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version change (early beta, do not change until everythin works

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Max Zwiessele 2014-01-24 11:59:54 +00:00
parent 4807967ce7
commit 06ad627f0a
3 changed files with 27 additions and 2 deletions
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25
GPy/util/datasets.py
View file

@ -431,6 +431,31 @@ def swiss_roll_generated(num_samples=1000, sigma=0.0):
c = c[so, :] c = c[so, :]
return {'Y':Y, 't':t, 'colors':c} return {'Y':Y, 't':t, 'colors':c}
def hapmapIII(data_set='hapmapIII'):
try:
from pandas import read_pickle
except ImportError as i:
raise i, "Need pandas for hapmap dataset, make sure to install pandas before loading the hapmap dataset"
if not data_available(data_set):
download_data(data_set)
datadf = read_pickle(os.path.join(data_path,'HapMapIII','hapmap3_r2_b36_fwd.consensus.qc.poly.snps.pickle'))
infodf = read_pickle(os.path.join(data_path,'HapMapIII','hapmap3_r2_b36_fwd.consensus.qc.poly.info.pickle'))
inan = read_pickle(os.path.join(data_path,'HapMapIII','hapmap3_r2_b36_fwd.consensus.qc.poly.nan.pickle'))
snps = datadf.iloc[:,6:].values
populations = datadf.population.values.astype('S3')
hapmap = dict(name='HapMapIII',
describtion='The HapMap phase three SNP dataset - '
'1184 samples out of 11 populations. inan is a '
'boolean array, containing wheather or not the '
'given entry is nan (nans are masked as '
'-128 in snps).',
datadf=datadf,
infodf=infodf,
snps=snps,
inan=inan,
populations=populations)
return hapmap
def swiss_roll_1000(): def swiss_roll_1000():
return swiss_roll(num_samples=1000) return swiss_roll(num_samples=1000)

2
GPy/version
View file

@ -1 +1 @@
0.4.8 0.4.9b

2
setup.py
View file

@ -24,7 +24,7 @@ setup(name = 'GPy',
package_data = {'GPy': ['GPy/examples', 'gpy_config.cfg', 'util/data_resources.json', 'version']}, package_data = {'GPy': ['GPy/examples', 'gpy_config.cfg', 'util/data_resources.json', 'version']},
py_modules = ['GPy.__init__'], py_modules = ['GPy.__init__'],
long_description=read('README.md'), long_description=read('README.md'),
install_requires=['scipy == 0.12','matplotlib >= 1.2', 'nose'], install_requires=['scipy >= 0.12','matplotlib >= 1.2', 'nose'],
extras_require = { extras_require = {
'docs':['Sphinx', 'ipython'], 'docs':['Sphinx', 'ipython'],
}, },