Merge pull request #104 from willu47/scaffold

Replaced versioneer with PyScaffold

.checkignore

@@ -1,3 +1 @@
 SALib/sample/directions.py
-versioneer.py
-SALib/_version.py

.coveragerc

@@ -2,11 +2,9 @@
 [run]
 branch = True
 source = SALib
-omit = */_version.py
+omit = tests/*
 
 [report]
-omit = */tests/*
-
 # Regexes for lines to exclude from consideration
 exclude_lines =
     # Have to re-enable the standard pragma

.coveralls.yml

@@ -0,0 +1 @@
+repo_token: pylBNeUbcFeKP3ZsJJuMlLJaWFkR2S4UP

.gitignore

@@ -1,14 +1,41 @@
-*.egg-info
-*.pyc
-dist
-model_input.txt
-model_output.txt
-y_rbf.txt
-tests/*.txt
-/build/
-/dist/
+# Temporary and binary files
+*~
+*.py[cod]
+*.so
+*.cfg
+!setup.cfg
+*.orig
 *.log
-.coveralls.yml
+*.pot
+__pycache__/*
+.cache/*
+.*.swp
+
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
 
+# Package files
+*.egg
+*.eggs/
+.installed.cfg
+*.egg-info
+
+# Unittest and coverage
+htmlcov/*
 .coverage
-./result_images/*
+.tox
+junit.xml
+coverage.xml
+
+# Build and docs folder/files
+build/*
+dist/*
+sdist/*
+docs/api/*
+docs/_build/*
+cover/*
+MANIFEST

.travis.yml

@@ -1,38 +1,27 @@
 # Travis config for SALib/SALib
+sudo: false
 language: python
-
-python:
-- "2.7"
-- "3.3"
-
-env: 
- # Workaround for image_comparison issue in v1.5.0 of matplotlib - fix matplotlib to 1.4.3
- - DEPS="numpy scipy matplotlib=1.4.3"
-
+virtualenv:
+  system_site_packages: true
+services:
+  - postgresql
+env:
+  matrix:
+  - DISTRIB="conda" PYTHON_VERSION="2.7" COVERAGE="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.5" COVERAGE="false"
+addons:
+  apt:
+    packages:
+    - git
+    - python-pip
 install:
- - sudo apt-get update
- - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-     wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
-   else
-     wget http://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:$PATH"
- - hash -r
- - conda config --set always_yes yes --set changeps1 no
- - conda install -c conda conda-env
- - conda update -q conda --no-deps
-  # Useful for debugging any issues with conda
- - conda info -a
-
-  # Replace dep1 dep2 ... with your dependencies
- - conda create -q -n testenv python=$TRAVIS_PYTHON_VERSION $DEPS pip
- - source activate testenv
- - python setup.py install
- - pip install coveralls
+- source tests/travis_install.sh
+- pip install -r test-requirements.txt
 script:
- - coverage run --source=SALib --omit=SALib/_version.py setup.py test
+- python setup.py test
 after_success:
- - coveralls
+- if [[ "$COVERAGE" == "true" ]]; then coveralls || echo "failed"; fi
+cache:
+- apt
 notifications:
  email: false

AUTHORS.rst

@@ -0,0 +1,5 @@
+==========
+Developers
+==========
+
+* Will Usher <william.usher@ouce.ox.ac.uk>

CHANGES.rst

@@ -0,0 +1,10 @@
+=========
+Changelog
+=========
+
+Version 0.1
+===========
+
+- Feature A added
+- FIX: nasty bug #1729 fixed
+- add your changes here!

SALib/__init__.py

@@ -1,7 +1,6 @@
-__version__ = "0.1"
+import pkg_resources
 
-from ._version import get_versions
-
-
-__version__ = get_versions()['version']
-del get_versions
+try:
+    __version__ = pkg_resources.get_distribution(__name__).version
+except:
+    __version__ = 'unknown'

SALib/analyze/morris.py

@@ -18,11 +18,11 @@ def analyze(problem, X, Y,
     """Perform Morris Analysis on model outputs.
 
     Returns a dictionary with keys 'mu', 'mu_star', 'sigma', and 'mu_star_conf',
-    where each entry is a list of size D (the number of parameters) containing
+    where each entry is a list of size D (the number of eters) containing
     the indices in the same order as the parameter file.
 
-    Parameters
-    ----------
+    Arguments
+    ---------
     problem : dict
         The problem definition
     X : numpy.matrix
@@ -59,6 +59,7 @@ def analyze(problem, X, Y,
     >>> Y = Ishigami.evaluate(X)
     >>> Si = morris.analyze(problem, X, Y, conf_level=0.95,
     >>>                     print_to_console=True, num_levels=4, grid_jump=2)
+
     """
 
     # Assume that there are no groups
@@ -203,12 +204,14 @@ def get_decreased_values(op_vec, up, lo):
 def compute_elementary_effects(model_inputs, model_outputs, trajectory_size, delta):
     '''
     Arguments:
-        - model_inputs - matrix of inputs to the model under analysis.
-                         x-by-r where x is the number of variables and
-                         r is the number of rows (a function of x and num_trajectories)
-        - model_outputs - an r-length vector of model outputs
-        - trajectory_size - a scalar indicating the number of rows in a
-                            trajectory
+    ----------
+    model_inputs : matrix of inputs to the model under analysis.
+        x-by-r where x is the number of variables and
+        r is the number of rows (a function of x and num_trajectories)
+    model_outputs
+        an r-length vector of model outputs
+    trajectory_size
+        a scalar indicating the number of rows in a trajectory
     '''
     num_vars = model_inputs.shape[1]
     num_rows = model_inputs.shape[0]