public License is a free, copyleft license for
+ software and other kinds of works.
+ .
+ The licenses for most software and other practical works are designed
+ to take away your freedom to share and change the works. By contrast,
+ the GNU General Public License is intended to guarantee your freedom to
+ share and change all versions of a program--to make sure it remains free
+ software for all its users. We, the Free Software Foundation, use the
+ GNU General Public License for most of our software; it applies also to
+ any other work released this way by its authors. You can apply it to
+ your programs, too.
+ .
+ When we speak of free software, we are referring to freedom, not
+ price. Our General Public Licenses are designed to make sure that you
+ have the freedom to distribute copies of free software (and charge for
+ them if you wish), that you receive source code or can get it if you
+ want it, that you can change the software or use pieces of it in new
+ free programs, and that you know you can do these things.
+ .
+ To protect your rights, we need to prevent others from denying you
+ these rights or asking you to surrender the rights. Therefore, you have
+ certain responsibilities if you distribute copies of the software, or if
+ you modify it: responsibilities to respect the freedom of others.
+ .
+ For example, if you distribute copies of such a program, whether
+ gratis or for a fee, you must pass on to the recipients the same
+ freedoms that you received. You must make sure that they, too, receive
+ or can get the source code. And you must show them these terms so they
+ know their rights.
+ .
+ Developers that use the GNU GPL protect your rights with two steps:
+ (1) assert copyright on the software, and (2) offer you this License
+ giving you legal permission to copy, distribute and/or modify it.
+ .
+ For the developers' and authors' protection, the GPL clearly explains
+ that there is no warranty for this free software. For both users' and
+ authors' sake, the GPL requires that modified versions be marked as
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+ .
+ You should also get your employer (if you work as a programmer) or school,
+ if any, to sign a "copyright disclaimer" for the program, if necessary.
+ For more information on this, and how to apply and follow the GNU GPL, see
+ <http://www.gnu.org/licenses/>.
+ .
+ The GNU General Public License does not permit incorporating your program
+ into proprietary programs. If your program is a subroutine library, you
+ may consider it more useful to permit linking proprietary applications with
+ the library. If this is what you want to do, use the GNU Lesser General
+ Public License instead of this License. But first, please read
+ <http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/debian/python-ete3.docs b/debian/python-ete3.docs
new file mode 100644
index 0000000..a1320b1
--- /dev/null
+++ b/debian/python-ete3.docs
@@ -0,0 +1 @@
+README.rst
diff --git a/debian/python-ete3.examples b/debian/python-ete3.examples
new file mode 100644
index 0000000..e39721e
--- /dev/null
+++ b/debian/python-ete3.examples
@@ -0,0 +1 @@
+examples/*
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..eddcf6e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,11 @@
+#! /usr/bin/make -f
+
+export PYBUILD_NAME=python-ete3
+export PYBUILD_DISABLE_python3=test
+export PYBUILD_DISABLE_python2=1
+
+%:
+ dh $@ --with python2,python3 --buildsystem=pybuild # --disable
test/python2
+ #PYBUILD_DISABLE_python3=test
+ #PYBUILD_DISABLE_python2=1
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/source/options b/debian/source/options
new file mode 100644
index 0000000..d81db3f
--- /dev/null
+++ b/debian/source/options
@@ -0,0 +1 @@
+extend-diff-ignore="^[^/]+.egg-info/"
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..8f4149c
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,6 @@
+Reference:
+ Author: Jaime Huerta-Cepas, François Serra and Peer Bork.
+ Title: "ETE 3: Reconstruction analysis and visualization of phylogenomic
data."
+ Journal: Mol Biol Evol
+ DOI: 10.1093/molbev/msw046
+ Year: 2016
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..0e605fe
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+# try also https://pypi.debian.net/ete3/watch
+version=3
+opts=uversionmangle=s/(rc|a|b|c)/~$1/ \
+https://pypi.python.org/simple/ete3-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
--
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