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

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jakirkham wants to merge 125 commits into

chaubold: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.
jakirkham
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0b8129b
pytz: Provides support for timezone definitions. Required by Matplotlib.
jakirkham
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706fa8a
python-dateutil: Added dateutil for Python. Provides support for date and/or time manipulation. Used by Matplotlib.
jakirkham
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275865c
pyparsing: Added pyparsing. Provides a Python implementation of a parser. Used by Matplotlib.
jakirkham
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ad1fa45
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.
jakirkham
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a296d31
tornado: Added tornado, which is a web framework and asynchronous networking library. Required by Matplotlib and iPython.
jakirkham
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97f0a5a
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…
jakirkham
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0086fe0
matplotlib: Added PyQt4 as a dependency as Matplotlib should use the Qt backend.
jakirkham
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19605aa
sphinx: Added sphinx. Generates nice documentation from docstrings.
jakirkham
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68b4ee0
readline: Added a cmake to build and install the right readline for Mac or Windows using anyreadline. Required by iPython.
jakirkham
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3f1d2c9
zeromq: Added zeromq. Provides an asynchronous message passing implementation. Need by iPython.
jakirkham
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8f9a397
nose: Added comment to reflect iPython dependency.
jakirkham
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2b968f1
pygments: Added. Provides syntax highlighting support in Python. Used by iPython.
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9462b7f
jinja: Added comment to reflect iPython dependency.
jakirkham
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7427e7c
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 ).
jakirkham
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d3e9bfa
patsy: Uses a mini-language for formulae in a way similar to R/S. Used by pandas and hence statsmodels.
jakirkham
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beb32d2
numexpr: An acceleration library for use with NumPy.
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f54dd62
bottleneck: Added bottleneck, which speeds up some corner cases with NumPy. In particular, when nan values are present.
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b6b19bc
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…
jakirkham
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5dcabac
statsmodels: Builds on pandas ( actually depends on it as well ). Provides more advanced statistical analysis.
jakirkham
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8914e34
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…
jakirkham
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6804156
gmpy: Provides Python bindings to gmp, mpfr, and mpc. In short, allows high precision numbers in Python.
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7b0a32c
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.
jakirkham
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d2188be
sympy: Corrected comment.
jakirkham
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251ec6f
pep8: Added. Provides support for PEP8.
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d1161f6
pyflakes: A passive Python analyzer and error detector. Used by Spyder.
jakirkham
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9ddd88c
pylint: Python analyzer and error detector. Also, checks for bad smells. Used by Spyder.
jakirkham
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9695aad
rope: Added to provide refactoring support for Python. Used by Spyder.
jakirkham
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8f9f3b1
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…
jakirkham
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b2c16b4
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.
jakirkham
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6e6fc71
gmp: Add / after url.
jakirkham
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c5fd53a
pylint: Add / after url.
jakirkham
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cc1a6a6
python-dateutil: Add / after URL.
jakirkham
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e7f691d
spyder: Add / after URL.
jakirkham
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53c7ee4
mpfr: Link used for downloading mpfr no longer works. Added a new one that does work. Verified that the md5 is a match.
jakirkham
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72fc1fb

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…
jakirkham
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964434c

Commits on Aug 3, 2014

Commits on Aug 21, 2014

updates openssl package to work on Fedora 20

Stephen Plaza
authored and
jakirkham
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a441f6c
pip.cmake: Added pip for installing Python packages.
jakirkham
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b1db86a

Commits on Aug 30, 2014

Commits on Aug 31, 2014

pyzmq.cmake: Requires Cython to build.
jakirkham
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cd0a055
spams-python: Created a cmake to install SPAMS with Python bindings. Requires a patch be applied to the setup.py file to ensure that ATLAS is being used to build.
jakirkham
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67e7ff1
Added jsonschema.cmake

stuarteberg
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jakirkham
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83e3723
ilastik.cmake: Changed remote url to ilastik/ilastik-meta, not janelia-flyem/ilastik

stuarteberg
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jakirkham
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22933fa
ilastik.cmake: Added a new dependency: jsonschema

stuarteberg
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jakirkham
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630b156
ilastik.cmake: Require opengm

stuarteberg
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jakirkham
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3782754
Added futures.cmake (python futures module backported from Python 3)

stuarteberg
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jakirkham
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1c034a9
ilastik.cmake: Updated default ilastik checkout sha

stuarteberg
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jakirkham
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adb5748
updates sha for ilastik.cmake

Steve Plaza
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jakirkham
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648a6b5
opengm.cmake: Compile with hdf5, boost, and python

stuarteberg
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jakirkham
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9200745
opengm: Build without CPLEX if it can't be found.

stuarteberg
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jakirkham
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b8df931
opengm: Added a patch to let us skip the sphinx docs build with a cmake switch.

stuarteberg
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jakirkham
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f35f498
openblas.cmake: Added an additional step for installing links. Previously, the links pointed to a non-existent libopenblas.so on Mac. Now, links on Mac point to libopenblas.dylib.
jakirkham
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3807a12
spams-python.cmake: Updated to pass environment variable namely BUILDEM_DIR, GCC, and GXX. The variables GCC and GXX should point to GNU gcc and g++ compilers, respectively.
jakirkham
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2f6fec5
ilastik.cmake: Added scikit-image as dependency.
jakirkham
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5c26b77

Commits on Sep 23, 2014

Commits on Oct 11, 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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db8de65

Commits on Oct 22, 2014

vigra.cmake: Eliminated extra spaces.
jakirkham
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14ac04b

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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f7166fb

Commits on Dec 18, 2014

ilastik.cmake: Update the ilastik version.
jakirkham
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123ddbe

Commits on Jan 6, 2015

Commits on Jan 10, 2015

Commits on Jan 14, 2015

Commits on Jan 15, 2015

ann.cmake: Turn off FORCE as it is already in downloads.
jakirkham
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9a127a4
dlib.cmake: Turn off FORCE as it is already in downloads.
jakirkham
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0a74b0a
libxml2.cmake: Turn off FORCE as it is already in downloads.
jakirkham
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1ec962a
psutil.cmake: Turn off FORCE as it is already in downloads.
jakirkham
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19fd88e
matplotlib.cmake: Bump version to 1.4.2.
jakirkham
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307dcfa
ipython.cmake: Bump version from 1.2.1 to 2.1.0.
jakirkham
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b7879f0
opencv.cmake: Correct spacing.
jakirkham
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ca333c9
python-markdown.cmake: Markdown parser for Python.
jakirkham
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b2f8382
ipython.cmake: Correct spacing.
jakirkham
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7a3c6fb
ipython.cmake: Make python-markdown a dependency.
jakirkham
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830ffbb

Commits on Jan 20, 2015

pylibtiff.cmake: Added pylibtiff to provide Python bindings to libtiff.
jakirkham
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228eb73

Commits on Jan 23, 2015

cloud_sptheme.cmake: Added cloud theme. A theme for Sphinx.
jakirkham
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7d054be
nanshe.cmake: Add cloud_sptheme as a dependency.
jakirkham
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d181e3a