Merge pull request #28 from jbkalmbach/issue/23/add_setup

Issue/23/add setup

.travis.yml

@@ -23,9 +23,7 @@ install:
   - conda info -a
 
   - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION
-  - conda install -c conda-forge numpy scipy matplotlib nose future scikit-learn
-  - conda install -c conda-forge codecov
-  - conda install -c conda-forge scikit-optimize 
+  - conda install -c conda-forge numpy scipy matplotlib nose future scikit-learn codecov scikit-optimize
   - source activate test-environment
   - conda install coverage
 

setup.py

@@ -0,0 +1,23 @@
+from setuptools import setup, find_packages
+
+setup(
+    name="siggi",
+    version="0.1.0",
+    author="Bryce Kalmbach",
+    author_email="[email protected]",
+    url="https://github.com/jbkalmbach/siggi",
+    packages=find_packages(),
+    description="Spectral Information Gain Optimization",
+    long_description=open("README.md").read(),
+    package_data={"": ["README.md", "LICENSE"],
+                  "siggi": ["data/*",
+                            "data/lsst_baseline_throughputs/*"]},
+    include_package_data=True,
+    classifiers=[
+        "Development Status :: 3 - Alpha",
+        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+        "Intended Audience :: Science/Research",
+        "Operating System :: OS Independent",
+        "Programming Language :: Python",
+        ],
+)

siggi/calcIG.py

@@ -63,7 +63,7 @@ def __init__(self, filter_dict, sed_list, sed_probs, sed_mags=22.0,
     def calc_colors(self, return_all=False):
 
         """
-        Calculate the colors and errors in color measurement 
+        Calculate the colors and errors in color measurement
         of the SEDs in the given filters.
         """
 

siggi/lsst_utils/BandpassDict.py

@@ -158,13 +158,17 @@ def loadBandpassesFromFiles(cls,
 
     @classmethod
     def addSystemBandpass(cls, filter_dict,
-                          bandpassDir=os.path.join(os.path.dirname(__file__),
-                                             '../../data/lsst_baseline_throughputs'),
+                          bandpassDir=None,
                           components=['detector.dat', 'm1.dat', 'm2.dat',
                                       'm3.dat', 'lens1.dat',
                                       'lens2.dat', 'lens3.dat'],
                           atmosFile='atmos_std.dat'):
 
+        if bandpassDir is None:
+            bandpassDir = os.path.join(os.path.dirname(__file__),
+                                       '..', 'data',
+                                       'lsst_baseline_throughputs')
+
         comp_list = [os.path.join(bandpassDir, comp) for comp in components]
         comp_atmos_list = comp_list + [os.path.join(bandpassDir, atmosFile)]
 

siggi/siggi.py

@@ -72,7 +72,7 @@ def __init__(self, spec_list, spec_weights, z_prior,
                 self.z_probs.append(z_prior(z_val)*weight)
 
         bp_dict_folder = os.path.join(os.path.dirname(__file__),
-                                      '../data',
+                                      'data',
                                       'lsst_baseline_throughputs')
         bp_dict = BandpassDict.loadTotalBandpassesFromFiles(
             bandpassDir=bp_dict_folder)

siggi/spectra.py

@@ -19,23 +19,23 @@ def get_red_spectrum(self):
 
         sed_obj = Sed()
         sed_obj.readSED_flambda(os.path.join(os.path.dirname(__file__),
-                                             '../data/Inst.10E10.1Z.spec.gz'))
+                                             'data/Inst.10E10.1Z.spec.gz'))
 
         return sed_obj
 
     def get_blue_spectrum(self):
 
         sed_obj = Sed()
         sed_obj.readSED_flambda(os.path.join(os.path.dirname(__file__),
-                                             '../data/Inst.64E08.1Z.spec.gz'))
+                                             'data/Inst.64E08.1Z.spec.gz'))
 
         return sed_obj
 
     def get_dark_sky_spectrum(self):
 
         sed_obj = Sed()
         sky_sed = os.path.join(os.path.dirname(__file__),
-                               '../data/lsst_baseline_throughputs',
+                               'data/lsst_baseline_throughputs',
                                'darksky.dat')
         sed_obj.readSED_flambda(sky_sed)
 

tests/test_calcIG.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append('..')
 import unittest
 import numpy as np
 from siggi import filters, spectra, calcIG

tests/test_filters.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append('..')
 import unittest
 import numpy as np
 from siggi import filters

tests/test_mathUtils.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append('..')
 import unittest
 import numpy as np
 from scipy.spatial.distance import cdist

tests/test_siggi.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append('..')
 import os
 import unittest
 import pickle
@@ -21,7 +19,7 @@ def setUpClass(cls):
         cls.frozen_dict = BandpassDict.loadTotalBandpassesFromFiles(
                         bandpassNames=['u', 'g'],
                         bandpassDir=os.path.join(os.path.dirname(__file__),
-                                                 '../data',
+                                                 '../siggi/data',
                                                  'lsst_baseline_throughputs'))
 
         return
@@ -51,7 +49,7 @@ def prior_z(z, z0=0.5):
                                            system_wavelen_max=1200.,
                                            n_opt_points=14,
                                            optimizer_verbosity=10,
-                                           procs=4, 
+                                           procs=4,
                                            acq_func_kwargs_dict={'kappa': 3},
                                            frozen_filt_dict=self.frozen_dict,
                                            frozen_filt_eff_wavelen=[365, 477],
@@ -65,7 +63,7 @@ def prior_z(z, z0=0.5):
                                            system_wavelen_max=1200.,
                                            n_opt_points=14,
                                            optimizer_verbosity=10,
-                                           procs=4, 
+                                           procs=4,
                                            acq_func_kwargs_dict={'kappa': 3},
                                            frozen_filt_dict=self.frozen_dict,
                                            frozen_filt_eff_wavelen=[365, 477],
@@ -85,7 +83,7 @@ def prior_z(z, z0=0.5):
                                            system_wavelen_max=1200.,
                                            n_opt_points=10,
                                            optimizer_verbosity=10,
-                                           procs=4, 
+                                           procs=4,
                                            acq_func_kwargs_dict={'kappa': 3},
                                            frozen_filt_dict=self.frozen_dict,
                                            frozen_filt_eff_wavelen=[365, 477],
@@ -104,21 +102,23 @@ def prior_z(z, z0=0.5):
                                            system_wavelen_max=1200.,
                                            n_opt_points=4,
                                            optimizer_verbosity=10,
-                                           procs=4, 
+                                           procs=4,
                                            acq_func_kwargs_dict={'kappa': 3},
                                            frozen_filt_dict=self.frozen_dict,
                                            frozen_filt_eff_wavelen=[365, 477],
                                            starting_points=None,
                                            load_optimizer=test_opt,
                                            rand_state=23)
-        
+
         np.testing.assert_array_equal(t_1.Xi, t_4.Xi)
         np.testing.assert_array_equal(t_1.yi, t_4.yi)
 
     @classmethod
     def tearDownClass(cls):
 
         os.remove('test.pkl')
+        os.remove('Xi.out')
+        os.remove('yi.out')
 
         return
 

tests/test_siggiBase.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append('..')
 import os
 import unittest
 from siggi import _siggiBase, filters, spectra, calcIG
@@ -20,7 +18,7 @@ def setUpClass(cls):
         cls.frozen_dict = BandpassDict.loadTotalBandpassesFromFiles(
                         bandpassNames=['u', 'g'],
                         bandpassDir=os.path.join(os.path.dirname(__file__),
-                                                 '../data',
+                                                 '../siggi/data',
                                                  'lsst_baseline_throughputs'))
 
         return