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base repository: biocore/burrito
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base: 0.9.1
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head repository: biocore/burrito
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compare: master
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  • 5 commits
  • 4 files changed
  • 3 contributors

Commits on May 22, 2015

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    583391c View commit details
  2. Merge pull request #12 from biocore/091-dev

    REL: updated to 0.9.1-dev
    jairideout committed May 22, 2015
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    aa40fd4 View commit details

Commits on Oct 13, 2015

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    e49b322 View commit details
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Commits on Mar 15, 2016

  1. Merge pull request #14 from RNAer/master

    Close files when raising ApplicationError
    gregcaporaso committed Mar 15, 2016
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    3b1dcc5 View commit details
Showing with 10 additions and 7 deletions.
  1. +2 −0 CHANGELOG.md
  2. +1 −1 burrito/__init__.py
  3. +6 −5 burrito/util.py
  4. +1 −1 setup.py
2 changes: 2 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
# burrito changelog

## Version 0.9.1-dev (changes since 0.9.1 go here)

## Version 0.9.1 (2015-05-22)

* Updated default temporary directory from ``/tmp`` to python's ``tempfile.gettempdir()``. This should address many of the issues with temporary files being written to ``/tmp``, which sometimes doesn't exist, doesn't provide a lot of storage, or is not shared across cluster nodes. It is still possible that individual burrito fillings (i.e., ``CommandLineApplication`` derived classes) can hard code ``/tmp``, so care should be taken when writing those derived classes to avoid that.
2 changes: 1 addition & 1 deletion burrito/__init__.py
Original file line number Diff line number Diff line change
@@ -6,4 +6,4 @@
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------

__version__ = "0.9.1"
__version__ = "0.9.1-dev"
11 changes: 6 additions & 5 deletions burrito/util.py
Original file line number Diff line number Diff line change
@@ -278,11 +278,12 @@ def __call__(self, data=None, remove_tmp=True):
# Determine if error should be raised due to exit status of
# appliciation
if not self._accept_exit_status(exit_status):
raise ApplicationError('Unacceptable application exit ' +
'status: %s\n' % str(exit_status) +
'Command:\n%s\n' % command +
'StdOut:\n%s\n' % open(outfile).read() +
'StdErr:\n%s\n' % open(errfile).read())
with open(outfile) as out, open(errfile) as err:
raise ApplicationError('Unacceptable application exit ' +
'status: %s\n' % str(exit_status) +
'Command:\n%s\n' % command +
'StdOut:\n%s\n' % out.read() +
'StdErr:\n%s\n' % err.read())

# open the stdout and stderr if not being suppressed
out = None
2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
@@ -10,7 +10,7 @@

from setuptools import find_packages, setup

__version__ = "0.9.1"
__version__ = "0.9.1-dev"

classes = """
Development Status :: 5 - Production/Stable