Merge branch 'support-py2-and-py3'

* make sources Python 3 compatible
* keep compatibility with Python 2 using the `six` tool
* rename module names to lowercase
* provide legacy import hook to support old names
* use noarch conda package

Closes #23.

Author: pavoljuhas

.readthedocs.yml

@@ -0,0 +1,7 @@
+python:
+  version: 3
+  setup_py_install: true
+  use_system_site_packages: true
+
+# For more fields that can be specified here, see:
+# http://docs.readthedocs.io/en/latest/yaml-config.html

.travis.yml

@@ -1,6 +1,4 @@
-# Use container-based travis workers
-sudo: false
-
+dist: xenial
 language: generic
 
 os:
@@ -9,46 +7,43 @@ 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.structure
   - 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
+  - MYMCREPO=https://repo.anaconda.com/miniconda
   - case ${TRAVIS_OS_NAME} in
     linux)
-        MYMCBUNDLE=Miniconda2-latest-Linux-x86_64.sh ;;
+        MYMCBUNDLE=Miniconda3-latest-Linux-x86_64.sh ;;
     osx)
-        MYMCBUNDLE=Miniconda2-latest-MacOSX-x86_64.sh ;;
+        MYMCBUNDLE=Miniconda3-latest-MacOSX-x86_64.sh ;;
     *)
         echo "Unsupported operating system." >&2;
         exit 2 ;;
@@ -65,16 +60,27 @@ before_install:
   - $NOMC || popd
   - $NOMC || source ~/mc/bin/activate base
   - $NOMC || conda update --yes conda
-  - $NOMC || conda install --yes conda-build jinja2
+  - $NOMC || conda install --yes conda-build conda-verify jinja2
   - $NOMC || conda create --name=testenv --yes python=${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 $?
   - $NOAPT || PATH="$(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-numpy python-setuptools 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:
@@ -84,26 +90,26 @@ install:
   - $NOMC || source activate testenv
   - $NOMC || conda install --yes --use-local --file=/tmp/mypackage.txt
 
-  - $NOAPT || pip install $MYPIPFLAGS coverage
-  # TODO - remove after fixup release of PyCifRW following 4.3.
-  - $NOAPT || pip install $MYPIPFLAGS "pycifrw==4.2.1"
-  - $NOAPT || easy_install --user "${MYTARBUNDLE}"
-
-  # We need to capitalize MYNAME to match Python module name.
-  - MYNAME=diffpy.Structure
+  - $NOSYS || $MYPIP install $MYPIPFLAGS coverage
+  - $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:
+  - $NOBREW || USER_BASE="$($MYPYTHON -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

@@ -5,42 +5,43 @@
    :target: https://codecov.io/gh/diffpy/diffpy.structure
 
 
-diffpy.Structure
+diffpy.structure
 ========================================================================
 
 storage and manipulation of crystal structure data
 
-The diffpy.Structure package provides objects for storing atomic
+The diffpy.structure package provides objects for storing atomic
 coordinates, displacement parameters and other crystal structure data.
-diffpy.Structure supports import and export of structure data in several
+diffpy.structure supports import and export of structure data in several
 structure formats such as CIF, PDB, and xyz.  It provides conversion
 between fractional and absolute Cartesian coordinates, functions for
 symmetry expansion of atom sites in the asymmetric unit and generation
 of symmetry constraints for atom positions and displacement parameters.
-diffpy.Structure includes definitions of all space groups in over 500
+diffpy.structure includes definitions of all space groups in over 500
 symmetry settings.
 
-To learn more about diffpy.Structure library see the
+To learn more about diffpy.structure library see the
 user manual at http://diffpy.github.io/diffpy.structure.
 
 
 REQUIREMENTS
 ------------------------------------------------------------------------
 
-The diffpy.Structure requires Python 2.7 and the following software:
+The diffpy.structure 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
 
 We recommend to use `Anaconda Python <https://www.anaconda.com/download>`_
 as it allows to install all software dependencies together with
-diffpy.Structure.  For other Python distributions it is necessary to
+diffpy.structure.  For other Python distributions it is necessary to
 install the required software separately.  As an example on Ubuntu
 Linux the required software can be installed with ::
 
-   sudo aptitude install python-setuptools python-numpy
+   sudo aptitude install python3-setuptools python3-numpy
 
-diffpy.Structure also uses the
+diffpy.structure also uses the
 `PyCifRW <https://bitbucket.org/jamesrhester/pycifrw>`_
 library, which is automatically deployed during the
 installation process.
@@ -55,7 +56,7 @@ The preferred method is to use Anaconda Python and install from the
    conda config --add channels diffpy
    conda install diffpy.structure
 
-diffpy.Structure is also included in the "diffpy-cmi" collection
+diffpy.structure is also included in the "diffpy-cmi" collection
 of packages for structure analysis ::
 
    conda install diffpy-cmi
@@ -64,7 +65,7 @@ Another installation option is to use ``easy_install`` to download and
 install the latest release from
 `Python Package Index <https://pypi.python.org>`_ ::
 
-   easy_install diffpy.Structure
+   easy_install diffpy.structure
 
 If you prefer to install from sources, navigate to the source archive
 directory and run ::
@@ -77,18 +78,18 @@ the usage info from ``python setup.py install --help`` for options to
 install to user-writable locations.  The installation integrity can be
 verified by changing to the HOME directory and running ::
 
-   python -m diffpy.Structure.tests.run
+   python -m diffpy.structure.tests.run
 
 
 DEVELOPMENT
 ------------------------------------------------------------------------
 
-diffpy.Structure is an open-source software developed as a part of the
+diffpy.structure is an open-source software developed as a part of the
 DiffPy-CMI complex modeling initiative at the Brookhaven National
-Laboratory.  The diffpy.Structure sources are hosted at
+Laboratory.  The diffpy.structure sources are hosted at
 https://github.com/diffpy/diffpy.structure.
 
-Feel free to fork the project and contribute.  To install diffpy.Structure
+Feel free to fork the project and contribute.  To install diffpy.structure
 in a development mode, where the sources are directly used by Python
 rather than copied to a system directory, use ::
 
@@ -105,7 +106,7 @@ originate from the pymmlib project, http://pymmlib.sourceforge.net.
 CONTACTS
 ------------------------------------------------------------------------
 
-For more information on diffpy.Structure please visit the project web-page
+For more information on diffpy.structure please visit the project web-page
 
 http://www.diffpy.org/
 

conda-recipe/meta.yaml

@@ -10,6 +10,8 @@ source:
 
 build:
   preserve_egg_dir: True
+  noarch: python
+
   # entry_points:
     # Put any entry points (scripts to be generated automatically) here. The
     # syntax is module:function.  For example
@@ -18,27 +20,33 @@ build:
     #
     # Would create an entry point called diffpy.structure that calls diffpy.structure.main()
 
-
   # If this is a new build for the same version, increment the build
   # number. If you do not include this key, it defaults to 0.
   # number: 0
 
 requirements:
   build:
-    - python
+    - python >=3.5|2.7*
     - setuptools
+    - six
     - pycifrw
 
   run:
-    - python
+    - python >=3.5|2.7*
     - setuptools
     - numpy >=1.3
     - pycifrw
+    - six
 
 test:
   # Python imports
   imports:
-    - diffpy
+    - diffpy.structure
+    - diffpy.structure.parsers
+    - diffpy.structure.applications
+    - diffpy.structure.expansion
+    - diffpy.structure.tests
+    # legacy imports
     - diffpy.Structure
     - diffpy.Structure.Parsers
     - diffpy.Structure.applications

conda-recipe/run_test.py

@@ -1,4 +1,4 @@
 #!/usr/bin/env python
 
-import diffpy.Structure.tests
-assert diffpy.Structure.tests.test().wasSuccessful()
+import diffpy.structure.tests
+assert diffpy.structure.tests.test().wasSuccessful()

devutils/sgtbx_extra_groups.py

@@ -13,14 +13,14 @@
 import re
 import math
 import numpy
-from diffpy.Structure.SpaceGroups import SpaceGroup, SymOp
-from diffpy.Structure.SpaceGroups import mmLibSpaceGroupList
-from diffpy.Structure.SpaceGroups import IsSpaceGroupIdentifier
+from diffpy.structure.spacegroups import SpaceGroup, SymOp
+from diffpy.structure.spacegroups import mmLibSpaceGroupList
+from diffpy.structure.spacegroups import IsSpaceGroupIdentifier
 from cctbx import sgtbx
 
 def tupleToSGArray(tpl):
     if not _rtarrays:
-        import diffpy.Structure.SpaceGroups as sgmod
+        import diffpy.structure.SpaceGroups as sgmod
         for n in dir(sgmod):
             if not n.startswith('Rot_') and not n.startswith('Tr_'): continue
             a = getattr(sgmod, n)
@@ -39,7 +39,6 @@ def mmSpaceGroupFromSymbol(symbol):
     """
     sginfo = sgtbx.space_group_info(symbol)
     symop_list = []
-    unique_rotations = set()
     symop_list = getSymOpList(sginfo.group())
     sgtype = sginfo.type()
     uhm = sgtype.lookup_symbol()
@@ -60,7 +59,7 @@ def mmSpaceGroupFromSymbol(symbol):
 
 
 def adjustMMSpaceGroupNumber(mmsg):
-    sg0 = filter(lambda x : x.number == mmsg.number, mmLibSpaceGroupList)
+    sg0 = [x for x in mmLibSpaceGroupList if x.number == mmsg.number]
     if sg0 and cmpSpaceGroups(sg0[0], mmsg):
         return
     while mmsg.number in sgnumbers:
@@ -121,13 +120,13 @@ def hashMMSpaceGroup(sg):
     s = '\n'.join(lines)
     return s
 
+
 def hashSgtbxGroup(grp):
     n = grp.type().number()
     lines = [str(n)] + sorted(map(str, getSymOpList(grp)))
     s = '\n'.join(lines)
     return s
 
-
 sgnumbers = [sg.number for sg in mmLibSpaceGroupList]
 
 _SGsrc = '''\
@@ -159,7 +158,7 @@ def SymOpsCode(mmsg):
 
 def SymOpCode(op):
     if not _rtnames:
-        import diffpy.Structure.SpaceGroups as sgmod
+        import diffpy.structure.SpaceGroups as sgmod
         for n in dir(sgmod):
             if not n.startswith('Rot_') and not n.startswith('Tr_'): continue
             a = getattr(sgmod, n)
@@ -185,7 +184,7 @@ def main():
         if hsg in duplicates: continue
         adjustMMSpaceGroupNumber(sg)
         duplicates.add(hsg)
-        print SGCode(sg)
+        print(SGCode(sg))
     return
 
 if __name__ == '__main__':