Merge pull request #243 from ConnectedSystems/scipy-import-comb

Updated import of scipy comb function
SALib · May 13, 2019 · 3083615 · 3083615
2 parents dfb1f30 + e184c80
commit 3083615
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diff --git a/.travis.yml b/.travis.yml
@@ -1,16 +1,14 @@
 sudo: false
 language: python
-virtualenv:
-  system_site_packages: true
 env:
   matrix:
   - DISTRIB="conda" PYTHON_VERSION="3.5" COVERAGE="true"
   - DISTRIB="conda" PYTHON_VERSION="3.6" COVERAGE="false"
   - DISTRIB="conda" PYTHON_VERSION="3.7" COVERAGE="false"
-
+  - DISTRIB="conda" PYTHON_VERSION="3.8" COVERAGE="false"
 matrix:
   allow_failures:
-    - env: DISTRIB="conda" PYTHON_VERSION="3.7" COVERAGE="false"
+    - env: DISTRIB="conda" PYTHON_VERSION="3.8" COVERAGE="false"
 addons:
   apt:
     packages:
@@ -26,12 +24,23 @@ after_success:
 - if [[ "$COVERAGE" == "true" ]]; then coveralls || echo "failed"; fi
 notifications:
   email: false
-deploy:
-  provider: pypi
-  user: jdherman
-  password:
-    secure: KiUygZVHWMR2a+fk092xeHh8J2c61VGrgq4v1l3bq41MxcZO745H7CLJJ3rfqo+G5/pqy4/tm+q3p8fHhbUmwMcuSC3vjRN6WAYjuNPs0FMVXiIkMQtevv2LdVF1zVKFBdYTuNrfugtZ/GXh/ReCydjEBWTrTaNYeNM4ZRIaj0Q=
-  on:
-    tags: true
-    distributions: sdist bdist_wheel
-  skip_upload_docs: true
+
+jobs:
+  include:
+    - stage: "deploy"
+      name: "Deploy to PyPI"
+      if: tag =~ ^v
+      env: DISTRIB="conda" PYTHON_VERSION="3.6" COVERAGE="false"
+      install:
+      - source tests/travis_install.sh
+      - pip install -r requirements.txt
+      script: echo "Deploying to PyPI"
+      deploy:
+        provider: pypi
+        user: jdherman
+        password:
+          secure: KiUygZVHWMR2a+fk092xeHh8J2c61VGrgq4v1l3bq41MxcZO745H7CLJJ3rfqo+G5/pqy4/tm+q3p8fHhbUmwMcuSC3vjRN6WAYjuNPs0FMVXiIkMQtevv2LdVF1zVKFBdYTuNrfugtZ/GXh/ReCydjEBWTrTaNYeNM4ZRIaj0Q=
+        on:
+          tags: true
+          all_branches: true
+        skip_cleanup: true
diff --git a/examples/rbd_fast/rbd_fast.bat b/examples/rbd_fast/rbd_fast.bat
@@ -44,21 +44,21 @@ REM Sensitivity indices will print to command line. Use ">" to write to file.
 
 salib analyze rbd_fast ^
 	-p ../../src/SALib/test_functions/params/Ishigami.txt ^
-	-Y ../data/model_output.txt ^
 	-X ../data/model_input.txt ^
+	-Y ../data/model_output.txt ^
 	--seed=100
 
 REM python -m SALib.analyze.rbd_fast ^
 REM 	-p ../../src/SALib/test_functions/params/Ishigami.txt ^
-REM 	-Y ../data/model_output.txt ^
 REM 	-X ../data/model_input.txt ^
+REM 	-Y ../data/model_output.txt ^
 REM 	--seed=100
 
 REM Options:
 REM -p, --paramfile: Your parameter range file (3 columns: parameter name, lower bound, upper bound)
 REM
-REM -Y, --model-output-file: File of model output values to analyze
 REM -X, --model-input-file: File of model input values to analyze
+REM -Y, --model-output-file: File of model output values to analyze
 REM
 REM --delimiter (optional): Model output file delimiter.
 REM

diff --git a/examples/rbd_fast/rbd_fast.py b/examples/rbd_fast/rbd_fast.py
@@ -18,7 +18,7 @@
 
 # Perform the sensitivity analysis using the model output
 # Specify which column of the output file to analyze (zero-indexed)
-Si = rbd_fast.analyze(problem, Y, param_values, print_to_console=False)
+Si = rbd_fast.analyze(problem, param_values, Y, print_to_console=False)
 # Returns a dictionary with keys 'S1' and 'ST'
 # e.g. Si['S1'] contains the first-order index for each parameter, in the
 # same order as the parameter file
diff --git a/examples/rbd_fast/rbd_fast.sh b/examples/rbd_fast/rbd_fast.sh
@@ -44,14 +44,14 @@ python -c "from SALib.test_functions import Ishigami; import numpy as np; np.sav
 
 salib analyze rbd_fast \
 	-p ../../src/SALib/test_functions/params/Ishigami.txt \
-	-Y ../data/model_output.txt \
 	-X ../data/model_input.txt \
+	-Y ../data/model_output.txt \
 	--seed=100
 
 # python -m SALib.analyze.rbd_fast \
 # 	-p ../../src/SALib/test_functions/params/Ishigami.txt \
-# 	-Y ../data/model_output.txt \
 # 	-X ../data/model_input.txt \
+# 	-Y ../data/model_output.txt \
 # 	--seed=100
 
 # Options:

diff --git a/examples/sobol/sobol.bat b/examples/sobol/sobol.bat
@@ -82,3 +82,8 @@ REM
 REM --parallel (optional): Flag to enable parallel execution with multiprocessing
 REM
 REM --processors (optional, int): Number of processors to be used with the parallel option
+
+REM First-order indices expected with Saltelli sampling:
+REM x1: 0.3139
+REM x2: 0.4424
+REM x3: 0.0
diff --git a/examples/sobol/sobol.py b/examples/sobol/sobol.py
@@ -21,10 +21,15 @@
 # Specify which column of the output file to analyze (zero-indexed)
 Si = sobol.analyze(problem, Y, calc_second_order=True, conf_level=0.95, print_to_console=True)
 # Returns a dictionary with keys 'S1', 'S1_conf', 'ST', and 'ST_conf'
-# e.g. Si['S1'] contains the first-order index for each parameter, 
+# e.g. Si['S1'] contains the first-order index for each parameter,
 # in the same order as the parameter file
 # The optional second-order indices are now returned in keys 'S2', 'S2_conf'
 # These are both upper triangular DxD matrices with nan's in the duplicate
 # entries.
 # Optional keyword arguments parallel=True and n_processors=(int) for parallel execution
 # using multiprocessing
+
+# First-order indices expected with Saltelli sampling:
+# x1: 0.3139
+# x2: 0.4424
+# x3: 0.0
diff --git a/examples/sobol/sobol.sh b/examples/sobol/sobol.sh
@@ -82,3 +82,8 @@ salib analyze sobol \
 # --parallel (optional): Flag to enable parallel execution with multiprocessing
 #
 # --processors (optional, int): Number of processors to be used with the parallel option
+
+# First-order indices expected with Saltelli sampling:
+# x1: 0.3139
+# x2: 0.4424
+# x3: 0.0
diff --git a/setup.cfg b/setup.cfg
@@ -17,7 +17,7 @@ classifier =
     Programming Language :: Python :: 3.5
     Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
-    License :: OSI Approved :: MIT License,
+    License :: OSI Approved :: MIT License
     Intended Audience :: End Users/Desktop
     Intended Audience :: Developers
     Intended Audience :: Science/Research

diff --git a/src/SALib/analyze/rbd_fast.py b/src/SALib/analyze/rbd_fast.py
@@ -11,7 +11,7 @@
 from ..util import read_param_file, ResultDict
 
 
-def analyze(problem, Y, X, M=10, print_to_console=False, seed=None):
+def analyze(problem, X, Y, M=10, print_to_console=False, seed=None):
     """Performs the Random Balanced Design - Fourier Amplitude Sensitivity Test
     (RBD-FAST) on model outputs.
 
@@ -23,10 +23,10 @@ def analyze(problem, Y, X, M=10, print_to_console=False, seed=None):
     ----------
     problem : dict
         The problem definition
-    Y : numpy.array
-        A NumPy array containing the model outputs
     X : numpy.array
         A NumPy array containing the model inputs
+    Y : numpy.array
+        A NumPy array containing the model outputs
     M : int
         The interference parameter, i.e., the number of harmonics to sum in
         the Fourier series decomposition (default 10)
@@ -58,7 +58,7 @@ def analyze(problem, Y, X, M=10, print_to_console=False, seed=None):
     --------
     >>> X = latin.sample(problem, 1000)
     >>> Y = Ishigami.evaluate(X)
-    >>> Si = rbd_fast.analyze(problem, Y, X, print_to_console=False)
+    >>> Si = rbd_fast.analyze(problem, X, Y, print_to_console=False)
     """
     if seed:
         np.random.seed(seed)
@@ -73,7 +73,7 @@ def analyze(problem, Y, X, M=10, print_to_console=False, seed=None):
     Si['names'] = problem['names']
 
     for i in range(D):
-        S1 = compute_first_order(permute_outputs(Y, X[:, i]), M)
+        S1 = compute_first_order(permute_outputs(X[:, i], Y), M)
         S1 = unskew_S1(S1, M, N)
         Si['S1'][i] = S1
         if print_to_console:
@@ -82,7 +82,7 @@ def analyze(problem, Y, X, M=10, print_to_console=False, seed=None):
     return Si
 
 
-def permute_outputs(Y, X):
+def permute_outputs(X, Y):
     """
     Permute the output according to one of the inputs as in [_2]
 
@@ -126,13 +126,12 @@ def cli_parse(parser):
 
 def cli_action(args):
     problem = read_param_file(args.paramfile)
+    X = np.loadtxt(args.model_input_file,
+                   delimiter=args.delimiter)
     Y = np.loadtxt(args.model_output_file,
                    delimiter=args.delimiter,
                    usecols=(args.column,))
-    X = np.loadtxt(args.model_input_file,
-                   delimiter=args.delimiter)
-
-    analyze(problem, Y, X, print_to_console=True, seed=args.seed)
+    analyze(problem, X, Y, print_to_console=True, seed=args.seed)
 
 
 if __name__ == "__main__":

diff --git a/src/SALib/sample/morris/gurobi.py b/src/SALib/sample/morris/gurobi.py
@@ -16,7 +16,11 @@
 from datetime import datetime as dt
 
 import numpy as np
-from scipy.misc import comb as nchoosek
+
+try:
+    from scipy.misc import comb as nchoosek
+except ImportError:
+    from scipy.special import comb as nchoosek
 
 from . strategy import Strategy
 

diff --git a/src/SALib/test_functions/Ishigami.py b/src/SALib/test_functions/Ishigami.py
@@ -6,7 +6,8 @@
 
 
 # Non-monotonic Ishigami Function (3 parameters)
-# First-order indices:
+# Using Saltelli sampling with a sample size of ~1000
+# the expected first-order indices would be:
 # x1: 0.3139
 # x2: 0.4424
 # x3: 0.0

diff --git a/test-requirements.txt b/test-requirements.txt
@@ -1,8 +1,4 @@
-nose
 pre-commit
 pytest
-# Add requirements only needed for your unittests and during development here.
-# They will be installed automatically when running `python setup.py test`.
-# ATTENTION: Don't remove pytest-cov and pytest as they are needed.
 pytest-cov
 recommonmark