Merge branch 'support-py2-and-py3'

* make sources Python-3 compatible
* keep compatibility with Python 2 using the `six` tool
* add homebrew CI-test on travis

Author: pavoljuhas

.travis.yml

@@ -1,6 +1,4 @@
-# Use container-based travis workers
-sudo: false
-
+dist: xenial
 language: generic
 
 os:
@@ -9,37 +7,35 @@ os:
 
 env:
   - MYUSEMC=true MYPYTHON_VERSION=2.7
+  - MYUSEMC=true MYPYTHON_VERSION=3.5
+  - MYUSEMC=true MYPYTHON_VERSION=3.6
+  - MYUSEMC=true MYPYTHON_VERSION=3.7
   - MYUSEMC=false
 
-matrix:
-  exclude:
-    - os: osx
-      env: MYUSEMC=false
-
 git:
   depth: 999999
 
 branches:
   except:
     - /^v[0-9]/
 
-addons:
-  apt:
-    packages:
-    - python-dev
-    - python-numpy
-    - python-setuptools
-    - build-essential
 
 before_install:
   - MYNAME=diffpy.srfit
   - MYCOMMIT="$(git rev-parse HEAD)"
   - umask 022
   - git fetch origin --tags
+  - MYPYTHON=python; MYPIP=pip
+  - NOSYS=true; NOAPT=true; NOBREW=true; NOMC=true
   - if ${MYUSEMC}; then
-        NOAPT=true; NOMC=false;
-    else
-        NOAPT=false; NOMC=true;
+        NOMC=false;
+    elif [[ ${TRAVIS_OS_NAME} == linux ]]; then
+        NOAPT=false; NOSYS=false;
+        MYPIPFLAGS="--user";
+    elif [[ ${TRAVIS_OS_NAME} == osx ]]; then
+        NOBREW=false; NOSYS=false;
+        MYPYTHON=python3;
+        MYPIP=pip3;
         MYPIPFLAGS="--user";
     fi
   - MYMCREPO=https://repo.continuum.io/miniconda
@@ -72,8 +68,19 @@ before_install:
   - $NOAPT || PATH="$(echo "$PATH" | sed 's,:/opt/pyenv/[^:]*,,g')"
   - $NOAPT || test "$(which python)" = "/usr/bin/python" || (
                   which python; exit 1)
-  - $NOAPT || devutils/makesdist
-  - $NOAPT || MYTARBUNDLE="$(ls -t "${PWD}"/dist/*.tar.gz | head -1)"
+  - $NOAPT || sudo apt-get update -qq
+  - $NOAPT || sudo apt-get install -y
+                  python-dev python-setuptools python-numpy
+                  build-essential
+
+  - $NOBREW || test "${TRAVIS_OS_NAME}" = "osx" || exit $?
+  - $NOBREW || brew update
+  - $NOBREW || brew upgrade python
+  - $NOBREW || brew install gcc || brew link --overwrite gcc
+
+  - $NOSYS || devutils/makesdist
+  - $NOSYS || MYTARBUNDLE="$(ls -t "${PWD}"/dist/*.tar.gz | head -1)"
+
 
 install:
   - $NOMC || conda build --python=${MYPYTHON_VERSION} conda-recipe
@@ -82,23 +89,35 @@ install:
   - $NOMC || source activate testenv
   - $NOMC || conda install --yes --use-local --file=/tmp/mypackage.txt
   - $NOMC || conda install --yes
-                diffpy.structure pyobjcryst diffpy.srreal srfit-sasview
+                diffpy.structure pyobjcryst diffpy.srreal
+  # TODO - always install srfit-sasview when ready for Python 3.
+  - if $MYUSEMC && [[ "$MYPYTHON_VERSION" == 2.7 ]]; then
+        conda install --yes srfit-sasview;
+    fi
 
-  - $NOAPT || pip install $MYPIPFLAGS coverage
-  - $NOAPT || easy_install --user diffpy.Structure
-  - $NOAPT || easy_install --user "${MYTARBUNDLE}"
+  - $NOSYS || $MYPIP install $MYPIPFLAGS coverage
+  - $NOSYS || $MYPIP install $MYPIPFLAGS pycifrw
+  - $NOSYS || $MYPIP install $MYPIPFLAGS diffpy.structure
+  - $NOSYS || $MYPIP install $MYPIPFLAGS "${MYTARBUNDLE}"
 
   - cd ${MYRUNDIR}
-  - MYGIT_REV=$(python -c "import ${MYNAME}.version as v; print(v.__git_commit__)")
+  - MYGIT_REV=$($MYPYTHON -c "import ${MYNAME}.version as v; print(v.__git_commit__)")
   - if [[ "${MYCOMMIT}" != "${MYGIT_REV}" ]]; then
         echo "Version mismatch ${MYCOMMIT} vs ${MYGIT_REV}.";
         exit 1;
     fi
 
+
+before_script:
+  - $NOBREW || USER_BASE="$(python3 -c 'import site; print(site.USER_BASE)')"
+  - $NOBREW || PATH="${USER_BASE}/bin:${PATH}"
+
+
 script:
   - coverage run --source ${MYNAME} -m ${MYNAME}.tests.run
 
+
 after_success:
   # do not post coverage reports when testing with system Python.
-  - $NOMC || pip install $MYPIPFLAGS codecov
+  - $NOMC || $MYPIP install $MYPIPFLAGS codecov
   - $NOMC || codecov

README.rst

@@ -1,8 +1,8 @@
 .. image:: https://travis-ci.org/diffpy/diffpy.srfit.svg?branch=master
    :target: https://travis-ci.org/diffpy/diffpy.srfit
 
-.. image:: http://codecov.io/github/diffpy/diffpy.srfit/coverage.svg?branch=master
-   :target: http://codecov.io/github/diffpy/diffpy.srfit?branch=master
+.. image:: https://codecov.io/gh/diffpy/diffpy.srfit/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/diffpy/diffpy.srfit/branch/master
 
 
 diffpy.srfit
@@ -38,7 +38,8 @@ http://diffpy.github.io/diffpy.srfit.
 REQUIREMENTS
 ------------------------------------------------------------------------
 
-The diffpy.srfit package requires Python 2.7 and the following software:
+The diffpy.srfit package requires Python 3.5 or later or 2.7 and
+the following software:
 
 * ``setuptools`` - software distribution tools for Python
 * ``NumPy`` - numerical mathematics and fast array operations for Python
@@ -49,8 +50,8 @@ Recommended software:
 
 Optimizations involving crystal structures or molecules require
 
-* ``diffpy.Structure`` - crystal structure container and parsers,
-  https://github.com/diffpy/diffpy.Structure
+* ``diffpy.structure`` - crystal structure container and parsers,
+  https://github.com/diffpy/diffpy.structure
 * ``pyobjcryst`` - Crystal and Molecule storage, rigid units, bond
   length and bond angle restraints, https://github.com/diffpy/pyobjcryst
 
@@ -73,7 +74,7 @@ install the required software separately.  As an example, on Ubuntu
 Linux some of the required software can be installed using ::
 
    sudo apt-get install \
-      python-setuptools python-numpy python-scipy python-matplotlib
+      python3-setuptools python3-numpy python3-scipy python3-matplotlib
 
 For other required packages see their respective web pages for installation
 instructions.

conda-recipe/meta.yaml

@@ -18,11 +18,13 @@ requirements:
   build:
     - python
     - setuptools
+    - six
 
   run:
     - python
     - setuptools
     - numpy >=1.3
+    - six
 
 test:
   # Python imports
@@ -51,7 +53,8 @@ test:
     - diffpy.structure
     - pyobjcryst
     - diffpy.srreal
-    - srfit-sasview
+    # FIXME - correct when packages become available for Python 3.
+    - srfit-sasview     # [py2k]
 
 about:
   home: https://github.com/diffpy/diffpy.srfit/

doc/examples/README

@@ -94,7 +94,7 @@ Advanced:
     instructive extension to gaussianrecipe.py_.
 
 * npintensity.py_
-    Use diffpy.Structure to build a nanoparticle intensity generator, and use
+    Use diffpy.structure to build a nanoparticle intensity generator, and use
     it to refine a structure to simulated data.
 
 * npintensityII.py_
@@ -111,7 +111,7 @@ should read through these use cases to gain an understanding of PDF and SAS
 refinement with SrFit.
 
 * crystalpdf.py_
-    Refine a diffpy.Structure crystal to PDF data using automatic explicit
+    Refine a diffpy.structure crystal to PDF data using automatic explicit
     space group constraints.
 
 * simplepdf.py_

doc/examples/crystalpdf.py

@@ -12,7 +12,8 @@
 # See LICENSE_DANSE.txt for license information.
 #
 ########################################################################
-"""Example of a PDF refinement using diffpy.Structure and PDFGenerator.
+
+"""Example of a PDF refinement using diffpy.structure and PDFGenerator.
 
 This is example of fitting the fcc nickel structure to measured PDF data. The
 purpose of this example is to demonstrate and describe the classes in
@@ -26,7 +27,7 @@
 
 import numpy
 
-from diffpy.Structure import Structure
+from diffpy.structure import Structure
 from diffpy.srfit.pdf import PDFGenerator, PDFParser
 from diffpy.srfit.fitbase import Profile
 from diffpy.srfit.fitbase import FitContribution, FitRecipe
@@ -56,7 +57,7 @@ def makeRecipe(ciffile, datname):
 
     ## The ProfileGenerator
     # The PDFGenerator is for configuring and calculating a PDF profile. Here,
-    # we want to refine a Structure object from diffpy.Structure. We tell the
+    # we want to refine a Structure object from diffpy.structure. We tell the
     # PDFGenerator that with the 'setStructure' method. All other configuration
     # options will be inferred from the metadata that is read by the PDFParser.
     # In particular, this will set the scattering type (x-ray or neutron), the

doc/examples/npintensity.py

@@ -59,7 +59,7 @@ class IntensityGenerator(ProfileGenerator):
     """A class for calculating intensity using the Debye equation.
 
     Calculating intensity from a structure is difficult in general. This class
-    takes a diffpy.Structure.Structure instance and from that generates a
+    takes a diffpy.structure.Structure instance and from that generates a
     theoretical intensity signal. Unlike the example in gaussianrecipe.py, the
     intensity generator is not simple. It must take a structure object and some
     Parameters, and from that generate a signal. At the same time, the
@@ -93,7 +93,7 @@ def setStructure(self, strufile):
         """Set the structure used in the calculation.
 
         strufile    --  The name of a structure file. A
-                        diffpy.Structure.Structure object will be created from
+                        diffpy.structure.Structure object will be created from
                         the file, and that object will be passed to the 'iofq'
                         function whenever it is called.
 
@@ -102,7 +102,7 @@ def setStructure(self, strufile):
         DiffpyStructureParSet is a ParameterSet object that organizes and gives
         attribute access to Parameters and ParameterSets adapted from a diffpy
         Structure object.  The Parameters embedded in the DiffpyStructureParSet
-        are proxies for attributes of the diffpy.Structure.Structure object
+        are proxies for attributes of the diffpy.structure.Structure object
         that is needed by the 'iofq' function. The Parameters will be
         accessible by name under the 'phase' attribute of this generator, and
         are organized hierarchically:
@@ -130,21 +130,21 @@ def setStructure(self, strufile):
               - Uiso
             - etc.
 
-        The diffpy.Structure.Structure instance is held within the
+        The diffpy.structure.Structure instance is held within the
         DiffpyStructureParSet as the 'stru' attribute.
 
         """
         # Load the structure from file
-        from diffpy.Structure import Structure
+        from diffpy.structure import Structure
         stru = Structure()
         stru.read(strufile)
 
         # Create a ParameterSet designed to interface with
-        # diffpy.Structure.Structure objects that organizes the Parameter
+        # diffpy.structure.Structure objects that organizes the Parameter
         # hierarchy. Note that the DiffpyStructureParSet holds a handle to the
         # loaded structure that we use in the __call__ method below.
         #
-        # We pass the diffpy.Structure.Structure instance, and give the
+        # We pass the diffpy.structure.Structure instance, and give the
         # DiffpyStructureParSet the name "phase".
         parset = DiffpyStructureParSet("phase", stru)
 
@@ -158,7 +158,7 @@ def __call__(self, q):
 
         This ProfileGenerator will be used in a FitContribution that will be
         optimized to fit some data.  By the time this function is evaluated,
-        the diffpy.Structure.Structure instance has been updated by the
+        the diffpy.structure.Structure instance has been updated by the
         optimizer via the DiffpyStructureParSet defined in setStructure.  Thus,
         we need only call iofq with the internal structure object.
 
@@ -353,7 +353,7 @@ def iofq(S, q):
     I(Q) = 2 sum(i,j) f_i(Q) f_j(Q) sinc(rij Q) exp(-0.5 ssij Q**2)
     (The exponential term is the Debye-Waller factor.)
 
-    S   --  A diffpy.Structure.Structure instance. It is assumed that the
+    S   --  A diffpy.structure.Structure instance. It is assumed that the
             structure is that of an isolated scatterer. Periodic boundary
             conditions are not applied.
     q   --  The q-points to calculate over.
@@ -378,14 +378,14 @@ def iofq(S, q):
     pairdict = {}
     elcount = {}
     n = len(S)
-    for i in xrange(n):
+    for i in range(n):
 
         # count the number of each element
         eli = S[i].element
         m = elcount.get(eli, 0)
         elcount[eli] = m + 1
 
-        for j in xrange(i+1,n):
+        for j in range(i + 1, n):
 
             elj = S[j].element
 
@@ -473,7 +473,7 @@ def makeData(strufile, q, datname, scale, a, Uiso, sig, bkgc, nl = 1):
 
     """
 
-    from diffpy.Structure import Structure
+    from diffpy.structure import Structure
     S = Structure()
     S.read(strufile)
 
@@ -507,7 +507,7 @@ def makeData(strufile, q, datname, scale, a, Uiso, sig, bkgc, nl = 1):
         y = numpy.random.poisson(y*nl) / nl
 
     # Now save it
-    numpy.savetxt(datname, zip(q, y, u))
+    numpy.savetxt(datname, numpy.transpose([q, y, u]))
     return
 
 

doc/examples/simplepdf.py

@@ -19,7 +19,7 @@
 It uses the PDFContribution class to simplify fit setup.
 """
 
-from diffpy.Structure import Structure
+from diffpy.structure import Structure
 from diffpy.srfit.pdf import PDFContribution
 from diffpy.srfit.fitbase import FitRecipe, FitResults
 

setup.py

@@ -14,7 +14,7 @@
 
 # Use this version when git data are not available, like in git zip archive.
 # Update when tagging a new release.
-FALLBACK_VERSION = '1.3.post0'
+FALLBACK_VERSION = '3.0a0.post0'
 
 # determine if we run with Python 3.
 PY3 = (sys.version_info[0] == 3)
@@ -85,7 +85,7 @@ def getversioncfg():
     package_dir = {'' : 'src'},
     test_suite = 'diffpy.srfit.tests',
     include_package_data = True,
-    install_requires = [],
+    install_requires = ['six'],
     zip_safe = False,
     author = "Simon J.L. Billinge",
     author_email = "[email protected]",
@@ -107,6 +107,9 @@ def getversioncfg():
         'Operating System :: MacOS',
         'Operating System :: POSIX',
         'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
         'Topic :: Scientific/Engineering :: Chemistry',
         'Topic :: Scientific/Engineering :: Physics',
         'Topic :: Software Development :: Libraries',