v4.1.7: Merge pull request #257 from SURGroup/Development

Changes:

• 84afdd3 Merge pull request #257 from SURGroup/Development
• 943a650 Merge pull request #258 from SURGroup/feature/scientific_machine_learning
• cd631a6 Update azure-pipelines.yml
• 35c14ad Update azure-pipelines.yml
• 23d7c37 Update azure-pipelines.yml
• 308ca05 Maximizes the Azure Pipeline job timeout
• c4fbf68 Merge branch 'Development' into feature/scientific_machine_learning
• 31317de added integration tests
• 19725d0 corrected history logging
• af400c2 applied black formatting

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• 16fb0a2 fixed extra_repr for correct string representation
• 925433f added tests to improve code coverage
• f327c74 removed unused file
• 654d2a5 improved comparison operators
• 0935992 deleted unused code
• 98f98b3 Update azure-pipelines.yml
• 4b17b02 Merge branch 'master' into Development
• 96ad483 Merge pull request #249 from SURGroup/feature/scientific_machine_learning
• f6a3e50 set all hypothesis tests to have max_example=1
• af0bdef reduce hypothesis parameters for simpler tests
• 272d69c reduce hypothesis parameters for simpler tests
• f7867a9 fixed failing tests
• dae7248 fixed grammar in documentation
• bbf09a5 fixed device testing so it works on a cpu
• f4bb367 reduced hypothesis parameters to save time during PyTest on azure pipelines
• c29b95f reduced max_examples in hypothesis to save time during PyTest on azure pipelines
• 6fd405d reduced max_examples in hypothesis to save time during PyTest on azure pipelines
• 36123a2 removed slowest SciML tests to decrease azure pipeline runtime
• bad113a gave unique filenames to integration tests
• 0657866 gave unique filenames to functional tests
• d3b3dd9 removed unused files
• eaed781 Merge remote-tracking branch 'origin/feature/scientific_machine_learning' into feature/scientific_machine_learning
• dc924f3 added hypothesis package to testing environment
• 5f1b0a5 Merge branch 'Development' into feature/scientific_machine_learning
• 3c0639d removed unused files
• 716abcc added torch to ignored-modules and disabled E1102: torch.fft.rfft is not callable caused by the torch package
• 36f1f33 improved docstring
• ef9ed1b finalized hmc example
• 9ad77bd cleaned up and finalized FNO example for sphinx
• 000d4ed updated HMC example
• 9f9b426 added FNO example
• fe363d2 added deterministic FNO example
• 785495a removing old and unused HMC
• ff0b9f4 Merge branch 'feature/scientific_machine_learning' of https://github.com/SURGroup/UQpy into feature/scientific_machine_learning
• 09e5e9b Modified pyro example with HMC, not working yet
• 174d72a ignored torch module from PyLint
• a67b7ad initialize history attribute with tensors to fix PyLint error
• c26ff82 corrected variable in extra_repr
• 441394c added torch and torchinfo
• 07d4578 merged commits from development branch
• d1c8a51 fixed typos in documentation
• 2b8a1db added scientific machine learning citations
• f137b26 removed unused file
• 07432a4 Merge branch 'feature/scientific_machine_learning' of https://github.com/SURGroup/UQpy into feature/scientific_machine_learning
• 1ae1c44 - Added Unet example and data
• 1a5e679 cleaned data loading in deeponet examples
• b70570d cleaned data loading in deeponet examples
• 783b21e corrected deeponet elasticity examples
• 1756e07 corrected deeponet elasticity examples
• 1f2de4c applied black formatting
• a9f40b3 added examples
• 1dd6cd6 Update azure-pipelines.yml
• 10178e6 Update azure-pipelines.yml
• b3ad351 Update azure-pipelines.yml
• 0b22cb3 Merge pull request #247 from SURGroup/feature/CI_improvements
• bc7de26 specific package versions for consistency with requirements.txt
• cbb634e cleaned up examples
• 63065cd removed unused examples
• ae3fe83 fixed minor warnings
• 07a7cdc disabled plotting in ReadTheDocs to save on compute time and memory
• 171a6d0 applied black formatting
• ce25471 improved documentation
• 4308f63 Fixes SonarCloud PR target
• fa76c57 Removes deprecated custom conda channel commands and disables Sonarqube for PRs to Development
• b135b0b corrected test for new class architecture
• 4cf3560 removed unused class
• 45c167e reformatted documentation for consistency
• bd550c1 improved documentation and associated examples
• 44c9c60 Small modification to the description and documentation of the Unet class
• 9999ec7 Updated Unet class description and documentation
• 4221ff7 corrected naming convention
• bdde45c fixed documentation typo
• a45c663 fixed documentation typo
• bfe8486 removed unused class
• c1c6111 unet improvements
• d3cf2c3 Added comments on the Unet neural code and documentation
• 828e5bb pull to commit
• 0b31f4b improved test
• ccd717d improved documentation
• 72c869e fixed test
• f68410b renamed lamda to beta
• 192d61a deleted unused loss
• 9dd1115 Merge branch 'feature/scientific_machine_learning' of https://github.com/SURGroup/UQpy into feature/scientific_machine_learning
• 5217336 Merge remote-tracking branch 'origin/feature/scientific_machine_learning' into feature/scientific_machine_learning
• ee6f3a6 simplified the valid input/output shapes
• 83d8881 implemented and standardized n_samples parameter in monte carlo sampling
• 4a4b203 Renamed KL weighting from beta to lamda
• 8101468 improved handling of tensor shapes and documentation
• 05d1a2f deleted code that is out of scope
• 42b1bf6 fixed typos
• 9a90624 corrected typo in latex
• 67842a4 added examples to documentation
• 3078833 added example for feed forward neural network
• b551e6e corrected extra_repr function to work with new keywords for prior and posterior distributions
• 3d9a9e3 improved documentation
• e3742a8 fixed documentation formatting
• 072493f added formula to documentation
• 8a19932 fixed documentation formatting
• 0b15cca added tests and documentation for LpLoss.py
• 768aaeb fixed documentation
• 2641ca2 fixed documentation formatting
• 3d1b0f8 fixed documentation typo
• 9b44140 Merge remote-tracking branch 'origin/feature/scientific_machine_learning' into feature/scientific_machine_learning
• 7a9135b replace dictionary of prior and initial posterior distributions with keyword inputs
• 5b08065 updated Modules for changes to relevant functional calls
• 2777744 updated Modules for changes to relevant functional calls
• 0af954f improved documentation
• 131a936 typed hinting alpha
• 48c149d updated references
• 10ccaec improved documentation
• 7cdded4 improved documentation
• 8cc5259 removed tests referring to deleted classes
• 0e42a49 added Torch6DComplexTensor for use in spectral convolutions
• 094b441 cleaned up documentation
• dbec99a combined weights for spectral convolution into a single tensor
• bd89a66 renamed parent BayesianLayer to NormalBayesianLayer
• e05eefa renamed dropout to ProbabilisticDropout to prevent naming conflicts with Torch
• a5c2a87 simplified documentation hierarchy
• c9c05f2 fixed typos in documentation
• c02ae43 added beartype
• 711235b corrected typos in documentation
• 566b453 moved all activations to layers. deleted all references to activations.
• 2263681 moved all activations to layers
• f7b2ba6 simplified methods and improved documentation
• 48b0143 Merge branch 'feature/scientific_machine_learning' of https://github.com/SURGroup/UQpy into feature/scientific_machine_learning
• f815d8d commit to pull
• 3d8a3c1 replaced deprecated torch.norm with stable torch.linalg.vector_norm
• b87b7b5 improved documentation and simplifed class methods
• 35ea09c added input to specify which dimensions to reduce over
• 34efb20 fixed and added tests for bias=False in Bayesian layers
• 0cf78d8 improved existing test, added device test
• 98b65f0 deleted tests from unused class
• 050f0c4 improved documentation
• 4f1321d improved documentation and added device support
• aa74b54 improved extra_repr
• bb350e6 added typehints and device support
• a7c9f7a fixed typos
• 55cc787 removed unused FourierNeuralOperator.py code
• faa9025 attempt at rewriting HMC trainer
• 011fb9c improved naming conventions and docstrings
• 2c73d13 improved docstring
• 11aba5e minor changes, many to-dos
• bb1056e improved docstring
• 830b8a3 deleted incorrect class
• aa1007f corrected device implementation
• 8812ce5 fixed spelling
• 5a4ccb5 cleaned up example
• f402474 added pairplot
• b19568f corrected einsum to handle multiple outputs
• a25344e added new histogram, improved print statements, added commentary
• 437b020 alphabetized
• 5805c7d improved documentation
• 93f1dc4 improved documentation
• dc636f2 improved documentation
• 8a931c2 improved documentation
• 4f5b12a improved documentation and spelling
• 64eb8b6 improved documentation and spelling
• b0b06e0 Pulled for updates
• 57d0c28 updated tests
• df0c807 applied formatting
• 6766838 deleted gaussianJS, replaced it with GeneralizedJensonShannonDivergence.py
• fcbcab4 Merge remote-tracking branch 'origin/feature/scientific_machine_learning' into feature/scientific_machine_learning
• 2121174 simplified keywords and for loop, added device
• 20c889a simplified keywords and for loop
• f7b7aec changed spectral weights to torch.float and convert to complex as needed
• 6628b06 Added loss function to evaluate Geometric JS divergence
• 98ec870 Added loss function to evaluate Geometric JS divergence
• 34f1b04 added self.bias attribute
• 54cf6a8 changed keywords
• 60f16ab added tests
• 7873306 improved docstrings
• fdecc4b added attributes to docstrings
• 7a62a71 fixed typos
• 248df4f improved docstrings
• d0d567f fixed typos
• 62e24ad improved tests
• 4bed626 moved to folder
• eee6624 made divegences consistent with BayesianLayer design
• b7f59bf Merge remote-tracking branch 'origin/feature/scientific_machine_learning' into feature/scientific_machine_learning
• 97cdf6a switched naming conventions for consistency with Pytorch
• 88096e5 improved documentation
• b9f2fbe overhauled for new BayesianLayer implementation
• e75eafa updated for new BayesianLayer implementation
• 3b1b202 improved documentation
• cc3c861 Added loss function for Monte Carlo KL evaluation
• 98b6362 Added loss function for Monte Carlo KL evaluation
• bdddd74 Added loss function for Monte Carlo KL evaluation
• bbb8b87 optimized MC computation
• 4c49c94 renamed test for clarity
• bc8763d Corrected naming convention in parameters (sigma to rho)
• 2d0d8bf Computing KL with Monte Carlo samples
• f0d0455 Initial commit of BayesianConv3d.py
• 2069024 Initial commit of BayesianConv3d.py
• decc4f2 Merge branch 'feature/scientific_machine_learning' of https://github.com/SURGroup/UQpy into feature/scientific_machine_learning
• 5247c2a improved tests
• bf17f5d improved init of parameters via reset_parameters
• 6888bbf added bias to convolution, improved init of parameters
• 1e85f02 added reset_parameters for standardization
• fedac57 cleaned up docstrings
• 55186e2 added bias to convolution and standardized parameter initialization
• 3b8a6bf updated attribute names
• bc8cd2e improved tests
• bcb8603 Moved sampling and dropping attributes to child class, BayesianLayer
• 0b66ab6 added arbitrary number of Bayesian parameters to BayesianLayer.py, implemented calls in all child classes
• 467e146 updated tests
• 15136c9 removed kwargs on init
• 4bda97d changed default tolerance, minor tweak to training loop
• 29929fe added device test
• a83bd7b improved device and dtype tests
• c23058b added device as init argument
• 8db5ff7 added device as init argument
• 98ded0d removed outdated tests
• f29c604 added test to standardize sampling, dropping, and training
• e6e85e9 changed to standard imports
• c692fb9 standardized sampling, dropping, and training on init
• 288edb4 added markdown
• 29eb27e added initialization arguments for device and dtype
• 285f3ef added markdown
• 02a9e7b improved scheduler to handle reduce on plateau
• 0e14bc9 removed todo
• fae5fd4 added bayesian quickstart examples
• 88bb9da updated scheduler code to handle ReduceLROnPlateau
• bf9b2d4 fixed docstring typo
• 7f6b57e fixed warning caused by docstring
• cf0a335 removed dependency on self.training. Now only sampling matters
• 4ef0b27 tried unpacking operator in forward
• 6d841be changed default reduction="sum"
• 78ee75a improved tests
• 998f3d3 improved tests
• 429d31e improved tests
• 8f4720d improved docstring, added shape and example
• 3497d4d improved docstring
• 8da7814 cleaned up extra_repr
• b5bcb0c fixed method return
• 5cf9dd8 cleaned up docstring
• a6bd92c cleaned up docstring
• 9aa940f added shape and example placeholder in docstring
• 89d54e8 cleaned up file structure
• 93ec335 removed unneeded standalone spectral layers
• 421fde9 standard normalizer implementation and documentation

This list of changes was auto generated.