Updated readme and license, cleaning up unneeded files.

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "gromacs"]
-	path = gromacs
-	url = git://git.gromacs.org/gromacs.git 

LICENSE

@@ -1,21 +1,30 @@
-MIT License
+Copyright (c) 2017, Niels Müller.
+All rights reserved.
 
-Copyright (c) 2016 Niels A. Müller
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+    * Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+    * Redistributions in binary form must reproduce the above
+       copyright notice, this list of conditions and the following
+       disclaimer in the documentation and/or other materials provided
+       with the distribution.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+    * Neither the name of the copyright holder nor the names of any
+       contributors may be used to endorse or promote products derived
+       from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,10 +1,10 @@
 # Pygmx
 
-A Cython wrapper for the shared library of GROMACS 5.1.
+A Cython wrapper for the shared library of GROMACS 2016
 
 ## Installation
 
-Pygmx requires some python packages and an installation of GROMACS 5.1.
+Pygmx requires some python packages and an installation of GROMACS 2016.
 
 ### Python requirements
 
@@ -15,48 +15,30 @@ Pygmx needs mainly two python packages to be installed, which are available in a
 
 ### Gromacs installation
 
-Pygmx requires the shared library and header files of Gromacs 5.1 or higher to be installed.
-
-Note that pygmx also supports the Gromacs-2016 version.
-Checkout the followng git branch if this version of Gromacs is desired:
-
-    git checkout gromacs-2016
-
-Note that Gromacs is backwards compatible, i. e. files produced by the 5.1 version will also work in the 2016 version.
-But Gromacs-2016 is required to load files of the 2016 version.
-
-#### Using a module
-
-If gromacs is installed as a module in your system, run
-
-    module load gromacs/5.1
-
-and skip to the section *Installing pygmx*.
-Note that on the AG Vogel intranet pygmx is available through the module `mdevaluate`.
+Pygmx requires the shared library and header files of Gromacs 2016 to be installed.
 
 #### Through package manager
 
-On many Unix distributions Gromacs may be installed through the package manager.
+On many Unix distributions, Gromacs may be installed through the package manager.
 The required packages, which provide the headers, are usually named `gromacs-devel` or `gromcas-dev`.
 
 #### Manual build
 
-To build the shared library manually, follow the [official installation instructions](http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html).
+To build the shared library manually, follow the [official installation instructions](http://manual.gromacs.org/documentation/2016.4/install-guide/index.html).
 Make sure to source the `GMXRC` script, which sets the environment variable `LD_LIBRARY_PATH` to the correct location or set this variable manually.
 Don't bother with advanced features like GPU support if the Gromacs installation will only be used for pygmx,
 since the file io functions do not use these features.
 
 ### Installing pygmx
 
-When the requirements are met, the installation should be easy.
-Navigate to the top folder of the repository and run the command
+When the requirements are met, installing pygmx into the local Python installation can be achieved by navigating to the top folder of the repository and running the command
 
     python setup.py install
 
 This builds the cython modules and installs them into the local python distribution.
-To check if everyting works run
+To check if everyting works, run the following command from a directory out of the repository
 
     python -c 'import pygmx'
 
-If this raises an error that refers to `libgromacs.so`, this means the Gromacs library could not be found.
+If this raises an error that refers to `libgromacs.so`, the Gromacs library could not be found.
 Make sure it is either in a standard location or `LD_LIBRARY_PATH` is set correctly.

bld.bat

@@ -1,3 +0,0 @@
-
-"%PYTHON%" setup.py install
-if errorlevel 1 exit 1

build.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-${PYTHON} setup.py install || exit 1;

deploy.sh

@@ -1,19 +0,0 @@
-#!/bin/bash -l
-
-module purge
-module load mdevaluate/dev
-python --version
-
-TMPDIR="./tmp"
-PYVERSION="$(python -c 'import sys; print("python{}.{}".format(sys.version_info.major, sys.version_info.minor))')"
-PYLIBDIR="$TMPDIR/lib/$PYVERSION/site-packages"
-
-rm -rf $TMPDIR
-mkdir -p $PYLIBDIR
-
-PYTHONPATH="$PYLIBDIR:$PYTHONPATH"
-
-if PYTHONPATH="$PYLIBDIR:$PYTHONPATH" python setup.py install --prefix=$TMPDIR
-then
-  scp -r $PYLIBDIR/*.egg niels@nas2:/nfsopt/mdevaluate/mdevaluate-dev/lib/$PYVERSION/site-packages
-fi

meta.yaml

@@ -1,13 +0,0 @@
-package:
-  name: "pygmx"
-  version: "0.2"
-
-source:
-  path: .
-
-requirements:
-  build:
-    - cython
-    - numpy
-  run:
-    - numpy