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change file headers to MIT
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@msuchard
msuchard committed Jan 24, 2022
1 parent aee7aae commit 1d4b21d
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Showing 40 changed files with 967 additions and 2,415 deletions.
674 changes: 0 additions & 674 deletions examples/standalone/epochtest/COPYING
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21 changes: 21 additions & 0 deletions examples/standalone/epochtest/LICENSE
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@@ -0,0 +1,21 @@
MIT License

Copyright (c) 2021 Phylogenetic Likelihood Working Group

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
16 changes: 3 additions & 13 deletions java/beagle/Beagle.java
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Expand Up @@ -5,19 +5,9 @@
*
* This file is part of BEAGLE.
*
* BEAGLE is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation, either version 3 of
* the License, or (at your option) any later version.
*
* BEAGLE 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAGLE. If not, see
* <http://www.gnu.org/licenses/>.
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
* @brief This file documents the API as well as header for the
* Broad-platform Evolutionary Analysis General Likelihood Evaluator
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74 changes: 32 additions & 42 deletions libhmsbeagle/BeagleImpl.h
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Expand Up @@ -6,20 +6,10 @@
*
* This file is part of BEAGLE.
*
* BEAGLE is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation, either version 3 of
* the License, or (at your option) any later version.
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
* BEAGLE 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAGLE. If not, see
* <http://www.gnu.org/licenses/>.
*
* @author Andrew Rambaut
* @author Marc Suchard
* @author Daniel Ayres
Expand All @@ -42,31 +32,31 @@ class BeagleImpl
{
public:
virtual ~BeagleImpl(){}

virtual int createInstance(int tipCount,
int partialsBufferCount,
int compactBufferCount,
int stateCount,
int patternCount,
int eigenBufferCount,
int matrixBufferCount,
int matrixBufferCount,
int categoryCount,
int scaleBufferCount,
int resourceNumber,
int pluginResourceNumber,
long preferenceFlags,
long requirementFlags) = 0;

virtual int getInstanceDetails(BeagleInstanceDetails* returnInfo) = 0;

virtual int setCPUThreadCount(int threadCount) = 0;

virtual int setTipStates(int tipIndex,
const int* inStates) = 0;

virtual int setTipPartials(int tipIndex,
const double* inPartials) = 0;

virtual int setPartials(int bufferIndex,
const double* inPartials) = 0;

Expand All @@ -77,28 +67,28 @@ class BeagleImpl
virtual int getPartials(int bufferIndex,
int scaleIndex,
double* outPartials) = 0;

virtual int setEigenDecomposition(int eigenIndex,
const double* inEigenVectors,
const double* inInverseEigenVectors,
const double* inEigenValues) = 0;

virtual int setStateFrequencies(int stateFrequenciesIndex,
const double* inStateFrequencies) = 0;
const double* inStateFrequencies) = 0;

virtual int setCategoryWeights(int categoryWeightsIndex,
const double* inCategoryWeights) = 0;

virtual int setPatternWeights(const double* inPatternWeights) = 0;

virtual int setPatternPartitions(int partitionCount,
const int* inPatternPartitions) = 0;

virtual int setCategoryRates(const double* inCategoryRates) = 0;

virtual int setCategoryRatesWithIndex(int categoryRatesIndex,
const double* inCategoryRates) = 0;

virtual int setTransitionMatrix(int matrixIndex,
const double* inMatrix,
double paddedValue) = 0;
Expand All @@ -109,8 +99,8 @@ class BeagleImpl
virtual int setTransitionMatrices(const int* matrixIndices,
const double* inMatrices,
const double* paddedValues,
int count) = 0;
int count) = 0;

virtual int getTransitionMatrix(int matrixIndex,
double* outMatrix) = 0;

Expand Down Expand Up @@ -149,7 +139,7 @@ class BeagleImpl
const int* secondDerivativeIndices,
const double* edgeLengths,
int count) = 0;

virtual int updatePartials(const int* operations,
int operationCount,
int cumulativeScalingIndex) = 0;
Expand All @@ -166,7 +156,7 @@ class BeagleImpl

virtual int waitForPartials(const int* destinationPartials,
int destinationPartialsCount) = 0;

virtual int accumulateScaleFactors(const int* scalingIndices,
int count,
int cumulativeScalingIndex) = 0;
Expand All @@ -175,7 +165,7 @@ class BeagleImpl
int count,
int cumulativeScaleIndex,
int partitionIndex) = 0;

virtual int removeScaleFactors(const int* scalingIndices,
int count,
int cumulativeScalingIndex) = 0;
Expand All @@ -184,18 +174,18 @@ class BeagleImpl
int count,
int cumulativeScaleIndex,
int partitionIndex) = 0;
virtual int resetScaleFactors(int cumulativeScalingIndex) = 0;

virtual int resetScaleFactors(int cumulativeScalingIndex) = 0;

virtual int resetScaleFactorsByPartition(int cumulativeScaleIndex,
int partitionIndex) = 0;
int partitionIndex) = 0;

virtual int copyScaleFactors(int destScalingIndex,
int srcScalingIndex) = 0;
int srcScalingIndex) = 0;

virtual int getScaleFactors(int srcScalingIndex,
double* scaleFactors) = 0;
double* scaleFactors) = 0;

virtual int calculateRootLogLikelihoods(const int* bufferIndices,
const int* categoryWeightsIndices,
const int* stateFrequenciesIndices,
Expand Down Expand Up @@ -263,14 +253,14 @@ class BeagleImpl
double* outSumFirstDerivative,
double* outSumSecondDerivativeByPartition,
double* outSumSecondDerivative) = 0;

virtual int getLogLikelihood(double* outSumLogLikelihood) = 0;

virtual int getDerivatives(double* outSumFirstDerivative,
double* outSumSecondDerivative) = 0;

virtual int getSiteLogLikelihoods(double* outLogLikelihoods) = 0;

virtual int getSiteDerivatives(double* outFirstDerivatives,
double* outSecondDerivatives) = 0;
//protected:
Expand All @@ -293,9 +283,9 @@ class BeagleImplFactory {
long preferenceFlags,
long requirementFlags,
int* errorCode) = 0; // pure virtual

virtual const char* getName() = 0; // pure virtual

virtual const long getFlags() = 0; // pure virtual
};

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16 changes: 3 additions & 13 deletions libhmsbeagle/CPU/AVXDefinitions.h
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Expand Up @@ -6,19 +6,9 @@
*
* This file is part of BEAGLE.
*
* BEAGLE is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation, either version 3 of
* the License, or (at your option) any later version.
*
* BEAGLE 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAGLE. If not, see
* <http://www.gnu.org/licenses/>.
* Use of this source code is governed by an MIT-style
* license that can be found in the LICENSE file or at
* https://opensource.org/licenses/MIT.
*
* @author Marc Suchard
*/
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