add iqtree to the tests

CONTRIBUTING.rst

@@ -1,51 +1,37 @@
 Contributing to ETE
 ===================
 
-Development status
-------------------
+Pull requests and development workflow
+-----------------------------------------
 
-Current stable version is ETE v2.3, which supports Python 2 only. Source code is in
-the following branch: https://github.com/jhcepas/ete/tree/2.3
+Official versioned releases are done via conda and pypi. However, the master
+branch at GitHub is also expected to stable and receives more frequent additions
+and fixes.
 
-ETE v3.0 is the development branch and should support Python 2.7 and Python
-3.4. Although it is mostly functional, this version is currently under active
-development. Problems are still expected. The module name for ETE v3.0 has
-changed form "ete2" to "ete3". Both versions (ETE v2.3 and ETE v3.0) can co-exist.
+All development should occur in feature specific git branches or forks from
+master. Pull requests to master are merged after reviewing changes and
+confirming that all tests are passed.
 
-BUGs and Feature Request
-------------------------
-
-The preferred way to report a problem or request/disccuss new features is by
-opening a new issue at http://github.com/jhcepas/ete/issues.  (Please, make sure
-there is no other issues pointing to the same topic)
+If you start working on a new feature or a fix, consider letting others know
+(i.e. opening a updating GitHub issues).
 
 
-Pull Requests (either code or documentation)
---------------------------------------------
+Bugs and Feature Requests
+---------------------------
 
-Contributions to the main code, unit-tests and documentation are very
-welcome. ETE's main source code is hosted at http://github.com/jhcepas/ete.
-There are currently 2 active branches:
-
-- "2.3" is the latest stable. Only bug fixes are accepted.
-- "master" is the development branch, focused on the upcoming version
-  3.0. Bug fixes, new features, tests and documentation are accepted and highly
-  appreciated.
-
-**contact info**
+The preferred way to report a problem or request/disccuss new features is by
+opening a new issue at http://github.com/jhcepas/ete/issues. (Please check for
+duplicate reports).
 
-- There is no mailing list for developers, but you can open a new github issue for
-  discussion or send an email directly to jhcepas [at] gmail.com.
-
-- There is also chat room for developers:
+  There is also chat room for developers:
 
 .. image:: https://badges.gitter.im/Join%20Chat.svg
    :alt: Join the chat at https://gitter.im/jhcepas/ete
    :target: https://gitter.im/jhcepas/ete?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge 
 
 
-Running tests (development version)
------------------------------------
+Running tests
+---------------------------------
 
 In order to run the tests, first clone ete::
 

README.rst

@@ -10,10 +10,11 @@
 
 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
@@ -31,7 +32,8 @@ 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
 --------------------

ete3/test/test_ete_build/test_genetree.py

@@ -19,14 +19,14 @@ def get_out_files(outdir, workflow, fasta):
     alg_trimmed = "%s/%s/%s.final_tree.fa" %(outdir, workflow, fasta)
     img = "%s/%s/%s.final_tree.png" %(outdir, workflow, fasta)
     cmd = "%s/%s/commands.log" %(outdir, workflow)
-    return clean_tree, extended_tree, alg_used, alg, alg_trimmed, img, cmd    
-    
+    return clean_tree, extended_tree, alg_used, alg, alg_trimmed, img, cmd
+
 class Test_ete_build_genetree(unittest.TestCase):
-    def test_01_aa_genetree_worflow(self):        
+    def test_01_aa_genetree_worflow(self):
         aligners = "muscle_default", "clustalo_default", "mafft_default"
         trimmers = "none", "trimal01"
         testers = "none", "pmodeltest_full_fast"
-        builders = "phyml_default", "raxml_default", "fasttree_default"
+        builders = "phyml_default", "raxml_default", "fasttree_default", "iqtree_default"
         for _aligner in aligners:
             for _trimmer in trimmers:
                 for _tester in testers:

utils/FILE_HEADER.txt

@@ -21,16 +21,16 @@
 #                     ABOUT THE ETE PACKAGE
 #                     =====================
 #
-# ETE is distributed under the GPL copyleft license (2008-2016).
+# ETE is distributed under the GPL copyleft license (2008-2017)
 #
 # If you make use of ETE in 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
 #
-# Note that extra references to the specific methods implemented in
-# the toolkit may be available in the documentation.
+# Additional references to third-party methods and software used by ETE can be
+# found in the documentation.
 #
 # More info at http://etetoolkit.org. Contact: [email protected]
 #

utils/conda_build/meta.yaml.template

@@ -50,4 +50,5 @@ test:
 about:
   home: http://etetoolkit.org
   license: GPL
-  summary: "A Framework for reconstructing, analysing and visualizing phylogenetic trees and multiple sequence alignments. Includes the Python API and Phylogenomic tools"
+  summary: "A Python framework for reconstructing, analysing and visualizing phylogenetic trees and multiple sequence alignments. Includes Python API and Phylogenomic tools"
+