PKG-INFO

 Metadata-Version: 1.1
 Name: ete3
-Version: 3.0.0b35
+Version: 3.1.1
 Summary: A Python Environment for (phylogenetic) Tree Exploration
 Home-page: http://etetoolkit.org
 Author: Jaime Huerta-Cepas
 Author-email: huerta@embl.de
 License: GPLv3
 Download-URL: http://etetoolkit.org/static/releases/ete3/
+Description-Content-Type: UNKNOWN
 Description: 
         The Environment for Tree Exploration (ETE) is a Python programming
         toolkit that assists in the recontruction, manipulation, analysis and

README.rst

-README
-=======
-
 .. image:: https://travis-ci.org/etetoolkit/ete.svg?branch=master
    :target: https://travis-ci.org/etetoolkit/ete
 
@@ -11,11 +8,13 @@ README
 ..
    .. image:: https://coveralls.io/repos/jhcepas/ete/badge.png
 
+Overview
+-----------
 
-ETE (Environment for Tree Exploration is a Python programming
-toolkit that assists in the automated manipulation, analysis and
-visualization of phylogenetic trees. Clustering trees or any
-other tree-like data structure are also supported. 
+ETE (Environment for Tree Exploration is a Python programming toolkit that
+assists in the automated manipulation, analysis and visualization of
+phylogenetic trees. 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. ETE provides specialized tools to reconstruct, compare and visualize
@@ -27,13 +26,14 @@ phylogenetic trees. If you use ETE for a published work, please cite:
    analysis and visualization of phylogenomic data."  Mol Biol Evol (2016) doi:
    10.1093/molbev/msw046
 
-Install/Documentation
+Install and Documentation
 -----------------------------
 
 - The official web site of ETE is http://etetoolkit.org. Downloading
   instructions and further documentation can be found there.
 
-- News and announcements are usually posted on twitter: http://twitter.com/etetoolkit
+- News and announcements are usually posted on twitter:
+  http://twitter.com/etetoolkit
 
 Gallery of examples
 --------------------
@@ -41,23 +41,31 @@ Gallery of examples
 .. image:: https://raw.githubusercontent.com/jhcepas/ete/master/sdoc/gallery.png
    :width: 600
   
+Getting Support
+------------------
+**Whenerver possible, please avoid sending support related emails directly to
+the developers. Keep communication public:**
 
-Contributing and BUG reporting
----------------------------------
-https://github.com/jhcepas/ete/blob/master/CONTRIBUTING.rst
+- For any type of question on how to use ETE in a bioinformatics context, the
+  BioStars community (http://biostars.org) provides an excellent help desk. ETE
+  developers contribute there with answers, but you will also get feedback from
+  other users. It is recommended to tag your questions with the "etetoolkit"
+  label.
 
+- For technical problems or more ETE specific questions, you can also use the
+  official ETE mailing list at https://groups.google.com/d/forum/etetoolkit. To
+  avoid spam, messages from new users are moderated. Expect some delay until
+  your first message and account is validated.
 
-Getting support
-------------------
+- Bug reports, feature requests and general discussion should be posted into github:
+  https://github.com/etetoolkit/ete/issues
 
-- There is a mailing list providing user support at
-  https://groups.google.com/d/forum/etetoolkit. In order to avoid spam,
-  messages from new users are moderated. Expect some delay until your first
-  message and account is validated.
+- For any other inquire please contact *huerta /at/ embl.de*
+   
+
+Contributing and BUG reporting
+---------------------------------
+https://github.com/etetoolkit/ete/wiki/Contributing
   
-- For general questions on how to use ETE in bioinformatic projects, the
-  BioStars community (http://biostars.org) provides an excellent and broader
-  help desk. Please feel free to raise any question there and tag it with the
-  "etetoolkit" label.
 
 

VERSION

-3.0.0b35
\ No newline at end of file
+3.1.1
\ No newline at end of file

debian/NEWS

-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: crespialba@gmail.com
-Message-ID: <CADQ1UCL2gB3TfKKJDYKFgD49gWt+vBCQo+72K1+0uwvOYGb+kQ@mail.gmail.com>
-Subject: ete toolkit copyright
-From: Alba Crespi <crespialba@gmail.com>
-To: Jaime Huerat-Cepas <jhcepas@gmail.com>, "François Serra" <serra.francois@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 <jhcepas@gmail.com>,
-Copyright (C) 2011-2017 Fran=C3=A7ois Serra <serra.francois@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 &lt;<a href=3D"mailto:jhcepas@gmail.com">jhcepas@gmail.com</a>&gt=
-;,<br></div>Copyright (C) 2011-2017 Fran=C3=A7ois Serra &lt;<a href=3D"mail=
-to:serra.francois@gmail.com">serra.francois@gmail.com</a>&gt;<br><br></div>=
-<div>(But I don&#39;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=
->
-
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-In-Reply-To: <CADQ1UCL2gB3TfKKJDYKFgD49gWt+vBCQo+72K1+0uwvOYGb+kQ@mail.gmail.com>
-References: <CADQ1UCL2gB3TfKKJDYKFgD49gWt+vBCQo+72K1+0uwvOYGb+kQ@mail.gmail.com>
-From: Jaime Huerta Cepas <jhcepas@gmail.com>
-Date: Mon, 29 May 2017 14:00:34 +0200
-Message-ID: <CANU7+zEB=wWGn3X73NcrswQwR1qfNfHFw0RTf0JnEDj4JeKMcQ@mail.gmail.com>
-Subject: Re: ete toolkit copyright
-To: Alba Crespi <crespialba@gmail.com>
-Cc: "François Serra" <serra.francois@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 <crespialba@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 <jhcepas@gmail.com>,
-> Copyright (C) 2011-2017 Fran=C3=A7ois Serra <serra.francois@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">&lt;<a href=3D"mailto:crespi=
-alba@gmail.com" target=3D"_blank">crespialba@gmail.com</a>&gt;</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 &lt;<a href=3D"mail=
-to:jhcepas@gmail.com" target=3D"_blank">jhcepas@gmail.com</a>&gt;,<br></div=
->Copyright (C) 2011-2017 Fran=C3=A7ois Serra &lt;<a href=3D"mailto:serra.fr=
-ancois@gmail.com" target=3D"_blank">serra.francois@gmail.com</a>&gt;<br><br=
-></div><div>(But I don&#39;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--
-

debian/changelog

-python-ete3 (3.0.0b35-1) unstable; urgency=medium
+python-ete3 (3.1.1+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release. (Closes: #861182)
 
- -- Alba Crespi <crespialba+debian@gmail.com>  Sat, 12 Aug 2017 19:28:33 +0000
-
+ -- Alba Crespi <crespialba+debian@gmail.com>  Mon, 29 Oct 2018 14:47:53 +0100

debian/compat

-9
+11

debian/control

@@ -2,22 +2,27 @@ Source: python-ete3
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Alba Crespi <crespialba+debian@gmail.com>
 Section: python
+Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                dh-python,
                python-all-dev,
                python-setuptools,
+               python-lxml,
+               python-numpy,
+               python-qt4,
+               python-scipy,
+               python-six,
                python3-all-dev,
                python3-setuptools,
-               python-qt4,
-               python3-pyqt4,
-               python-numpy,
                python3-numpy,
-               python-lxml,
-               python3-lxml
-Standards-Version: 4.0.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-ete3.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/python-ete3.git
+               python3-lxml,
+               python3-pyqt4,
+               python3-scipy,
+               python3-six
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/python-ete3
+Vcs-Git: https://salsa.debian.org/med-team/python-ete3.git
 Homepage: http://etetoolkit.org
 
 Package: python-ete3

debian/rules

 #! /usr/bin/make -f
 
-export PYBUILD_NAME=python-ete3
-export PYBUILD_DISABLE_python3=test
-export PYBUILD_DISABLE_python2=1
+export PYBUILD_NAME=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
+	dh $@ --with python2,python3 --buildsystem=pybuild
 

debian/upstream/metadata

@@ -4,3 +4,5 @@ Reference:
   Journal:  Mol Biol Evol 
   DOI: 10.1093/molbev/msw046
   Year: 2016
+  URL: https://academic.oup.com/mbe/article/33/6/1635/2579822
+  eprint: https://academic.oup.com/mbe/article-pdf/33/6/1635/7953632/msw046.pdf

debian/watch

-# 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)))
+version=4
+
+opts="uversionmangle=s/(rc|a|b|c)/~$1/,repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
+  https://pypi.org/simple/ete3 .*/ete3-@ANY_VERSION@@ARCHIVE_EXT@#sha256=.*

doc/_sources/tutorial/tutorial_adaptation.txt

@@ -314,6 +314,8 @@ The most usual comparison, and perhaps the most robust, is the comparison of mod
 
 Each sites model, contains a dictionary 'model.sites' in which are stored the results of CodeML. These are displayed through the histface, but they are still accessible by digging a bit. 'site' dictionary usually contains the result of the NEB and BEB analysis (prefer the BEB when available). For each of BEB and NEB, the probability of belonging from one category of site is summarized by 'p0', 'p1' and 'p2' in the case of M2 model that have only 3 class of sites (p0, the probability of belonging to the first class of sites with :math:`\omega < 1`; p1, the probability of belonging to the second class of sites with :math:`\omega = 1`; p2, the probability of belonging to the third class of sites with :math:`\omega > 1`). *For details on the models and outputs, it is recommended to read PAML documentation.*
 
+*Note that M1 and M2 models are making reference to the new versions of these models, with continuous omega rates (namely M1a and M2a in the PAML user guide).*
+
 
 Test on branches
 ------------------

doc/about.html

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@@ -190,7 +190,7 @@ Environment for Tree Exploration.</strong> <em>BMC Bioinformatics 2010, 11:24.</
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doc/changelog/changelog2.1.html

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@@ -321,7 +321,7 @@ it totally inefficient. Now, the same expression returns always <em>True</em></l
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@@ -343,7 +343,7 @@ it totally inefficient. Now, the same expression returns always <em>True</em></l
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doc/changelog/changelog2.2.html

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@@ -208,7 +208,7 @@ format</li>
 adaptation-test extension recently developed by François Serra (see
 <a class="reference internal" href="../tutorial/tutorial_adaptation.html"><em>Testing Evolutionary Hypothesis</em></a> in the tutorial).</p>
 <div class="figure">
-<a class="reference internal image-reference" href="../_images/M2_super_profesional.png"><img alt="../_images/M2_super_profesional.png" src="../_images/M2_super_profesional.png" style="width: 812.0px; height: 135.0px;" /></a>
+<a class="reference internal image-reference" href="../_images/M2_super_profesional.png"><img alt="../_images/M2_super_profesional.png" src="../_images/M2_super_profesional.png" /></a>
 </div>
 </li>
 </ul>
@@ -309,7 +309,7 @@ described in <a class="reference external" href="http://treeko.cgenomics.org">Tr
 <div class="admonition seealso">
 <p class="first admonition-title">See also</p>
 <div class="figure">
-<a class="reference internal image-reference" href="../_images/treeko_logo.png"><img alt="../_images/treeko_logo.png" src="../_images/treeko_logo.png" style="width: 55.3px; height: 58.1px;" /></a>
+<a class="reference internal image-reference" href="../_images/treeko_logo.png"><img alt="../_images/treeko_logo.png" src="../_images/treeko_logo.png" /></a>
 </div>
 <p><a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/21335609">TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.</a></p>
 <p>Marcet-Houben M, Gabaldón T.</p>
@@ -382,7 +382,7 @@ individual faces even when a global <code class="xref py py-attr docutils litera
 used.</p>
 <blockquote>
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+<a class="reference internal image-reference" href="../_images/rotated_faces.png"><img alt="../_images/rotated_faces.png" src="../_images/rotated_faces.png" /></a>
 </div>
 </div></blockquote>
 </li>
@@ -399,7 +399,7 @@ points. Gaps can also be taken into account and therefore shown as
 as a black space or a flat line.</p>
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+<a class="reference internal image-reference" href="../_images/seqmotif.png"><img alt="../_images/seqmotif.png" src="../_images/seqmotif.png" /></a>
 </div>
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 </li>
@@ -407,10 +407,10 @@ as a black space or a flat line.</p>
 for built-in representation of statistics attached to nodes.</p>
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+<a class="reference internal image-reference" href="../_images/float_piechart.png"><img alt="../_images/float_piechart.png" src="../_images/float_piechart.png" /></a>
 </div>
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+<a class="reference internal image-reference" href="../_images/barcharts.png"><img alt="../_images/barcharts.png" src="../_images/barcharts.png" /></a>
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 </li>
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doc/changelog/changelog2.3.html

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-  <dt><a href="reference/reference_treeview.html#ete3.SequenceFace.InteractiveLetterItem.hoverEnterEvent">hoverEnterEvent() (SequenceFace.InteractiveLetterItem method)</a>
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