reinit the tree, so we can have metadata

4 files changed, 86 insertions, 0 deletions

diff --git a/sci-mathematics/pymc/Manifest b/sci-mathematics/pymc/Manifest
new file mode 100644
index 000000000000..b6b91b7cd09c
--- /dev/null
+++ b/sci-mathematics/pymc/Manifest
@@ -0,0 +1,6 @@
+AUX pymc-2.3.6-remove-hardcoded-blas.patch 414 SHA256 041bec5d7eccff7e47438e228f030046dd1d442c17dc7f7118e58f2cfc82b190 SHA512 776ecd9876342215c925ad4a2dfa123e9f6656c6e5a8f3b8d208cc89befc84164b5355d4c1afce8be8962951c3343629cfacb0449d6d0b05d9333886803bbb4a WHIRLPOOL 7c979609c33cd1d86503293ceda1cc2771f4c504a26356e33b61897d7d379f38c312bc8237135256ef1ed49634adbf681611d952d6eb4c5b664dca4ae6c0a087
+DIST pymc-2.3.6.zip 402827 SHA256 70b00a9d722d9bba95d975f0a0836e41d8792b8d6fe0dd21b4af209747da3dc5 SHA512 4b5e0663ca296efd8d242a0b6362a12d475cdabf661a430de5455e60999acf8a4a30d053303c2f79e8aec3e5e7d120f56cb341e283aa87f31c224e4e57300d13 WHIRLPOOL 4a0774e0362baef7c6390ec499ba6f605766c614974f04bd9c04e78916b91e0e7f4d35d39e8ba002c654ad15c7158b8b670e6c7010eb1fd8513bfd43e0fe61db
+EBUILD pymc-2.3.6.ebuild 1303 SHA256 9265842164269b4c72750d04684080c85a8df344bfb4f7ac3689d3af7776ee5b SHA512 28d1d613dcbb25025bbf1cc3963af6afc495a8d201ab74d6ba05fb3e6455a5dfe13e480d5768b6d8a02c59764a858eda6c8e60da18739d9c7f0d7521d9115dcc WHIRLPOOL 6efe235202675cac9ff7455909a7ff0b856f57f8959974b9fb3f78bb28c4a8f491ec3397a307cc601393537f87c003b3e0cb1e3e296913aedf64baa1e50bce1e
+MISC ChangeLog 2949 SHA256 89815941f7f0985dc21a39f615084d2b1cc6d8d12f7e61e4c2e88d179b1cf00b SHA512 21c4ede1a8bbb8c6b19652465916916b064314558e3d4d5ae8a42925c2161a7e94901620dbcf35dea6a36358a1054a5e6e27e04bd1f8906772a0c6f20718c0e3 WHIRLPOOL 34dd173bf88708053c15ab9e327cc42c88c2f9fed17f14cf4e7029fa86a4fa4738bc4e5a6db0327f1f8cfedeeafacfde0fadc0dbe1e556d867e849976a3ad391
+MISC ChangeLog-2015 632 SHA256 8861fa0871d0830370195c3004083e79f19434d91a93da5021198858515f7856 SHA512 6c2f3597157f495662802d36f7e5215d15354d7cc186fb9ef3ce4a224fda6ebf9ace68e050ed1174de55e738cd0b46e77af0f3a835bdcb84376a492e25a7dd10 WHIRLPOOL 62dab4ea5544cd57fc16f78398a5b1ac3942057399934b244c3ed79dfa54889a6be076a8b150b4c950d54217a6fd93c1c347600f23d26ab9c1f346bcfca207b3
+MISC metadata.xml 554 SHA256 2dc5dbb5e5bdb7c2d515fda347795f52da76604c9e46ce48ecd5fee83714bb6c SHA512 0d9ac09e21100370ed731a23cbce01c73a734a4e2adb282a2c0cc185c75d011f3aeafc75283d27e30635f00cf7fb27a6a502e1a9cb922892d10016d6e9770d65 WHIRLPOOL f6a19c790e57c3620fb9dedacc83ccecfee7315824dbba9bfdca54c9949660c8cbf3e9ce439e4808bef3076882be6a4177fa1663e88e4b2d0d2c7afd6fb39ac5
diff --git a/sci-mathematics/pymc/files/pymc-2.3.6-remove-hardcoded-blas.patch b/sci-mathematics/pymc/files/pymc-2.3.6-remove-hardcoded-blas.patch
new file mode 100644
index 000000000000..93ce86f5c717
--- /dev/null
+++ b/sci-mathematics/pymc/files/pymc-2.3.6-remove-hardcoded-blas.patch
@@ -0,0 +1,11 @@
+--- a/setup.py
++++ b/setup.py
+@@ -80,7 +80,7 @@
+ 
+ # Compile covariance functions
+ config.add_extension(name='gp.cov_funs.isotropic_cov_funs',\
+-sources=['pymc/gp/cov_funs/isotropic_cov_funs.f','blas/BLAS/dscal.f'],\
++sources=['pymc/gp/cov_funs/isotropic_cov_funs.f'],\
+ extra_info=lapack_info)
+ 
+ config.add_extension(name='gp.cov_funs.distances',sources=['pymc/gp/cov_funs/distances.f'], extra_info=lapack_info)
diff --git a/sci-mathematics/pymc/metadata.xml b/sci-mathematics/pymc/metadata.xml
new file mode 100644
index 000000000000..0b8c7cb3f0e5
--- /dev/null
+++ b/sci-mathematics/pymc/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>heroxbd@gentoo.org</email>
+    <name>Benda Xu</name>
+  </maintainer>
+  <longdescription lang="en">
+PyMC is a python module that implements Bayesian statistical models
+and fitting algorithms, including Markov chain Monte Carlo.
+  </longdescription>
+  <upstream>
+    <remote-id type="github">pymc-devs/pymc</remote-id>
+    <remote-id type="pypi">pymc</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-mathematics/pymc/pymc-2.3.6.ebuild b/sci-mathematics/pymc/pymc-2.3.6.ebuild
new file mode 100644
index 000000000000..dc48d2559a46
--- /dev/null
+++ b/sci-mathematics/pymc/pymc-2.3.6.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_4,3_5} )
+
+inherit distutils-r1 flag-o-matic fortran-2 toolchain-funcs
+
+DESCRIPTION="Markov Chain Monte Carlo sampling toolkit"
+HOMEPAGE="https://github.com/${PN}-devs/${PN} https://pypi.python.org/pypi/${PN}"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.zip"
+
+SLOT=0
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE=AFL-3.0
+IUSE="test"
+
+RDEPEND=">=dev-python/numpy-1.6[${PYTHON_USEDEP},lapack]
+	>=dev-python/matplotlib-1.0[${PYTHON_USEDEP}]"
+DEPEND="
+	test? (
+		${RDEPEND}
+		dev-python/nose[${PYTHON_USEDEP}]
+	)"
+
+PATCHES=( "${FILESDIR}/${PN}-2.3.6-remove-hardcoded-blas.patch" )
+
+# tests freeze at some point
+#RESTRICT="test"
+
+python_prepare_all() {
+	# forcibly remove bundled libs, just to be sure...
+	rm -r blas || die
+
+	distutils-r1_python_prepare_all
+}
+
+python_configure_all() {
+	append-fflags -fPIC
+	append-ldflags -shared
+
+	[[ $(tc-getFC) == *gfortran* ]] && mydistutilsargs=( config_fc --fcompiler=gnu95 )
+}
+
+python_test() {
+	distutils_install_for_testing
+	cd "${TEST_DIR}" || die
+	# Use agg backend instead of gtk
+	echo 'backend      : agg' > matplotlibrc || die
+
+	${EPYTHON} -c "import pymc; pymc.test()" || die "Tests failed on ${EPYTHON}"
+}