Merge branch 'maint'

* Merge branch 'common-diffpy-patches' into maint
* Merge branch 'update-conda-recipe' into maint

Author: pavoljuhas

.codecov.yml

@@ -0,0 +1,2 @@
+fixes:
+  - ".*/site-packages/::src/"

.travis.yml

@@ -1,6 +1,4 @@
-# Use container-based travis workers
-sudo: false
-
+dist: xenial
 language: generic
 
 os:
@@ -23,15 +21,6 @@ branches:
   except:
     - /^v[0-9]/
 
-addons:
-  apt:
-    packages:
-    - build-essential
-    - libgsl0-dev
-    - python-dev
-    - python-numpy
-    - python-setuptools
-    - python-wxtools
 
 before_install:
   - MYNAME=diffpy.pdfgui
@@ -44,12 +33,12 @@ before_install:
         NOAPT=false; NOMC=true;
         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 ;;
@@ -66,28 +55,36 @@ 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
 
+  # TODO - remove after update to wxpython 4
+  - $NOMC || conda config --set restore_free_channel true
+
   - $NOAPT || test "${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 || sudo apt-get update -qq
+  - $NOAPT || sudo apt-get install -y
+                  build-essential libgsl0-dev python-dev
+                  python-numpy python-setuptools python-pip python-wxtools
   - $NOAPT || devutils/makesdist
   - $NOAPT || MYTARBUNDLE="$(ls -t "${PWD}"/dist/*.tar.gz | head -1)"
 
 install:
-  - $NOMC || conda build --python=${MYPYTHON_VERSION} conda-recipe
+  - $NOMC || conda build --python=${MYPYTHON_VERSION} --no-test conda-recipe
   - $NOMC || conda render --python=${MYPYTHON_VERSION} --output conda-recipe |
                 sed 's,.*/,,; s/[.]tar[.]bz2$//; s/-/=/g' > /tmp/mypackage.txt
   - $NOMC || source activate testenv
   - $NOMC || conda install --yes --use-local --file=/tmp/mypackage.txt
 
+  # TODO - remove after fix of libgsl.a location in pdffit2
+  - $NOAPT || sudo ln -si /usr/lib/x86_64-linux-gnu/libgsl.a /usr/lib/libgsl.a
+
   - $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}"
+  - $NOAPT || pip install $MYPIPFLAGS "${MYTARBUNDLE}"
 
   - cd ${MYRUNDIR}
   - MYGIT_REV=$(python -c "import ${MYNAME}.version as v; print(v.__git_commit__)")

README.rst

@@ -1,8 +1,8 @@
 .. image:: https://travis-ci.org/diffpy/diffpy.pdfgui.svg?branch=master
    :target: https://travis-ci.org/diffpy/diffpy.pdfgui
 
-.. image:: http://codecov.io/github/diffpy/diffpy.pdfgui/coverage.svg?branch=master
-   :target: http://codecov.io/github/diffpy/diffpy.pdfgui?branch=master
+.. image:: https://codecov.io/gh/diffpy/diffpy.pdfgui/branch/master/graph/badge.svg
+  :target: https://codecov.io/gh/diffpy/diffpy.pdfgui
 
 
 PDFgui

conda-recipe/bld.bat

@@ -1,4 +1,4 @@
-%PYTHON% setup.py install
+%PYTHON% -m pip install --no-deps -vv .
 if errorlevel 1 exit 1
 
 :: Add more build steps here, if they are necessary.

conda-recipe/build.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-$PYTHON setup.py install
+$PYTHON -m pip install --no-deps -vv .
 
 # Add more build steps here, if they are necessary.
 

conda-recipe/conda_build_config.yaml

@@ -0,0 +1,2 @@
+python:
+  - 2.7

conda-recipe/meta.yaml

@@ -27,12 +27,10 @@ app:
   summary: materials structure analysis from Pair Distribution Function
 
 requirements:
-  build:
-    - python
+  host:
+    - python {{ python }}
+    - pip
     - setuptools
-    - diffpy.pdffit2
-    - diffpy.structure 1.*
-    - diffpy.utils 1.*
 
   run:
     - python
@@ -41,8 +39,8 @@ requirements:
     - wxpython 3.*
     - menuinst                  [win]
     - diffpy.pdffit2
-    - diffpy.structure 1.*
-    - diffpy.utils 1.*
+    - diffpy.structure
+    - diffpy.utils
 
 test:
   # Python imports

conda-recipe/run_test.py

@@ -1,4 +1,4 @@
 #!/usr/bin/env python
 
-import diffpy.pdffit2.tests
-assert diffpy.pdffit2.tests.testdeps().wasSuccessful()
+import diffpy.pdfgui.tests
+assert diffpy.pdfgui.tests.testdeps().wasSuccessful()

setup.py

@@ -9,12 +9,17 @@
 """
 
 import os
+import re
+import sys
 from setuptools import setup, find_packages
 
 # Use this version when git data are not available, like in git zip archive.
 # Update when tagging a new release.
 FALLBACK_VERSION = '1.1.2.post0'
 
+# determine if we run with Python 3.
+PY3 = (sys.version_info[0] == 3)
+
 # versioncfgfile holds version data for git commit hash and date.
 # It must reside in the same directory as version.py.
 MYDIR = os.path.dirname(os.path.abspath(__file__))
@@ -23,7 +28,7 @@
 
 def gitinfo():
     from subprocess import Popen, PIPE
-    kw = dict(stdout=PIPE, cwd=MYDIR)
+    kw = dict(stdout=PIPE, cwd=MYDIR, universal_newlines=True)
     proc = Popen(['git', 'describe', '--match=v[[:digit:]]*'], **kw)
     desc = proc.stdout.read()
     proc = Popen(['git', 'log', '-1', '--format=%H %ct %ci'], **kw)
@@ -35,8 +40,10 @@ def gitinfo():
 
 
 def getversioncfg():
-    import re
-    from ConfigParser import RawConfigParser
+    if PY3:
+        from configparser import RawConfigParser
+    else:
+        from ConfigParser import RawConfigParser
     vd0 = dict(version=FALLBACK_VERSION, commit='', date='', timestamp=0)
     # first fetch data from gitarchivecfgfile, ignore if it is unexpanded
     g = vd0.copy()
@@ -65,18 +72,24 @@ def getversioncfg():
         cp.set('DEFAULT', 'commit', g['commit'])
         cp.set('DEFAULT', 'date', g['date'])
         cp.set('DEFAULT', 'timestamp', g['timestamp'])
-        cp.write(open(versioncfgfile, 'w'))
+        with open(versioncfgfile, 'w') as fp:
+            cp.write(fp)
     return cp
 
 versiondata = getversioncfg()
 
+
 def dirglob(d, *patterns):
     from glob import glob
     rv = []
     for p in patterns:
         rv += glob(os.path.join(d, p))
     return rv
 
+
+with open(os.path.join(MYDIR, 'README.rst')) as fp:
+    long_description = fp.read()
+
 # define distribution
 setup_args = dict(
     name = 'diffpy.pdfgui',
@@ -100,9 +113,9 @@ def dirglob(d, *patterns):
     # manual and tutorial files should not be zipped
     zip_safe = False,
     install_requires = [
-        'diffpy.Structure>=1.2',
-        'diffpy.pdffit2>=1.1a0',
-        'diffpy.utils>=1.1',
+        'diffpy.structure',
+        'diffpy.pdffit2',
+        'diffpy.utils',
     ],
 
     author = 'Simon J.L. Billinge',
@@ -111,6 +124,8 @@ def dirglob(d, *patterns):
     maintainer_email = 'pavol.juhas@gmail.com',
     url = 'https://github.com/diffpy/diffpy.pdfgui',
     description = "GUI for PDF simulation and structure refinement.",
+    long_description = long_description,
+    long_description_content_type = 'text/x-rst',
     license = 'BSD',
     keywords = 'PDF structure refinement GUI',
     classifiers = [