SciPy stack support, nanshe dependencies, some changes from upstream (old)#8

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jakirkham wants to merge 125 commits intochaubold:fix/OSX10.9from

jakirkham:fix__OSX_10_9__SciPy_Stack

Commits on Apr 22, 2014

six: Added six, which provides access to utilities in a compatible way between Python 2 and 3. Required by Matplotlib.
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pytz: Provides support for timezone definitions. Required by Matplotlib.
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python-dateutil: Added dateutil for Python. Provides support for date and/or time manipulation. Used by Matplotlib.
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pyparsing: Added pyparsing. Provides a Python implementation of a parser. Used by Matplotlib.
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backports-ssl_match_hostname: Added backports-ssl_match_hostname. Provides match_hostname from Python 3 for Python 2. Required for tornado, which is used by both Matplotlib and iPython.
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tornado: Added tornado, which is a web framework and asynchronous networking library. Required by Matplotlib and iPython.
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matplotlib: Missing various dependencies, which now have their own cmake files ( six, pytz, python-dateutil, pyparsing, tornado ). These have now been included and added as dependencies. Did not ad…
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matplotlib: Added PyQt4 as a dependency as Matplotlib should use the Qt backend.
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sphinx: Added sphinx. Generates nice documentation from docstrings.
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readline: Added a cmake to build and install the right readline for Mac or Windows using anyreadline. Required by iPython.
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zeromq: Added zeromq. Provides an asynchronous message passing implementation. Need by iPython.
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nose: Added comment to reflect iPython dependency.
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pygments: Added. Provides syntax highlighting support in Python. Used by iPython.
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jinja: Added comment to reflect iPython dependency.
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ipython: Added iPython and dependencies. This includes install readline in a compatiable way for Mac and Windows. Uses the 1.2.1 ( last of version 1 ).
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patsy: Uses a mini-language for formulae in a way similar to R/S. Used by pandas and hence statsmodels.
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numexpr: An acceleration library for use with NumPy.
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bottleneck: Added bottleneck, which speeds up some corner cases with NumPy. In particular, when nan values are present.
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pandas: Data analysis library. Part of SciPy stack. Used in particular for linear analysis. Included essential dependencies. Did not include optional dependencies to deal with input and output form…
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statsmodels: Builds on pandas ( actually depends on it as well ). Provides more advanced statistical analysis.
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mpc: Added mpc, which is commonly used in conjunction with gmp and mpfr ( already included ). This is also required by gmpy, which provides Python bindings to these three libraries to allow the use…
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gmpy: Provides Python bindings to gmp, mpfr, and mpc. In short, allows high precision numbers in Python.
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sympy: Provides support for symbolic on top of numeric calculations. Provides support for high precision calculation using gmpy with its bindings to gmp, mpfr, and mpc. Part of the SciPy stack.
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sympy: Corrected comment.
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pep8: Added. Provides support for PEP8.
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pyflakes: A passive Python analyzer and error detector. Used by Spyder.
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pylint: Python analyzer and error detector. Also, checks for bad smells. Used by Spyder.
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rope: Added to provide refactoring support for Python. Used by Spyder.
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spyder: Added Spyder. However, it currently is broken. Until WebKit is added back to Qt and PyQt, it will remain broken. It raises an error message to this effect if anyone tries to build it. If We…
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scipy-stack: Provides a custom target for installing the full SciPy stack. Includes everything in the SciPy stack and in a few cases a little extra. Does not include Spyder.
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gmp: Add / after url.
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pylint: Add / after url.
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python-dateutil: Add / after URL.
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spyder: Add / after URL.
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mpfr: Link used for downloading mpfr no longer works. Added a new one that does work. Verified that the md5 is a match.
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Commits on Apr 23, 2014

Commits on Apr 24, 2014

Commits on May 27, 2014

joblib: Provided a separate cmake for joblib. Tested and it works. This isn't strictly necessary if scikit-learn is installed as it will have joblib under sklearn.externals. However, it doesn't hur…
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Commits on Aug 3, 2014

Commits on Aug 21, 2014

updates openssl package to work on Fedora 20

Stephen Plaza
authored and
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pip.cmake: Added pip for installing Python packages.
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Commits on Aug 30, 2014

Commits on Aug 31, 2014

Commits on Sep 23, 2014

Commits on Oct 14, 2014

Update psutil to fix https://github.com/ilastik/ilastik/issues/891

chaubold
authored and
jakirkham
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Commits on Oct 22, 2014

vigra.cmake: Eliminated extra spaces.
jakirkham
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Commits on Nov 21, 2014

Commits on Dec 12, 2014

Commits on Dec 15, 2014

templates/exec.template: Make exec.template an executable. This way, when it is copied to bin, it should be an executable.
jakirkham
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Commits on Dec 18, 2014

ilastik.cmake: Update the ilastik version.
jakirkham
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Commits on Jan 6, 2015

Commits on Jan 10, 2015

Commits on Jan 15, 2015

Commits on Jan 20, 2015

pylibtiff.cmake: Added pylibtiff to provide Python bindings to libtiff.
jakirkham
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Commits on Jan 23, 2015