Merged 0.15.0 release into master

.coveragerc

@@ -3,7 +3,6 @@ branch = True
 source = MDAnalysis
 omit =
     */migration/*
-    */analysis/*
     */visualization/*
     */MDAnalysis/tests/*
 

.github/CONTRIBUTING.md

@@ -0,0 +1,15 @@
+## Contributing to MDAnalysis
+
+Thanks for contributing to MDAnalysis!
+
+#### Reporting issues
+
+If you've found a defect with MDAnalysis we'd love to know so we can fix it.  Please follow the Issue template so we can quickly diagnose the problem, in particular the piece of code that causes the problem.
+
+If your issue isn't a defect with the code and instead you require help using MDAnalysis, drop by the [discussion board](http://help.mdanalysis.org).
+
+#### Contributing code
+
+If you're contributing code, please check out the [Style guide](https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide).
+
+MDAnalysis devs are most easily reached through the [development board](http://developers.mdanalysis.org).

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,19 @@
+### Expected behaviour
+
+
+### Actual behaviour
+
+
+### Code to reproduce the behaviour
+
+``` python
+import MDAnalysis as mda
+
+u = mda.Universe(top, trj)
+
+....
+
+```
+
+### Currently version of MDAnalysis:
+(run `python -c "import MDAnalysis as mda; print(mda.__version__)"`)

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,12 @@
+Fixes #
+
+Changes made in this Pull Request:
+ - 
+
+
+PR Checklist
+------------
+ - [ ] Tests?
+ - [ ] Docs?
+ - [ ] CHANGELOG updated?
+ - [ ] Issue raised/referenced?

.gitignore

@@ -34,3 +34,5 @@ doc/html/
 *.sw[a-z]
 # Ignore MDAnalysis log files
 MDAnalysis.log
+# Ignore the authors.py files as they are generated files
+authors.py

.travis.yml

@@ -4,7 +4,9 @@ branches:
     - master
     - develop
 
-language: python
+os:
+  - linux
+  - osx
 env:
   global:
     - secure: "HIj3p+p2PV8DBVg/KGUx6n83KwB0ASE5FwOn0SMB9zxnzAqe8sapwdBQdMdq0sXB7xT1spJqRxuxOMVEVn35BNLu7bxMLfa4287C8YXcomnvmv9xruxAsjsIewnNQ80vtPVbQddBPxa4jKbqgPby5QhhAP8KANAqYe44pIV70fY="
@@ -13,39 +15,29 @@ env:
     - GIT_CI_USER: TravisCI
     - GIT_CI_EMAIL: [email protected]
     - MDA_DOCDIR: package/doc/html
+  matrix:
+    - SETUP=minimal PYTHON_VERSION=2.7
+    - SETUP=full PYTHON_VERSION=2.7
+    - SETUP=minimal PYTHON_VERSION=3.3
+    - SETUP=full PYTHON_VERSION=3.3
 matrix:
   allow_failures:
-     - python: "3.3"
-       env: SETUP=full 
-  include:
-     - python: "2.7"
-       env: SETUP=minimal
-     - python: "2.7"
-       env: SETUP=full
-     - python: "3.3"
-       env: SETUP=full
-# command to install dependencies
-addons:
-  apt:
-    packages:
-      - gfortran
-      - libgfortran3
-      - libhdf5-serial-dev
-      - libnetcdf-dev
-      - liblapack-dev
-      - libatlas-dev
+    - env: SETUP=minimal PYTHON_VERSION=3.3
+    - env: SETUP=full PYTHON_VERSION=3.3
+
 before_install:
-  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+  - if [[ $TRAVIS_OS_NAME == 'osx' ]]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh -O miniconda.sh; fi
+  - if [[ $TRAVIS_OS_NAME == 'linux' ]]; then wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh; fi
   - chmod +x miniconda.sh
-  - ./miniconda.sh -b -p /home/travis/miniconda
-  - export PATH=/home/travis/miniconda/bin:$PATH
+  - ./miniconda.sh -b -p $(pwd)/miniconda
+  - export PATH=$(pwd)/miniconda/bin:$PATH
   - conda update --yes conda
 install:
-  - if [[ $SETUP == 'full' ]]; then conda create --yes -q -n pyenv python=2.7 numpy=1.9.2 scipy=0.16.0 nose=1.3.7 sphinx=1.3; fi
-  - if [[ $SETUP == 'minimal' ]]; then conda create --yes -q -n pyenv python=2.7 numpy=1.9.2 nose=1.3.7 sphinx=1.3; fi
+  - if [[ $SETUP == 'full' ]]; then conda create --yes -q -n pyenv python=$PYTHON_VERSION numpy scipy nose=1.3.7 sphinx=1.3; fi
+  - if [[ $SETUP == 'minimal' ]]; then conda create --yes -q -n pyenv python=$PYTHON_VERSION numpy nose=1.3.7 sphinx=1.3; fi
   - source activate pyenv
-  - if [[ $SETUP == 'full' ]]; then conda install --yes python=$TRAVIS_PYTHON_VERSION cython biopython matplotlib networkx netcdf4; fi
-  - if [[ $SETUP == 'minimal' ]]; then conda install --yes python=$TRAVIS_PYTHON_VERSION cython biopython networkx; fi
+  - if [[ $SETUP == 'full' ]]; then conda install --yes python=$PYTHON_VERSION cython biopython matplotlib networkx netcdf4; fi
+  - if [[ $SETUP == 'minimal' ]]; then conda install --yes python=$PYTHON_VERSION cython biopython networkx; fi
 # ensure that cython files are rebuilt
   - find . -name '*.pyx' -exec touch '{}' \;
   - pip install -v package/

README.rst

@@ -4,7 +4,7 @@
 
 |build| |cov| [*]_
 
-|docs| |devdocs| |usergroup| |developergroup|
+|docs| |devdocs| |usergroup| |developergroup| |anaconda|
 
 MDAnalysis_ is a Python toolkit to analyze molecular dynamics
 trajectories generated by a wide range of popular simulation packages
@@ -14,18 +14,18 @@ lists of  supported `trajectory formats`_ and `topology formats`_.)
 .. code:: python
 
    import MDAnalysis as mda
-   
+
    # Load simulation results with a single line
    u = mda.Universe('topol.tpr','traj.trr')
-   
+
    # Select atoms
    ag = u.select_atoms('name OH')
-   
+
    # Atom data made available as Numpy arrays
    ag.positions
    ag.velocities
    ag.forces
-   
+
    # Iterate through trajectories
    for ts in u.trajectory:
        print(ag.center_of_mass())
@@ -61,9 +61,9 @@ MDAnalysis issue tracker.)
 
 .. Footnotes
 
-.. [*] **build**: Unit testing is for the whole package; **coverage** is shown for the core library 
-       modules (which excludes `MDAnalysis.analysis`_ and `MDAnalysis.visualization`_ at
-       the moment). For more details and discussion see issue `#286`_.
+.. [*] **build**: Unit testing is for the whole package; **coverage** is
+       shown for the core library modules and the analysis modules (which
+       excludes `MDAnalysis.visualization`_ at the moment).
 
 .. _trajectory formats: http://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1
 .. _topology formats: http://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats
@@ -77,11 +77,11 @@ MDAnalysis issue tracker.)
 .. |usergroup| image:: https://img.shields.io/badge/Google%20Group-Users-lightgrey.svg
    :alt: User Google Group
    :target: http://users.mdanalysis.org
-   
+
 .. |developergroup| image:: https://img.shields.io/badge/Google%20Group-Developers-lightgrey.svg
    :alt: Developer Google Group
    :target: http://developers.mdanalysis.org
-   
+
 .. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg
    :alt: Documentation (latest release)
    :target: http://docs.mdanalysis.org
@@ -93,7 +93,11 @@ MDAnalysis issue tracker.)
 .. |build| image:: https://travis-ci.org/MDAnalysis/mdanalysis.svg?branch=develop
     :alt: Build Status
     :target: https://travis-ci.org/MDAnalysis/mdanalysis
-    
+
 .. |cov|   image:: https://coveralls.io/repos/MDAnalysis/mdanalysis/badge.svg?branch=develop
     :alt: Coverage Status
     :target: https://coveralls.io/r/MDAnalysis/mdanalysis?branch=develop
+
+.. |anaconda| image:: https://anaconda.org/mdanalysis/mdanalysis/badges/version.svg
+    :alt: Anaconda
+    :target: https://anaconda.org/MDAnalysis/mdanalysis

maintainer/change_release.sh

@@ -10,7 +10,7 @@ like '0.7.6' or 0.7.6-dev'.
 Run from the top directory of the git checkout.
 "
 
-FILES="package/setup.py package/MDAnalysis/version.py testsuite/setup.py testsuite/MDAnalysisTests/__init__.py"
+FILES="package/setup.py package/MDAnalysis/version.py testsuite/setup.py testsuite/MDAnalysisTests/__init__.py maintainer/conda/MDAnalysis/meta.yaml"
 
 die () {
     echo "ERROR: $1"
@@ -19,40 +19,40 @@ die () {
 
 findcommand() {
     for name in $*; do
-	path=$(which $name)
-	if [ -n "$path" ]; then
-	    echo $path
-	    return 0
-	fi
+    path=$(which $name)
+    if [ -n "$path" ]; then
+        echo $path
+        return 0
+    fi
     done
     die "None of the commands $* found." 2
 }
 
 sed_eregex () {
-  # does this sed understand extended regular expressions?
-  # - FreeBSD (Mac OS X) sed -E
-  # - GNU sed --regexp-extended (undocumented: also -E ...)
-  local SED=$1
-  if [ "good" = "$(echo 'bad' | $SED -E 's/(abc)?bad|foo/good/')" ]; then
-     echo "$SED -E"
-     return 0
-  elif [ "good" = "$(echo 'bad' | $SED --regexp-extended 's/(abc)?bad|foo/good/')" ]; then     
-     echo "$SED --regexp-extended"
-     return 0
-  elif [ "good" = "$(echo 'bad' | $SED 's/(abc)?bad|foo/good/')" ]; then
-     echo "$SED"
-     return 0
-  fi
-  echo "false"
-  return 1
+    # does this sed understand extended regular expressions?
+    # - FreeBSD (Mac OS X) sed -E
+    # - GNU sed --regexp-extended (undocumented: also -E ...)
+    local SED=$1
+    if [ "good" = "$(echo 'bad' | $SED -E 's/(abc)?bad|foo/good/')" ]; then
+       echo "$SED -E"
+       return 0
+    elif [ "good" = "$(echo 'bad' | $SED --regexp-extended 's/(abc)?bad|foo/good/')" ]; then
+       echo "$SED --regexp-extended"
+       return 0
+    elif [ "good" = "$(echo 'bad' | $SED 's/(abc)?bad|foo/good/')" ]; then
+       echo "$SED"
+       return 0
+    fi
+    echo "false"
+    return 1
 }
 
 while getopts h OPT; do
     case $OPT in
-	h) echo "$usage";
-	   exit 0
-	   ;;
-	\?) exit 2;;
+    h) echo "$usage";
+       exit 0
+       ;;
+    \?) exit 2;;
     esac
 done
 
@@ -62,20 +62,24 @@ RELEASE=$1
 test -n "$RELEASE" || die "Required argument missing. See -h for help." 2
 
 # find a sed with -i and -E
-for cmd in gsed sed; do 
+for cmd in gsed sed; do
    SED=$(sed_eregex $(findcommand $cmd))
    [ "$SED" != "false" ] && break
 done
-[ "$SED" = "false" ] && { echo "ERROR: cannot find suitable sed."; exit 1; } 
+[ "$SED" = "false" ] && { echo "ERROR: cannot find suitable sed."; exit 1; }
 # should check for -i but we just hope for the best ...
 # modern(ish) seds have -i
 echo "Using sed = $SED"
 
 echo "Setting RELEASE/__version__ in MDAnalysis to $RELEASE"
 
-git grep -E -l 'RELEASE.*[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(dev|rc*[0-9])?' $FILES  \
-   | xargs -I FILE $SED '/RELEASE/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(dev|rc*[0-9])?/'${RELEASE}'/' -i.bak FILE
-git grep -E -l '__version__ =.*[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(dev|rc*[0-9])?'  $FILES \
-   | xargs -I FILE $SED '/__version__/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(dev|rc*[0-9])?/'${RELEASE}'/' -i.bak FILE
-git status
+git grep -E -l 'RELEASE.*[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?' $FILES  \
+   | xargs -I FILE $SED '/RELEASE/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?/'${RELEASE}'/' -i.bak FILE
+
+git grep -E -l '__version__ *=.*[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?'  $FILES \
+   | xargs -I FILE $SED '/__version__/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?/'${RELEASE}'/' -i.bak FILE
 
+git grep -E -l 'version:.*[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?'  $FILES \
+   | xargs -I FILE $SED '/version:/s/[0-9]+\.[0-9]+\.[0-9]+(\.[0-9]+)?(-dev[0-9]*|-rc[0-9]*)?/'${RELEASE}'/' -i.bak FILE
+
+git status

maintainer/conda/MDAnalysis/build.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+MDA_USE_OPENMP=FALSE pip install package/
+pip install testsuite/

maintainer/conda/MDAnalysis/meta.yaml

@@ -0,0 +1,73 @@
+package:
+  name: mdanalysis
+  # This has to be changed after a release
+  version: "0.14.0"
+
+source:
+   # to build from source you can speficy the path to the code directly.
+   # path: ../../../
+   # This ensures that you will build from a clean checkout
+   git_url: https://github.com/MDAnalysis/mdanalysis
+   git_branch: master
+   # git_tag: release-0.14.0
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - pip
+    - numpy
+    - cython
+    - biopython
+    - networkx
+    - griddataformats
+    - nose
+
+  run:
+    - python
+    - numpy
+    - scipy
+    - griddataformats
+    - networkx
+    - biopython
+    - matplotlib
+    - seaborn
+    - six
+    - netcdf4
+    - nose
+
+test:
+  imports:
+    - MDAnalysis
+    - MDAnalysis.analysis
+    # check that distance cython modules have been build
+    - MDAnalysis.lib.c_distances_openmp
+    - MDAnalysis.lib.c_distances
+
+  requires:
+    # this is the same list as the run requirements
+    - python
+    - numpy
+    - scipy
+    - griddataformats
+    - networkx
+    - biopython
+    - matplotlib
+    - seaborn
+    - six
+    - netcdf4
+    - nose
+
+  commands:
+    # run the testsuite with 2 processes
+    - python -c 'import MDAnalysisTests; MDAnalysisTests.run(label="full", extra_argv=["-v", "--processes=2", "--process-timeout=120"])'
+
+about:
+  home: http://www.mdanalysis.org
+  license: GPLv2
+  license_file: package/LICENSE
+  summary: 'MDAnalysis is a Python library to analyze molecular dynamics trajectories.'
+
+# See
+# http://docs.continuum.io/conda/build.html for
+# more information about meta.yaml