[med-svn] [python-treetime] 05/06: Install example scripts and data into separate package

[Andreas Tille]

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tille pushed a commit to branch master
in repository python-treetime.

commit 174e0376a143c102781d7c8e1b270b2591a929b8
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jun 15 09:58:30 2017 +0200

    Install example scripts and data into separate package
---
 debian/control                              | 43 ++++++++++++++++++++++++++++-
 debian/patches/fix_test.patch               | 11 ++++++++
 debian/python-treetime-examples.install     |  2 ++
 debian/{install => python-treetime.install} |  0
 4 files changed, 55 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 149c647..641b215 100644
--- a/debian/control
+++ b/debian/control
@@ -12,7 +12,7 @@ Vcs-Git: https://anonscm.debian.org/git/debian-med/treetime.git
 Homepage: https://github.com/neherlab/treetime
 
 Package: python-treetime
-Architecture: any
+Architecture: all
 Section: python
 Depends: ${python:Depends},
          ${misc:Depends},
@@ -48,3 +48,44 @@ Description: inference of time stamped phylogenies and ancestral reconstruction
   * inference of GTR models
   * rerooting to obtain best root-to-tip regression
   * auto-correlated relaxed molecular clock (with normal prior)
+
+Package: python-treetime-examples
+Architecture: all
+Section: python
+Depends: ${python:Depends},
+         ${misc:Depends},
+         python-numpy,
+         python-scipy,
+         python-biopython,
+         python-pandas
+Description: inference of time stamped phylogenies and ancestral reconstruction (example)
+ TreeTime provides routines for ancestral sequence reconstruction and the
+ maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree
+ where all branches are scaled such that the locations of terminal nodes
+ correspond to their sampling times and internal nodes are placed at the
+ most likely time of divergence.
+ .
+ TreeTime aims at striking a compromise between sophisticated
+ probabilistic models of evolution and fast heuristics. It implements GTR
+ models of ancestral inference and branch length optimization, but takes
+ the tree topology as given. To optimize the likelihood of time-scaled
+ phylogenies, treetime uses an iterative approach that first infers
+ ancestral sequences given the branch length of the tree, then optimizes
+ the positions of unconstraine d nodes on the time axis, and then repeats
+ this cycle. The only topology optimization are (optional) resolution of
+ polytomies in a way that is most (approximately) consistent with the
+ sampling time constraints on the tree. The package is designed to be
+ used as a stand-alone tool or as a library used in larger phylogenetic
+ analysis workflows.
+ .
+ Features
+  * ancestral sequence reconstruction (marginal and joint maximum
+    likelihood)
+  * molecular clock tree inference (marginal and joint maximum
+    likelihood)
+  * inference of GTR models
+  * rerooting to obtain best root-to-tip regression
+  * auto-correlated relaxed molecular clock (with normal prior)
+ .
+ This package contains example scripts and data to test the usage of
+ treetime.
diff --git a/debian/patches/fix_test.patch b/debian/patches/fix_test.patch
index 926d1b3..7937489 100644
--- a/debian/patches/fix_test.patch
+++ b/debian/patches/fix_test.patch
@@ -22,3 +22,14 @@ Description: No idea how this test is run - but at least fix syntax issues
  
  
  
+--- a/test/tree_time_test.py
++++ b/test/tree_time_test.py
+@@ -5,7 +5,7 @@ Test time tree class
+ import unittest,os,sys
+ from Bio import AlignIO
+ 
+-from ..treetime import treeanc
++from treetime import treeanc
+ 
+ resources_dir = os.path.join(path.dirname(__file__), '../data/')
+ 
diff --git a/debian/python-treetime-examples.install b/debian/python-treetime-examples.install
new file mode 100644
index 0000000..7c2712c
--- /dev/null
+++ b/debian/python-treetime-examples.install
@@ -0,0 +1,2 @@
+data	usr/share/doc/python-treetime
+test	usr/share/doc/python-treetime
diff --git a/debian/install b/debian/python-treetime.install
similarity index 100%
rename from debian/install
rename to debian/python-treetime.install

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