ports/129567: [New Port]math/py-pymc:Markov Chain Monte Carlo Sampling Toolkit

Wen Heping wenheping at gmail.com
Thu Dec 11 09:30:01 UTC 2008 

>Number:         129567
>Category:       ports
>Synopsis:       [New Port]math/py-pymc:Markov Chain Monte Carlo Sampling Toolkit
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Thu Dec 11 09:30:00 UTC 2008
>Closed-Date:
>Last-Modified:
>Originator:     Wen Heping
>Release:        FreeBSD-8.0 Current
>Organization:
ChangAn Middle School
>Environment:
FreeBSD fb8.wenjing.com 8.0-CURRENT FreeBSD 8.0-CURRENT #0: Sun Sep 21 18:56:51 HKT 2008     root at fb8.wenjing.com:/usr/obj/usr/src/sys/GENERIC  i386
>Description:
Bayesian estimation, particularly using Markov chain Monte
Carlo (MCMC), is an increasingly relevant approach to
statistical estimation. However, few statistical software
packages implement MCMC samplers, and they are non-trivial
 to code by hand. pymc is a python package that implements
the Metropolis-Hastings algorithm as a python class, and is
extremely flexible and applicable to a large suite of problems.
pymc includes methods for summarizing output, plotting,
goodness-of-fit and convergence diagnostics.

WWW:    http://pypi.python.org/pypi/pymc/
>How-To-Repeat:

>Fix:


Patch attached with submission follows:

# This is a shell archive.  Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file".  Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
#	py-pymc
#	py-pymc/pkg-plist
#	py-pymc/pkg-descr
#	py-pymc/distinfo
#	py-pymc/Makefile
#
echo c - py-pymc
mkdir -p py-pymc > /dev/null 2>&1
echo x - py-pymc/pkg-plist
sed 's/^X//' >py-pymc/pkg-plist << 'b53346d5093e09b427e94645320d457d'
X%%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.py
X%%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.pyc
X%%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.pyo
X%%PYTHON_SITELIBDIR%%/pymc/Container.py
X%%PYTHON_SITELIBDIR%%/pymc/Container.pyc
X%%PYTHON_SITELIBDIR%%/pymc/Container.pyo
X%%PYTHON_SITELIBDIR%%/pymc/Container_values.so
X%%PYTHON_SITELIBDIR%%/pymc/InstantiationDecorators.py
X%%PYTHON_SITELIBDIR%%/pymc/InstantiationDecorators.pyc
X%%PYTHON_SITELIBDIR%%/pymc/InstantiationDecorators.pyo
X%%PYTHON_SITELIBDIR%%/pymc/LazyFunction.so
X%%PYTHON_SITELIBDIR%%/pymc/MCMC.py
X%%PYTHON_SITELIBDIR%%/pymc/MCMC.pyc
X%%PYTHON_SITELIBDIR%%/pymc/MCMC.pyo
X%%PYTHON_SITELIBDIR%%/pymc/Matplot.py
X%%PYTHON_SITELIBDIR%%/pymc/Matplot.pyc
X%%PYTHON_SITELIBDIR%%/pymc/Matplot.pyo
X%%PYTHON_SITELIBDIR%%/pymc/Model.py
X%%PYTHON_SITELIBDIR%%/pymc/Model.pyc
X%%PYTHON_SITELIBDIR%%/pymc/Model.pyo
X%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/ModelPosterior.py
X%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/ModelPosterior.pyc
X%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/ModelPosterior.pyo
X%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/__init__.py
X%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/__init__.pyc
X%%PYTHON_SITELIBDIR%%/pymc/MultiModelInference/__init__.pyo
X%%PYTHON_SITELIBDIR%%/pymc/Node.py
X%%PYTHON_SITELIBDIR%%/pymc/Node.pyc
X%%PYTHON_SITELIBDIR%%/pymc/Node.pyo
X%%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.py
X%%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.pyc
X%%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.pyo
X%%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.py
X%%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.pyc
X%%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.pyo
X%%PYTHON_SITELIBDIR%%/pymc/ScipyDistributions.py
X%%PYTHON_SITELIBDIR%%/pymc/ScipyDistributions.pyc
X%%PYTHON_SITELIBDIR%%/pymc/ScipyDistributions.pyo
X%%PYTHON_SITELIBDIR%%/pymc/StepMethods.py
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X%%PYTHON_SITELIBDIR%%/pymc/StepMethods.pyo
X%%PYTHON_SITELIBDIR%%/pymc/__init__.py
X%%PYTHON_SITELIBDIR%%/pymc/__init__.pyc
X%%PYTHON_SITELIBDIR%%/pymc/__init__.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/database/__init__.pyc
X%%PYTHON_SITELIBDIR%%/pymc/database/__init__.pyo
X%%PYTHON_SITELIBDIR%%/pymc/database/base.py
X%%PYTHON_SITELIBDIR%%/pymc/database/base.pyc
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X%%PYTHON_SITELIBDIR%%/pymc/database/hdf5.py
X%%PYTHON_SITELIBDIR%%/pymc/database/hdf5.pyc
X%%PYTHON_SITELIBDIR%%/pymc/database/hdf5.pyo
X%%PYTHON_SITELIBDIR%%/pymc/database/mysql.py
X%%PYTHON_SITELIBDIR%%/pymc/database/mysql.pyc
X%%PYTHON_SITELIBDIR%%/pymc/database/mysql.pyo
X%%PYTHON_SITELIBDIR%%/pymc/database/no_trace.py
X%%PYTHON_SITELIBDIR%%/pymc/database/no_trace.pyc
X%%PYTHON_SITELIBDIR%%/pymc/database/no_trace.pyo
X%%PYTHON_SITELIBDIR%%/pymc/database/pickle.py
X%%PYTHON_SITELIBDIR%%/pymc/database/pickle.pyc
X%%PYTHON_SITELIBDIR%%/pymc/database/pickle.pyo
X%%PYTHON_SITELIBDIR%%/pymc/database/ram.py
X%%PYTHON_SITELIBDIR%%/pymc/database/ram.pyc
X%%PYTHON_SITELIBDIR%%/pymc/database/ram.pyo
X%%PYTHON_SITELIBDIR%%/pymc/database/sqlite.py
X%%PYTHON_SITELIBDIR%%/pymc/database/sqlite.pyc
X%%PYTHON_SITELIBDIR%%/pymc/database/sqlite.pyo
X%%PYTHON_SITELIBDIR%%/pymc/database/txt.py
X%%PYTHON_SITELIBDIR%%/pymc/database/txt.pyc
X%%PYTHON_SITELIBDIR%%/pymc/database/txt.pyo
X%%PYTHON_SITELIBDIR%%/pymc/decorators.py
X%%PYTHON_SITELIBDIR%%/pymc/decorators.pyc
X%%PYTHON_SITELIBDIR%%/pymc/decorators.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/diagnostics.pyc
X%%PYTHON_SITELIBDIR%%/pymc/diagnostics.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/examples/__init__.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/examples/custom_step.pyo
X%%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.py
X%%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.pyc
X%%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/examples/model_1.pyc
X%%PYTHON_SITELIBDIR%%/pymc/examples/model_1.pyo
X%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.py
X%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.pyc
X%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.pyo
X%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.py
X%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.pyc
X%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/examples/model_2.pyc
X%%PYTHON_SITELIBDIR%%/pymc/examples/model_2.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/examples/straightlinefit.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/examples/weibull_fit.pyc
X%%PYTHON_SITELIBDIR%%/pymc/examples/weibull_fit.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/gp/Mean.py
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X%%PYTHON_SITELIBDIR%%/pymc/gp/NearlyFullRankCovariance.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/gp/PyMC_objects.pyc
X%%PYTHON_SITELIBDIR%%/pymc/gp/PyMC_objects.pyo
X%%PYTHON_SITELIBDIR%%/pymc/gp/Realization.py
X%%PYTHON_SITELIBDIR%%/pymc/gp/Realization.pyc
X%%PYTHON_SITELIBDIR%%/pymc/gp/Realization.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/gp/__init__.pyc
X%%PYTHON_SITELIBDIR%%/pymc/gp/__init__.pyo
X%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/__init__.py
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X%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/bases.py
X%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/bases.pyc
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X%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/cov_utils.py
X%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/cov_utils.pyc
X%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/cov_utils.pyo
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X%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/isotropic_cov_funs.so
X%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.py
X%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.pyc
X%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.pyo
X%%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.py
X%%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.pyc
X%%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.pyo
X%%PYTHON_SITELIBDIR%%/pymc/gp/incomplete_chol.so
X%%PYTHON_SITELIBDIR%%/pymc/gp/linalg_utils.so
X%%PYTHON_SITELIBDIR%%/pymc/graph.py
X%%PYTHON_SITELIBDIR%%/pymc/graph.pyc
X%%PYTHON_SITELIBDIR%%/pymc/graph.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/__init__.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/__init__.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/__init__.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/check_dependencies.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/check_dependencies.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/check_dependencies.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/objectmodel.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/objectmodel.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/objectmodel.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/screen.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/screen.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/screen.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_GP_MCMC.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_GP_MCMC.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_GP_MCMC.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_LazyFunction.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_LazyFunction.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_LazyFunction.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_MCMCSampler.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_MCMCSampler.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_MCMCSampler.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_adaptive.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_adaptive.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_adaptive.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_basiscov.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_basiscov.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_basiscov.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_binary_step.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_binary_step.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_binary_step.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_container.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_container.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_container.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_convergence.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_convergence.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_convergence.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_cov.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_cov.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_cov.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_database.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_database.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_database.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_distributions.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_distributions.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_distributions.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_graph.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_graph.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_graph.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_instantiation.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_instantiation.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_instantiation.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_interactive.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_interactive.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_interactive.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_joint.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_joint.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_joint.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_mean.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_mean.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_mean.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_model_ave.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_model_ave.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_model_ave.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_norm_approx.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_norm_approx.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_norm_approx.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_observation.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_observation.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_observation.pyo
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.py
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.pyc
X%%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.pyo
X%%PYTHON_SITELIBDIR%%/pymc/utils.py
X%%PYTHON_SITELIBDIR%%/pymc/utils.pyc
X%%PYTHON_SITELIBDIR%%/pymc/utils.pyo
X at dirrm %%PYTHON_SITELIBDIR%%/pymc/MultiModelInference
X at dirrm %%PYTHON_SITELIBDIR%%/pymc/database
X at dirrm %%PYTHON_SITELIBDIR%%/pymc/examples
X at dirrm %%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs
X at dirrm %%PYTHON_SITELIBDIR%%/pymc/gp
X at dirrm %%PYTHON_SITELIBDIR%%/pymc/tests
X at dirrm %%PYTHON_SITELIBDIR%%/pymc
b53346d5093e09b427e94645320d457d
echo x - py-pymc/pkg-descr
sed 's/^X//' >py-pymc/pkg-descr << '028581d951f44e8b077ccfbd8423b8f4'
XBayesian estimation, particularly using Markov chain Monte
XCarlo (MCMC), is an increasingly relevant approach to
Xstatistical estimation. However, few statistical software
Xpackages implement MCMC samplers, and they are non-trivial
X to code by hand. pymc is a python package that implements
Xthe Metropolis-Hastings algorithm as a python class, and is
Xextremely flexible and applicable to a large suite of problems.
Xpymc includes methods for summarizing output, plotting,
Xgoodness-of-fit and convergence diagnostics.
X
XWWW:	http://pypi.python.org/pypi/pymc/
028581d951f44e8b077ccfbd8423b8f4
echo x - py-pymc/distinfo
sed 's/^X//' >py-pymc/distinfo << '4701a20f5e0f2e6342883d84867903f6'
XMD5 (pymc-2.0rc1.tar.gz) = b8e8bc8e72b23a0215d10e13839738d8
XSHA256 (pymc-2.0rc1.tar.gz) = fdb7b27c01509e2293d8905697feee3a157478393683eab3deb46a02f486f70a
XSIZE (pymc-2.0rc1.tar.gz) = 978218
4701a20f5e0f2e6342883d84867903f6
echo x - py-pymc/Makefile
sed 's/^X//' >py-pymc/Makefile << 'b70d98f3f14233c734202ca4805d7059'
X# New ports collection makefile for:	py-pymc
X# Date created:		2008-12-10
X# Whom:			Wen Heping <wenheping at gmail.com>
X#
X# $FreeBSD$
X#
X
XPORTNAME=	pymc
XPORTVERSION=	2.0r1
XCATEGORIES=	math python
XMASTER_SITES=	CHEESESHOP
XPKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
XDISTNAME=	${PORTNAME}-2.0rc1
X
XMAINTAINER=	wenheping at gmail.com
XCOMMENT=	Markov Chain Monte Carlo Sampling Toolkit
X
XBUILD_DEPENDS=	${PYNUMPY}
XRUN_DEPENDS=	${BUILD_DEPENDS}
X#LIB_DEPENDS=	lapack.4:${PORTSDIR}/math/lapack
X
XUSE_PYTHON=	yes
XUSE_PYDISTUTILS=	yes
XPYDISTUTILS_EGGINFO=	${DISTNAME}-${PYTHON_VERSION:S/thon//}.egg-info
X
X.include <bsd.port.mk>
b70d98f3f14233c734202ca4805d7059
exit



>Release-Note:
>Audit-Trail:
>Unformatted:

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