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 u...

v4.1.6: Merge pull request #245 from SURGroup/Development

Changes:

• bd510fb Merge pull request #245 from SURGroup/Development
• 03e338d Update setup.py
• 33b03e2 Update requirements.txt
• 0f515a6 Update setup.py
• fea65a3 Merge branch 'master' into Development
• 93c2e63 Merge pull request #244 from SURGroup/bugfix/trapz_import
• 2d64dc7 commented bad tests
• d5271f4 corrected import of function to compute trapezoidal sum from scipy.integrate
• 1a93808 Merge pull request #239 from SURGroup/feature/update-packages-to-latest
• cda2284 Adds long description and dev requirements in setup.py

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• b2c3df6 Updates required beartype version
• 7abb1d5 Reverts change due to failing tests
• 9aae410 reverted tests to previous values
• d12f199 Fixes minor static code analysis issues
• fa8f5de Tries to fix failing tests due to scipy version update
• 85aee9e Fixes failing tests due to scipy version bump
• 05644a5 Merge remote-tracking branch 'origin/feature/update-packages-to-latest' into feature/update-packages-to-latest
• c81cc20 Removes deprecated argument from Lars input parameters
• 3d8501f Updates logo link according to #234
• b20d0e4 Update README.rst
• 70fcc10 Python umbridge example

This list of changes was auto generated.

v4.1.5: Merge pull request #233 from SURGroup/Development

Changes:

• f8d0b1d Merge pull request #233 from SURGroup/Development
• f695e37 Merge branch 'master' into Development
• ff07e3a Removes seaborn from example dependencies

This list of changes was auto generated.

v4.1.4

Changes:

• cce5c3a Physics-informed PCE capability
• c9a47c2 Merge branch 'master' into Development
• 58ea332 Merge pull request #231 from SURGroup/feature/PC2
• d35d561 Type hints in PdeData and PdePCE
• edbce33 Sonarcloud bugfix
• b718315 Sonarcloud bugfix
• a7f6dca Merge pull request #229 from SURGroup/feature/PC2
• 7a51ba0 Tries to fix Pylint errors
• a565587 Tries to fix Pylint errors
• 6f19146 Changes to resolve failing import statements

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• e07eb59 Implementation of PC2
• a7a609b Implementation of PC2
• caa4928 Implementation of PC2
• da1e62a Implementation of PC2
• 68648b7 Implementation of PC2
• dc711f5 Implementation of PC2
• 3c72db4 Merge pull request #228 from SURGroup/bugfix/karcher_mean
• 5a75881 Update README.rst
• 6201115 corrected documentation
• c14bae8 new and improved test for simple analytic examples on Karcher mean of grassman manifold
• 5c76e06 deleted test
• c2b2ccd added test for two point mean on Gr(1,2)

This list of changes was auto generated.

v4.1.3: Merge pull request #227 from SURGroup/Development

Changes:

• 1ea42a6 Merge pull request #227 from SURGroup/Development
• 98761fd Merge branch 'master' into Development
• 4e2142d Disables flaky tests
• 62696ed Merge pull request #225 from SURGroup/feature/inverse_form
• bc50b1c Merge remote-tracking branch 'origin/Development' into feature/inverse_form
• 52743a0 Merge pull request #224 from SURGroup/feature/documentation_improvements
• d8c3b73 deleted unneeded attribute
• 1aa56e0 fixes dummy syntax
• 9704aa0 added logic to run InverseFORM.run() if seed is provided in init
• 6236297 added logic to prevent seed_x and see_u from being specified at the same time in init

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• 8995220 Merge remote-tracking branch 'origin/Development' into feature/documentation_improvements
• 738e25b changed title font to match existing documentation
• 6359c16 cleaned up and added docstrings to public and hidden methods, renamed internal variables for clarity and consistency with literature
• adad1d0 deleted unused file
• a75aac5 cleaned up notation and attribute documentation
• d992388 fixed minor bug with state_function attribute
• 5a6a1ce added state_function attribute, correct attribute behavior when max number of iterations is reached
• 8133538 grammatical and notation edits to make documentation more consistent with literature references
• adafcdf added references to the new child class InverseFORM
• fa02302 editted docstrings for clarity and notational consistency
• 770256b edited markdown for clarity and notational consistency
• b74b418 corrected vector notation in math statement
• 935d45d improved docstrings and markdown for cleaniness and consistency in readthedocs
• bd5c57d added InverseFORM to paths so the examples would show up in the ReadTheDocs
• 55db785 scripts to config and run examples for InverseFORM
• 48b6204 documentation for InverseFORM as a child of the TaylorSeries class
• c3e5459 tests for accuracy and behavior under various inputs for InverseFORM class
• 9cd9d75 initial commit of the InverseFORM class
• bbb4341 Disables example execution
• 333be9b Disables FORM and SORM examples execution
• 7a5bd24 Corrects equation display in plot_pce_sparsity_lars.py
• 174d578 Minor changes to fix reliability examples
• ee0fa3e added Connor to development team
• ec3f6e9 passes test for seed_u_is_none in FORM.run()
• 06c413a Merge remote-tracking branch 'origin/feature/documentation_improvements' into feature/documentation_improvements
• 80f3609 added test for seed_u is None in FORM.run()

This list of changes was auto generated.

v4.1.2: Merge pull request #222 from SURGroup/Development

Changes:

• 9e98a62 Merge pull request #222 from SURGroup/Development
• 8e4d074 Merge branch 'master' into Development
• ca196b8 Merge pull request #220 from SURGroup/feature/documentation_improvements
• 83cd4b8 Adds SORM reference
• 8575027 Corrects SORM documentation
• bcb171b Adds citation for FORM structural reliability example
• f15aee5 made the FORM plots more accurate, useful, and the code more legible
• eb0eca1 Hides auxiliary file in SORM example
• 4435f59 Merge remote-tracking branch 'origin/feature/documentation_improvements' into feature/documentation_improvements
• 5b61847 updated documentation to improve legibility

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• 8324ebe Fixes minor SORM error
• c133c3d updated local variable names to match class attribute names
• 79a3dd0 updated local variable names to match class attribute names
• 9319cc1 Fixes FORM attributes inside SORM
• 4a3d2c8 Merge remote-tracking branch 'origin/Development' into feature/documentation_improvements
• 013a6bd Fixes figures in FORM structural reliability example
• 25a9f44 fixed typo in LaTeX in docstring
• 3cb5fcd Fixes issue #194 - removed duplicate import statement
• 1e7844b fixed minor formatting error in math statement, alphabetized class attributes
• c20aeba added specific versions to packages for compatability
• 9d2f3d0 removed tabs
• ce3d906 improved documentation, cleaned up and renamed attributes, simplified variable storage after FORM.run() completes
• 653558b updated input and attribute names for improved FORM.py
• 717328f fixing examples for updated FORM.py
• 655d0f6 improved docstrings
• d416434 removed incorrected and unneeded example statements
• 00b9119 optimized import statements

This list of changes was auto generated.

v4.1.1: Merge pull request #216 from SURGroup/Development

Changes:

• 680b267 Merge pull request #216 from SURGroup/Development
• 32d2dc5 Merge branch 'master' into Development
• 5136dae Tries to fix Sphinx error
• 89e6509 Tries to fix Sphinx error
• 9e6a00b Fixes sphinx warnings
• d2f3722 Removes Kernel cross-ref
• 8fb4eea Minor documentation fixes
• 100f783 Disables plotting of Nataf example
• 2135024 Merge pull request #215 from SURGroup/feature/unify_kernels
• 3dc0086 Merge branch 'Development' into feature/unify_kernels

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• 1080c15 Fixes failing import statements due to kernels restructuring
• 73b258c Fixes failing import statements due to kernels restructuring
• 0f44a14 Refactors Dimension Reduction kernels to match GP kernels signatures
• 2917cca Moves GP kernels to utilities
• 5564ab8 Refactors Gaussian process kernels to abstract from hyperparameters

This list of changes was auto generated.

v4.1.0: Merge pull request #214 from SURGroup/Development

Changes:

• c2f3e5c Merge pull request #214 from SURGroup/Development
• bb2c0ce Merge branch 'master' into Development
• 9fe7e31 Merge pull request #213 from SURGroup/feature/increment_minor_version
• 4724b58 +semver: minor
• 888209e Merge pull request #212 from SURGroup/feature/Active_Learning_PCE
• 36269b1 Updates standardization code for Uniform and Normal
• e059b2e Update documentation of ThetaActiveLearning
• 6284575 Added one unit test for standardization
• e859d3c Updates documentation files
• f52aa94 Fixes failing ThetaCriterion test

See More

• 1697947 Example for Theta Criterion
• e33a673 Update ThetaCriterionPCE.py
• 441e35b Update test_pce.py
• 07d2673 Adds theta criterion PCE to init.py
• 1790f37 Minor naming conventions changes
• b4502ed Active learning for PCE Class
• fd26576 New functions for PCE basis
• d8f2de0 Adds missing file copy in ClusterExecution.py
• 9e5f072 Merge pull request #205 from SURGroup/feature/RunModel_updates
• e6c48a2 Merge branch 'Development' into feature/RunModel_updates
• 45f446c Merge pull request #202 from SURGroup/feature/v4/TMCMC
• 15e8d4d Merge branch 'Development' into feature/v4/TMCMC
• ee6540a Updates numpy version from 1.24.2 to 1.22.0
• bdba54a Updates numpy version from 1.21.4 to 1.24.2
• dec5d72 Updates test values @promitchakroborty
• e5ee158 STMCMC test error debug push 2
• 9533703 Merge remote-tracking branch 'origin/feature/v4/TMCMC' into feature/v4/TMCMC
• accae15 STMCMC test error debug push
• c8db82e Minor formatting changes in cluster execution example
• 15cbf30 Merge branch 'Development' into feature/RunModel_updates
• 291bd55 Merge pull request #196 from shellshocked2003/frontera
• 475df6c Merge remote-tracking branch 'origin/Development' into feature/v4/TMCMC
• 6e2f2b7 Finalizes TMCMC docs
• 3d87f70 Merge remote-tracking branch 'origin/feature/v4/TMCMC' into feature/v4/TMCMC
• 8921f9b STMCMC documentation and docstrings
• ed1b5bd STMCMC bug fixes and unit tests
• 1cf219e Merge remote-tracking branch 'origin/feature/v4/TMCMC' into feature/v4/TMCMC
• 0fcdb28 Update run_script.sh to tile jobs using bash loop and mpirun
• 21fb695 parallel tempering docstrings: changes to output docs
• 885bcfd tempering and parallel tempering documentation
• 5e9dbed first try at tempering / parallel tempering docstrings
• d897bfc Merge remote-tracking branch 'upstream/master' into frontera
• d7db12b Added documentation and example for launching parallel job on cluster
• 02a53b6 Correction for FORM
• 8917c83 Allows either a single MCMC sampler or list to be provided in ParallelTemperingMCMC.py
• 8fae052 Moves TemperingMCMC files inside mcmc folder
• 8982763 Port TMCMC examples to v4
• 1b479bd Ports SequentialTemperingMCMC.py to v4
• e758876 Ports ParallelTemperingMCMC.py to v4
• b87cf47 Starts TMCMC porting
• cfdf3df Adds Parallel and Sequential Tempering files
• 8d93c72 Finished adding cluster exectution model, will test multi-node deployment on HPC next
• bc6fda0 Update to fix issue related to Iterable
• 283f40a Merge remote-tracking branch 'upstream/master' into frontera
• 8dc7cd4 Adding cluster execution model
• 179306f Merge remote-tracking branch 'upstream/master' into frontera
• a023a25 Changes to run on Frontera: separate preprocessing, model run, and post processing to only use ibrun on computationally intensive portions
• d52d06f Changes to RunModel to execute tiled MPI jobs on Frontera

This list of changes was auto generated.

v4.0.7: Merge pull request #207 from SURGroup/Development

Changes:

• 859921b Merge pull request #207 from SURGroup/Development
• 43a5804 Merge branch 'master' into Development
• 9476b0b Merge pull request #204 from SURGroup/bugfix/KLE_2D
• 8be0d82 Merge branch 'Development' into bugfix/KLE_2D
• 031cbe7 Merge pull request #206 from SURGroup/bugfix/form_convergence_condition
• 1caef56 Merge branch 'Development' into bugfix/form_convergence_condition
• 4f2b840 removed print statements and added tests
• 682dc25 correct quasi correlation computation
• 1241fed Adds simple descriptions to UML diagrams
• 103d8e6 Adds UML diagrams to docs

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• b166584 Merge pull request #178 from SURGroup/feature/v4/KLE_2D
• 8ea79d1 Merge remote-tracking branch 'origin/Development' into feature/v4/KLE_2D
• ace9ebe Changes while loop convergence condition of FORM.py
• 2dcd16a Changes logging error to logging info inside FORM.py
• 92241c0 Tries to fix FORM convergence condition
• 8bd92a8 Merge remote-tracking branch 'origin/feature/v4/KLE_2D' into feature/v4/KLE_2D
• 05ba57a modified the example code plot for KLE 2D
• cb0f6f2 Merge remote-tracking branch 'origin/feature/v4/KLE_2D' into feature/v4/KLE_2D
• f97fde8 KLE2D documentation fixes
• d01eb72 corrected 2d test
• 07e34fc added example file and documentation for the method along with another test for KLE 2d code
• c179ed8 Extracts KLE2D to separate file
• 7987f31 corrected a typo in the file test_karhunen_loeve_2d.py
• 19c1434 updated the docstrings for the class KarhunenLoeveExpansionTwoDimension
• cde3b52 corrected the sample value in pytest
• cdd2031 corrected the samples shape test and print the value of the samples at a specific index
• c60520b reduced the number of samples in the test to reduce the test time
• 7c41dce fixed samples shape error
• fabe62a added debug print statements
• 0da8242 added import from KarhunenLoeveExpansionTwoDimension in the 'init' file of the stochastic_process module
• 3a4cbc9 added the code for KarhunenLoeveExpansionTwoDimension and added tests - test_karhunen_loeve_2d.py

This list of changes was auto generated.

v4.0.6: Merge pull request #193 from SURGroup/Development

Changes:

• bfbb5eb Merge pull request #193 from SURGroup/Development
• 55fed0b Merge remote-tracking branch 'origin/Development' into Development
• bb06927 Changes default number of Nataf integration points
• 498091a Merge branch 'master' into Development
• 13c5539 Disables execution of monte carlo example
• 5cc7e42 Adds option to increase gauss points also in Nataf initializer
• a5f9fc1 Update requirements.txt
• e8eb6fe Merge pull request #195 from SURGroup/feature/remove_old_kriging_files
• 32bdd29 Fixes RSS tests
• 1ed0540 Fixes RSS tests

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• 38c96f5 Fixes RSS tests
• 2818b25 Fixes RSS tests
• 08b5f33 Fixes AKMCS tests
• 80c3b03 Removes old kriging files
• 1bfec7c Merge pull request #192 from SURGroup/bugfix/nataf_stability
• 293f374 Test fix
• e1cee93 Fixes matplotlib 3d projection issue
• 10a3822 Fixes matplotlib 3d projection issue
• 5a9c338 Fixes Nataf Stability issue by adding an n_gauss_points optional parameter to distortion_z2x function

This list of changes was auto generated.