Merge pull request #26 from kaklise/master

Updates to support Pandas 1.0 and other minor changes

.travis.yml

@@ -8,10 +8,6 @@ sudo: false # if false, use TravisCI's container based build
 
 matrix:
     include:
-    - python: 2.7
-      env: CONDA_ENV=py27
-      services:
-      - xvfb
     - python: 3.5
       env: CONDA_ENV=py35
       services:
@@ -47,11 +43,7 @@ before_script:
 before_install:
     - echo "before install"
     - export PATH=/usr/lib/ccache:$PATH
-    - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-        wget http://repo.continuum.io/miniconda/Miniconda-3.16.0-Linux-x86_64.sh -O miniconda.sh;
-      else
-        wget http://repo.continuum.io/miniconda/Miniconda3-3.16.0-Linux-x86_64.sh -O miniconda.sh;
-      fi
+    - wget http://repo.continuum.io/miniconda/Miniconda3-3.16.0-Linux-x86_64.sh -O miniconda.sh
     - bash miniconda.sh -b -p $HOME/miniconda
     - export PATH="$HOME/miniconda/bin:$PATH"
     - hash -r

LICENSE.txt

@@ -1 +1 @@
-License Notice==============Copyright 2016-2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights in this software.This software is distributed under the Revised BSD License.Chama also leverages a variety of third-party software packages, whichhave separate licensing policies. Revised BSD License-------------------Redistribution and use in source and binary forms, with or withoutmodification, are permitted provided that the following conditionsare met:* Redistributions of source code must retain the above copyright notice, this   list of conditions and the following disclaimer.* Redistributions in binary form must reproduce the above copyright notice,   this list of conditions and the following disclaimer in the documentation   and/or other materials provided with the distribution.* Neither the name of Sandia National Laboratories, nor the names of  its contributors may be used to endorse or promote products derived from  this software without specific prior written permission.THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOTLIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FORA PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHTOWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITEDTO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, ORPROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OFLIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDINGNEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THISSOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License Notice==============Copyright 2016 National Technology & Engineering Solutions of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights in this software.This software is distributed under the Revised BSD License.Chama also leverages a variety of third-party software packages, whichhave separate licensing policies. Revised BSD License-------------------Redistribution and use in source and binary forms, with or withoutmodification, are permitted provided that the following conditionsare met:* Redistributions of source code must retain the above copyright notice, this   list of conditions and the following disclaimer.* Redistributions in binary form must reproduce the above copyright notice,   this list of conditions and the following disclaimer in the documentation   and/or other materials provided with the distribution.* Neither the name of Sandia National Laboratories, nor the names of  its contributors may be used to endorse or promote products derived from  this software without specific prior written permission.THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOTLIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FORA PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHTOWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITEDTO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, ORPROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OFLIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDINGNEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THISSOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,9 +1,10 @@
 ![Chama](documentation/figures/logo.png)
-=======================================
+=========================================
 
 [![TravisCI](https://travis-ci.org/sandialabs/chama.svg?branch=master)](https://travis-ci.org/sandialabs/chama)
 [![Coverage Status](https://coveralls.io/repos/github/sandialabs/chama/badge.svg?branch=master)](https://coveralls.io/github/sandialabs/chama?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/chama/badge/?version=latest)](http://chama.readthedocs.io/en/latest/?badge=latest)
+[![Downloads](https://pepy.tech/badge/chama)](https://pepy.tech/project/chama)
 
 Continuous or regularly scheduled monitoring has the potential to quickly 
 identify changes in the environment. However, even with low-cost sensors, only 

chama/__init__.py

@@ -4,9 +4,9 @@
 from chama import optimize
 from chama import graphics
 
-__version__ = '0.1.2'
+__version__ = '0.1.3'
 
-__copyright__ = """Copyright 2016-2019 National Technology & Engineering 
+__copyright__ = """Copyright 2016 National Technology & Engineering 
     Solutions of Sandia, LLC (NTESS). Under the terms of Contract 
 	DE-NA0003525 with NTESS, the U.S. Government retains certain rights 
 	in this software."""

chama/sensors.py

@@ -312,8 +312,21 @@ def _get_signal_at_sample_points(self, signal, sample_points,
 
         # Get subset of signal. If a sample point is not in signal then NaN
         # is inserted
-        signal_subset = signal.loc[sample_points, :]
-
+        try:
+            signal_subset = signal.loc[sample_points, :]
+        except: # Some sample points are not in the signal
+            if ['T', 'X', 'Y', 'Z'] == signal.index.names:
+                signal_subset = pd.DataFrame(data=np.nan, columns=signal.columns, 
+                                         index=pd.MultiIndex.from_tuples(sample_points, names=['T', 'X', 'Y', 'Z']))
+            elif ['T', 'Node'] == signal.index.names:
+                signal_subset = pd.DataFrame(data=np.nan, columns=signal.columns, 
+                                         index=pd.MultiIndex.from_tuples(sample_points, names=['T', 'Node']))
+            else:
+                raise ValueError('Unrecognized signal format')
+
+            sample_points_in_signal = list(set(sample_points).intersection(set(signal.index)))
+            signal_subset.loc[sample_points_in_signal, :] = signal.loc[sample_points_in_signal, :]
+
         if interp_method is None:
             return signal_subset
 

documentation/conf.py

@@ -15,6 +15,7 @@
 import sys
 import os
 import shlex
+from chama import __version__
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -66,17 +67,17 @@
 
 # General information about the project.
 project = u'Chama'
-copyright = u'2016-2019, National Technology & Engineering Solutions of Sandia, LLC (NTESS)'
+copyright = u'2016 National Technology & Engineering Solutions of Sandia, LLC (NTESS)'
 author = u'Sandia National Laboratories'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.1.2'
+version = __version__
 # The full version, including alpha/beta/rc tags.
-release = '0.1.2'
+release = __version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

documentation/environment.yml

@@ -1,7 +1,4 @@
 name: chama
-channels:
-    - conda-forge
-    - defaults
 dependencies:
     - python=3.7
     - numpy
@@ -10,4 +7,4 @@ dependencies:
     - sphinx
     - numpydoc
     - matplotlib
-    - pyomo
+

documentation/installation.rst

@@ -5,7 +5,7 @@
 Installation
 ======================================
 
-Chama requires Python (2.7, 3.5, 3.6, or 3.7) along with several Python package dependencies.  
+Chama requires Python (tested on 3.5, 3.6, and 3.7) along with several Python package dependencies.  
 Information on installing and using Python can be found at 
 https://www.python.org/.  
 Python distributions, such as Anaconda, are recommended to manage the Python interface.  

documentation/license.rst

@@ -14,7 +14,7 @@ Copyright
 ------------
 .. code-block:: none 
 
-	Copyright 2016-2019 National Technology & Engineering Solutions of Sandia, 
+	Copyright 2016 National Technology & Engineering Solutions of Sandia, 
 	LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S. 
 	Government retains certain rights in this software.
 

documentation/whatsnew.rst

@@ -5,6 +5,8 @@
 Release notes
 ================
 
+.. include:: whatsnew/v0.1.3.rst
+
 .. include:: whatsnew/v0.1.2.rst
 
 .. include:: whatsnew/v0.1.1.rst

documentation/whatsnew/v0.1.3.rst

@@ -0,0 +1,7 @@
+v0.1.3 (February 28, 2020)
+----------------------------
+
+* Updated methods to be compatible with Pandas 1.0
+* Added required dependencies to setup.py
+* Dropped Python 2.7 tests
+* Updated documentation

setup.py

@@ -1,24 +1,38 @@
 from setuptools import setup, find_packages
 from distutils.core import Extension
+import os
+import re
 
 DISTNAME = 'chama'
-VERSION = '0.1.2'
 PACKAGES = ['chama']
 EXTENSIONS = []
 DESCRIPTION = 'Sensor Placement Optimization.'
-LONG_DESCRIPTION = open('README.md').read()
 AUTHOR = 'Chama developers'
 MAINTAINER_EMAIL = '[email protected]'
 LICENSE = 'Revised BSD'
 URL = 'https://github.com/sandialabs/chama'
+DEPENDENCIES = ['pyomo', 'pandas', 'numpy', 'scipy']
 
-setuptools_kwargs = {
-    'zip_safe': False,
-    'install_requires': [],
-    'scripts': [],
-    'include_package_data': True
-}
+# use README file as the long description
+file_dir = os.path.abspath(os.path.dirname(__file__))
+with open(os.path.join(file_dir, 'README.md'), encoding='utf-8') as f:
+    LONG_DESCRIPTION = f.read()
 
+# use README file as the long description
+file_dir = os.path.abspath(os.path.dirname(__file__))
+with open(os.path.join(file_dir, 'README.md'), encoding='utf-8') as f:
+    LONG_DESCRIPTION = f.read()
+
+# get version from __init__.py
+with open(os.path.join(file_dir, 'chama', '__init__.py')) as f:
+    version_file = f.read()
+    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
+                              version_file, re.M)
+    if version_match:
+        VERSION = version_match.group(1)
+    else:
+        raise RuntimeError("Unable to find version string.")
+
 setup(name=DISTNAME,
       version=VERSION,
       packages=PACKAGES,
@@ -29,4 +43,7 @@
       maintainer_email=MAINTAINER_EMAIL,
       license=LICENSE,
       url=URL,
-      **setuptools_kwargs)
+      zip_safe=False,
+      install_requires=DEPENDENCIES,
+      scripts=[],
+      include_package_data=True)