...
 
Commits (4)
......@@ -22,19 +22,3 @@ nose*.egg
# .eggs directory
.eggs
# quilt
.pc/
.pybuild/
# Debian-generated files
debian/debhelper-build-stamp
debian/files
debian/python-bx.debhelper.log
debian/python-bx.substvars
debian/python-bx/
debian/python3-bx.debhelper.log
debian/python3-bx.substvars
debian/python3-bx/
debian/tmp/
......@@ -5,6 +5,7 @@ os:
## - osx
python:
- 2.7
- 3.3
addons:
apt:
packages:
......
......@@ -3,7 +3,7 @@ python-bx for Debian
The situation is somewhat unfortunate in that both python2 and python3 occupy the same location in /usr/bin. The -tools packages separate those binaries from the modules.
The language suffix ".py" was left for the time being, uncertain about reverse dependencies.
The language suffix ".py" was left for the time being for compatibility with the installation of the same on other distributions and wary of reverse dependencies.
--
Steffen Moeller <moeller@debian.org> Sat, 14 Jan 2017 10:43:03 +0100
python-bx (0.7.4-1) unstable; urgency=low
python-bx (0.8.1-1) unstable; urgency=low
* New upstream version.
* Initial release (Closes: #851242)
* Policy compliance with 4.1.4.
-- Steffen Moeller <moeller@debian.org> Mon, 11 Jun 2018 00:33:54 +0200
python-bx (0.7.4-1) unstable; urgency=low
* Added Michael and Steffen as uploaders
* Removing generated files from source tree in debian/copyright
* Added -tools packages to separate command line interface
......
......@@ -19,10 +19,10 @@ Build-Depends:
python3-nose,
python3-numpy,
cython3
Standards-Version: 3.9.8
Standards-Version: 4.1.4
Homepage: https://github.com/bxlab/bx-python
Vcs-Git: https://anonscm.debian.org/git/debian-med/python-bx.git
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-bx.git
Vcs-Git: https://salsa.debian.org/med-team/python-bx.git
Vcs-Browser: https://salsa.debian.org/med-team/python-bx
Package: python-bx
Architecture: any
......
This diff is collapsed.
......@@ -6,7 +6,7 @@ Index: python-bx/setup.py
===================================================================
--- python-bx.orig/setup.py
+++ python-bx/setup.py
@@ -7,8 +7,8 @@ if sys.version_info < (2, 4):
@@ -9,8 +9,8 @@ elif sys.version_info > (3, ) and sys.ve
try:
from setuptools import setup, find_packages
except ImportError:
......
https://bitbucket.org/james_taylor/python-lzo-static/get/63987d89fd1b.zip
numpy
six
This diff is collapsed.
......@@ -15,9 +15,9 @@ Contents
========
.. toctree::
:maxdepth: 2
:maxdepth: 5
modules/index.rst
Application Documentation <lib/modules>
Indices and tables
==================
......
bx.align.axt module
===================
.. automodule:: bx.align.axt
:members:
:undoc-members:
:show-inheritance:
bx.align.core module
====================
.. automodule:: bx.align.core
:members:
:undoc-members:
:show-inheritance:
bx.align.epo module
===================
.. automodule:: bx.align.epo
:members:
:undoc-members:
:show-inheritance:
bx.align.epo_tests module
=========================
.. automodule:: bx.align.epo_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.lav module
===================
.. automodule:: bx.align.lav
:members:
:undoc-members:
:show-inheritance:
bx.align.lav_tests module
=========================
.. automodule:: bx.align.lav_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.maf module
===================
.. automodule:: bx.align.maf
:members:
:undoc-members:
:show-inheritance:
bx.align.maf_tests module
=========================
.. automodule:: bx.align.maf_tests
:members:
:undoc-members:
:show-inheritance:
bx.align package
================
Subpackages
-----------
.. toctree::
bx.align.sitemask
bx.align.tools
Submodules
----------
.. toctree::
bx.align.axt
bx.align.core
bx.align.epo
bx.align.epo_tests
bx.align.lav
bx.align.lav_tests
bx.align.maf
bx.align.maf_tests
bx.align.score
bx.align.score_tests
Module contents
---------------
.. automodule:: bx.align
:members:
:undoc-members:
:show-inheritance:
bx.align.score module
=====================
.. automodule:: bx.align.score
:members:
:undoc-members:
:show-inheritance:
bx.align.score_tests module
===========================
.. automodule:: bx.align.score_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.core module
=============================
.. automodule:: bx.align.sitemask.core
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.cpg module
============================
.. automodule:: bx.align.sitemask.cpg
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.quality module
================================
.. automodule:: bx.align.sitemask.quality
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask package
=========================
Submodules
----------
.. toctree::
bx.align.sitemask.core
bx.align.sitemask.cpg
bx.align.sitemask.quality
bx.align.sitemask.sitemask_tests
Module contents
---------------
.. automodule:: bx.align.sitemask
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.sitemask_tests module
=======================================
.. automodule:: bx.align.sitemask.sitemask_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.tools.chop module
==========================
.. automodule:: bx.align.tools.chop
:members:
:undoc-members:
:show-inheritance:
bx.align.tools.fuse module
==========================
.. automodule:: bx.align.tools.fuse
:members:
:undoc-members:
:show-inheritance:
bx.align.tools package
======================
Submodules
----------
.. toctree::
bx.align.tools.chop
bx.align.tools.fuse
bx.align.tools.thread
bx.align.tools.tile
Module contents
---------------
.. automodule:: bx.align.tools
:members:
:undoc-members:
:show-inheritance:
bx.align.tools.thread module
============================
.. automodule:: bx.align.tools.thread
:members:
:undoc-members:
:show-inheritance:
bx.align.tools.tile module
==========================
.. automodule:: bx.align.tools.tile
:members:
:undoc-members:
:show-inheritance:
bx.arrays.array_tree module
===========================
.. automodule:: bx.arrays.array_tree
:members:
:undoc-members:
:show-inheritance:
bx.arrays.array_tree_tests module
=================================
.. automodule:: bx.arrays.array_tree_tests
:members:
:undoc-members:
:show-inheritance:
bx.arrays.bed module
====================
.. automodule:: bx.arrays.bed
:members:
:undoc-members:
:show-inheritance:
bx.arrays package
=================
Submodules
----------
.. toctree::
bx.arrays.array_tree
bx.arrays.array_tree_tests
bx.arrays.bed
bx.arrays.wiggle
Module contents
---------------
.. automodule:: bx.arrays
:members:
:undoc-members:
:show-inheritance:
bx.arrays.wiggle module
=======================
.. automodule:: bx.arrays.wiggle
:members:
:undoc-members:
:show-inheritance:
bx.bbi.bbi_file module
======================
.. automodule:: bx.bbi.bbi_file
:members:
:undoc-members:
:show-inheritance:
bx.bbi.bigbed_file module
=========================
.. automodule:: bx.bbi.bigbed_file
:members:
:undoc-members:
:show-inheritance:
bx.bbi.bigwig_file module
=========================
.. automodule:: bx.bbi.bigwig_file
:members:
:undoc-members:
:show-inheritance:
bx.bbi.bigwig_tests module
==========================
.. automodule:: bx.bbi.bigwig_tests
:members:
:undoc-members:
:show-inheritance:
bx.bbi.bpt_file module
======================
.. automodule:: bx.bbi.bpt_file
:members:
:undoc-members:
:show-inheritance:
bx.bbi.cirtree_file module
==========================
.. automodule:: bx.bbi.cirtree_file
:members:
:undoc-members:
:show-inheritance:
bx.bbi package
==============
Submodules
----------
.. toctree::
bx.bbi.bbi_file
bx.bbi.bigbed_file
bx.bbi.bigwig_file
bx.bbi.bigwig_tests
bx.bbi.bpt_file
bx.bbi.cirtree_file
Module contents
---------------
.. automodule:: bx.bbi
:members:
:undoc-members:
:show-inheritance:
bx.binned_array module
======================
.. automodule:: bx.binned_array
:members:
:undoc-members:
:show-inheritance:
bx.binned_array_tests module
============================
.. automodule:: bx.binned_array_tests
:members:
:undoc-members:
:show-inheritance:
bx.bitset module
================
.. automodule:: bx.bitset
:members:
:undoc-members:
:show-inheritance:
bx.bitset_builders module
=========================
.. automodule:: bx.bitset_builders
:members:
:undoc-members:
:show-inheritance:
bx.bitset_tests module
======================
.. automodule:: bx.bitset_tests
:members:
:undoc-members:
:show-inheritance:
bx.bitset_utils module
======================
.. automodule:: bx.bitset_utils
:members:
:undoc-members:
:show-inheritance:
bx.cookbook.argparse module
===========================
.. automodule:: bx.cookbook.argparse
:members:
:undoc-members:
:show-inheritance:
bx.cookbook.attribute module
============================
.. automodule:: bx.cookbook.attribute
:members:
:undoc-members:
:show-inheritance:
bx.cookbook.doc_optparse module
===============================
.. automodule:: bx.cookbook.doc_optparse
:members:
:undoc-members:
:show-inheritance:
bx.cookbook.progress_bar module
===============================
.. automodule:: bx.cookbook.progress_bar
:members:
:undoc-members:
:show-inheritance:
bx.cookbook package
===================
Submodules
----------
.. toctree::
bx.cookbook.argparse
bx.cookbook.attribute
bx.cookbook.doc_optparse
bx.cookbook.progress_bar
Module contents
---------------
.. automodule:: bx.cookbook
:members:
:undoc-members:
:show-inheritance:
bx.filter module
================
.. automodule:: bx.filter
:members:
:undoc-members:
:show-inheritance:
bx.gene_reader module
=====================
.. automodule:: bx.gene_reader
:members:
:undoc-members:
:show-inheritance:
bx.interval_index_file module
=============================
.. automodule:: bx.interval_index_file
:members:
:undoc-members:
:show-inheritance:
bx.interval_index_file_tests module
===================================
.. automodule:: bx.interval_index_file_tests
:members:
:undoc-members:
:show-inheritance:
bx.intervals.cluster module
===========================
.. automodule:: bx.intervals.cluster
:members:
:undoc-members:
:show-inheritance:
bx.intervals.cluster_tests module
=================================
.. automodule:: bx.intervals.cluster_tests
:members:
:undoc-members:
:show-inheritance:
bx.intervals.intersection module
================================
.. automodule:: bx.intervals.intersection
:members:
:undoc-members:
:show-inheritance:
bx.intervals.intersection_tests module
======================================
.. automodule:: bx.intervals.intersection_tests
:members:
:undoc-members:
:show-inheritance:
bx.intervals.io module
======================
.. automodule:: bx.intervals.io
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.base_coverage module
============================================
.. automodule:: bx.intervals.operations.base_coverage
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.complement module
=========================================
.. automodule:: bx.intervals.operations.complement
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.concat module
=====================================
.. automodule:: bx.intervals.operations.concat
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.coverage module
=======================================
.. automodule:: bx.intervals.operations.coverage
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.find_clusters module
============================================
.. automodule:: bx.intervals.operations.find_clusters
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.intersect module
========================================
.. automodule:: bx.intervals.operations.intersect
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.join module
===================================
.. automodule:: bx.intervals.operations.join
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.merge module
====================================
.. automodule:: bx.intervals.operations.merge
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.quicksect module
========================================
.. automodule:: bx.intervals.operations.quicksect
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations package
===============================
Submodules
----------
.. toctree::
bx.intervals.operations.base_coverage
bx.intervals.operations.complement
bx.intervals.operations.concat
bx.intervals.operations.coverage
bx.intervals.operations.find_clusters
bx.intervals.operations.intersect
bx.intervals.operations.join
bx.intervals.operations.merge
bx.intervals.operations.quicksect
bx.intervals.operations.subtract
Module contents
---------------
.. automodule:: bx.intervals.operations
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.subtract module
=======================================
.. automodule:: bx.intervals.operations.subtract
:members:
:undoc-members:
:show-inheritance:
bx.intervals.random_intervals module
====================================
.. automodule:: bx.intervals.random_intervals
:members:
:undoc-members:
:show-inheritance:
bx.intervals package
====================
Subpackages
-----------
.. toctree::
bx.intervals.operations
Submodules
----------
.. toctree::
bx.intervals.cluster
bx.intervals.cluster_tests
bx.intervals.intersection
bx.intervals.intersection_tests
bx.intervals.io
bx.intervals.random_intervals
Module contents
---------------
.. automodule:: bx.intervals
:members:
:undoc-members:
:show-inheritance:
bx.intseq.ngramcount module
===========================
.. automodule:: bx.intseq.ngramcount
:members:
:undoc-members:
:show-inheritance:
bx.intseq package
=================
Submodules
----------
.. toctree::
bx.intseq.ngramcount
Module contents
---------------
.. automodule:: bx.intseq
:members:
:undoc-members:
:show-inheritance:
bx.misc.bgzf module
===================
.. automodule:: bx.misc.bgzf
:members:
:undoc-members:
:show-inheritance:
bx.misc.bgzf_tests module
=========================
.. automodule:: bx.misc.bgzf_tests
:members:
:undoc-members:
:show-inheritance:
bx.misc.binary_file module
==========================
.. automodule:: bx.misc.binary_file
:members:
:undoc-members:
:show-inheritance:
bx.misc.cdb module
==================
.. automodule:: bx.misc.cdb
:members:
:undoc-members:
:show-inheritance:
bx.misc.cdb_tests module
========================
.. automodule:: bx.misc.cdb_tests
:members:
:undoc-members:
:show-inheritance:
bx.misc.filecache module
========================
.. automodule:: bx.misc.filecache
:members:
:undoc-members:
:show-inheritance:
bx.misc.filecache_tests module
==============================
.. automodule:: bx.misc.filecache_tests
:members:
:undoc-members:
:show-inheritance:
bx.misc.readlengths module
==========================
.. automodule:: bx.misc.readlengths
:members:
:undoc-members:
:show-inheritance:
bx.misc package
===============
Submodules
----------
.. toctree::
bx.misc.bgzf
bx.misc.bgzf_tests
bx.misc.binary_file
bx.misc.cdb
bx.misc.cdb_tests
bx.misc.filecache
bx.misc.filecache_tests
bx.misc.readlengths
bx.misc.seekbzip2
bx.misc.seekbzip2_tests
bx.misc.seeklzop
bx.misc.seeklzop_tests
Module contents
---------------
.. automodule:: bx.misc
:members:
:undoc-members:
:show-inheritance:
bx.misc.seekbzip2 module
========================
.. automodule:: bx.misc.seekbzip2
:members:
:undoc-members:
:show-inheritance:
bx.misc.seekbzip2_tests module
==============================
.. automodule:: bx.misc.seekbzip2_tests
:members:
:undoc-members:
:show-inheritance:
bx.misc.seeklzop module
=======================
.. automodule:: bx.misc.seeklzop
:members:
:undoc-members:
:show-inheritance:
bx.misc.seeklzop_tests module
=============================
.. automodule:: bx.misc.seeklzop_tests
:members:
:undoc-members:
:show-inheritance:
bx.motif.io package
===================
Submodules
----------
.. toctree::
bx.motif.io.transfac
bx.motif.io.transfac_tests
Module contents
---------------
.. automodule:: bx.motif.io
:members:
:undoc-members:
:show-inheritance:
bx.motif.io.transfac module
===========================
.. automodule:: bx.motif.io.transfac
:members:
:undoc-members:
:show-inheritance:
bx.motif.io.transfac_tests module
=================================
.. automodule:: bx.motif.io.transfac_tests
:members:
:undoc-members:
:show-inheritance:
bx.motif.logo package
=====================
Module contents
---------------
.. automodule:: bx.motif.logo
:members:
:undoc-members:
:show-inheritance:
bx.motif.pwm module
===================
.. automodule:: bx.motif.pwm
:members:
:undoc-members:
:show-inheritance:
bx.motif.pwm_tests module
=========================
.. automodule:: bx.motif.pwm_tests
:members:
:undoc-members:
:show-inheritance:
bx.motif package
================
Subpackages
-----------
.. toctree::
bx.motif.io
bx.motif.logo
Submodules
----------
.. toctree::
bx.motif.pwm
bx.motif.pwm_tests
Module contents
---------------
.. automodule:: bx.motif
:members:
:undoc-members:
:show-inheritance:
bx.phylo.newick module
======================
.. automodule:: bx.phylo.newick
:members:
:undoc-members:
:show-inheritance:
bx.phylo.newick_tests module
============================
.. automodule:: bx.phylo.newick_tests
:members:
:undoc-members:
:show-inheritance:
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