[med-svn] [pbsuite] 03/11: Remove dependency on python-intervaltree-bio

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository pbsuite.

commit c25b41a78617d45377d0c5aca824da1f2913c9ef
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Mon Feb 8 19:26:58 2016 -0800

    Remove dependency on python-intervaltree-bio
    
    That package depends on python-intervaltree, which is currently
    held up by incompatibility with Python 3.5.
---
 debian/control                                  |  1 -
 debian/patches/rm-intervaltree-dependency.patch | 39 +++++++++++++++++++++++++
 debian/patches/series                           |  1 +
 3 files changed, 40 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 260cc1e..2c07496 100644
--- a/debian/control
+++ b/debian/control
@@ -64,7 +64,6 @@ Depends:
 	${python:Depends},
 	python-pbsuite-utils (= ${source:Version}),
 	python-pbbanana (= ${source:Version}),
-	python-intervaltree-bio,
 	python-pysam (>= 0.8.0),
 	python-networkx,
 	python-h5py (>= 2.0.1),
diff --git a/debian/patches/rm-intervaltree-dependency.patch b/debian/patches/rm-intervaltree-dependency.patch
new file mode 100644
index 0000000..4d2b43d
--- /dev/null
+++ b/debian/patches/rm-intervaltree-dependency.patch
@@ -0,0 +1,39 @@
+Description: Disable ComplexResolver while intervaltree-bio isn't yet in Debian
+ See ITP #807803. It's currently held up by Python3.5 incompatibility in
+ its dependency python-intervaltree.
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2016-02-08
+--- pbsuite.orig/pbsuite/honey/__init__.py
++++ pbsuite/pbsuite/honey/__init__.py
+@@ -1 +1 @@
+-__all__ = ["bampie", "Honey", "TGraf", "HSpots", "Force", "ComplexResolver", "massivePhrap"]
++__all__ = ["bampie", "Honey", "TGraf", "HSpots", "Force", "massivePhrap"]
+--- pbsuite.orig/pbsuite/honey/Honey.py
++++ pbsuite/pbsuite/honey/Honey.py
+@@ -2,15 +2,14 @@
+ 
+ import argparse, sys
+ from pbsuite.utils.setupLogging import *
+-from pbsuite.honey import bampie, TGraf, HSpots, Force, ComplexResolver, \
++from pbsuite.honey import bampie, TGraf, HSpots, Force, \
+                          massivePhrap
+ 
+ STAGES = {"pie":   bampie.run, \
+           "tails": TGraf.run, \
+           "spots": HSpots.run, \
+           "force": Force.run , \
+-          "asm":  massivePhrap.run, \
+-          "cpxres": ComplexResolver.run}
++          "asm":  massivePhrap.run}
+ 
+ USAGE = """\
+    Honey - genomic variant calling with long sequencing reads
+@@ -21,7 +20,6 @@
+      spots      Find genomic variants within reads' spans.
+      force      Given a BedFile of predicted variants, force search for matching
+      asm        Assemble reads around a variant and remap contigs to a reference
+-     cpxres     Complex multi-break-point resolution (beta)
+     
+    See HoneyReadme.txt for documentation or --help for details\
+ """
diff --git a/debian/patches/series b/debian/patches/series
index 93f72fe..330b576 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 fix-syntax-error.patch
 intervaltree-import-statement.patch
+rm-intervaltree-dependency.patch

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