git: 7c0a02b1bf8e - main - science/py-PyNE: New port: PyNE: The Nuclear Engineering Toolkit

From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 10 Oct 2021 05:21:38 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=7c0a02b1bf8eed6ccf4a0543fb6eb5c4b18eb424

commit 7c0a02b1bf8eed6ccf4a0543fb6eb5c4b18eb424
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2021-10-10 04:45:26 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2021-10-10 05:21:33 +0000

    science/py-PyNE: New port: PyNE: The Nuclear Engineering Toolkit
---
 science/Makefile                                   |   1 +
 science/py-PyNE/Makefile                           |  60 +++++
 science/py-PyNE/distinfo                           |  11 +
 .../files/patch-cmake_SetupSubPyInstall.cmake.in   |  12 +
 science/py-PyNE/pkg-descr                          |   6 +
 science/py-PyNE/pkg-plist                          | 252 +++++++++++++++++++++
 6 files changed, 342 insertions(+)

diff --git a/science/Makefile b/science/Makefile
index 3019d3e97cd6..b1371a5909d0 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -233,6 +233,7 @@
     SUBDIR += py-OpenFermion
     SUBDIR += py-PubChemPy
     SUBDIR += py-PyFR
+    SUBDIR += py-PyNE
     SUBDIR += py-SimpleSpectral
     SUBDIR += py-abipy
     SUBDIR += py-access
diff --git a/science/py-PyNE/Makefile b/science/py-PyNE/Makefile
new file mode 100644
index 000000000000..70882d74548d
--- /dev/null
+++ b/science/py-PyNE/Makefile
@@ -0,0 +1,60 @@
+PORTNAME=	PyNE
+DISTVERSION=	0.7.5
+CATEGORIES=	science
+MASTER_SITES=	http://raw.githubusercontent.com/pyne/data/master/:decay \
+		http://raw.githubusercontent.com/pyne/data/master/:cram \
+		http://raw.githubusercontent.com/pyne/data/master/:dlc \
+		http://raw.githubusercontent.com/pyne/data/master/:clc
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+DISTFILES=	decay.tar.gz:decay \
+		cram.tar.gz:cram \
+		decay-linux-clang.tar.gz:dlc \
+		cram-linux-clang.tar.gz:clc
+DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}
+EXTRACT_ONLY=	${DISTNAME}.tar.gz
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	PyNE: The Nuclear Engineering Toolkit
+
+LICENSE=	BSD2CLAUSE
+LICENSE_FILE=	${WRKSRC}/license.txt
+
+PY_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}tables>0:devel/py-tables@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR}
+BUILD_DEPENDS=	cmake:devel/cmake \
+		${PY_DEPENDS}
+LIB_DEPENDS=	libhdf5.so:science/hdf5 \
+		libsz.so:science/szip
+RUN_DEPENDS=	${PY_DEPENDS}
+
+USES=		compiler:c++17-lang fortran python:3.7+
+USE_PYTHON=	distutils cython flavors
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	pyne
+GH_PROJECT=	pyne
+
+MAKE_ENV=	DESTDIR=${STAGEDIR}
+FFLAGS+=	-fallow-argument-mismatch
+
+PYDISTUTILS_BUILDARGS=	--slow	# this chooses slow compilation of sources from {decay,cram}.tar.gz
+				# over incompatible pre-compiled assembly from {decay,cram}-linux-clang.tar.gz
+
+post-extract:
+.for f in decay.tar.gz cram.tar.gz decay-linux-clang.tar.gz cram-linux-clang.tar.gz
+	@${CP} ${DISTDIR}/${DIST_SUBDIR}/${f} ${WRKSRC}/src
+.endfor
+
+do-install:
+	# install
+	cd ${INSTALL_WRKSRC} && \
+		${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYDISTUTILS_SETUP} ${PYDISTUTILS_INSTALL_TARGET}
+	# strip
+	${STRIP_CMD} \
+		${STAGEDIR}${LOCALBASE}/lib/lib*.so \
+		${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/*.so \
+		${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/xs/models.so
+
+.include <bsd.port.mk>
diff --git a/science/py-PyNE/distinfo b/science/py-PyNE/distinfo
new file mode 100644
index 000000000000..fc8c2dadf0b6
--- /dev/null
+++ b/science/py-PyNE/distinfo
@@ -0,0 +1,11 @@
+TIMESTAMP = 1633733586
+SHA256 (PyNE-0.7.5/decay.tar.gz) = aa1aa69cb84685731eb234c046c56f9167a0bcc9686ccd5437f62186ac9bd441
+SIZE (PyNE-0.7.5/decay.tar.gz) = 8012492
+SHA256 (PyNE-0.7.5/cram.tar.gz) = 5ea1443226234787e0b8ef7f1d4c9cb0a6846b9da00bc843557051ad74e4a2f5
+SIZE (PyNE-0.7.5/cram.tar.gz) = 2110526
+SHA256 (PyNE-0.7.5/decay-linux-clang.tar.gz) = 6fa05231e7fbfe5994e9a6705131bdcac2fc5845e362d3607e96c46ed418a0db
+SIZE (PyNE-0.7.5/decay-linux-clang.tar.gz) = 18904467
+SHA256 (PyNE-0.7.5/cram-linux-clang.tar.gz) = 0a7a04b5268db91fea7bec75dbefe3ec23036f9e250aacc6fb353d17d8e84538
+SIZE (PyNE-0.7.5/cram-linux-clang.tar.gz) = 20477898
+SHA256 (PyNE-0.7.5/pyne-pyne-0.7.5_GH0.tar.gz) = 80143d5e232b89ffd89121363c0e1e615acc28c26f5d7682521eb9baf98311c4
+SIZE (PyNE-0.7.5/pyne-pyne-0.7.5_GH0.tar.gz) = 9262728
diff --git a/science/py-PyNE/files/patch-cmake_SetupSubPyInstall.cmake.in b/science/py-PyNE/files/patch-cmake_SetupSubPyInstall.cmake.in
new file mode 100644
index 000000000000..e70e7905f014
--- /dev/null
+++ b/science/py-PyNE/files/patch-cmake_SetupSubPyInstall.cmake.in
@@ -0,0 +1,12 @@
+- make 'install' DESTDIR-aware
+
+--- cmake/SetupSubPyInstall.cmake.in.orig	2021-10-09 05:02:12 UTC
++++ cmake/SetupSubPyInstall.cmake.in
+@@ -9,6 +9,7 @@ message("  CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFI
+ message("  CMAKE_CURRENT_BINARY_DIR: ${CMAKE_CURRENT_BINARY_DIR}")
+ execute_process(COMMAND ${PYTHON_EXECUTABLE} setup_sub.py install
+                         "--prefix=${CMAKE_INSTALL_PREFIX}"
++                        "--root=$ENV{DESTDIR}"
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                 RESULT_VARIABLE res_var)
+ if(NOT "${res_var}" STREQUAL "0")
diff --git a/science/py-PyNE/pkg-descr b/science/py-PyNE/pkg-descr
new file mode 100644
index 000000000000..0a0ecb6320fa
--- /dev/null
+++ b/science/py-PyNE/pkg-descr
@@ -0,0 +1,6 @@
+PyNE is a suite of tools to aid in computational nuclear science & engineering.
+PyNE seeks to provide native implementations of common nuclear algorithms, as
+well as Python bindings and I/O support for other industry standard nuclear
+codes.
+
+WWW: https://pyne.io/
diff --git a/science/py-PyNE/pkg-plist b/science/py-PyNE/pkg-plist
new file mode 100644
index 000000000000..0e0196d6cbb8
--- /dev/null
+++ b/science/py-PyNE/pkg-plist
@@ -0,0 +1,252 @@
+bin/aceviewer
+bin/activation_responses.py
+bin/expand_tags.py
+bin/gtcadis.py
+bin/meshtal_to_mesh
+bin/nuc_data_make
+bin/ptrac_to_hdf5
+bin/r2s.py
+bin/ssw_combine.py
+bin/tape9
+include/pyne/_atomic_data.h
+include/pyne/_decay.h
+include/pyne/atomic_data.h
+include/pyne/cram.h
+include/pyne/cram.hpp
+include/pyne/dagmc_bridge.h
+include/pyne/data.h
+include/pyne/decay.h
+include/pyne/enrichment.h
+include/pyne/enrichment_cascade.h
+include/pyne/enrichment_symbolic.h
+include/pyne/extra_types.h
+include/pyne/h5wrap.h
+include/pyne/json-forwards.h
+include/pyne/json.h
+include/pyne/jsoncustomwriter.h
+include/pyne/material.h
+include/pyne/material_library.h
+include/pyne/measure.h
+include/pyne/nucname.h
+include/pyne/particle.h
+include/pyne/pyne.h
+include/pyne/rxname.h
+include/pyne/source.h
+include/pyne/source_sampling.h
+include/pyne/tally.h
+include/pyne/transmuters.h
+include/pyne/utils.h
+lib/libpyne.so
+%%PYTHON_SITELIBDIR%%/pyne-0.7.1-py%%PYTHON_VER%%.egg-info
+%%PYTHON_SITELIBDIR%%/pyne/__init__.pxd
+%%PYTHON_SITELIBDIR%%/pyne/__init__.py
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/_argparse%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/alara%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/api%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/binaryreader%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/cccc%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/decay_tape9%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/endl%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/ensdf%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/ensdf_processing%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/fispact%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/fluka%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/gammaspec%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/mcnp%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/mesh%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/njoy%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/openmc_utils%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/origen22%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/partisn%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/ptrac_to_hdf5%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/r2s%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/rxdata%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/serpent%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/spatialsolver%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/spectanalysis%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/utils%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/__pycache__/variancereduction%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/_argparse.py
+%%PYTHON_SITELIBDIR%%/pyne/_utils.so
+%%PYTHON_SITELIBDIR%%/pyne/ace.so
+%%PYTHON_SITELIBDIR%%/pyne/alara.py
+%%PYTHON_SITELIBDIR%%/pyne/api.py
+%%PYTHON_SITELIBDIR%%/pyne/apigen/__init__.py
+%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/enrich_multi_sym%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/main%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/apigen/__pycache__/utils%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/apigen/enrich_multi_sym.py
+%%PYTHON_SITELIBDIR%%/pyne/apigen/main.py
+%%PYTHON_SITELIBDIR%%/pyne/apigen/utils.py
+%%PYTHON_SITELIBDIR%%/pyne/base_tape9.inp
+%%PYTHON_SITELIBDIR%%/pyne/binaryreader.py
+%%PYTHON_SITELIBDIR%%/pyne/bins.so
+%%PYTHON_SITELIBDIR%%/pyne/c_cram.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cccc.py
+%%PYTHON_SITELIBDIR%%/pyne/cli/__init__.py
+%%PYTHON_SITELIBDIR%%/pyne/cli/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/cli/__pycache__/tape9%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/cli/tape9.py
+%%PYTHON_SITELIBDIR%%/pyne/cpp_dagmc_bridge.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_data.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_enrichment.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_jsoncpp.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_material.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_material_library.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_nucname.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_particle.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_rxname.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_source.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_source_sampling.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_tally.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_transmuters.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cpp_utils.pxd
+%%PYTHON_SITELIBDIR%%/pyne/cram.so
+%%PYTHON_SITELIBDIR%%/pyne/data.pxd
+%%PYTHON_SITELIBDIR%%/pyne/data.so
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__init__.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/api%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/atomic_mass%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/cinder%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/decay%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/dosefactors%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/eaf%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/hashtools%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/isotopic_abundance%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/kaeri%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/materials_library%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/ndsfpy%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/nuc_data_make%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/q_val%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/scattering_lengths%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/simple_xs%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/__pycache__/wimsdfpy%%PYTHON_EXT_SUFFIX%%.pyc
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/abundances.txt
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/api.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/atomic_mass.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/cinder.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/decay.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/dosefactors.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/dosefactors_external_air.csv
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/dosefactors_external_soil.csv
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/dosefactors_ingest.csv
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/dosefactors_inhale.csv
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/eaf.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/hashtools.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/isotopic_abundance.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/kaeri.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/mass.mas16
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/materials_compendium.csv
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/materials_library.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/mednew.dat
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/ndsfpy.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/nuc_data_make.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/q_val.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/q_val_actinides.csv
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/q_val_fissionproducts.csv
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/q_val_light.csv
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/scattering_lengths.html
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/scattering_lengths.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/simple_xs.py
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/wimsd-fpyield.html
+%%PYTHON_SITELIBDIR%%/pyne/dbgen/wimsdfpy.py
+%%PYTHON_SITELIBDIR%%/pyne/decay_tape9.py
+%%PYTHON_SITELIBDIR%%/pyne/dtypes.pxd
+%%PYTHON_SITELIBDIR%%/pyne/dtypes.so
+%%PYTHON_SITELIBDIR%%/pyne/endf.so
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+%%PYTHON_SITELIBDIR%%/pyne/ensdf_processing.py
+%%PYTHON_SITELIBDIR%%/pyne/extra_types.pxd
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+%%PYTHON_SITELIBDIR%%/pyne/fortranformat/FortranRecordWriter.py
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+%%PYTHON_SITELIBDIR%%/pyne/fortranformat/_edit_descriptors.py
+%%PYTHON_SITELIBDIR%%/pyne/fortranformat/_exceptions.py
+%%PYTHON_SITELIBDIR%%/pyne/fortranformat/_input.py
+%%PYTHON_SITELIBDIR%%/pyne/fortranformat/_lexer.py
+%%PYTHON_SITELIBDIR%%/pyne/fortranformat/_misc.py
+%%PYTHON_SITELIBDIR%%/pyne/fortranformat/_output.py
+%%PYTHON_SITELIBDIR%%/pyne/fortranformat/_parser.py
+%%PYTHON_SITELIBDIR%%/pyne/fortranformat/config.py
+%%PYTHON_SITELIBDIR%%/pyne/gammaspec.py
+%%PYTHON_SITELIBDIR%%/pyne/gui/__init__.py
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