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        "author": "Jerome Kelleher",
        "author_email": "jerome.kelleher@ed.ac.uk",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Other Environment",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Operating System :: POSIX",
            "Programming Language :: C",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "===================================================\nEfficient coalescent simulation in continuous space\n===================================================\n\nSimulates the coalescent for populations evolving in a spatial \ncontinuum under the extinction/recolonisation model. This \npackage is a specialisation of the `ercs <https://pypi.python.org/pypi/ercs>`_\npackage, and provides a much more efficient method of \nsimulating the spatial coalescent for the disc model. \nA very similar (but not identical) interface to ``ercs``\nis provided.\n\n\nThe simulations \nsupport:\n        \n- A sample of ``n`` individuals with ``m`` loci at arbitrary locations on a \n  torus of diameter ``L``.\n- A fixed recombination rate between pairs of adjacent loci. \n- An arbitrary number of classes of event occuring at fixed\n  rates. \n- Simulations in one and two dimensions.\n- Access to the locations of ancestors at any time in the past.\n- Simulations of the locations of all pedigree ancestors, as well \n  as the genetic ancestors.\n\nThe ``discsim`` module supports Python 2 and 3.\n\n-------------\nDocumentation\n-------------\n\nHere's a quick example for the impatient::\n\n        import ercs\n        import discsim\n        sim = discsim.Simulator(10)\n        sim.sample = [None, (3, 2), (6, 4), (7, 0)]\n        sim.event_classes = [ercs.DiscEventClass(u=0.5, r=1)]\n        sim.run()\n        pi, tau = sim.get_history()\n\n\nFull documentation for ``discsim`` is available at \n`<http://pythonhosted.org/discsim>`_.\n\n------------\nInstallation\n------------\n\n*******************************\nQuick install for Debian/Ubuntu\n*******************************\n\nIf you are running Debian or Ubuntu, this should get you up and running quickly::\n\n        $ sudo apt-get install python-dev libgsl0-dev \n        $ sudo pip install ercs discsim\n\nFor Python 3, use ``python3-dev`` and ``pip3``.\n\n********************\nGeneral instructions\n********************\n\nThe ``discsim`` module \ndepends on the `GNU Scientific Library <http://www.gnu.org/software/gsl/>`_,\nwhich must be installed before it can be built.\nFortunately, this is straightforward on most platforms. For example, \non Debian or Ubuntu use::\n\n        $ sudo apt-get install libgsl0-dev\n\nor on Fedora::\n\n        $ sudo yum install gsl-devel\n\nGSL is available on most packaging systems; if it is not available on your\nplatform, it can be installed from source.\n\nThe ``discsim`` module also depends on the \n`ercs <https://pypi.python.org/pypi/ercs>`_\nPython module, which \nmust also be installed, using the same methods as outlined below.\n\nOnce GSL has been installed we can build the ``discsim`` module using the \nstandard Python `methods <http://docs.python.org/install/index.html>`_. For \nexample, using pip we have ::\n        \n        $ sudo pip install discsim\n\nOr, we can manually download the package, unpack it and then run::\n        \n        $ python setup.py build\n        $ sudo python setup.py install\n\nMost of the time this will compile and install the module without difficulty.\n\nIt is also possible to download the latest development version of \n``discsim`` from `github <https://github.com/jeromekelleher/discsim>`_. \n\n******************\nPotential problems\n******************\n\nOn platforms that GSL is not available as part of the native packaging \nsystem (or GSL was installed locally because of non-root access)\nthere can be issues with finding the correct headers and libraries\nwhen compiling ``ercs`` and ``discsim``. For example, on FreeBSD we get something \nlike this::\n\n        $ python setup.py build\n        ... [Messages cut for brevity] ...\n        _discsimmodule.c:515: error: 'sim_t' has no member named 'time'\n        _discsimmodule.c: In function 'Simulator_get_num_reproduction_events':\n        _discsimmodule.c:529: error: 'sim_t' has no member named 'num_reproduction_events'\n        _discsimmodule.c: In function 'Simulator_get_history':\n        _discsimmodule.c:743: error: 'sim_t' has no member named 'pi'\n        _discsimmodule.c:748: error: 'sim_t' has no member named 'tau'\n        _discsimmodule.c: In function 'Simulator_run':\n        _discsimmodule.c:789: error: 'sim_t' has no member named 'time'\n        error: command 'cc' failed with exit status 1\n        \nThis can be remedied by using the ``gsl-config`` program to set the \nthe ``LDFLAGS`` and ``CFLAGS`` environment variables to \ntheir correct values::\n        \n         $ CFLAGS=`gsl-config --cflags` LDFLAGS=`gsl-config --libs` python setup.py build\n\n*****\nTests\n*****\n\n``discsim`` provides some test cases to ensure that the installation has gone smoothly.\nIt is a good idea to run these immediately after installation::\n\n        $ python tests.py\n\n\n****************\nTested platforms\n****************\n\nDiscsim has been successfully built and tested on the following platforms:\n\n================        ========        ======          ========\nOperating system        Platform        Python          Compiler\n================        ========        ======          ========\nDebian wheezy           x86_64          2.7.3           gcc 4.7.2\t\nDebian wheezy           x86_64          3.2.3           gcc 4.7.2\t\nDebian wheezy           x86             2.7.3           gcc 4.7.2\t\nDebian squeeze          ppc64           2.6.6           gcc 4.4.5\t\nDebian squeeze          ppc64           3.1.3           gcc 4.4.5\t\nDebian squeeze          x86_64          2.6.6           gcc 4.4.5\t\nDebian squeeze          x86_64          3.1.3           gcc 4.4.5\t\nFreeBSD 9.2             x86_64          2.7.5           gcc 4.2.1\nFreeBSD 9.2             x86_64          3.3.2           gcc 4.2.1\nFedora 19               x86_64          2.7.5           gcc 4.8.1\nFedora 19               x86_64          3.3.2           gcc 4.8.1\nSunOS 5.10              SPARC           3.3.2           gcc 4.8.0 \n================        ========        ======          ========",
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        "keywords": "Coalescent simulation,Continuous space",
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