Merge branch 'support-python3'.

Add support for Python 3.4, 3.5, 3.6 and stay compatible with 2.7.
Test all supported versions on travis with conda.
Test Python 2.7 with Linux system Python and
Python 3.6 with homebrew Python on Mac OS X.

Author: pavoljuhas

.travis.yml

@@ -8,13 +8,11 @@ os:
 
 env:
   - MYUSEMC=true MYPYTHON_VERSION=2.7
+  - MYUSEMC=true MYPYTHON_VERSION=3.4
+  - MYUSEMC=true MYPYTHON_VERSION=3.5
+  - MYUSEMC=true MYPYTHON_VERSION=3.6
   - MYUSEMC=false
 
-matrix:
-  exclude:
-    - os: osx
-      env: MYUSEMC=false
-
 git:
   depth: 999999
 
@@ -26,10 +24,17 @@ before_install:
   - MYNAME=diffpy.srreal
   - 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
@@ -54,23 +59,36 @@ before_install:
   - $NOMC || popd
   - $NOMC || source ~/mc/bin/activate root
   - $NOMC || conda update --yes conda
-  - $NOMC || conda install --yes conda-build jinja2
+  - $NOMC || conda install --yes conda-build jinja2 scons numpy
+  # Make scons available globally.
+  - $NOMC || mkdir -p ~/bin
+  - $NOMC || cp ~/mc/bin/scons ~/bin/
   - $NOMC || conda create --name=testenv --yes python=${MYPYTHON_VERSION} coverage
   - $NOMC || conda config --add channels diffpy
+  # FIXME - keep just the "diffpy" channel for public release.
+  - $NOMC || conda config --add channels diffpy/channel/dev
 
   - $NOAPT || test "${TRAVIS_OS_NAME}" = "linux" || exit $?
   - $NOAPT || sudo apt-get update -qq
   - $NOAPT || sudo apt-get install -y
                   libgsl0-dev libboost-all-dev python-dev
                   python-setuptools python-numpy python-pyparsing
                   python-lxml python-pip build-essential scons
-  - $NOAPT || devutils/makesdist
-  - $NOAPT || MYTARBUNDLE="$(ls -t "${PWD}"/dist/*.tar.gz | head -1)"
-  - $NOAPT || pushd ~/pkgs
-  - $NOAPT || git clone https://github.com/diffpy/libObjCryst.git
-  - $NOAPT || git clone https://github.com/diffpy/libdiffpy.git
-  - $NOAPT || popd
 
+  - $NOBREW || test "${TRAVIS_OS_NAME}" = "osx" || exit $?
+  - $NOBREW || brew update
+  - $NOBREW || brew install gsl
+  - $NOBREW || brew install scons
+  - $NOBREW || brew install python3
+  - $NOBREW || brew install boost-python --with-python3
+  - $NOBREW || brew install numpy --without-python --with-python3
+
+  - $NOSYS || devutils/makesdist
+  - $NOSYS || MYTARBUNDLE="$(ls -t "${PWD}"/dist/*.tar.gz | head -1)"
+  - $NOSYS || pushd ~/pkgs
+  - $NOSYS || git clone https://github.com/diffpy/libObjCryst.git
+  - $NOSYS || git clone https://github.com/diffpy/libdiffpy.git
+  - $NOSYS || popd
 
 install:
   - $NOMC || conda build --python=${MYPYTHON_VERSION} --dirty conda-recipe
@@ -80,25 +98,40 @@ install:
   - $NOMC || source activate testenv
   - $NOMC || conda install --yes --use-local --file=/tmp/mypackage.txt
 
-  - $NOAPT || pip install $MYPIPFLAGS coverage
-  - $NOAPT || pip install $MYPIPFLAGS periodictable
-  - $NOAPT || easy_install --user "pycifrw==4.2.1"
-  - $NOAPT || easy_install --user diffpy.Structure
+  - $NOAPT || $MYPIP install $MYPIPFLAGS coverage
+  - $NOAPT || $MYPIP install $MYPIPFLAGS periodictable
+  - $NOAPT || $MYPIP install $MYPIPFLAGS "pycifrw==4.2.1"
+  - $NOAPT || $MYPIP install $MYPIPFLAGS diffpy.structure
   - $NOAPT || sudo scons -C ~/pkgs/libObjCryst install
-  - $NOAPT || easy_install --user pyobjcryst
+  - $NOAPT || $MYPIP install $MYPIPFLAGS pyobjcryst
   - $NOAPT || sudo scons -C ~/pkgs/libdiffpy install
-  - $NOAPT || easy_install --user "${MYTARBUNDLE}"
+  - $NOAPT || $MYPIP install $MYPIPFLAGS "${MYTARBUNDLE}"
+
+  - $NOBREW || $MYPIP install $MYPIPFLAGS coverage
+  - $NOBREW || $MYPIP install $MYPIPFLAGS periodictable
+  - $NOBREW || $MYPIP install $MYPIPFLAGS pycifrw
+  # install diffpy.structure from the python3 development branch.
+  # TODO - replace with PyPI version later.
+  - $NOBREW || $MYPIP install $MYPIPFLAGS https://github.com/diffpy/diffpy.structure/archive/python3.tar.gz
+  - $NOBREW || scons -C ~/pkgs/libObjCryst install
+  - $NOBREW || $MYPIP install $MYPIPFLAGS pyobjcryst
+  - $NOBREW || scons -C ~/pkgs/libdiffpy install
+  - $NOBREW || $MYPIP install $MYPIPFLAGS "${MYTARBUNDLE}"
 
   - cd ${MYRUNDIR}
-  - MYGIT_REV=$(python -c "import ${MYNAME}.version as v; print(v.__gitsha__)")
+  - MYGIT_REV=$($MYPYTHON -c "import ${MYNAME}.version as v; print(v.__gitsha__)")
   - if [[ "${TRAVIS_COMMIT}" != "${MYGIT_REV}" ]]; then
         echo "Version mismatch ${TRAVIS_COMMIT} 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:
-  - pip install $MYPIPFLAGS codecov
+  - $MYPIP install $MYPIPFLAGS codecov
   - codecov

README.rst

@@ -14,7 +14,7 @@ function (PDF), bond valence sums (BVS), atom overlaps for a hard-sphere
 model, bond distances and directions up to specified maximum distance.   The
 atomic structure models are represented with internal classes as non-periodic,
 periodic or structures with space group symmetries.  The package provides
-implicit adapters from diffpy.Structure class or from Crystal or Molecule
+implicit adapters from diffpy.structure classes or from Crystal or Molecule
 objects from pyobjcryst.  Adapters can be easily defined for any other
 structure representations in Python allowing their direct use with the
 calculators.  Calculators support two evaluation models - BASIC, which
@@ -46,18 +46,18 @@ http://diffpy.github.io/diffpy.srreal.
 REQUIREMENTS
 ------------------------------------------------------------------------
 
-The diffpy.srreal requires Python 2.7, C++ compiler and
-the following software:
+The diffpy.srreal package requires Python 3.6, 3.5, 3.4 or 2.7,
+C++ compiler and the following software:
 
 * ``setuptools`` - tools for installing Python packages
 * ``NumPy`` - library for scientific computing with Python
-* ``scons`` - software constructions tool (1.0 or later)
 * ``python-dev`` - header files for interfacing Python with C
 * ``libboost-all-dev`` - Boost C++ libraries and development files (1.43 or later)
 * ``libdiffpy`` - C++ library for PDF, bond valence sum and other pair
   quantity calculators https://github.com/diffpy/libdiffpy
-* ``diffpy.Structure`` - simple storage and manipulation of atomic structures
-  https://github.com/diffpy/diffpy.Structure
+* ``diffpy.structure`` - simple storage and manipulation of atomic structures
+  https://github.com/diffpy/diffpy.structure
+* ``scons`` - software construction tool (optional)
 
 Optional software:
 
@@ -103,13 +103,14 @@ You may need to use ``sudo`` with system Python so the process is
 allowed to copy files to the system directories.  If administrator (root)
 access is not available, see the output from
 ``python setup.py install --help`` for options to install to
-a user-writable location.  The installation integrity can be verified by
-changing to the HOME directory and running ::
+a user-writable location.  The installation integrity can be
+verified by executing the included tests with ::
 
    python -m diffpy.srreal.tests.run
 
 An alternative way of installing diffpy.srreal is to use the SCons tool,
-which can speed up the process by compiling the C++ files in parallel (-j4) ::
+which can speed up the process by compiling C++ files in several
+parallel jobs (-j4) ::
 
    sudo scons -j4 install
 

conda-recipe/meta.yaml

@@ -19,17 +19,16 @@ requirements:
   build:
     - python
     - setuptools
-    - numpy 1.9.2
-    - libdiffpy >=1.3.3,1.3.*
+    - numpy 1.11.2
+    - libdiffpy >=1.3.4,1.3.*
     - pycifrw
     - diffpy.structure
-    - scons
 
   run:
     - python
     - setuptools
-    - numpy >=1.9.2
-    - libdiffpy >=1.3.3,1.3.*
+    - numpy >=1.11.2
+    - libdiffpy >=1.3.4,1.3.*
     - pycifrw
     - diffpy.structure
     - pyobjcryst 2.0*

devutils/tunePeakPrecision.py

@@ -27,7 +27,7 @@
 
 import numpy
 
-from diffpy.Structure import Structure
+from diffpy.structure import Structure
 from diffpy.srreal.pdf_ext import PDFCalculator
 import diffpy.pdffit2
 # make PdfFit silent

doc/manual/source/index.rst

@@ -19,7 +19,7 @@ function (PDF), bond valence sums (BVS), atom overlaps for a hard-sphere
 model, bond distances and directions up to specified maximum distance.   The
 atomic structure models are represented with internal classes as non-periodic,
 periodic or structures with space group symmetries.  The package provides
-implicit adapters from diffpy.Structure class or from Crystal or Molecule
+implicit adapters from diffpy.structure classes or from Crystal or Molecule
 objects from pyobjcryst.  Adapters can be easily defined for any other
 structure representations in Python allowing their direct use with the
 calculators.  Calculators support two evaluation models - BASIC, which

examples/compareC60PDFs.py

@@ -1,19 +1,19 @@
 #!/usr/bin/env python
 
 """Plot C60 PDFs calculated with PDFCalculator and DebyePDFCalculator.
-The C60 molecule is held in a diffpy.Structure object.
+The C60 molecule is held in a diffpy Structure object.
 """
 
 import sys
 import os
 from matplotlib.pyplot import plot, show, clf, draw
-from diffpy.Structure import Structure
+from diffpy.structure import Structure
 from diffpy.srreal.pdfcalculator import PDFCalculator, DebyePDFCalculator
 
 mydir = os.path.dirname(os.path.abspath(sys.argv[0]))
 buckyfile = os.path.join(mydir, 'datafiles', 'C60bucky.stru')
 
-# load C60 molecule as a diffpy.Structure object
+# load C60 molecule as a diffpy.structure object
 bucky = Structure(filename=buckyfile)
 cfg = { 'qmax' : 25,
         'rmin' : 0,

examples/compareC60PDFs_objcryst.py

@@ -5,13 +5,13 @@
 """
 
 from matplotlib.pyplot import plot, show, clf, draw
-from diffpy.Structure import Structure
+from diffpy.structure import Structure
 from pyobjcryst.crystal import Crystal
 from pyobjcryst.molecule import Molecule
 from pyobjcryst.scatteringpower import ScatteringPowerAtom
 from diffpy.srreal.pdfcalculator import PDFCalculator, DebyePDFCalculator
 
-# load C60 molecule as a diffpy.Structure object
+# load C60 molecule as a diffpy.structure object
 bucky_diffpy = Structure(filename='datafiles/C60bucky.stru')
 
 # convert to an ObjCryst molecule

examples/distanceprinter.py

@@ -5,7 +5,7 @@
 """
 
 from diffpy.srreal.pairquantity import PairQuantity
-from diffpy.Structure import Structure
+from diffpy.structure import Structure
 
 class DistancePrinter(PairQuantity):
 
@@ -45,8 +45,8 @@ def _addPairContribution(self, bnds, sumscale):
 distprint._setDoubleAttr('rmax', 10)
 
 def get_pyobjcryst_sphalerite():
-    from pyobjcryst.crystal import CreateCrystalFromCIF
-    crst = CreateCrystalFromCIF(open('datafiles/sphalerite.cif'))
+    from pyobjcryst import loadCrystal
+    crst = loadCrystal('datafiles/sphalerite.cif')
     return crst
 
 def main():
@@ -72,7 +72,7 @@ def main():
     crst = get_pyobjcryst_sphalerite()
     distprint.eval(crst)
     print(linesep)
-    input('Press enter for distances in diffpy.Structure sphalerite.cif.')
+    input('Press enter for distances in diffpy.structure sphalerite.cif.')
     crst = Structure(filename='datafiles/sphalerite.cif')
     distprint.eval(crst)
     return

examples/lennardjones/ljcalculator.py

@@ -8,7 +8,7 @@
 
 import sys
 from diffpy.srreal.pairquantity import PairQuantity
-from diffpy.Structure import Structure
+from diffpy.structure import Structure
 
 class LennardJonesCalculator(PairQuantity):
 

examples/parallelPDF.py

@@ -11,7 +11,7 @@
 import optparse
 import time
 import multiprocessing
-from diffpy.Structure import Structure
+from diffpy.structure import Structure
 from diffpy.srreal.pdfcalculator import PDFCalculator
 from diffpy.srreal.parallel import createParallelCalculator
 
@@ -30,14 +30,14 @@
 # load menthol structure and make sure Uiso values are non-zero
 if opts.pyobjcryst:
     # use pyobjcryst if requested by the user
-    from pyobjcryst.crystal import CreateCrystalFromCIF
+    from pyobjcryst import loadCrystal
     from numpy import pi
-    menthol = CreateCrystalFromCIF(open(mentholcif))
+    menthol = loadCrystal(mentholcif)
     for sc in menthol.GetScatteringComponentList():
         sp = sc.mpScattPow
         sp.Biso = sp.Biso or 8 * pi**2 * Uisodefault
 else:
-    # or use diffpy.Structure by default
+    # or use diffpy.structure by default
     menthol = Structure(filename=mentholcif)
     for a in menthol:
         a.Uisoequiv = a.Uisoequiv or Uisodefault