Changeset 1143:1a3ef9702843
- Timestamp:
- 04/01/08 21:08:04
(9 months ago)
- Author:
- Nate Coraor <nate@bx.psu.edu>
- branch:
- default
- convert_revision:
- svn:9bcadc22-80f8-0310-8a53-c8f022958886/galaxy/trunk@2502
- Message:
Updates for Python 2.5 compatibility.
phastOdds was using numarray, test passes with numpy. Not really a
requirement for py2.5, but it was the only tool not using numpy.
cElementTree is part of the standard distribution in py2.5, updated
megablast xml parser accordingly.
Need simplejson > 1.4 for py2.5 - all tests pass w/ 1.5.
The only showstopper now is Cheetah...
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Files:
-
Legend:
- Unmodified
- Added
- Removed
- Modified
- Copied
- Moved
| r1132 |
r1143 |
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| 33 | 33 | PasteScript = 1.3.6 http://cheeseshop.python.org/packages/source/P/PasteScript/PasteScript-1.3.6.tar.gz |
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| 34 | 34 | Routes = 1.6.3 http://pypi.python.org/packages/source/R/Routes/Routes-1.6.3.tar.gz |
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| 35 | | simplejson = 1.4 http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.4.tar.gz |
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| | 35 | simplejson = 1.5 http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.tar.gz |
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| 36 | 36 | SQLAlchemy = 0.3.11 http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.3.11.tar.gz |
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| 37 | 37 | Tempita = 0.1 http://pypi.python.org/packages/source/T/Tempita/Tempita-0.1.tar.gz |
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| r1125 |
r1143 |
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| 5 | 5 | |
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| 6 | 6 | pyver=`$GALAXY_PYTHON -c 'import sys; print sys.version[:3]'` |
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| 7 | | export PYTHONPATH=$PYTHONPATH:eggs/py$pyver-noplatform/NoseHTML-0.2-py$pyver.egg |
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| | 7 | PYTHONPATH=$PYTHONPATH:eggs/py$pyver-noplatform/NoseHTML-0.2-py$pyver.egg |
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| | 8 | export PYTHONPATH |
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| 8 | 9 | |
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| 9 | 10 | $GALAXY_PYTHON ./scripts/nosetests.py $@ |
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| r1129 |
r1143 |
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| 9 | 9 | |
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| 10 | 10 | import sys |
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| 11 | | from numarray import * |
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| 12 | | from numarray.ieeespecial import * |
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| | 11 | from numpy import * |
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| 13 | 12 | from tables import * |
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| 14 | 13 | |
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| … | … | |
| 17 | 16 | |
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| 18 | 17 | from bx import intervals |
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| | 18 | |
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| | 19 | # ignore wanrnings about NumArray flavor |
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| | 20 | from warnings import filterwarnings |
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| | 21 | from tables.exceptions import FlavorWarning |
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| | 22 | filterwarnings("ignore", category=FlavorWarning) |
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| 19 | 23 | |
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| 20 | 24 | assert sys.version_info[:2] >= ( 2, 4 ) |
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| r1107 |
r1143 |
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| 1 | 1 | #! /usr/bin/python |
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| 2 | 2 | |
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| 3 | | import cElementTree |
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| 4 | 3 | import sys, os |
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| | 4 | if float( sys.version[:3] ) >= 2.5: |
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| | 5 | import xml.etree.cElementTree as cElementTree |
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| | 6 | else: |
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| | 7 | import cElementTree |
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| 5 | 8 | |
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| 6 | 9 | def parse_megablast_xml_output(infile_name,outfile_name): |
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Galaxy