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‎LICENSE‎

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‎README.md‎

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@@ -6,8 +6,9 @@ Singularity Python is a python module and command line tool for working with <a
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We currently require Python > version 3 to use various timezone functions. If you are unable to install version 3.0, we provide a [Singularity.container](Singularity.container) for you to use instead. This is the recommended approach as some older versions of Python do not support generation of the timestamp. See the [installation docs](https://github.com/singularityware/singularity-python/wiki/Installation) for your different options.
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The Singularity-Python code is licensed under the MIT open source license, which is a highly permissive license that places few limits upon reuse. This ensures that the code will be usable by the greatest number of researchers, in both academia and industry. The following examples are provided:
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## License
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This code is licensed under the Affero GPL, version 3.0 or later [LICENSE](LICENSE).
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Please see our [complete docs](https://github.com/singularityware/singularity-python/wiki)
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## Help and Contribution

‎setup.py‎

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'''
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Copyright (C) 2017 The Board of Trustees of the Leland Stanford Junior
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University.
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Copyright (C) 2017 Vanessa Sochat.
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This program is free software: you can redistribute it and/or modify it
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under the terms of the GNU Affero General Public License as published by
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the Free Software Foundation, either version 3 of the License, or (at your
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option) any later version.
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This program is distributed in the hope that it will be useful, but WITHOUT
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ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public
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License for more details.
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You should have received a copy of the GNU Affero General Public License
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along with this program. If not, see <https://www.gnu.org/licenses/>.
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'''
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from setuptools import setup, find_packages
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import codecs
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import os
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classifiers=[
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'Intended Audience :: Science/Research',
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'Intended Audience :: Developers',
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'License :: OSI Approved :: MIT License',
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'License :: OSI Approved :: GPLv3 License',
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'Programming Language :: C',
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'Programming Language :: Python',
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'Topic :: Software Development',

‎singularity/__init__.py‎

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'''
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3-
The MIT License (MIT)
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Copyright (C) 2017 The Board of Trustees of the Leland Stanford Junior
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University.
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Copyright (C) 2016-2017 Vanessa Sochat.
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5-
Copyright (c) 2016-2017 Vanessa Sochat
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This program is free software: you can redistribute it and/or modify it
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under the terms of the GNU Affero General Public License as published by
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the Free Software Foundation, either version 3 of the License, or (at your
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option) any later version.
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7-
Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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This program is distributed in the hope that it will be useful, but WITHOUT
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ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public
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License for more details.
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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You should have received a copy of the GNU Affero General Public License
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along with this program. If not, see <https://www.gnu.org/licenses/>.
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'''
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‎singularity/analysis/apps.py‎

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'''
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apps.py: part of singularity package
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functions to assess SCI-F apps
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Copyright (c) 2016-2017 Vanessa Sochat
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
14-
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Copyright (C) 2017 The Board of Trustees of the Leland Stanford Junior
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University.
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Copyright (C) 2016-2017 Vanessa Sochat.
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7+
This program is free software: you can redistribute it and/or modify it
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under the terms of the GNU Affero General Public License as published by
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the Free Software Foundation, either version 3 of the License, or (at your
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option) any later version.
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This program is distributed in the hope that it will be useful, but WITHOUT
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ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public
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License for more details.
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You should have received a copy of the GNU Affero General Public License
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along with this program. If not, see <https://www.gnu.org/licenses/>.
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'''
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‎singularity/analysis/classify.py‎

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'''
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classify.py: part of singularity package
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functions to tag and classify images
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The MIT License (MIT)
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Copyright (c) 2016-2017 Vanessa Sochat
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Copyright (C) 2017 The Board of Trustees of the Leland Stanford Junior
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University.
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Copyright (C) 2016-2017 Vanessa Sochat.
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This program is free software: you can redistribute it and/or modify it
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under the terms of the GNU Affero General Public License as published by
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the Free Software Foundation, either version 3 of the License, or (at your
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option) any later version.
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This program is distributed in the hope that it will be useful, but WITHOUT
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ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public
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License for more details.
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You should have received a copy of the GNU Affero General Public License
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along with this program. If not, see <https://www.gnu.org/licenses/>.
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'''
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‎singularity/analysis/compare.py‎

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'''
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compare.py: part of singularity package
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functions to compare packages and images
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The MIT License (MIT)
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Copyright (c) 2016-2017 Vanessa Sochat
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
25-
SOFTWARE.
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Copyright (C) 2017 The Board of Trustees of the Leland Stanford Junior
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University.
5+
Copyright (C) 2016-2017 Vanessa Sochat.
6+
7+
This program is free software: you can redistribute it and/or modify it
8+
under the terms of the GNU Affero General Public License as published by
9+
the Free Software Foundation, either version 3 of the License, or (at your
10+
option) any later version.
11+
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This program is distributed in the hope that it will be useful, but WITHOUT
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ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public
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License for more details.
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You should have received a copy of the GNU Affero General Public License
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along with this program. If not, see <https://www.gnu.org/licenses/>.
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'''
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‎singularity/analysis/metrics.py‎

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'''
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The MIT License (MIT)
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Copyright (c) 2016-2017 Vanessa Sochat
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
11-
furnished to do so, subject to the following conditions:
12-
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
15-
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17-
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18-
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19-
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21-
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
22-
SOFTWARE.
2+
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Copyright (C) 2017 The Board of Trustees of the Leland Stanford Junior
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University.
5+
Copyright (C) 2016-2017 Vanessa Sochat.
6+
7+
This program is free software: you can redistribute it and/or modify it
8+
under the terms of the GNU Affero General Public License as published by
9+
the Free Software Foundation, either version 3 of the License, or (at your
10+
option) any later version.
11+
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This program is distributed in the hope that it will be useful, but WITHOUT
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ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
14+
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public
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License for more details.
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You should have received a copy of the GNU Affero General Public License
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along with this program. If not, see <https://www.gnu.org/licenses/>.
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'''
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‎singularity/analysis/reproduce/criteria.py‎

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'''
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criteria.py: part of singularity package, functions to assess
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reproducibility of images
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The MIT License (MIT)
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Copyright (c) 2016-2017 Vanessa Sochat
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9-
Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
11-
in the Software without restriction, including without limitation the rights
12-
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
13-
copies of the Software, and to permit persons to whom the Software is
14-
furnished to do so, subject to the following conditions:
15-
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The above copyright notice and this permission notice shall be included in all
17-
copies or substantial portions of the Software.
18-
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
20-
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
21-
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
22-
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
23-
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
24-
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
25-
SOFTWARE.
2+
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Copyright (C) 2017 The Board of Trustees of the Leland Stanford Junior
4+
University.
5+
Copyright (C) 2016-2017 Vanessa Sochat.
6+
7+
This program is free software: you can redistribute it and/or modify it
8+
under the terms of the GNU Affero General Public License as published by
9+
the Free Software Foundation, either version 3 of the License, or (at your
10+
option) any later version.
11+
12+
This program is distributed in the hope that it will be useful, but WITHOUT
13+
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
14+
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public
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License for more details.
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You should have received a copy of the GNU Affero General Public License
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along with this program. If not, see <https://www.gnu.org/licenses/>.
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'''
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‎singularity/analysis/reproduce/hash.py‎

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'''
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hash.py: part of singularity package, functions to assess
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reproducibility of images
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The MIT License (MIT)
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Copyright (c) 2016-2017 Vanessa Sochat
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
13-
copies of the Software, and to permit persons to whom the Software is
14-
furnished to do so, subject to the following conditions:
15-
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The above copyright notice and this permission notice shall be included in all
17-
copies or substantial portions of the Software.
18-
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
20-
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
21-
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
22-
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
23-
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
24-
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
25-
SOFTWARE.
2+
3+
Copyright (C) 2017 The Board of Trustees of the Leland Stanford Junior
4+
University.
5+
Copyright (C) 2016-2017 Vanessa Sochat.
6+
7+
This program is free software: you can redistribute it and/or modify it
8+
under the terms of the GNU Affero General Public License as published by
9+
the Free Software Foundation, either version 3 of the License, or (at your
10+
option) any later version.
11+
12+
This program is distributed in the hope that it will be useful, but WITHOUT
13+
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
14+
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public
15+
License for more details.
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17+
You should have received a copy of the GNU Affero General Public License
18+
along with this program. If not, see <https://www.gnu.org/licenses/>.
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'''
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