{
    "info": {
        "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 :: 3",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "==============================================\nExtinction/recolonisation coalescent simulator\n==============================================\n\nSimulates the coalescent for populations evolving in a spatial \ncontinuum under the extinction/recolonisation model. The simulations \nsupport:\n        \n- A sample of ``n`` individuals with ``m`` loci at arbitrary locations on a \n  torus of diameter ``L``.\n- Arbitrary recombination rates between adjacent loci.\n- An arbitrary number of classes of event occuring at fixed\n  rates. \n\nErcs supports both Python 2 and 3.\n\n\n-------------\nDocumentation\n-------------\n\nHere's a quick example for the impatient::\n\n        import ercs\n        sim = ercs.Simulator(10)\n        sim.sample = [None, (3, 2), (6, 4), (7, 0)]\n        sim.event_classes = [ercs.DiscEventClass(u=0.5, r=1)]\n        pi, tau = sim.run(1)\n\nFull documentation for ``ercs`` is available at `<http://jeromekelleher.github.com/ercs>`_.\n\n------------\nInstallation\n------------\n\nErcs depends on the `GNU Scientific Library <http://www.gnu.org/software/gsl/>`_,\nwhich must be installed before the ``ercs`` module 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\nOnce GSL has been installed we can build the ``ercs`` module using the \nstandard Python `methods <http://docs.python.org/install/index.html>`_. For \nexample, using pip we have ::\n        \n        $ sudo pip install ercs\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``ercs`` from `github <https://github.com/jeromekelleher/ercs>`_. \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``. For example, on FreeBSD we get something \nlike this::\n\n        $ python setup.py build\n        ... [Messages cut for brevity] ...\n        In file included from _ercsmodule.c:27:\n        lib/ercs.h:26:25: error: gsl/gsl_rng.h: No such file or directory\n        In file included from _ercsmodule.c:27:\n        lib/ercs.h:73: error: expected declaration specifiers or '...' before 'gsl_rng'\n        lib/ercs.h:94: error: expected specifier-qualifier-list before 'gsl_rng'\n        _ercsmodule.c: In function 'pyercs_simulate':\n        _ercsmodule.c:351: error: 'ercs_t' has no member named 'pi'\n        _ercsmodule.c:356: error: 'ercs_t' has no member named 'tau'\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\nErcs 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\nIt is also possible to run some tests on the low-level C library.\nTo do this, ``cd`` to the ``lib`` directory and run::\n\n        $ make check \n\nThis will build the C library test cases and run them. If compilation fails, it \nmay be necessary set ``LDFLAGS`` and ``CFLAGS`` as before:: \n\n        $ make CFLAGS=\"`gsl-config --cflags`\" LDFLAGS=\"`gsl-config --libs`\" check \n\n\n****************\nTested platforms\n****************\n\nErcs has been successfully built and tested on the following platforms:\n\n================        ========        ======          ========\nOperating system        Platform        Python          Compiler\n================        ========        ======          ========\nUbuntu 8.04             i386            2.5.2           gcc 4.2.3 \nNetBSD 5.0              i386            2.7.3           gcc 4.1.3\nFedora 17               i386            2.7.3           gcc 4.7.2\nFedora 17               i386            3.2.3           gcc 4.7.2\nCygwin                  i386            2.6.8           gcc 4.5.3\nUbuntu 12.04            x86-64          2.7.3           gcc 4.6.3\nUbuntu 12.04            x86-64          3.2.3           gcc 4.6.3\nFreeBSD 9.0             i386            3.2.2           gcc 4.2.2        \nFreeBSD 9.0             i386            2.7.2           gcc 4.2.2        \nFreeBSD 9.0             i386            3.1.4           clang 3.0 \nSolaris 11              x86-64          2.6.4           Sun C 5.12\nMac OSX 10.6.8          x86-64          2.6.1           gcc 4.2.1\nMac OSX 10.6.8          x86-64          3.2.3           gcc 4.2.1\nMac OS X 10.4.11        ppc             3.2.3           gcc 4.0.1\nMac OS X 10.4.11        ppc             2.7.3           gcc 4.0.1\nDebian wheezy           armv6l          2.7.3           gcc 4.6.3\nDebian squeeze          ppc64           2.6.6           gcc 4.4.5\t\nDebian squeeze          ppc64           3.1.3           gcc 4.4.5\t\n================        ========        ======          ========\n\nThe C library has additionally been compiled and tested with the \nfollowing processors and compilers:\n\n==========================================        ========\nPlatform                                          Compiler\n==========================================        ========\nLinux 2.6.18-164.15.1.el5 x86_64 GNU/Linux        Intel(R) C 11.0\nLinux 2.6.32-5-amd64 x86_64 GNU/Linux             gcc 4.4.5\nLinux 2.6.32-5-amd64 x86_64 GNU/Linux             clang 1.1 \nLinux 3.2.0-32-generic x86_64 GNU/Linux           gcc 4.6.3\nLinux 3.2.0-32-generic x86_64 GNU/Linux           clang 3.0 \nLinux 3.2.27+ armv6l GNU/Linux                    gcc 4.6.3\nLinux 2.6.32-5-powerpc64 ppc64 GNU/Linux          gcc 4.4.5\nLinux 2.6.32-5-powerpc64 ppc64 GNU/Linux          clang 1.1 \nSunOS 5.11 11.0 i86pc i386 i86pc                  Sun C 5.12\nSunOS 5.10 sun4u sparc SUNW,Ultra-4               Sun C 5.8\n==========================================        ========",
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