Merge pull request #5 from cosmo-ethz/r060

R060

.travis.yml

@@ -1,15 +1,24 @@
 language: python
 python:
   - "2.7"
-  - "3.3"
+  - "3.4"
 
 before_install:
-  - sudo apt-get update -qq
-  - sudo apt-get install -qq libatlas-dev libatlas-base-dev liblapack-dev gfortran
-  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b
-  - export PATH=/home/travis/miniconda/bin:$PATH
+  - sudo apt-get update
+  - sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+  - sudo apt-get -qq update
+  - sudo apt-get -qq install g++-4.8 gcc-4.8
+  - sudo ln -sf /usr/bin/gcc-4.8 /usr/bin/gcc
+  - sudo ln -sf /usr/bin/g++-4.8 /usr/bin/g++
+  # We do this conditionally because it saves us some downloading if the
+  # version is the same.
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
   - conda update --yes conda
   - travis_retry conda install --yes python=$TRAVIS_PYTHON_VERSION pip numpy scipy
 

HISTORY.rst

@@ -3,6 +3,13 @@
 History
 -------
 
+0.6.0 (2016-08-15)
+++++++++++++++++++
+- Order preserving parameter objects
+- Fixing logging issue
+- Prettified examples
+
+
 0.5.0 (2015-05-12)
 ++++++++++++++++++
 - Flat package structure

cosmoHammer/__init__.py

@@ -6,7 +6,7 @@
 This is the CosmoHammer package.
 """
 
-__version__   = '0.5.0'
+__version__   = '0.6.0'
 __author__    = 'Joel Akeret'
 __credits__   = 'Institute for Astronomy ETHZ, Institute of 4D Technologies FHNW'
 

cosmoHammer/pso/BestFitPositionGenerator.py

@@ -7,7 +7,6 @@
 
 import numpy
 from cosmoHammer.pso.ParticleSwarmOptimizer import ParticleSwarmOptimizer
-from cosmoHammer.pso.ParaboloidFitter import ParaboloidFitter
 from cosmoHammer.pso.CurvatureFitter import CurvatureFitter
 
 class BestFitPositionGenerator(object):

doc/source/user/usage.rst

@@ -16,15 +16,14 @@ To run CosmoHammer in order to sample the WMAP 9 year likelihood, you would do s
     from pycambWrapper import PyCambCoreModule
 
     #parameter start center, min, max, start width
-    params = np.array(
-            [[70, 40, 100, 3],
-            [0.0226, 0.005, 0.1, 0.001],
-            [0.122, 0.01, 0.99, 0.01],
-            [2.1e-9, 1.48e-9, 5.45e-9, 1e-10],
-            [0.96, 0.5, 1.5, 0.02],
-            [0.09, 0.01, 0.8, 0.03],
-            [1,0,2,0.4] ])
-    
+    params = Params(("hubble",                [70, 65, 80, 3]),
+                    ("ombh2",                 [0.0226, 0.01, 0.03, 0.001]),
+                    ("omch2",                 [0.122, 0.09, 0.2, 0.01]),
+                    ("scalar_amp",            [2.1e-9, 1.8e-9, 2.35e-9, 1e-10]),
+                    ("scalar_spectral_index", [0.96, 0.8, 1.2, 0.02]),
+                    ("re_optical_depth",      [0.09, 0.01, 0.1, 0.03]),
+                    ("sz_amp",                [1,0,2,0.4]))
+
     chain = LikelihoodComputationChain(
                         min=params[:,1], 
                         max=params[:,2])

examples/DerivedParamterFileUtil.py

@@ -11,8 +11,8 @@
 '''
 from cosmoHammer.util import SampleFileUtil
 
-VALUE_1_KEY = "value1"
-VALUE_2_KEY = "value2"
+VALUE_1_KEY = "derived_params_key"
+VALUE_2_KEY = "derived_params_key"
 
 OUTPUT_ORDER = [VALUE_2_KEY, VALUE_1_KEY]
 
@@ -35,7 +35,8 @@ def persistValues(self, posFile, probFile, pos, prob, data):
 
         #handle special parameters
         for derParams in data:
-            self.paramsFile.write("\t".join(derParams[key] for key in OUTPUT_ORDER))
+            if len(derParams) > 0:
+                self.paramsFile.write("\t".join([str(derParams[key]) for key in OUTPUT_ORDER]))
             self.paramsFile.write("\n")
 
         self.paramsFile.flush();

examples/wmap_tester.py

@@ -16,7 +16,7 @@
 
 
 pyCambCore = PyCambCoreModule.PyCambCoreModule()
-cambCore = CambCoreModule.CambCoreModule()
+cambCore = CambCoreModule()
 wmap3Likelihood = wmap3.WmapLikelihoodModule()
 wmap5Likelihood = wmap5.WmapLikelihoodModule()
 wmap7Likelihood = wmap7.WmapLikelihoodModule()

setup.py

@@ -34,7 +34,7 @@ def run_tests(self):
 
 setup(
     name="cosmoHammer",
-    version='0.5.0',
+    version='0.6.0',
     author='Joel Akeret',
     author_email="jakeret@phys.ethz.ch",
     url="http://www.cosmology.ethz.ch/research/software-lab/cosmohammer.html",
@@ -60,6 +60,6 @@ def run_tests(self):
         'Natural Language :: English',
         'Programming Language :: Python :: 2.6',
         'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3.3',
+        'Programming Language :: Python :: 3.4',
     ],
 )

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = py26, py27, docs-ci
+envlist = py26, py27, py34, docs-ci
 
 [testenv]
 setenv =