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Date: Thu, 14 Nov 2013 13:02:46 +0200 (EET)
From: Johannes Jost Meixner <xmj@chaot.net>
To: FreeBSD-gnats-submit@freebsd.org
Cc: wenheping@gmail.com
Subject: [PATCH] math/py-pymc: update to 2.3,1
X-Send-Pr-Version: 3.113
X-GNATS-Notify: wenheping@gmail.com

>Number:         183951
>Category:       ports
>Synopsis:       [PATCH] math/py-pymc: update to 2.3,1
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    wen
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Thu Nov 14 11:10:00 UTC 2013
>Closed-Date:    Fri Dec 06 15:42:36 UTC 2013
>Last-Modified:  Fri Dec  6 15:50:00 UTC 2013
>Originator:     Johannes Jost Meixner
>Release:        FreeBSD 11.0-CURRENT amd64
>Organization:
>Environment:
System: FreeBSD mx12.chaot.net 11.0-CURRENT FreeBSD 11.0-CURRENT #3: Thu Nov  7 16:08:22 EET
>Description:
- Update to 2.3,1
- Add license
- Add matplotlib dependency as per docs/INSTALL.rst
- Add DOCS option
- Add stage support

Port maintainer (wenheping@gmail.com) is cc'd.

Generated with FreeBSD Port Tools 0.99_8 (mode: update, diff: ports)
>How-To-Repeat:
>Fix:

--- py27-pymc-2.3,1.patch begins here ---
diff -ruN /usr/ports/math/py-pymc/Makefile ./Makefile
--- /usr/ports/math/py-pymc/Makefile	2013-10-26 03:52:33.000000000 +0300
+++ ./Makefile	2013-11-14 12:58:21.017349595 +0200
@@ -1,9 +1,8 @@
 # Created by: Wen Heping <wenheping@gmail.com>
-# $FreeBSD: math/py-pymc/Makefile 331644 2013-10-26 00:52:33Z gerald $
+# $FreeBSD$
 
 PORTNAME=	pymc
-PORTVERSION=	2.0
-PORTREVISION=	1
+PORTVERSION=	2.3
 PORTEPOCH=	1
 CATEGORIES=	math python
 MASTER_SITES=	CHEESESHOP
@@ -12,11 +11,35 @@
 MAINTAINER=	wenheping@gmail.com
 COMMENT=	Markov Chain Monte Carlo Sampling Toolkit
 
-BUILD_DEPENDS=	${PYNUMPY}
-RUN_DEPENDS:=	${BUILD_DEPENDS}
+LICENSE=	AFL
+LICENSE_NAME=	Academic Free License
+LICENSE_FILE=	${WRKSRC}/LICENSE
+LICENSE_PERMS=	auto-accept dist-mirror dist-sell pkg-mirror pkg-sell
+
+BUILD_DEPENDS=	${PYNUMPY} \
+				${PYTHON_PKGNAMEPREFIX}matplotlib>0:${PORTSDIR}/math/py-matplotlib
+LIB_DEPENDS=	liblapack.so:${PORTSDIR}/math/lapack \
+	libblas.so:${PORTSDIR}/math/blas
+RUN_DEPENDS=	${PYNUMPY} \
+				${PYTHON_PKGNAMEPREFIX}matplotlib>0:${PORTSDIR}/math/py-matplotlib
+
+OPTIONS_DEFINE=	DOCS
+DOCSDIR=	${PREFIX}/share/doc/py-${PORTNAME}
 
 USE_PYTHON=	yes
 USE_PYDISTUTILS=	yes
+PYTHON_P3K_PLIST_HACK=	yes
+PORTDOCS=	*
+
+post-install:
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/flib.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/cov_funs/distances.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/cov_funs/isotropic_cov_funs.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/incomplete_chol.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/linalg_utils.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/Container_values.so
+	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/LazyFunction.so
+	${MKDIR} ${STAGEDIR}${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/docs/*.rst ${STAGEDIR}${DOCSDIR}
 
-NO_STAGE=	yes
 .include <bsd.port.mk>
diff -ruN /usr/ports/math/py-pymc/distinfo ./distinfo
--- /usr/ports/math/py-pymc/distinfo	2012-07-14 16:54:48.000000000 +0300
+++ ./distinfo	2013-11-14 10:22:13.226930415 +0200
@@ -1,2 +1,2 @@
-SHA256 (pymc-2.0.tar.gz) = 15bbf1e0df9e080d367d639462c4b2b9290826ca069a76ac2bc79d795fe6e653
-SIZE (pymc-2.0.tar.gz) = 1200416
+SHA256 (pymc-2.3.tar.gz) = db029c59d6a04f0c97d88993151c4ee58c76b9ad5c71ead7ee250088ba4cce0d
+SIZE (pymc-2.3.tar.gz) = 13080085
diff -ruN /usr/ports/math/py-pymc/pkg-descr ./pkg-descr
--- /usr/ports/math/py-pymc/pkg-descr	2012-07-14 16:54:48.000000000 +0300
+++ ./pkg-descr	2013-11-14 10:43:55.937529554 +0200
@@ -1,11 +1,9 @@
-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.
+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/
+WWW: http://pypi.python.org/pypi/pymc/
diff -ruN /usr/ports/math/py-pymc/pkg-plist ./pkg-plist
--- /usr/ports/math/py-pymc/pkg-plist	2012-07-14 16:54:48.000000000 +0300
+++ ./pkg-plist	2013-11-14 12:27:27.886763032 +0200
@@ -1,3 +1,7 @@
+%%PYTHON_SITELIBDIR%%/pymc-2.3-py2.7.egg-info
+%%PYTHON_SITELIBDIR%%/pymc/CircularStochastic.py
+%%PYTHON_SITELIBDIR%%/pymc/CircularStochastic.pyc
+%%PYTHON_SITELIBDIR%%/pymc/CircularStochastic.pyo
 %%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.py
 %%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.pyc
 %%PYTHON_SITELIBDIR%%/pymc/CommonDeterministics.pyo
@@ -24,6 +28,9 @@
 %%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.py
 %%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.pyc
 %%PYTHON_SITELIBDIR%%/pymc/NormalApproximation.pyo
+%%PYTHON_SITELIBDIR%%/pymc/NumpyDeterministics.py
+%%PYTHON_SITELIBDIR%%/pymc/NumpyDeterministics.pyc
+%%PYTHON_SITELIBDIR%%/pymc/NumpyDeterministics.pyo
 %%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.py
 %%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.pyc
 %%PYTHON_SITELIBDIR%%/pymc/PyMCObjects.pyo
@@ -36,6 +43,9 @@
 %%PYTHON_SITELIBDIR%%/pymc/__init__.py
 %%PYTHON_SITELIBDIR%%/pymc/__init__.pyc
 %%PYTHON_SITELIBDIR%%/pymc/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pymc/calc_utils.py
+%%PYTHON_SITELIBDIR%%/pymc/calc_utils.pyc
+%%PYTHON_SITELIBDIR%%/pymc/calc_utils.pyo
 %%PYTHON_SITELIBDIR%%/pymc/database/__init__.py
 %%PYTHON_SITELIBDIR%%/pymc/database/__init__.pyc
 %%PYTHON_SITELIBDIR%%/pymc/database/__init__.pyo
@@ -45,9 +55,9 @@
 %%PYTHON_SITELIBDIR%%/pymc/database/hdf5.py
 %%PYTHON_SITELIBDIR%%/pymc/database/hdf5.pyc
 %%PYTHON_SITELIBDIR%%/pymc/database/hdf5.pyo
-%%PYTHON_SITELIBDIR%%/pymc/database/mysql.py
-%%PYTHON_SITELIBDIR%%/pymc/database/mysql.pyc
-%%PYTHON_SITELIBDIR%%/pymc/database/mysql.pyo
+%%PYTHON_SITELIBDIR%%/pymc/database/hdf5ea.py
+%%PYTHON_SITELIBDIR%%/pymc/database/hdf5ea.pyc
+%%PYTHON_SITELIBDIR%%/pymc/database/hdf5ea.pyo
 %%PYTHON_SITELIBDIR%%/pymc/database/no_trace.py
 %%PYTHON_SITELIBDIR%%/pymc/database/no_trace.pyc
 %%PYTHON_SITELIBDIR%%/pymc/database/no_trace.pyo
@@ -63,6 +73,9 @@
 %%PYTHON_SITELIBDIR%%/pymc/database/txt.py
 %%PYTHON_SITELIBDIR%%/pymc/database/txt.pyc
 %%PYTHON_SITELIBDIR%%/pymc/database/txt.pyo
+%%PYTHON_SITELIBDIR%%/pymc/datatypes.py
+%%PYTHON_SITELIBDIR%%/pymc/datatypes.pyc
+%%PYTHON_SITELIBDIR%%/pymc/datatypes.pyo
 %%PYTHON_SITELIBDIR%%/pymc/decorators.py
 %%PYTHON_SITELIBDIR%%/pymc/decorators.pyc
 %%PYTHON_SITELIBDIR%%/pymc/decorators.pyo
@@ -72,39 +85,72 @@
 %%PYTHON_SITELIBDIR%%/pymc/distributions.py
 %%PYTHON_SITELIBDIR%%/pymc/distributions.pyc
 %%PYTHON_SITELIBDIR%%/pymc/distributions.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/DisasterModel.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/DisasterModel.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/DisasterModel.pyo
 %%PYTHON_SITELIBDIR%%/pymc/examples/__init__.py
 %%PYTHON_SITELIBDIR%%/pymc/examples/__init__.pyc
 %%PYTHON_SITELIBDIR%%/pymc/examples/__init__.pyo
 %%PYTHON_SITELIBDIR%%/pymc/examples/custom_step.py
 %%PYTHON_SITELIBDIR%%/pymc/examples/custom_step.pyc
 %%PYTHON_SITELIBDIR%%/pymc/examples/custom_step.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_gof.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_gof.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_gof.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_linear.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_linear.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_linear.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_missing.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_missing.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_missing.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_null.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_null.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/disaster_model_null.pyo
 %%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.py
 %%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.pyc
 %%PYTHON_SITELIBDIR%%/pymc/examples/gelman_bioassay.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_gof.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_1_missing.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_2.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_2.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_2.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_3.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_3.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/model_3.pyo
-%%PYTHON_SITELIBDIR%%/pymc/examples/straightlinefit.py
-%%PYTHON_SITELIBDIR%%/pymc/examples/straightlinefit.pyc
-%%PYTHON_SITELIBDIR%%/pymc/examples/straightlinefit.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/MCMC.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/MCMC.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/MCMC.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/PyMCmodel.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/PyMCmodel.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/PyMCmodel.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/__init__.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/basiscov.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/basiscov.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/basiscov.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/cov.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/cov.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/cov.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/covparams.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/covparams.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/covparams.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/mean.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/mean.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/mean.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/mesh_choice.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/mesh_choice.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/mesh_choice.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/observation.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/observation.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/observation.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/realizations.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/realizations.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/gp/realizations.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/melanoma.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/melanoma.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/melanoma.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/melanoma_data.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/melanoma_data.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/melanoma_data.pyo
 %%PYTHON_SITELIBDIR%%/pymc/examples/weibull_fit.py
 %%PYTHON_SITELIBDIR%%/pymc/examples/weibull_fit.pyc
 %%PYTHON_SITELIBDIR%%/pymc/examples/weibull_fit.pyo
+%%PYTHON_SITELIBDIR%%/pymc/examples/zip.py
+%%PYTHON_SITELIBDIR%%/pymc/examples/zip.pyc
+%%PYTHON_SITELIBDIR%%/pymc/examples/zip.pyo
 %%PYTHON_SITELIBDIR%%/pymc/flib.so
 %%PYTHON_SITELIBDIR%%/pymc/gp/BasisCovariance.py
 %%PYTHON_SITELIBDIR%%/pymc/gp/BasisCovariance.pyc
@@ -124,9 +170,6 @@
 %%PYTHON_SITELIBDIR%%/pymc/gp/NearlyFullRankCovariance.py
 %%PYTHON_SITELIBDIR%%/pymc/gp/NearlyFullRankCovariance.pyc
 %%PYTHON_SITELIBDIR%%/pymc/gp/NearlyFullRankCovariance.pyo
-%%PYTHON_SITELIBDIR%%/pymc/gp/PyMC_objects.py
-%%PYTHON_SITELIBDIR%%/pymc/gp/PyMC_objects.pyc
-%%PYTHON_SITELIBDIR%%/pymc/gp/PyMC_objects.pyo
 %%PYTHON_SITELIBDIR%%/pymc/gp/Realization.py
 %%PYTHON_SITELIBDIR%%/pymc/gp/Realization.pyc
 %%PYTHON_SITELIBDIR%%/pymc/gp/Realization.pyo
@@ -147,38 +190,44 @@
 %%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/cov_utils.pyo
 %%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/distances.so
 %%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/isotropic_cov_funs.so
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/nsmatern.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/nsmatern.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/nsmatern.pyo
 %%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.py
 %%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.pyc
 %%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs/wrapped_distances.pyo
+%%PYTHON_SITELIBDIR%%/pymc/gp/gp_submodel.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/gp_submodel.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/gp_submodel.pyo
 %%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.py
 %%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.pyc
 %%PYTHON_SITELIBDIR%%/pymc/gp/gpplots.pyo
 %%PYTHON_SITELIBDIR%%/pymc/gp/incomplete_chol.so
 %%PYTHON_SITELIBDIR%%/pymc/gp/linalg_utils.so
+%%PYTHON_SITELIBDIR%%/pymc/gp/step_methods.py
+%%PYTHON_SITELIBDIR%%/pymc/gp/step_methods.pyc
+%%PYTHON_SITELIBDIR%%/pymc/gp/step_methods.pyo
 %%PYTHON_SITELIBDIR%%/pymc/graph.py
 %%PYTHON_SITELIBDIR%%/pymc/graph.pyc
 %%PYTHON_SITELIBDIR%%/pymc/graph.pyo
+%%PYTHON_SITELIBDIR%%/pymc/progressbar.py
+%%PYTHON_SITELIBDIR%%/pymc/progressbar.pyc
+%%PYTHON_SITELIBDIR%%/pymc/progressbar.pyo
+%%PYTHON_SITELIBDIR%%/pymc/six.py
+%%PYTHON_SITELIBDIR%%/pymc/six.pyc
+%%PYTHON_SITELIBDIR%%/pymc/six.pyo
 %%PYTHON_SITELIBDIR%%/pymc/tests/__init__.py
 %%PYTHON_SITELIBDIR%%/pymc/tests/__init__.pyc
 %%PYTHON_SITELIBDIR%%/pymc/tests/__init__.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/check_dependencies.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/check_dependencies.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/check_dependencies.pyo
 %%PYTHON_SITELIBDIR%%/pymc/tests/objectmodel.py
 %%PYTHON_SITELIBDIR%%/pymc/tests/objectmodel.pyc
 %%PYTHON_SITELIBDIR%%/pymc/tests/objectmodel.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/screen.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/screen.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/screen.pyo
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_AM.py
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_AM.pyc
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_AM.pyo
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_GP_MCMC.py
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_GP_MCMC.pyc
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_GP_MCMC.pyo
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_LazyFunction.py
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_LazyFunction.pyc
-%%PYTHON_SITELIBDIR%%/pymc/tests/test_LazyFunction.pyo
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_MCMCSampler.py
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_MCMCSampler.pyc
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_MCMCSampler.pyo
@@ -206,6 +255,9 @@
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_distributions.py
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_distributions.pyc
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_distributions.pyo
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_gradients.py
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_gradients.pyc
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_gradients.pyo
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_graph.py
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_graph.pyc
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_graph.pyo
@@ -218,6 +270,9 @@
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_mean.py
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_mean.pyc
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_mean.pyo
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_missing.py
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_missing.pyc
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_missing.pyo
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_norm_approx.py
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_norm_approx.pyc
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_norm_approx.pyo
@@ -227,12 +282,36 @@
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.py
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.pyc
 %%PYTHON_SITELIBDIR%%/pymc/tests/test_realization.pyo
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_special_methods.py
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_special_methods.pyc
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_special_methods.pyo
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_utils.py
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_utils.pyc
+%%PYTHON_SITELIBDIR%%/pymc/tests/test_utils.pyo
+%%PYTHON_SITELIBDIR%%/pymc/threadpool.py
+%%PYTHON_SITELIBDIR%%/pymc/threadpool.pyc
+%%PYTHON_SITELIBDIR%%/pymc/threadpool.pyo
 %%PYTHON_SITELIBDIR%%/pymc/utils.py
 %%PYTHON_SITELIBDIR%%/pymc/utils.pyc
 %%PYTHON_SITELIBDIR%%/pymc/utils.pyo
-@dirrm %%PYTHON_SITELIBDIR%%/pymc/tests
-@dirrm %%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs
-@dirrm %%PYTHON_SITELIBDIR%%/pymc/gp
-@dirrm %%PYTHON_SITELIBDIR%%/pymc/examples
-@dirrm %%PYTHON_SITELIBDIR%%/pymc/database
-@dirrm %%PYTHON_SITELIBDIR%%/pymc
+%%PORTDOCS%%%%DOCSDIR%%/INSTALL.rst
+%%PORTDOCS%%%%DOCSDIR%%/README.rst
+%%PORTDOCS%%%%DOCSDIR%%/conclusion.rst
+%%PORTDOCS%%%%DOCSDIR%%/database.rst
+%%PORTDOCS%%%%DOCSDIR%%/distributions.rst
+%%PORTDOCS%%%%DOCSDIR%%/extending.rst
+%%PORTDOCS%%%%DOCSDIR%%/index.rst
+%%PORTDOCS%%%%DOCSDIR%%/modelbuilding.rst
+%%PORTDOCS%%%%DOCSDIR%%/modelchecking.rst
+%%PORTDOCS%%%%DOCSDIR%%/modelfitting.rst
+%%PORTDOCS%%%%DOCSDIR%%/references.rst
+%%PORTDOCS%%%%DOCSDIR%%/theory.rst
+%%PORTDOCS%%%%DOCSDIR%%/tutorial.rst
+@dirrmtry %%PYTHON_SITELIBDIR%%/pymc/tests
+@dirrmtry %%PYTHON_SITELIBDIR%%/pymc/gp/cov_funs
+@dirrmtry %%PYTHON_SITELIBDIR%%/pymc/gp
+@dirrmtry %%PYTHON_SITELIBDIR%%/pymc/examples/gp
+@dirrmtry %%PYTHON_SITELIBDIR%%/pymc/examples
+@dirrmtry %%PYTHON_SITELIBDIR%%/pymc/database
+@dirrmtry %%PYTHON_SITELIBDIR%%/pymc
+%%PORTDOCS%%@dirrmtry %%DOCSDIR%%
--- py27-pymc-2.3,1.patch ends here ---

>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->wen 
Responsible-Changed-By: edwin 
Responsible-Changed-When: Thu Nov 14 11:10:09 UTC 2013 
Responsible-Changed-Why:  
wenheping@gmail.com => wen@ (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=183951 
State-Changed-From-To: open->feedback 
State-Changed-By: edwin 
State-Changed-When: Thu Nov 14 11:10:11 UTC 2013 
State-Changed-Why:  
Awaiting maintainers feedback (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=183951 

From: Edwin Groothuis <edwin@FreeBSD.org>
To: wenheping@gmail.com
Cc: bug-followup@FreeBSD.org
Subject: Re: ports/183951: [PATCH] math/py-pymc: update to 2.3,1
Date: Thu, 14 Nov 2013 11:10:11 UT

 Maintainer of math/py-pymc,
 
 Please note that PR ports/183951 has just been submitted.
 
 If it contains a patch for an upgrade, an enhancement or a bug fix
 you agree on, reply to this email stating that you approve the patch
 and a committer will take care of it.
 
 The full text of the PR can be found at:
     http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/183951
 
 -- 
 Edwin Groothuis via the GNATS Auto Assign Tool
 edwin@FreeBSD.org
State-Changed-From-To: feedback->closed 
State-Changed-By: mat 
State-Changed-When: Fri Dec 6 15:42:35 UTC 2013 
State-Changed-Why:  
Committed, thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=183951 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/183951: commit references a PR
Date: Fri,  6 Dec 2013 15:42:41 +0000 (UTC)

 Author: mat
 Date: Fri Dec  6 15:42:33 2013
 New Revision: 335765
 URL: http://svnweb.freebsd.org/changeset/ports/335765
 
 Log:
   - Update to 2.3,1
   - Add license
   - Add matplotlib dependency as per docs/INSTALL.rst
   - Add DOCS option
   - Add stage support
   
   maintainer timeout.
   
   PR:		ports/183951
   Submitted by:	Johannes Jost Meixner
 
 Deleted:
   head/math/py-pymc/pkg-plist
 Modified:
   head/math/py-pymc/Makefile
   head/math/py-pymc/distinfo
   head/math/py-pymc/pkg-descr
 
 Modified: head/math/py-pymc/Makefile
 ==============================================================================
 --- head/math/py-pymc/Makefile	Fri Dec  6 15:35:13 2013	(r335764)
 +++ head/math/py-pymc/Makefile	Fri Dec  6 15:42:33 2013	(r335765)
 @@ -2,8 +2,7 @@
  # $FreeBSD$
  
  PORTNAME=	pymc
 -PORTVERSION=	2.0
 -PORTREVISION=	1
 +PORTVERSION=	2.3
  PORTEPOCH=	1
  CATEGORIES=	math python
  MASTER_SITES=	CHEESESHOP
 @@ -12,11 +11,37 @@ PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
  MAINTAINER=	wenheping@gmail.com
  COMMENT=	Markov Chain Monte Carlo Sampling Toolkit
  
 -BUILD_DEPENDS=	${PYNUMPY}
 -RUN_DEPENDS:=	${BUILD_DEPENDS}
 +LICENSE=	AFL
 +LICENSE_NAME=	Academic Free License
 +LICENSE_FILE=	${WRKSRC}/LICENSE
 +LICENSE_PERMS=	auto-accept dist-mirror dist-sell pkg-mirror pkg-sell
 +
 +BUILD_DEPENDS=	${PYNUMPY} \
 +		${PYTHON_PKGNAMEPREFIX}matplotlib>0:${PORTSDIR}/math/py-matplotlib \
 +		${PYTHON_PKGNAMEPREFIX}scipy>0:${PORTSDIR}/science/py-scipy
 +LIB_DEPENDS=	liblapack.so:${PORTSDIR}/math/lapack \
 +		libblas.so:${PORTSDIR}/math/blas
 +RUN_DEPENDS=	${PYNUMPY} \
 +		${PYTHON_PKGNAMEPREFIX}matplotlib>0:${PORTSDIR}/math/py-matplotlib \
 +		${PYTHON_PKGNAMEPREFIX}scipy>0:${PORTSDIR}/science/py-scipy
 +
 +OPTIONS_DEFINE=	DOCS
 +DOCSDIR=	${PREFIX}/share/doc/py-${PORTNAME}
  
  USE_PYTHON=	yes
  USE_PYDISTUTILS=	yes
 +PYDISTUTILS_AUTOPLIST=	yes
 +PORTDOCS=	*
 +
 +post-install:
 +	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/flib.so
 +	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/cov_funs/distances.so
 +	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/cov_funs/isotropic_cov_funs.so
 +	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/incomplete_chol.so
 +	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/gp/linalg_utils.so
 +	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/Container_values.so
 +	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/LazyFunction.so
 +	${MKDIR} ${STAGEDIR}${DOCSDIR}
 +	${INSTALL_DATA} ${WRKSRC}/docs/*.rst ${STAGEDIR}${DOCSDIR}
  
 -NO_STAGE=	yes
  .include <bsd.port.mk>
 
 Modified: head/math/py-pymc/distinfo
 ==============================================================================
 --- head/math/py-pymc/distinfo	Fri Dec  6 15:35:13 2013	(r335764)
 +++ head/math/py-pymc/distinfo	Fri Dec  6 15:42:33 2013	(r335765)
 @@ -1,2 +1,2 @@
 -SHA256 (pymc-2.0.tar.gz) = 15bbf1e0df9e080d367d639462c4b2b9290826ca069a76ac2bc79d795fe6e653
 -SIZE (pymc-2.0.tar.gz) = 1200416
 +SHA256 (pymc-2.3.tar.gz) = db029c59d6a04f0c97d88993151c4ee58c76b9ad5c71ead7ee250088ba4cce0d
 +SIZE (pymc-2.3.tar.gz) = 13080085
 
 Modified: head/math/py-pymc/pkg-descr
 ==============================================================================
 --- head/math/py-pymc/pkg-descr	Fri Dec  6 15:35:13 2013	(r335764)
 +++ head/math/py-pymc/pkg-descr	Fri Dec  6 15:42:33 2013	(r335765)
 @@ -1,11 +1,9 @@
 -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.
 +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: https://pypi.python.org/pypi/pymc/
 +WWW: http://pypi.python.org/pypi/pymc/
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>Unformatted:
