Merge branch 'main' into NeSyEBMLearning

linqs · Feb 22, 2024 · da7765e · da7765e
2 parents e6d5e18 + e1f7a61
commit da7765e
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Showing 327 changed files with 462 additions and 347 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -36,29 +36,29 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0  # Needs to be deep enough to hit the last tagged version.
 
       - name: Set up JDK 8
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 8
           distribution: adopt
 
       - name: Set up Python 3.7
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.7'
 
       - name: Cache Maven
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.m2/repository
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
 
       - name: Cache Python Dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('psl-python/setup.py') }}-${{ hashFiles('psl-python/dev_requirements.txt') }}-${{ hashFiles('psl-python/optional_requirements.txt') }}
@@ -75,7 +75,7 @@ jobs:
         run: tar cvf psl.tar */target
 
       - name: Upload Archived Build
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
             name: psl
             path: psl.tar
@@ -86,29 +86,29 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0  # Needs to be deep enough to hit the last tagged version.
 
       - name: Set up JDK 8
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 8
           distribution: adopt
 
       - name: Set up Python 3.7
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.7'
 
       - name: Cache Maven
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.m2/repository
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
 
       - name: Cache Python Dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('psl-python/setup.py') }}-${{ hashFiles('psl-python/dev_requirements.txt') }}-${{ hashFiles('psl-python/optional_requirements.txt') }}
@@ -131,29 +131,29 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0  # Needs to be deep enough to hit the last tagged version.
 
       - name: Set up JDK 8
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 8
           distribution: adopt
 
       - name: Set up Python 3.7
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.7'
 
       - name: Cache Maven
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.m2/repository
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
 
       - name: Cache Python Dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('psl-python/setup.py') }}-${{ hashFiles('psl-python/dev_requirements.txt') }}-${{ hashFiles('psl-python/optional_requirements.txt') }}
@@ -211,29 +211,29 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0  # Needs to be deep enough to hit the last tagged version.
 
       - name: Set up JDK ${{ matrix.java-version }}
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: ${{ matrix.java-version }}
           distribution: adopt
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Cache Maven
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.m2/repository
           key: ${{ runner.os }}-maven-java${{ matrix.java-version }}-${{ hashFiles('**/pom.xml') }}
 
       - name: Cache Python Dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('psl-python/setup.py') }}-${{ hashFiles('psl-python/dev_requirements.txt') }}-${{ hashFiles('psl-python/optional_requirements.txt') }}

diff --git a/NOTICE b/NOTICE
@@ -1,6 +1,6 @@
 PSL Software
 Copyright 2011-2015 University of Maryland
-Copyright 2013-2023 The Regents of the University of California
+Copyright 2013-2024 The Regents of the University of California
 
 This product includes software developed by
 the University of Maryland and the University of California.

diff --git a/pom.xml b/pom.xml
@@ -2,7 +2,7 @@
 <!--
   - This file is part of the PSL software.
   - Copyright 2011-2015 University of Maryland
-  - Copyright 2013-2023 The Regents of the University of California
+  - Copyright 2013-2024 The Regents of the University of California
   -
   - Licensed under the Apache License, Version 2.0 (the "License");
   - you may not use this file except in compliance with the License.

diff --git a/psl-cli/pom.xml b/psl-cli/pom.xml
@@ -2,7 +2,7 @@
 <!--
   - This file is part of the PSL software.
   - Copyright 2011-2015 University of Maryland
-  - Copyright 2013-2023 The Regents of the University of California
+  - Copyright 2013-2024 The Regents of the University of California
   -
   - Licensed under the Apache License, Version 2.0 (the "License");
   - you may not use this file except in compliance with the License.

diff --git a/psl-cli/src/main/java/org/linqs/psl/cli/CommandLineLoader.java b/psl-cli/src/main/java/org/linqs/psl/cli/CommandLineLoader.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-cli/src/main/java/org/linqs/psl/cli/Launcher.java b/psl-cli/src/main/java/org/linqs/psl/cli/Launcher.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-cli/src/test/java/org/linqs/psl/cli/CLITest.java b/psl-cli/src/test/java/org/linqs/psl/cli/CLITest.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-cli/src/test/java/org/linqs/psl/cli/MiscTest.java b/psl-cli/src/test/java/org/linqs/psl/cli/MiscTest.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-cli/src/test/java/org/linqs/psl/cli/SimpleAcquaintancesTest.java b/psl-cli/src/test/java/org/linqs/psl/cli/SimpleAcquaintancesTest.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-core/pom.xml b/psl-core/pom.xml
@@ -2,7 +2,7 @@
 <!--
   - This file is part of the PSL software.
   - Copyright 2011-2015 University of Maryland
-  - Copyright 2013-2023 The Regents of the University of California
+  - Copyright 2013-2024 The Regents of the University of California
   -
   - Licensed under the Apache License, Version 2.0 (the "License");
   - you may not use this file except in compliance with the License.

diff --git a/psl-core/src/main/java/org/linqs/psl/application/ModelApplication.java b/psl-core/src/main/java/org/linqs/psl/application/ModelApplication.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-core/src/main/java/org/linqs/psl/application/inference/InferenceApplication.java b/psl-core/src/main/java/org/linqs/psl/application/inference/InferenceApplication.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/ADMMInference.java b/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/ADMMInference.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/...re/src/main/java/org/linqs/psl/application/inference/mpe/DistributedDualBCDInference.java b/...re/src/main/java/org/linqs/psl/application/inference/mpe/DistributedDualBCDInference.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/DualBCDInference.java b/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/DualBCDInference.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/GradientDescentInference.java b/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/GradientDescentInference.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/MPEInference.java b/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/MPEInference.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/SGDInference.java b/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/SGDInference.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/SGDStreamingInference.java b/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/SGDStreamingInference.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/gurobi/GurobiInference.java b/psl-core/src/main/java/org/linqs/psl/application/inference/mpe/gurobi/GurobiInference.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/psl-core/src/main/java/org/linqs/psl/application/learning/weight/TrainingMap.java b/psl-core/src/main/java/org/linqs/psl/application/learning/weight/TrainingMap.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/...re/src/main/java/org/linqs/psl/application/learning/weight/WeightLearningApplication.java b/...re/src/main/java/org/linqs/psl/application/learning/weight/WeightLearningApplication.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/...ore/src/main/java/org/linqs/psl/application/learning/weight/gradient/GradientDescent.java b/...ore/src/main/java/org/linqs/psl/application/learning/weight/gradient/GradientDescent.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/...ava/org/linqs/psl/application/learning/weight/gradient/batchgenerator/BatchGenerator.java b/...ava/org/linqs/psl/application/learning/weight/gradient/batchgenerator/BatchGenerator.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/...application/learning/weight/gradient/batchgenerator/ConnectedComponentBatchGenerator.java b/...application/learning/weight/gradient/batchgenerator/ConnectedComponentBatchGenerator.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/...org/linqs/psl/application/learning/weight/gradient/batchgenerator/FullBatchGenerator.java b/...org/linqs/psl/application/learning/weight/gradient/batchgenerator/FullBatchGenerator.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/...g/linqs/psl/application/learning/weight/gradient/batchgenerator/NeuralBatchGenerator.java b/...g/linqs/psl/application/learning/weight/gradient/batchgenerator/NeuralBatchGenerator.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/...java/org/linqs/psl/application/learning/weight/gradient/minimizer/BinaryCrossEntropy.java b/...java/org/linqs/psl/application/learning/weight/gradient/minimizer/BinaryCrossEntropy.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

diff --git a/...src/main/java/org/linqs/psl/application/learning/weight/gradient/minimizer/Minimizer.java b/...src/main/java/org/linqs/psl/application/learning/weight/gradient/minimizer/Minimizer.java
@@ -1,7 +1,7 @@
 /*
  * This file is part of the PSL software.
  * Copyright 2011-2015 University of Maryland
- * Copyright 2013-2023 The Regents of the University of California
+ * Copyright 2013-2024 The Regents of the University of California
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.