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Conda #112
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Conda #112
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from ${PY_PKG_OLD} import * |
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#!/usr/bin/env python | ||
# -*- coding: utf-8 -*- | ||
try: | ||
from setuptools import setup | ||
except ImportError: | ||
from distutils.core import setup | ||
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__author__ = "Casper da Costa-Luis <imaging@caspersci.uk.to>" | ||
__version__ = "1.0.0" | ||
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setup( | ||
name='sirf', | ||
version=__version__, | ||
description='CCP PET-MR SIRF', | ||
license='Apache 2.0', | ||
author='CCP PET-MR', | ||
author_email='ccppetmr@stfc.ac.uk', | ||
url='https://github.com/CCPPETMR/SIRF', | ||
platforms=['any'], | ||
package_data={'sirf': ['*.so']}, | ||
packages=[${PYTHON_SETUP_PKGS_CSV}], | ||
long_description='', | ||
classifiers=[ | ||
# Trove classifiers | ||
# (https://pypi.python.org/pypi?%3Aaction=list_classifiers) | ||
'Development Status :: 5 - Production/Stable', | ||
'Programming Language :: Python :: 2', | ||
'Programming Language :: Python :: 2.6', | ||
'Programming Language :: Python :: 2.7', | ||
'Programming Language :: Python :: 3', | ||
'Programming Language :: Python :: 3.2', | ||
'Programming Language :: Python :: 3.3', | ||
'Programming Language :: Python :: 3.4', | ||
'Programming Language :: Python :: 3.5', | ||
'Programming Language :: Python :: 3.6', | ||
'Programming Language :: Python :: 3.7' | ||
], | ||
keywords='image reconstruction pet mr medical imaging', | ||
) |
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#!/bin/bash | ||
# | ||
# Script to install/update the CCP-PETMR VM. It could also be used for any other system | ||
# but will currently change your .sirfrc. This is to be avoided later on. | ||
# | ||
# Author: Edoardo Pasca | ||
# Copyright 2016-2018 University College London | ||
# Copyright 2016-2018 Rutherford Appleton Laboratory STFC | ||
# | ||
# This is software developed for the Collaborative Computational | ||
# Project in Positron Emission Tomography and Magnetic Resonance imaging | ||
# (http://www.ccppetmr.ac.uk/). | ||
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# Licensed under the Apache License, Version 2.0 (the "License"); | ||
# you may not use this file except in compliance with the License. | ||
# You may obtain a copy of the License at | ||
# | ||
# http://www.apache.org/licenses/LICENSE-2.0.txt | ||
# | ||
# Unless required by applicable law or agreed to in writing, software | ||
# distributed under the License is distributed on an "AS IS" BASIS, | ||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
# See the License for the specific language governing permissions and | ||
# limitations under the License. | ||
# | ||
#========================================================================= | ||
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#if [ -z "$SIRF_VERSION" ]; then | ||
# echo "Need to set SIRF_VERSION" | ||
# exit 1 | ||
#fi | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. until we fix this, will need to add it to the checklist |
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mkdir "$SRC_DIR/build" | ||
mkdir "$SRC_DIR/SIRF-SuperBuild" | ||
cp -rv "$RECIPE_DIR/../" "$SRC_DIR/SIRF-SuperBuild" | ||
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cd $SRC_DIR/build | ||
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echo "$SRC_DIR/ccpi/Python" | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. really? There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Really what? There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. ccpi... There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. You know, I'm torn |
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#site-packages ${SP_DIR}/sirf | ||
cmake ../SIRF-SuperBuild \ | ||
-DCMAKE_INSTALL_PREFIX=${PREFIX} \ | ||
-DPYTHON_DEST_DIR=${PREFIX}/python\ | ||
-USIRF_URL \ | ||
-USIRF_TAG \ | ||
-DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\ | ||
-USTIR_URL \ | ||
-USTIR_TAG \ | ||
-UGadgetron_URL \ | ||
-UGadgetron_TAG \ | ||
-UISMRMRD_URL \ | ||
-UISMRMRD_TAG \ | ||
-DBUILD_GADGETRON=On \ | ||
-DUSE_SYSTEM_SWIG=On \ | ||
-DUSE_SYSTEM_Boost=Off \ | ||
-DUSE_SYSTEM_Armadillo=On \ | ||
-DUSE_SYSTEM_FFTW3=On \ | ||
-DUSE_SYSTEM_HDF5=ON \ | ||
-DBUILD_siemens_to_ismrmrd=On \ | ||
-DUSE_SYSTEM_GTEST=On\ | ||
-DCONDA_BUILD=On | ||
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make -j1 | ||
cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml | ||
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cd ${PREFIX}/python | ||
${PYTHON} setup.py install | ||
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# add to | ||
#echo "${PREFIX}/python" > ${PREFIX} | ||
#${PREFIX}/python |
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package: | ||
name: sirf | ||
# version: {{ environ['SIRF_VERSION'] }} | ||
version: 1.0.0 | ||
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build: | ||
preserve_egg_dir: False | ||
# number: 0 | ||
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requirements: | ||
build: | ||
#- boost ==1.64.0 | ||
#- boost-cpp ==1.64.0 | ||
# - boost | ||
# - boost-cpp | ||
- python 3.6 # [py36] | ||
- python 2.7 # [py27] | ||
- cmake >=3.1 | ||
- vc 14 # [win and py36] | ||
- vc 9 # [win and py27] | ||
- numpy | ||
- scipy | ||
- matplotlib | ||
- docopt | ||
- h5py | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. 99% sure we don't need this |
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- libxml2 | ||
- psutil | ||
- nose | ||
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- coverage | ||
- fftw | ||
- swig >=3 | ||
- libxslt | ||
- armadillo | ||
- gtest | ||
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run: | ||
- vc 14 # [win and py35] | ||
- vc 9 # [win and py27] | ||
- python 3.6 # [py36] | ||
- python 2.7 # [py27] | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. drop this of course |
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#- boost-dev ==1.63 | ||
- numpy | ||
- scipy | ||
- matplotlib | ||
- docopt | ||
- h5py | ||
- psutil | ||
- fftw | ||
- libgcc-ng | ||
- libstdcxx-ng | ||
- openblas | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. not for build? There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. I feel like there's a difference between build, install (runtime), and test. I'd think nose and coverage fall into the last category, and things like h5py for install? Is there a way to specify these three categories for conda? I'm sure at least two are possible. At least split into sections with comments There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Indeed there is. Currently The tricky bit is afaik that the install phase of the external packages is run during the make phase. |
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- armadillo | ||
- gtest | ||
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about: | ||
home: http://www.ccppetmr.ac.uk | ||
license: Apache 2.0 license | ||
summary: 'Synergistic Image Reconstruction Framework' |
Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,72 @@ | ||
#!/bin/bash | ||
# | ||
# Script to install/update the CCP-PETMR VM. It could also be used for any other system | ||
# but will currently change your .sirfrc. This is to be avoided later on. | ||
# | ||
# Author: Edoardo Pasca | ||
# Copyright 2016-2018 University College London | ||
# Copyright 2016-2018 Rutherford Appleton Laboratory STFC | ||
# | ||
# This is software developed for the Collaborative Computational | ||
# Project in Positron Emission Tomography and Magnetic Resonance imaging | ||
# (http://www.ccppetmr.ac.uk/). | ||
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# Licensed under the Apache License, Version 2.0 (the "License"); | ||
# you may not use this file except in compliance with the License. | ||
# You may obtain a copy of the License at | ||
# | ||
# http://www.apache.org/licenses/LICENSE-2.0.txt | ||
# | ||
# Unless required by applicable law or agreed to in writing, software | ||
# distributed under the License is distributed on an "AS IS" BASIS, | ||
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
# See the License for the specific language governing permissions and | ||
# limitations under the License. | ||
# | ||
#========================================================================= | ||
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#if [ -z "$SIRF_VERSION" ]; then | ||
# echo "Need to set SIRF_VERSION" | ||
# exit 1 | ||
#fi | ||
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mkdir "$SRC_DIR/build" | ||
mkdir "$SRC_DIR/SIRF-SuperBuild" | ||
cp -rv "$RECIPE_DIR/../../" "$SRC_DIR/SIRF-SuperBuild" | ||
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cd $SRC_DIR/build | ||
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#site-packages ${SP_DIR}/sirf | ||
cmake ../SIRF-SuperBuild \ | ||
-DCMAKE_INSTALL_PREFIX=${PREFIX} \ | ||
-DPYTHON_DEST_DIR=${PREFIX}/python\ | ||
-USIRF_URL \ | ||
-USIRF_TAG \ | ||
-DSIRF_TAG=v2.0.0\ | ||
-USTIR_URL \ | ||
-USTIR_TAG \ | ||
-UGadgetron_URL \ | ||
-UGadgetron_TAG \ | ||
-UISMRMRD_URL \ | ||
-UISMRMRD_TAG \ | ||
-DBUILD_GADGETRON=On \ | ||
-DUSE_SYSTEM_SWIG=Off \ | ||
-DUSE_SYSTEM_Boost=On \ | ||
-DUSE_SYSTEM_Armadillo=Off \ | ||
-DUSE_SYSTEM_FFTW3=On \ | ||
-DUSE_SYSTEM_HDF5=ON \ | ||
-DBUILD_siemens_to_ismrmrd=Off \ | ||
-DUSE_SYSTEM_GTest=Off\ | ||
-DCONDA_BUILD=On | ||
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make -j1 Armadillo | ||
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#cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml | ||
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#cd ${PREFIX}/python | ||
#${PYTHON} setup.py install | ||
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# add to | ||
#echo "${PREFIX}/python" > ${PREFIX} | ||
#${PREFIX}/python |
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python: | ||
- 2.7 | ||
numpy: | ||
- 1.11 |
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package: | ||
name: armadillo | ||
version: 7.800.0 | ||
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build: | ||
preserve_egg_dir: False | ||
# number: 0 | ||
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requirements: | ||
build: | ||
#- boost ==1.64.0 | ||
- boost-cpp >=1.63.0 | ||
- boost >=1.63 | ||
# - boost-cpp | ||
# - python 3.6 # [py36] | ||
# - python 2.7 # [py27] | ||
- cmake >=3.1 | ||
- vc 14 # [win and py36] | ||
- vc 9 # [win and py27] | ||
# - numpy | ||
# - scipy | ||
# - matplotlib | ||
# - docopt | ||
- h5py | ||
# - libxml2 | ||
- psutil | ||
- nose | ||
- coverage | ||
- fftw | ||
# - swig >=3 | ||
# - libxslt | ||
# - armadillo | ||
# - gtest | ||
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run: | ||
- boost >=1.63 | ||
- vc 14 # [win and py35] | ||
- vc 9 # [win and py27] | ||
# - python 3.6 # [py36] | ||
# - python 2.7 # [py27] | ||
# - numpy | ||
# - scipy | ||
# - matplotlib | ||
# - docopt | ||
- h5py | ||
- psutil | ||
- fftw | ||
- libgcc-ng | ||
- libstdcxx-ng | ||
- openblas | ||
# - armadillo | ||
# - gtest | ||
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||
about: | ||
home: http://www.ccppetmr.ac.uk | ||
license: Apache 2.0 license | ||
summary: 'Synergistic Image Reconstruction Framework' |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
incorrect comment