Skip to content

Commit

Permalink
cleanup of README/INSTALL/LICENSE
Browse files Browse the repository at this point in the history 
- removed all licensing with respect to KD-tree/Biopython: we do not ship any
  Biopython code anymore
- changed license description for Gromacs xdrlib: it is now BSD-2-clause (like);
  the LICENSE file is correct
- removed any mentioning of LGPL for libmdaxdr because it is GPL v2 like everything else
- changed wiki and doc links to use our redirects docs.mdanalysis.org and wiki.mdanalysis.org
- cleaned up INSTALL: added quick install at top, removed most of the crud, and just link
  to the wiki
- changed the copyright in README to be in line with #993
  • Loading branch information
@orbeckst
orbeckst committed Nov 29, 2016
1 parent 8db4b39 commit 3c3eeae
Show file tree
Hide file tree
Showing 4 changed files with 58 additions and 334 deletions.
285 changes: 28 additions & 257 deletions package/INSTALL
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,56 +2,44 @@
Installing MDAnalysis
=====================

Installing using binary packages (for Ubuntu/Debian users)
==========================================================
Quick installation instructions
===============================

Binary packages of MDAnalysis are available for Ubuntu and Debian users.
They can be downloaded from the following PPA:
http://www.mdanalysis.org/pages/installation_quick_start/

https://launchpad.net/~seb-buch/+archive/mdanalysis

It is possible to add this PPA to your software sources. To do so,
run the following command ::
From the Python package index (pip)
-----------------------------------

To install the latest stable release with pip
http://www.pip-installer.org/en/latest/index.html do::

sudo add-apt-repository ppa:seb-buch/mdanalysis
pip install --upgrade MDAnalysis

After updating your package index files, you should be able to install
the following packages:
To run the test cases and examples, also install the unit tests (about 20 MiB in size)::

* python-mdanalysis (main package - required to used MDAnalysis)
* python-mdanalysis-doc (documentation - optional)
* python-mdanalysis.tests (test suite - optional)
* python-mdanalysis.tests-data (data used by tests - optional
but required to run tests)
* python-griddataformats (additional package - optional)
pip install --upgrade MDAnalysisTests
python -c 'import MDAnalysisTests; MDAnalysisTests.run()'

Note 1: Dependencies such python-numpy or python-biopython will also be installed (if needed).
(The tests can take a long time to run.)

Note 2: Not-required (but yet recommended) packages such as netCDF4,
matplotlib or python-scipy will not be installed automatically!

Requirements for installing from source
=======================================
With conda
----------

In order to build MDAnalysis from source, you will need
To install the lastest stable release with conda
http://conda.pydata.org/docs/ do::

* python (>=2.6)
* a C and a C++ compiler (e.g. GNU gcc),
* the python header files (typically in a package python-dev),
* numpy to compile the DCD and XTC reader and other extensions,
conda config --add channels MDAnalysis
conda install mdanalysis

See *Additional non-standard packages* below for what else you need at
run time.
To upgrade to the latest stable release.

Stable releases are distributed as tar files from
https://pypi.python.org/pypi/MDAnalysis/. The current source code can
als be obtained from the SVN (subversion) source code repository
https://github.com/MDAnalysis/mdanalysis.
conda update mdanalysis

The primary dependency is NumPy http://numpy.scipy.org, which needs to
be installed before MDAnalysis can be installed itself. (matplotlib
http://matplotlib.org/ is a useful addition to plot results generated
with MDAnalysis and is recommended.)
The conda packages currently only support serial calculations. If you
plan to use the parallel OpenMP algorithms you need to install
MDAnalysis with pip and have a working OpenMP installation.


Help
Expand Down Expand Up @@ -79,226 +67,9 @@ mention your operating system (e.g. Ubuntu 14.04) and Python version
problem.


Getting the source
==================

Download a tar ball from https://pypi.python.org/pypi/MDAnalysis/; these
instructions apply to versions 0.6.0-rc2 or higher.

Alternatively, check out the MDAnalysis directory from the git
repository at https://github.com/MDAnalysis/mdanalysis. In most cases
simply do ::

git clone https://github.com/MDAnalysis/mdanalysis
cd mdanalysis



Installation from source
========================

You will need a C compiler to compile the DCD and XTC reader and other
extensions.

In principle, installation should be as simple as ::

python setup.py build
python setup.py install

This installs MDAnalysis in the system wide python directory; this may
require administrative privileges.

It is also possible to use --prefix, --home, or --user options for
setup.py to install in a different (probably your private) python
directory hierarchy. ``python setup.py install --help`` should show
you your options.

If you have problem at this stage then have a look at the operating
system specific notes at the end of this file or look in the issue
tracker --- maybe the problem is recognized and a work around can be
found in the comments



Selecting an installation directory
-----------------------------------

In order to install in a non-default directory one can use various
options to setup (see --help) such as ::

python setup.py install --prefix LOCAL_DIRECTORY

or any of the other options of distutil's setup.py to install in
alternative directories, for instance

python setup.py install --user



Easy Install
------------

We are also exploring the use of easy_install. This is experimental
but you might be able to do ::

easy_install [options] ./mdanalysis

A developer installation (that immediately reflects changes to the
sources) with ::

cd ./mdanalysis
python setup develop [options]


If you want to use optional functionality (such as running some of the
analysis code in the MDAnalysis.analysis module or running the test
suite) then you can have easy_install fetch and install additionaly
required packages if you have not been able to install them through
your package manager (always preferred!). For instance,

cd mdanalysis
easy_install [options] . mdanalysis[AMBER,analysis]

should also install packages required for analysis and the AMBER
netcdf reader/writer (but see below for hints on the packages required
to make AMBER work).



Additional non-standard python packages
=======================================

See the operating system specific notes above for hints how to get the
necessary packages through the native package management
system. Please add your own (eg for RPM based systems which the
developers are not using heavily).

python-dev includes Python.h, which is required for compiling. numpy
is used at the compilation stage to find maths libraries. scipy and
biopython are only needed when one wants to use all MDAnalysis
functions but are not required for compiling.

Required python packages
------------------------

In order to use the library in your own python code you will need at least

* numpy of version 1.0.3 or greater (http://numpy.scipy.org/)
* scipy (http://www.scipy.org/)
* BioPython's Bio.PDB (http://biopython.org)
* networkx (http://networkx.lanl.gov/) --- for analysis of lipid
leaflets via MDAnalysis.analysis.leaflet
* GridDataFormats (http://pypi.python.org/pypi/GridDataFormats)

If you want to operate on AMBER binary trajectories (NetCDF) then you
will need to have working NetCDF support based on the netcdf4-python
package:

* netcdf4-python (https://github.com/Unidata/netcdf4-python)

If you get a 'ValueError: did not find HDF5 headers' during
installation then you should install the hdf5 development
package through your package manager (see below for some hints
on how to do this for Linux and Mac OS X).

See also https://github.com/MDAnalysis/mdanalysis/wiki/netcdf
for notes on how to compile HDF5 and netcdf.

Optional python packages (used in MDAnalysis.analysis):

* nose (http://somethingaboutorange.com/mrl/projects/nose/) -- for testing


Running test cases
==================

If you want to check that your installation works correctly you can
run the test suite. It requires that you have a recent version of
NumPy, the Python package 'nose', and the MDAnalysisTests (the test
code and a collection of structures and trajectories that are used as
test input).

Download and install MDAnalysisTestData from

https://pypi.python.org/pypi/MDAnalysisTests

(or get the development version from https://github.com/MDAnalysis/mdanalysis)

Pick a file named `MDAnalysisTests-X.Y.Z.tar.gz` where the release
number X.Y.Z should match the release number of MDAnalysis
itself. E.g. For MDAnalysis-0.7.6 you would get MDAnalysisTests-0.7.6.

For more details on the test cases see https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests


.. Note:: In order to install the other packages you can use
easy_install with the special `test` specifier::

easy_install MDAnalysis[tests]


OS specific notes
=================

Linux
-----

* The GNU gcc compiler is the default and should be used
automatically; in particular you will not have to do anything with
setup.cfg. This should work if you have no file named setup.cfg in
your MDAnalysis directory. (If you want to use setup.cfg and use GNU
gcc simply comment out the compiler=intel line in the template:

# compiler=intel

(However, compiling with Intel compilers has not been tested for a
while. Send questions and feedback to the mailing list
http://groups.google.com/group/mdnalysis-discussion )

* To compile with the Intel compilers, set in setup.cfg ::

[build]
compiler=intel

(Although, in some instances the KDTree does not compile with
Intel. In this case please file a bug and use gcc in the mean time.)


* Install prerequisite packages on Ubuntu or Debian with

sudo aptitude install python-dev python-cython python-numpy g++

Install packages needed for full functionality

sudo aptitude install python-scipy python-matplotlib python-biopython \
python-netcdf4 libhdf5-dev

(The netcdf and libhdf5-dev packages are only required if you want
to be able to process AMBER netcdf (binary) trajectories. If you
don't have netcdf4 available from your package manager (eg Ubuntu
10.04) then follow the instructions for installing netcdf4 given at
and http://code.google.com/p/mdanalysis/wiki/netcdf.


Mac OS X
--------
OS specific notes


* Tested with Mac OS X 10.4.11+fink and 10.6.2+MacPorts.

* MacPorts hints::

port install py26-numpy py26-cython
port install py26-scipy py26-matplotlib py26-biopython hdf5 netcdf+dap+netcdf4

(The netcdf and libhdf5-dev packages are only required if you want
to be able to process AMBER netcdf (binary) trajectories.)
Installing from source
======================

* fink also worked in the past but the developers have not had any
recent experience with fink and MDAnalysis
Source code is available at https://github.com/MDAnalysis/mdanalysis

* NOTE: Use the Apple-provided gcc, not the fink provided
one. Apparently, only Apple's gcc has the -arch flag that appears to
be required for python setup.py install. (Thanks to Justin Lemkul
for pointing it out).
See http://wiki.mdanalysis.org/Install for further instructions.
22 changes: 0 additions & 22 deletions package/LICENSE
View file
Original file line number Diff line number Diff line change
Expand Up @@ -421,28 +421,6 @@ 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 WITH THE SOFTWARE.

==========================================================================

Biopython License Agreement

Permission to use, copy, modify, and distribute this software and its
documentation with or without modifications and for any purpose and
without fee is hereby granted, provided that any copyright notices
appear in all copies and that both those copyright notices and this
permission notice appear in supporting documentation, and that the
names of the contributors or copyright holders not be used in
advertising or publicity pertaining to distribution of the software
without specific prior permission.

THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE


==========================================================================

transformations module
Expand Down
Loading

0 comments on commit 3c3eeae

Please sign in to comment.