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daniaki merged 2 commits into from
Apr 15, 2020
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Relicense from GPLv3 to BSD 3-clause #8

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145fe7c
rewrite main docs page
afrubin Mar 20, 2020
9856b6d
relicense from GPLv3 to BSD 3-clause
afrubin Mar 20, 2020
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29 changes: 29 additions & 0 deletions LICENSE
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BSD 3-Clause License

Copyright (c) 2016-2020, Alan F Rubin and Daniel C Esposito
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
674 changes: 0 additions & 674 deletions License.txt
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14 changes: 5 additions & 9 deletions docs/index.rst
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Enrich2: deep mutational scanning data analysis
===============================================
CountESS: Count-based Experiment Scoring and Statistics
=======================================================

Enrich2 is a general software tool for processing, analyzing, and visualizing data from deep mutational scanning experiments.
CountESS is a general software tool for processing, analyzing, and visualizing data from multiplexed assays of variant effect.

The software is freely available from https://github.com/FowlerLab/Enrich2/ under the `GPLv3 license <https://www.gnu.org/licenses/gpl-3.0.txt>`_.
The software is freely available from https://github.com/CountESS-Project/CountESS/ under the BSD 3-clause license.

For an example dataset, visit https://github.com/FowlerLab/Enrich2-Example/.

To cite Enrich2, please reference `Enrich2: a statistical framework for analyzing deep mutational scanning data <http://biorxiv.org>`_.

Enrich2 was written by `Alan F Rubin <mailto:alan.rubin@wehi.edu.au>`_ |ORCID_icon| http://orcid.org/0000-0003-1474-605X
CountESS is maintained by `Alan F Rubin <mailto:alan.rubin@wehi.edu.au>`_ |ORCID_icon| http://orcid.org/0000-0003-1474-605X

.. |ORCID_icon| image:: _static/iD_icon.png
:target: http://orcid.org
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18 changes: 0 additions & 18 deletions enrich2/__init__.py
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# Copyright 2016-2017 Alan F Rubin, Daniel Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


__all__ = [
"base",
"config",
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17 changes: 0 additions & 17 deletions enrich2/base/__init__.py
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# Copyright 2016-2017 Alan F Rubin, Daniel Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.

"""
Enrich2 base module
===================
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18 changes: 0 additions & 18 deletions enrich2/base/config_constants.py
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# Copyright 2016-2017 Alan F Rubin, Daniel Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 configuration constants module
======================================
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18 changes: 0 additions & 18 deletions enrich2/base/constants.py
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# Copyright 2016-2017 Alan F Rubin, Daniel Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 constants module
========================
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18 changes: 0 additions & 18 deletions enrich2/base/dataframe.py
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# Copyright 2016-2017 Alan F Rubin, Daniel Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 dataframe module
========================
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18 changes: 0 additions & 18 deletions enrich2/base/store_wrappers.py
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# Copyright 2016-2017 Alan F Rubin, Daniel C Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 base wrapper module
=================================
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18 changes: 0 additions & 18 deletions enrich2/base/storemanager.py
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# Copyright 2016-2017 Alan F Rubin, Daniel C Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 base storemanager module
================================
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18 changes: 0 additions & 18 deletions enrich2/base/utils.py
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# Copyright 2016-2017 Alan F Rubin, Daniel C Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 base utility module
===========================
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18 changes: 0 additions & 18 deletions enrich2/config/__init__.py
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# Copyright 2016-2017 Alan F Rubin, Daniel C Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 config module
=====================
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18 changes: 0 additions & 18 deletions enrich2/config/config_check.py
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# Copyright 2016-2017 Alan F Rubin, Daniel C Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 config_check module
===========================
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18 changes: 0 additions & 18 deletions enrich2/config/types.py
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# Copyright 2016-2017 Alan F Rubin, Daniel C Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 config types module
===========================
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18 changes: 0 additions & 18 deletions enrich2/experiment/__init__.py
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# Copyright 2016-2017 Alan F Rubin, Daniel C Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 experiment module
=========================
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# Copyright 2016-2017 Alan F Rubin, Daniel C Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 experiment experiment module
====================================
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18 changes: 0 additions & 18 deletions enrich2/experiment/experiment.py
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# Copyright 2016-2017 Alan F Rubin, Daniel C Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 experiment experiment module
====================================
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18 changes: 0 additions & 18 deletions enrich2/gui/__init__.py
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# Copyright 2016-2017 Alan F Rubin, Daniel C Esposito
#
# This file is part of Enrich2.
#
# Enrich2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Enrich2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Enrich2. If not, see <http://www.gnu.org/licenses/>.


"""
Enrich2 gui module
==================
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