Merge pull request #48 from pygridtools/master

Release 0.7.7

.travis.yml

@@ -3,22 +3,36 @@ python:
   - 2.6
   - 2.7
   - 3.3
+  - 3.4
+  - 3.5
+  - 3.6
+  - 3.6-dev
+
+sudo: required
+
+addons:
+  hostname: drmaa.travis-ci.org
+  hosts:
+    - localhost
+    - localhost.localdomain
+    - drmaa.travis-ci.org
+
 
 notifications:
   email: false
 
+cache: pip
+
 # Install stuff
-virtualenv:
-  system_site_packages: true
 before_install:
   - travis/install_sge.sh
-  - export GRID_MAP_REDIS_PORT=12345
   - export SGE_ROOT=/var/lib/gridengine
   - export SGE_CELL=default
   - export DRMAA_LIBRARY_PATH=/usr/lib/libdrmaa.so.1.0
+  - pip install --upgrade pip
 install:
-  - pip install python-coveralls --use-mirrors
-  - pip install nose-cov --use-mirrors
+  - pip install python-coveralls
+  - pip install nose-cov
   - python setup.py install
 
 # Run test

README.rst

@@ -1,90 +1,80 @@
 DRMAA Python
 ------------
 
-.. image:: https://travis-ci.org/drmaa-python/drmaa-python.png
-   :target: https://travis-ci.org/drmaa-python/drmaa-python
-   :alt: Travis build status
+.. image:: https://img.shields.io/travis/pygridtools/drmaa-python/stable.svg
+   :alt: Build status
+   :target: https://travis-ci.org/pygridtools/drmaa-python
 
-.. image:: https://coveralls.io/repos/drmaa-python/drmaa-python/badge.png
-  :target: https://coveralls.io/r/drmaa-python/drmaa-python
-  :alt: Test coverage
+.. image:: https://img.shields.io/coveralls/pygridtools/drmaa-python/stable.svg
+    :target: https://coveralls.io/r/pygridtools/drmaa-python
 
-.. image:: https://pypip.in/d/drmaa/badge.png
-   :target: https://crate.io/packages/drmaa
+.. image:: https://img.shields.io/pypi/dm/drmaa.svg
+   :target: https://warehouse.python.org/project/drmaa/
    :alt: PyPI downloads
 
-.. image:: https://pypip.in/v/drmaa/badge.png
-   :target: https://crate.io/packages/drmaa
+.. image:: https://img.shields.io/pypi/v/drmaa.svg
+   :target: https://warehouse.python.org/project/drmaa/
    :alt: Latest version on PyPI
 
-.. image:: https://d2weczhvl823v0.cloudfront.net/drmaa-python/drmaa-python/trend.png
-   :alt: Bitdeli badge
-   :target: https://bitdeli.com/free
+.. image:: https://img.shields.io/pypi/l/drmaa.svg
+   :alt: License
 
 `Distributed Resource Management Application API <http://en.wikipedia.org/wiki/DRMAA>`__
 (DRMAA) bindings for Python. For more information
-`read the docs <http://drmaa-python.readthedocs.org>`__.
+`read the docs <http://drmaa-python.readthedocs.org>`__.  
+
+If you simply want to run Python functions on a DRMAA-compatible grid, use
+`GridMap <https://github.com/pygridtools/gridmap>`__.
 
 Requirements
 ~~~~~~~~~~~~
 
 -  Python 2.6+
 -  A DRMAA-compatible cluster (e.g., Grid Engine)
 
-License
-~~~~~~~
+Installation
+~~~~~~~~~~~~
 
--  BSD (3 Clause)
+To use the DRMAA Python library, you need to install it via ``pip``:
 
-Changelog
-~~~~~~~~~
 
--  v0.7.6
+.. code-block:: bash
 
-   -  Fix a typo in ``DictAttribute`` that was causing a crash.
+   pip install drmaa
 
--  v0.7.5
 
-   -  Fix an issue where dictionary attributes (like ``jtEnvironment``) could
-      encounter ``UnicodeDecodeError``s upon assignment.
+and then setup any environment variables that are necessary for your particular DRM system.
+For SGE, this means ``SGE_ROOT`` and ``SGE_CELL``, which should be set as follows:
 
--  v0.7.4
-   
-   -  Switch to using preferred encoding from ``locale`` module for converting 
-      strings to binary. This should prevent some lingering ``UnicodeEncodeError`` 
-      crashes on Python 2.7.
 
--  v0.7.3
+.. code-block:: bash
    
-   -  Fix a couple crashes when certain functions that expect ``str`` were passed 
-      integers.
+   export SGE_ROOT=/path/to/gridengine
+   export SGE_CELL=default
 
--  v0.7.2
-
-   -  Fix a couple inconsistencies with ``str`` vs ``bytes`` in Python 3 in 
-      ``drmaa.session``.
-
--  v0.7.1
-
-   -  Add `Read The Docs documentation <http://drmaa-python.readthedocs.org>`__
-   -  Add ``const`` module identifiers back into package namespace
-   -  Remove ``b`` prefixes from strings inserted into error messages.
-
--  v0.7.0
-
-   -  String attribute issues with Python 3 have all been resolved, and now each
-      function that takes a string can handle unicode strings, and returns
-      unicode strings.
-   -  All code has been updated to use future imports for ``unicode_literals``
-      and ``print_function``, so we're effectively writing Python 3 code now.
-   -  PEP8 compliance changes all over the place, except those that would break
-      names required by underlying C DRMAA library.
-   -  Now automatically run unit tests of Travis-CI with SGE, and all tests pass
-      for Python 2.6, 2.7, and 3.3.  SGE is installed using scripts I describe
-      in `this gist <https://gist.github.com/dan-blanchard/6586533>`__.
-   -  Unit tests are now in a top-level directory instead of a sub-directory
-      under the drmaa package.
-   -  There is now a `session.py` module that contains most of the code that was
-      in ``__init__.py`` before, and ``__init__`` just imports things and sets
-      ``__all__`` and ``__version__``, as is typically recommended now.
-   -  Drops support for Python 2.5.
+
+where ``/path/to/gridengine/`` is replaced with the actual path to your Grid Engine installation, 
+and ``default`` is replaced with your installation's actual cell. The path is typically 
+``/var/lib/gridengine``.
+
+You will also need access to the ``libdrmaa.so.1.0`` C library, which can often be installed as
+part of the ``libdrmaa-dev`` package on most Unixes. Once you have installed that, you may need to 
+tell DRMAA Python where it is installed by setting the ``DRMAA_LIBRARY_PATH`` environment variable,
+if it is not installed in a location that Python usually looks for libraries.
+
+
+.. code-block:: bash
+
+   export DRMAA_LIBRARY_PATH=/usr/lib/libdrmaa.so.1.0
+
+Acknowledgments
+~~~~~~~~~~~~~~~
+
+Thank you to `StatPro <http://www.statpro.com/>`__ and 
+`Educational Testing Service <https://github.com/EducationalTestingService>`__ for
+funding the development of DRMAA Python.
+
+Changelog
+~~~~~~~~~
+
+`See GitHub releases <https://github.com/drmaa-python/drmaa-python/releases>`__.

drmaa/helpers.py

@@ -231,11 +231,15 @@ def attributes_iterator(attributes):
 
 def adapt_rusage(rusage):
     """
-    transform a rusage data structure into a dict
+    Transform a rusage data structure into a dict.
+
+    Due to the value possibly containing a equal sign make sure we
+    limit the splits to only the first occurrence.
     """
     rv = dict()
     for attr in attributes_iterator(rusage.contents):
-        k, v = attr.split('=')
+
+        k, v = attr.split('=',1)
         rv[k] = v
     return rv
 

drmaa/session.py

@@ -477,11 +477,13 @@ def wait(jobId, timeout=-1):
         signaled = c_int()
         c(drmaa_wifsignaled, byref(signaled), stat)
         coredumped = c_int()
-        c(drmaa_wcoredump, byref(coredumped), stat)
+        if exited.value == 0:
+            c(drmaa_wcoredump, byref(coredumped), stat)
         exit_status = c_int()
         c(drmaa_wexitstatus, byref(exit_status), stat)
         term_signal = create_string_buffer(SIGNAL_BUFFER)
-        c(drmaa_wtermsig, term_signal, sizeof(term_signal), stat)
+        if signaled.value == 1:
+            c(drmaa_wtermsig, term_signal, sizeof(term_signal), stat)
         return JobInfo(jid_out.value.decode(), bool(exited), bool(signaled),
                        term_signal.value.decode(), bool(coredumped),
                        bool(aborted), int(exit_status.value), res_usage)

drmaa/version.py

@@ -22,5 +22,5 @@
 :author: Dan Blanchard ([email protected])
 '''
 
-__version__ = '0.7.6'
+__version__ = '0.7.7'
 VERSION = tuple(int(x) for x in __version__.split('.'))

setup.py

@@ -41,7 +41,7 @@ def readme():
       long_description=readme(),
       license="BSD",
       keywords="python grid hpc drmaa",
-      url="https://github.com/drmaa-python/drmaa-python",
+      url="https://github.com/pygridtools/drmaa-python",
       tests_require='nose',
       test_suite='nose.collector',
       classifiers=["Development Status :: 4 - Beta",

travis/install_sge.sh

@@ -5,7 +5,6 @@
 # Written by Dan Blanchard ([email protected]), September 2013
 
 cd travis
-sudo sed -i -r "s/^(127.0.0.1\s)(localhost\.localdomain\slocalhost)/\1localhost localhost.localdomain $(hostname) /" /etc/hosts
 sudo apt-get update -qq
 echo "gridengine-master shared/gridenginemaster string localhost" | sudo debconf-set-selections
 echo "gridengine-master shared/gridenginecell string default" | sudo debconf-set-selections