Merge pull request #529 from jay-m-dev/master

old files, gitmodule, headers
EpistasisLab · Jan 12, 2023 · d7c7de6 · d7c7de6
2 parents 6ba9fe3 + 52e8f51
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diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,3 @@
-[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
diff --git a/ai/__init__.py b/ai/__init__.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/ai.py b/ai/ai.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/api_utils.py b/ai/api_utils.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/knowledgebase_utils.py b/ai/knowledgebase_utils.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/metalearning/__init__.py b/ai/metalearning/__init__.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/metalearning/dataset_describe.py b/ai/metalearning/dataset_describe.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/metalearning/export_to_mongo.py b/ai/metalearning/export_to_mongo.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/metalearning/get_metafeatures.py b/ai/metalearning/get_metafeatures.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/metalearning/make_meta_ml_dataset.py b/ai/metalearning/make_meta_ml_dataset.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/metalearning/tests/test_dataset_describe.py b/ai/metalearning/tests/test_dataset_describe.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/metalearning/tests/test_get_metafeatures.py b/ai/metalearning/tests/test_get_metafeatures.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/metrics.py b/ai/metrics.py
@@ -1,3 +1,30 @@
+"""~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.

diff --git a/ai/q_utils.py b/ai/q_utils.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/recommender/__init__.py b/ai/recommender/__init__.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/recommender/average_recommender.py b/ai/recommender/average_recommender.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/recommender/base.py b/ai/recommender/base.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/recommender/knn_meta_recommender.py b/ai/recommender/knn_meta_recommender.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/recommender/random_recommender.py b/ai/recommender/random_recommender.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/recommender/surprise_recommenders.py b/ai/recommender/surprise_recommenders.py
@@ -1,12 +1,12 @@
 """~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

diff --git a/ai/request_manager.py b/ai/request_manager.py
@@ -1,12 +1,12 @@
 """~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