Merge pull request #223 from willu47/update_pyscaffold

Update pyscaffold to version 3

.coveragerc

@@ -1,7 +1,7 @@
 # .coveragerc to control coverage.py
 [run]
 branch = True
-source = SALib
+source = src/SALib/*
 omit = tests/*
 
 [report]

.gitignore

@@ -10,6 +10,7 @@
 __pycache__/*
 .cache/*
 .*.swp
+*/.ipynb_checkpoints/*
 
 # Project files
 .ropeproject
@@ -39,10 +40,3 @@ docs/api/*
 docs/_build/*
 cover/*
 MANIFEST
-
-# System files
-.DS_Store
-*.lp
-.vscode
-.tex*
-*.ipynb

.travis.yml

@@ -4,8 +4,13 @@ virtualenv:
   system_site_packages: true
 env:
   matrix:
-  - DISTRIB="conda" PYTHON_VERSION="2.7" COVERAGE="true"
-  - DISTRIB="conda" PYTHON_VERSION="3.5" COVERAGE="false"
+  - DISTRIB="conda" PYTHON_VERSION="3.5" COVERAGE="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.6" COVERAGE="false"
+  - DISTRIB="conda" PYTHON_VERSION="3.7" COVERAGE="false"
+
+matrix:
+  allow_failures:
+    - env: DISTRIB="conda" PYTHON_VERSION="3.7" COVERAGE="false"
 addons:
   apt:
     packages:

README-advanced.md

@@ -18,7 +18,7 @@ Parameter files can also be comma-delimited if your parameter names or group nam
 ```
 salib sample saltelli \
      -n 1000 \
-     -p ./SALib/test_functions/params/Ishigami.txt \
+     -p ./src/SALib/test_functions/params/Ishigami.txt \
      -o model_input.txt
 ```
 
@@ -27,7 +27,7 @@ salib sample saltelli \
 **Run the analysis**
 ```
 salib analyze sobol \
-     -p ./SALib/test_functions/params/Ishigami.txt \
+     -p ./src/SALib/test_functions/params/Ishigami.txt \
      -Y model_output.txt \
      -c 0
 ```

README.rst

@@ -0,0 +1,120 @@
+Sensitivity Analysis Library (SALib)
+------------------------------------
+
+Python implementations of commonly used sensitivity analysis methods.
+Useful in systems modeling to calculate the effects of model inputs or
+exogenous factors on outputs of interest.
+
+**Documentation:** `ReadTheDocs <http://salib.readthedocs.org>`__
+
+**Requirements:** `NumPy <http://www.numpy.org/>`__,
+`SciPy <http://www.scipy.org/>`__,
+`matplotlib <http://matplotlib.org/>`__,
+`pandas <http://https://pandas.pydata.org/>`__,
+Python 3 (from SALib v1.2 onwards SALib does not officially support Python 2)
+
+**Installation:** ``pip install SALib`` or ``python setup.py install`` or ``conda install SALib``
+
+**Build Status:** |Build Status| **Test Coverage:** |Coverage Status|
+
+**SALib Paper:** |status|
+
+``Herman, J., Usher, W., (2017), SALib: An open-source Python library for Sensitivity Analysis, Journal of Open Source Software, 2(9), 97, doi:10.21105/joss.00097``
+
+**Methods included:** 
+
+* Sobol Sensitivity Analysis (`Sobol 2001 <http://www.sciencedirect.com/science/article/pii/S0378475400002706>`__,
+  `Saltelli 2002 <http://www.sciencedirect.com/science/article/pii/S0010465502002801>`__,
+  `Saltelli et al. 2010 <http://www.sciencedirect.com/science/article/pii/S0010465509003087>`__)
+
+* Method of Morris, including groups and optimal trajectories (`Morris
+  1991 <http://www.tandfonline.com/doi/abs/10.1080/00401706.1991.10484804>`__,
+  `Campolongo et al. 2007 <http://www.sciencedirect.com/science/article/pii/S1364815206002805>`__)
+
+* Fourier Amplitude Sensitivity Test (FAST) (`Cukier et al. 1973 <http://scitation.aip.org/content/aip/journal/jcp/59/8/10.1063/1.1680571>`__,
+  `Saltelli et al. 1999 <http://amstat.tandfonline.com/doi/abs/10.1080/00401706.1999.10485594>`__)
+
+* Random Balance Designs - Fourier Amplitude Sensitivity Test (RBD-FAST) (`Tarantola et al. 2006 <https://hal.archives-ouvertes.fr/hal-01065897/file/Tarantola06RESS_HAL.pdf>`__,
+  `Plischke 2010 <https://doi.org/10.1016/j.ress.2009.11.005>`__, 
+  `Tissot et al. 2012 <https://doi.org/10.1016/j.ress.2012.06.010>`__) 
+
+* Delta
+  Moment-Independent Measure (`Borgonovo 2007 <http://www.sciencedirect.com/science/article/pii/S0951832006000883>`__,
+  `Plischke et al. 2013 <http://www.sciencedirect.com/science/article/pii/S0377221712008995>`__)
+
+* Derivative-based Global Sensitivity Measure (DGSM) (`Sobol and
+  Kucherenko 2009 <http://www.sciencedirect.com/science/article/pii/S0378475409000354>`__)
+
+* Fractional Factorial Sensitivity Analysis 
+  (`Saltelli et al. 2008 <http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470059974.html>`__)
+
+**Contributing:** see `here <CONTRIBUTING.md>`__
+
+Quick Start
+~~~~~~~~~~~
+
+.. code:: python
+
+    from SALib.sample import saltelli
+    from SALib.analyze import sobol
+    from SALib.test_functions import Ishigami
+    import numpy as np
+
+    problem = {
+      'num_vars': 3,
+      'names': ['x1', 'x2', 'x3'],
+      'bounds': [[-np.pi, np.pi]]*3
+    }
+
+    # Generate samples
+    param_values = saltelli.sample(problem, 1000)
+
+    # Run model (example)
+    Y = Ishigami.evaluate(param_values)
+
+    # Perform analysis
+    Si = sobol.analyze(problem, Y, print_to_console=True)
+    # Returns a dictionary with keys 'S1', 'S1_conf', 'ST', and 'ST_conf'
+    # (first and total-order indices with bootstrap confidence intervals)
+
+It's also possible to specify the parameter bounds in a file with 3
+columns:
+
+::
+
+    # name lower_bound upper_bound
+    P1 0.0 1.0
+    P2 0.0 5.0
+    ...etc.
+
+Then the ``problem`` dictionary above can be created from the
+``read_param_file`` function:
+
+.. code:: python
+
+    from SALib.util import read_param_file
+    problem = read_param_file('/path/to/file.txt')
+    # ... same as above
+
+Lots of other options are included for parameter files, as well as a
+command-line interface. See the `advanced
+readme <README-advanced.md>`__.
+
+Also check out the
+`examples <https://github.com/SALib/SALib/tree/master/examples>`__ for a
+full description of options for each method.
+
+License
+~~~~~~~
+
+Copyright (C) 2012-2019 Jon Herman, Will Usher, and others. Versions v0.5 and
+later are released under the `MIT license <LICENSE.md>`__.
+
+.. |Build Status| image:: https://travis-ci.org/SALib/SALib.svg?branch=master
+   :target: https://travis-ci.org/SALib/SALib
+.. |Coverage Status| image:: https://img.shields.io/coveralls/SALib/SALib.svg
+   :target: https://coveralls.io/r/SALib/SALib
+.. |Code Issues| image:: https://www.quantifiedcode.com/api/v1/project/ed62e70f899e4ec8af4ea6b2212d4b30/badge.svg
+   :target: https://www.quantifiedcode.com/app/project/ed62e70f899e4ec8af4ea6b2212d4b30
+.. |status| image:: http://joss.theoj.org/papers/431262803744581c1d4b6a95892d3343/status.svg
+   :target: http://joss.theoj.org/papers/431262803744581c1d4b6a95892d3343