Added/updated copyright info. Change package name to provis.

salesforce · Jun 25, 2020 · b23402d · b23402d
1 parent 1a2e4af
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diff --git a/LICENSE b/LICENSE
@@ -1,31 +1,14 @@
-BSD 3-Clause License
-
-Copyright (c) 2020, Salesforce.
+Copyright (c) 2020, Salesforce.com, Inc.
 All rights reserved.
 
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
-* Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
+* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 
-* 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.
+* 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.
 
-* 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.
+* Neither the name of Salesforce.com 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.
+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
 
 See attribution.txt for additional licensing information.
diff --git a/notebooks/provis.ipynb b/notebooks/provis.ipynb
@@ -13,7 +13,7 @@
     "### Notes\n",
     "* The tool visualizes attention between different positions in a sequence.\n",
     "* It does not currently visualize attention from a given position to itself.\n",
-    "* Attention is visualized as unidirectional using the maximum of the two directed attention weights. "
+    "* Attention is visualized as unidirectional using the maximum of the two directed attention weights. \n"
    ]
   },
   {
@@ -27,6 +27,13 @@
    },
    "outputs": [],
    "source": [
+    "\"\"\"\n",
+    "Copyright (c) 2018, salesforce.com, inc.\n",
+    "All rights reserved.\n",
+    "SPDX-License-Identifier: BSD-3-Clause\n",
+    "For full license text, see the LICENSE file in the repo root or https://opensource.org/licenses/BSD-3-Clause\n",
+    "\"\"\"\n",
+    "\n",
     "import io\n",
     "import urllib\n",
     "\n",

diff --git a/protein_attention/attention_analysis/compute_edge_features.py b/protein_attention/attention_analysis/compute_edge_features.py
@@ -1,4 +1,10 @@
-"""Compute aggregate statistics of attention edge features over a dataset"""
+"""Compute aggregate statistics of attention edge features over a dataset
+
+Copyright (c) 2020, salesforce.com, inc.
+All rights reserved.
+SPDX-License-Identifier: BSD-3-Clause
+For full license text, see the LICENSE file in the repo root or https://opensource.org/licenses/BSD-3-Clause
+"""
 
 from collections import defaultdict
 

diff --git a/protein_attention/attention_analysis/features.py b/protein_attention/attention_analysis/features.py
@@ -1,3 +1,10 @@
+"""
+Copyright (c) 2020, salesforce.com, inc.
+All rights reserved.
+SPDX-License-Identifier: BSD-3-Clause
+For full license text, see the LICENSE file in the repo root or https://opensource.org/licenses/BSD-3-Clause
+"""
+
 from abc import ABC, abstractmethod
 
 

diff --git a/protein_attention/attention_analysis/report_aa_correlations.py b/protein_attention/attention_analysis/report_aa_correlations.py
@@ -1,4 +1,10 @@
-"""Report pairwise correlations of attention to specific amino acids, and compare to blosum"""
+"""Report pairwise correlations of attention to specific amino acids, and compare to blosum
+
+Copyright (c) 2020, salesforce.com, inc.
+All rights reserved.
+SPDX-License-Identifier: BSD-3-Clause
+For full license text, see the LICENSE file in the repo root or https://opensource.org/licenses/BSD-3-Clause
+"""
 
 import json
 import pickle

diff --git a/protein_attention/attention_analysis/report_edge_features.py b/protein_attention/attention_analysis/report_edge_features.py
@@ -1,3 +1,10 @@
+"""
+Copyright (c) 2020, salesforce.com, inc.
+All rights reserved.
+SPDX-License-Identifier: BSD-3-Clause
+For full license text, see the LICENSE file in the repo root or https://opensource.org/licenses/BSD-3-Clause
+"""
+
 import json
 import pathlib
 

diff --git a/protein_attention/attention_analysis/report_edge_features_combined.py b/protein_attention/attention_analysis/report_edge_features_combined.py
@@ -1,4 +1,10 @@
-"""Create combined plot from multiple features"""
+"""Create combined plot from multiple features
+
+Copyright (c) 2020, salesforce.com, inc.
+All rights reserved.
+SPDX-License-Identifier: BSD-3-Clause
+For full license text, see the LICENSE file in the repo root or https://opensource.org/licenses/BSD-3-Clause
+"""
 
 import json
 import pathlib

diff --git a/protein_attention/attention_analysis/utils.py b/protein_attention/attention_analysis/utils.py
@@ -1,3 +1,9 @@
+"""Copyright (c) 2020, salesforce.com, inc.
+All rights reserved.
+SPDX-License-Identifier: BSD-3-Clause
+For full license text, see the LICENSE file in the repo root or https://opensource.org/licenses/BSD-3-Clause
+"""
+
 import torch
 
 

diff --git a/protein_attention/probing/metrics.py b/protein_attention/probing/metrics.py
@@ -1,4 +1,10 @@
-"""Metrics for evaluating probing classifiers"""
+"""Metrics for evaluating probing classifiers
+
+Copyright (c) 2020, salesforce.com, inc.
+All rights reserved.
+SPDX-License-Identifier: BSD-3-Clause
+For full license text, see the LICENSE file in the repo root or https://opensource.org/licenses/BSD-3-Clause
+"""
 
 from typing import Sequence, Union
 

diff --git a/protein_attention/probing/report.py b/protein_attention/probing/report.py
@@ -1,4 +1,10 @@
-"""Report on diagnostic classifiers for probing analysis"""
+"""Report on diagnostic classifiers for probing analysis
+
+Copyright (c) 2020, salesforce.com, inc.
+All rights reserved.
+SPDX-License-Identifier: BSD-3-Clause
+For full license text, see the LICENSE file in the repo root or https://opensource.org/licenses/BSD-3-Clause
+"""
 
 import json
 import pathlib

diff --git a/protein_attention/utils.py b/protein_attention/utils.py
@@ -1,3 +1,9 @@
+"""Copyright (c) 2020, salesforce.com, inc.
+All rights reserved.
+SPDX-License-Identifier: BSD-3-Clause
+For full license text, see the LICENSE file in the repo root or https://opensource.org/licenses/BSD-3-Clause
+"""
+
 from pathlib import Path
 
 

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
     requirements = reqs.read().split()
 
 setup(
-    name='protein-attention',
+    name='provis',
     packages=["protein_attention"],
     version='0.0.1',
     install_requires=requirements,