savu2.3.2_install

install/2_3_2_install/__init__.py

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+# Copyright 2014 Diamond Light Source Ltd.
+#
+# 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
+#
+# 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.
+
+"""
+All the plugin architecture for Savu is contained here
+
+
+.. moduleauthor:: Mark Basham <scientificsoftware@diamond.ac.uk>
+
+"""
+

install/2_3_2_install/conda-recipes/__init__.py

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+# Copyright 2014 Diamond Light Source Ltd.
+#
+# 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
+#
+# 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.
+
+"""
+All the plugin architecture for Savu is contained here
+
+
+.. moduleauthor:: Mark Basham <scientificsoftware@diamond.ac.uk>
+
+"""
+

install/2_3_2_install/conda-recipes/astra/astra.pth

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+./astra/python
+

install/2_3_2_install/conda-recipes/astra/build.sh

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+#!/bin/bash
+
+nvcc=`command -v nvcc`
+cuda=${nvcc%/bin/nvcc}
+
+savu_path=`command -v savu`
+ana_path=${savu_path%/savu}
+prefix=${ana_path%/bin}/lib/python2.7/site-packages/astra
+export PATH=$ana_path:$PATH
+
+cd build/linux
+
+if [ "$cuda" ]; then
+    ./configure --with-cuda=$cuda --with-python --prefix=$prefix
+else
+    echo "cuda has not been found."
+    ./configure --with-python --prefix=$prefix
+fi
+
+make -j 4
+make install
+

install/2_3_2_install/conda-recipes/astra/meta.yaml

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+{% set version = "1.8" %}
+
+package:
+  name: astra-toolbox
+  version: 1.8
+
+source:
+  fn: astra-{{ version }}.tar.bz2
+  url: http://www.astra-toolbox.com/files/astra-{{ version }}/astra-{{ version }}.tar.bz2
+  sha256: 44602e0eb0789a557622eae959fc0a067d81396bcb79ec315cb39b59d52322e7
+
+requirements:
+  build:
+    - python
+    - numpy
+    - cython
+
+build:
+  number: 2
+
+about:
+  home: http://www.astra-toolbox.com
+  license: GPLv3
+  summary: 'The ASTRA Toolbox is a Python toolbox of high-performance GPU primitives for 2D and 3D tomography.'
+

install/2_3_2_install/conda-recipes/h5py/build.sh

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+#!/bin/bash
+
+# set compiler wrapper
+mpicc=$(command -v mpicc)
+mpi=`dirname $mpicc`
+
+# set anaconda distribution
+ana_path=$(command -v savu)
+ana_path=${ana_path%/bin/savu}
+hdf5_version=1.10.1
+hdf5_build_no=1
+
+export LD_LIBRARY_PATH=$mpi/lib:$mpi/include:$ana_path/lib:$LD_LIBRARY_PATH
+export LD_RUN_PATH=$LD_LIBRARY_PATH
+export PYTHONPATH=$PYTHONPATH:$ana_path/lib/python2.7/site-packages
+export PATH=$PATH:$ana_path/bin/
+export CC=$mpicc
+
+$PYTHON setup.py configure --hdf5=$ana_path
+$PYTHON setup.py configure --hdf5-version=$hdf5_version
+$PYTHON setup.py configure --mpi
+$PYTHON setup.py build
+$PYTHON setup.py install
+

install/2_3_2_install/conda-recipes/h5py/meta.yaml

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+{% set version = "2.7.1" %} # change this
+
+package:
+  name: h5py
+  version: {{ version }}
+
+source:
+  fn: h5py-{{ version }}.tar.gz
+  url: https://github.com/h5py/h5py/archive/{{ version }}.tar.gz
+requirements:
+  build:
+    - python
+    - numpy
+    - hdf5
+    - cython
+    - pkgconfig
+    - six
+
+build:
+  number: 1
+
+about:
+  home: http://www.h5py.org/
+  license: New BSD (http://opensource.org/licenses/bsd-license.php)
+

install/2_3_2_install/conda-recipes/hdf5/build.sh

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+#!/bin/bash
+
+# set compiler wrapper
+mpicc=$(command -v mpicc)
+mpi=${mpicc%/bin/mpicc}
+export LD_LIBRARY_PATH=$mpi:$mpi/lib:$mpi/include:$LD_LIBRARY_PATH
+export LD_RUN_PATH=$LD_LIBRARY_PATH
+
+# check anaconda distribution
+ana_path=$(command -v savu)
+
+CC=$mpicc ./configure --with-zlib --enable-parallel --enable-shared --prefix=$PREFIX
+make
+make install
+
+rm -rf $PREFIX/share/hdf5_examples
+

install/2_3_2_install/conda-recipes/hdf5/meta.yaml

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+{% set version = "1.10.1" %}
+{% set release = "hdf5-1.10" %}
+{% set patch = "hdf5-1.10.1" %}
+
+package:
+  name: hdf5
+  version: {{ version }}
+
+source:
+  fn: {{ patch }}.tar.bz2
+  url: https://www.hdfgroup.org/ftp/HDF5/releases/{{ release }}/{{ patch }}/src/{{ patch }}.tar.bz2
+  md5: d89893c05ee7ea8611b51bb39450d64e
+
+build:
+  number: 1
+
+about:
+  home: http://www.hdfgroup.org/HDF5/
+  license: BSD-style (http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING)
+

install/2_3_2_install/conda-recipes/xdesign/build.sh

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+#!/bin/bash
+
+$PYTHON setup.py install
+

install/2_3_2_install/conda-recipes/xdesign/meta.yaml

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+package:
+  name: xdesign
+  version: '0.3.0'
+
+source:
+  git_url: https://github.com/tomography/xdesign.git
+
+build:
+  number: 0
+
+requirements:
+  build:
+    - python
+    - setuptools
+
+about:
+  home: http://xdesign.readthedocs.io
+  license: BSD-3
+  summary: 'Benchmarking and optimization tools for tomography.'
+
+# See
+# http://docs.continuum.io/conda/build.html for
+# more information about meta.yaml
+

install/2_3_2_install/conda-recipes/xraylib/build.sh

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+
+./configure --enable-python --disable-perl --disable-java \
+	    --disable-fortran2003 --disable-lua --prefix=$PREFIX
+make
+make check
+make install
+

install/2_3_2_install/conda-recipes/xraylib/meta.yaml

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+{% set version = "3.3.0" %}
+
+package:
+  name: xraylib
+  version: {{ version }}
+
+source:
+  fn: xraylib-{{ version }}.tar.gz
+  url: https://xraylib.tomschoonjans.eu/xraylib-{{ version }}.tar.gz
+  sha256: a22a73b8d90eb752b034bab1a4cf6abdd81b8c7dc5020bcb22132d2ee7aacd42
+
+build:
+  number: 0
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - numpy
+    - scipy >=0.7.0
+    - cython
+    - swig
+    - autoconf
+    - libtool
+    - automake
+

install/2_3_2_install/savu_v2.3.2/environment.yml

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+name: root
+channels:
+- defaults
+dependencies:
+- scipy==1.1.0
+- colorama==0.3.9
+- setuptools==39.2.0
+- jinja2==2.10
+- numpy==1.14.5
+- pandas==0.23.3
+- mock==2.0.0
+- PyWavelets==0.5.2
+- scikit-image==0.14.0
+- scikit-learn==0.19.1
+- pytest==3.6.2
+- spyder==3.3.0
+- ipython==5.7.0
+- cython==0.28.3
+- boost==1.67.0
+- pip:
+  - fabio==0.4.0
+  - pyfftw==0.10.4
+  - nvidia-ml-py==7.352.0
+  - PeakUtils==1.1.1
+  - pymca==5.3.1
+  - tifffile==0.4.0
+  - pyreadline==2.1
+  - gnureadline==6.3.8
+  - sphinx_rtd_theme==0.4.1
+

install/2_3_2_install/savu_v2.3.2/savu/build.sh

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+#!/bin/bash
+
+$PYTHON setup.py install --facility $FACILITY   # Python command to install the script.
+

install/2_3_2_install/savu_v2.3.2/savu/meta.yaml

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+{% set version = "2.3.2" %}
+
+package:
+  name: savu
+  version: {{ version }}
+
+source:
+  url: https://github.com/DiamondLightSource/Savu/archive/v{{ version }}.tar.gz
+
+requirements:
+  build:
+    - python
+
+build:
+  preserve_egg_dir: True
+  script_env:
+    - FACILITY
+
+about:
+  home: https://github.com/diamondlightsource/Savu
+  license: Apache V2 and GPL V3
+  license_file: LICENCE.txt
+