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old files, gitmodule, headers #529

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Jan 12, 2023
Merged

old files, gitmodule, headers #529

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14c2071
removed yml, .sh files and commented out .gitmodules
jay-m-dev Jan 12, 2023
cb9f4f0
updated setup.py names from pennai -> aliro
jay-m-dev Jan 12, 2023
52e8f51
updated source headers
jay-m-dev Jan 12, 2023
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6 changes: 3 additions & 3 deletions .gitmodules
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[submodule "docker/pennai-arm64-deps"]
path = docker/pennai-arm64-deps
url = https://github.com/EpistasisLab/pennai-arm64-deps
; [submodule "docker/pennai-arm64-deps"]
; path = docker/pennai-arm64-deps
; url = https://github.com/EpistasisLab/pennai-arm64-deps
10 changes: 5 additions & 5 deletions ai/__init__.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
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10 changes: 5 additions & 5 deletions ai/ai.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
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10 changes: 5 additions & 5 deletions ai/api_utils.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
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10 changes: 5 additions & 5 deletions ai/knowledgebase_utils.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/metalearning/__init__.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/metalearning/dataset_describe.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/metalearning/export_to_mongo.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/metalearning/get_metafeatures.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/metalearning/make_meta_ml_dataset.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/metalearning/tests/test_dataset_describe.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/metalearning/tests/test_get_metafeatures.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
27 changes: 27 additions & 0 deletions ai/metrics.py
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"""~This file is part of the Aliro library~

Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program 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.

This program 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 this program. If not, see <https://www.gnu.org/licenses/>.

(Autogenerated header, do not modify)

"""
# -*- coding: utf-8 -*-

"""This scoring file is part of the TPOT library.
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10 changes: 5 additions & 5 deletions ai/q_utils.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/recommender/__init__.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/recommender/average_recommender.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/recommender/base.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/recommender/knn_meta_recommender.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/recommender/random_recommender.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/recommender/surprise_recommenders.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
10 changes: 5 additions & 5 deletions ai/request_manager.py
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"""~This file is part of the Aliro library~

Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
Copyright (C) 2023 Epistasis Lab, Cedars-Sinai Medical Center

Aliro is maintained by:
- Heather Williams (hwilli@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- William La Cava (lacava@upenn.edu)
- Michael Stauffer (stauffer@upenn.edu)
- Jun Choi (hyunjun.choi@cshs.org)
- Miguel Hernandez (miguel.e.hernandez@cshs.org)
- Nick Matsumoto (nicholas.matsumoto@cshs.org)
- Jay Moran (jay.moran@cshs.org)
- and many other generous open source contributors

This program is free software: you can redistribute it and/or modify
Expand Down
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