Uqpy

Changes:

* 680b2676f4df3a3e79fe797ddede4550001b5c8f Merge pull request 216 from SURGroup/Development
* 32d2dc5b80bbb3165b26be9540724a55d63684d9 Merge branch 'master' into Development
* 5136daebec39fb5395c658479cbba1ff05da88a1 Tries to fix Sphinx error
* 89e650986be28a08f9f72772bb96573fc93ab175 Tries to fix Sphinx error
* 9e6a00b9be42bac46f22deee589958953c46594b Fixes sphinx warnings
* d2f3722936bc174d4c4e7c0df3b3d436dd08525f Removes Kernel cross-ref
* 8fb4eea61b90d908facffa603435460dd5f43176 Minor documentation fixes
* 100f7832c69366d16d70aa3e3d1627e5edfe3a98 Disables plotting of Nataf example
* 2135024cafd7b26ba1cad0de63762c11049ab787 Merge pull request 215 from SURGroup/feature/unify_kernels
* 3dc0086665990db16e6f2ea5a41bcfbf4a1ed947 Merge branch 'Development' into feature/unify_kernels
<details><summary><b>See More</b></summary>

* 1080c1543de1b2c2143ba7f6e23a22d045bcf222 Fixes failing import statements due to kernels restructuring
* 73b258c8d8f4a1d23388722ea73fbf20b86a359e Fixes failing import statements due to kernels restructuring
* 0f44a14004e34b2ced255ba88acf07fe17bb1a67 Refactors Dimension Reduction kernels to match GP kernels signatures
* 2917ccae68638025bb5fe743046d82e3aa7892ef Moves GP kernels to utilities
* 5564ab8048dc632ab005628b19b17fcc8d30dbe4 Refactors Gaussian process kernels to abstract from hyperparameters

This list of changes was [auto generated](https://dev.azure.com/UQpy/UQpy/_build/results?buildId=1043&view=logs).</details>

Changes:

* c2f3e5cee83b67f633cc82e7096f6acf2c681432 Merge pull request 214 from SURGroup/Development
* bb2c0ce7086c616f9671d21117cbe62470dbb112 Merge branch 'master' into Development
* 9fe7e31ed00f34ac8fe9b04a2dc41f141b2c884d Merge pull request 213 from SURGroup/feature/increment_minor_version
* 4724b58d563a6c131236ecd2443b6a05aea2054b +semver: minor
* 888209e44cea3dfa6124cbb3009eea1b4bdbc600 Merge pull request 212 from SURGroup/feature/Active_Learning_PCE
* 36269b15d4593e97f9f459353fc99089c3dae9bc Updates standardization code for Uniform and Normal
* e059b2e3a7c07aee7a0c1274a4f770acb458c479 Update documentation of ThetaActiveLearning
* 62845753ade9947526158d1a75d776f8f4c8e547 Added one unit test for standardization
* e859d3cad4c8ec905d520fb3dc3e6f3c0389b07f Updates documentation files
* f52aa944a1e73b9a71aa8f4b32e0f4eaea9ef243 Fixes failing ThetaCriterion test
<details><summary><b>See More</b></summary>

* 1697947ae5779f706096d4ffbfb52f135fc348e1 Example for Theta Criterion
* e33a67385e04131fcca1f2605c6838fc19d63d9c Update ThetaCriterionPCE.py
* 441e35b572b5e9411164fc0606e734be4eb25c51 Update test_pce.py
* 07d267330dc9f0adc1809aff6716008d7bab7f92 Adds theta criterion PCE to __init__.py
* 1790f3728c015b332b01c4a380ec45e100d262c2 Minor naming conventions changes
* b4502edaddad0e3946fb4d8de80fb60c0ed634e9 Active learning for PCE Class
* fd26576517e0178f137f26d0752c5dffe7fd0549 New functions for PCE basis
* d8f2de03978cd5d2825ad19187bcd29692dd9edd Adds missing file copy in ClusterExecution.py
* 9e5f07258d557428bb44a179cc66edab517bd8d2 Merge pull request 205 from SURGroup/feature/RunModel_updates
* e6c48a2a9c6b1a8a32b26c8bdc70192a86dd4f23 Merge branch 'Development' into feature/RunModel_updates
* 45f446cd062b5f9d6110c51cce3ab398d5ae794b Merge pull request 202 from SURGroup/feature/v4/TMCMC
* 15e8d4d2fc7a9bc31dc8811bdd6ff0184405d458 Merge branch 'Development' into feature/v4/TMCMC
* ee6540a852541c9fced90b2098be8541da51415d Updates numpy version from 1.24.2 to 1.22.0
* bdba54a6302b4208d2a596d0b033b23988dafa70 Updates numpy version from 1.21.4 to 1.24.2
* dec5d7220dccd6a219652518c9d4dd11d241f438 Updates test values promitchakroborty
* e5ee158821f80105787304b96ca6f47471c92610 STMCMC test error debug push 2
* 95337031d203d8dcb907cea872f7b8673c3fe621 Merge remote-tracking branch 'origin/feature/v4/TMCMC' into feature/v4/TMCMC
* accae159a44929ec111791c4194d2cda823b1d86 STMCMC test error debug push
* c8db82ec649205b4fc528cbe459bd79b3fc69f1e Minor formatting changes in cluster execution example
* 15cbf30e008a5a6bef567743a63370d5e9643ef5 Merge branch 'Development' into feature/RunModel_updates
* 291bd558eca5fb34598e0533b65c96c86fed5fc5 Merge pull request 196 from shellshocked2003/frontera
* 475df6cdbf03311da2f4dbb91b78191cea0542d2 Merge remote-tracking branch 'origin/Development' into feature/v4/TMCMC
* 6e2f2b7786beed5bdbde03fb3cdc34ee32de1113 Finalizes TMCMC docs
* 3d87f7026e71729b6f78b3aee7823a7d30ed9be1 Merge remote-tracking branch 'origin/feature/v4/TMCMC' into feature/v4/TMCMC
* 8921f9bccac6707bae98157bbbf1e6a5ea366e09 STMCMC documentation and docstrings
* ed1b5bd142ce7753ab6394843caf60f69e0d4e93 STMCMC bug fixes and unit tests
* 1cf219ea7b95cbe72a30c869c2357e291b4f3b7d Merge remote-tracking branch 'origin/feature/v4/TMCMC' into feature/v4/TMCMC
* 0fcdb28349fac0b5f9a22f15fd4477137bef7c9d Update run_script.sh to tile jobs using bash loop and mpirun
* 21fb69509e460ead4bd54f4b593127757acb17cf parallel tempering docstrings: changes to output docs
* 885bcfddbd90b1026f1030b5aafb35778d0d44a5 tempering and parallel tempering documentation
* 5e9dbed5ca49fb9b2bb4fe237983d12b42f9b307 first try at tempering / parallel tempering docstrings
* d897bfc836dddae4f11ee5d77d0294633407e696 Merge remote-tracking branch 'upstream/master' into frontera
* d7db12b28a476d9b16dd46c130d46e622d6c2a77 Added documentation and example for launching parallel job on cluster
* 02a53b6e7d30ff528f9090c0c0ab38d80aceb2a9 Correction for FORM
* 8917c83cfaf1872d474ee2a49edc5d84eb0a9e07 Allows either a single MCMC sampler or list to be provided in ParallelTemperingMCMC.py
* 8fae05274ecc266c03c595fec54ae4be4d40f674 Moves TemperingMCMC files inside mcmc folder
* 89827631c7fa5091f0ed2270a288fbe4125b578c Port TMCMC examples to v4
* 1b479bdfbd21439c1433588a060cfaa7a5de90eb Ports SequentialTemperingMCMC.py to v4
* e758876f4393805f45f8edd3d45571e1de4cb842 Ports ParallelTemperingMCMC.py to v4
* b87cf474ab6f2ca054ee8bd23e9d89d24a777c85 Starts TMCMC porting
* cfdf3dfd512b910f8c3ec7d58d0ebeb8d78fa9ae Adds Parallel and Sequential Tempering files
* 8d93c72ca078339a9b5fb36ab6fc97edbc99e822 Finished adding cluster exectution model, will test multi-node deployment on HPC next
* bc6fda0c50af9f75af22d7fffe0e8416264044f1 Update to fix issue related to Iterable
* 283f40a0139abc5751a8799ba950e9a451279e5f Merge remote-tracking branch 'upstream/master' into frontera
* 8dc7cd49910a5d8920655dc3ce62d6ea2e1a2399 Adding cluster execution model
* 179306f6a51dfa7c6484b919af5e27ae7341ac7b Merge remote-tracking branch 'upstream/master' into frontera
* a023a25d888685798361057c9077e707bbb8e287 Changes to run on Frontera: separate preprocessing, model run, and post processing to only use ibrun on computationally intensive portions
* d52d06f660e434ff8640f1a13d23b0ee51cddc65 Changes to RunModel to execute tiled MPI jobs on Frontera

This list of changes was [auto generated](https://dev.azure.com/UQpy/UQpy/_build/results?buildId=1028&view=logs).</details>

Changes:

* 859921b37a0b8f7a1d9df402340f087a0c234873 Merge pull request 207 from SURGroup/Development
* 43a580484708a71349e8d3fcbe520f19ffe5bae1 Merge branch 'master' into Development
* 9476b0bf3ec039a47a6b34b2ba99ac754a171eca Merge pull request 204 from SURGroup/bugfix/KLE_2D
* 8be0d824f5e043a518bee301032bd36008bda3e5 Merge branch 'Development' into bugfix/KLE_2D
* 031cbe74803a88112de4c9646ff41266aa56b32e Merge pull request 206 from SURGroup/bugfix/form_convergence_condition
* 1caef560682c0b0041b4299b3e2755611aa6d3bc Merge branch 'Development' into bugfix/form_convergence_condition
* 4f2b840fd8fea26b284d9424ed64198df0a3af3c removed print statements and added tests
* 682dc25e9917d9f41b7639816b447dee16f97872 correct quasi correlation computation
* 1241fedfe9696fe6735bcfa895676ab2f1430188 Adds simple descriptions to UML diagrams
* 103d8e619be2be99e41493468e0fce9da594f0b1 Adds UML diagrams to docs
<details><summary><b>See More</b></summary>

* b16658465d0af96387e9109b4e55465e09f56293 Merge pull request 178 from SURGroup/feature/v4/KLE_2D
* 8ea79d1e5fd2aa76e890a005b19c70396662e1e0 Merge remote-tracking branch 'origin/Development' into feature/v4/KLE_2D
* ace9ebe7055d01f8a7c119d554c5f1ccfe41fec5 Changes while loop convergence condition of FORM.py
* 2dcd16a59161c4e7c388a1e30f1db2aba4cb07bd Changes logging error to logging info inside FORM.py
* 92241c0f321b5719137b6b74fb28849cc6563165 Tries to fix FORM convergence condition
* 8bd92a8d736233a339532e5a32a101103e958e1f Merge remote-tracking branch 'origin/feature/v4/KLE_2D' into feature/v4/KLE_2D
* 05ba57abdb13405eb85e0cb3c2a81c911289a7cf modified the example code plot for KLE 2D
* cb0f6f2afbfac41c9cc69571cfd4cdb672b0ae71 Merge remote-tracking branch 'origin/feature/v4/KLE_2D' into feature/v4/KLE_2D
* f97fde86626c842a29a0f361df09d6cd92a0cb67 KLE2D documentation fixes
* d01eb728e5a20f7ba6bc25091463f5c0044e0d70 corrected 2d test
* 07e34fc6769e872bdc1efa2feac72ea946f5b1fe added example file and documentation for the method along with another test for KLE 2d code
* c179ed8f0b1ca9596e7bac6aa03136ee28f6bbab Extracts KLE2D to separate file
* 7987f31745fc57646bf49d0c219d282ee3c38642 corrected a typo in the file test_karhunen_loeve_2d.py
* 19c14344a76bb206a6c90a6edb4c7b72a4dbd139 updated the docstrings for the class KarhunenLoeveExpansionTwoDimension
* cde3b523f5d2f8c8be8820b899f96dd9f97df61e corrected the sample value in pytest
* cdd20316d4aa6702d8e7ff5532d0a8e97d030311 corrected the samples shape test and print the value of the samples at a specific index
* c60520be459b0210aadef57fd8eef60cecc0f6b5 reduced the number of samples in the test to reduce the test time
* 7c41dce80068f0972d54a470b52151959e29e021 fixed samples shape error
* fabe62a3b3b023f128cd35b0b44909163644159a added debug print statements
* 0da82429c2c39dccd511724384eb336e234af926 added import from KarhunenLoeveExpansionTwoDimension in the '__init__' file of the stochastic_process module
* 3a4cbc9e5e08eb015afc5ff702ad52f67690be89 added the code for KarhunenLoeveExpansionTwoDimension and added tests - test_karhunen_loeve_2d.py

This list of changes was [auto generated](https://dev.azure.com/UQpy/UQpy/_build/results?buildId=970&view=logs).</details>

Changes:

* bfbb5eb8d14938991551ff735833883545c365b1 Merge pull request 193 from SURGroup/Development
* 55fed0b9615cab710b90245f9e1f3790fb9339d8 Merge remote-tracking branch 'origin/Development' into Development
* bb06927f5d1d2a0443167f537e6ad39f8be16c9e Changes default number of Nataf integration points
* 498091a2398b939c966a8c31f3cfd77ccb7693d9 Merge branch 'master' into Development
* 13c55395299fd53edb25070a7ee5b52f7b12fea1 Disables execution of monte carlo example
* 5cc7e42fb19e711273d53a5a6470be3dbe6c7f73 Adds option to increase gauss points also in Nataf initializer
* a5f9fc13edc9b4b54e5bbbf4209197495469cabf Update requirements.txt
* e8eb6fe35a26a166508d98024a3df76da9ad2fda Merge pull request 195 from SURGroup/feature/remove_old_kriging_files
* 32bdd299f9f9f94df7d96d4e1187a8e962549c62 Fixes RSS tests
* 1ed054000f8080d5e76d5abbbda8d944113709d7 Fixes RSS tests
<details><summary><b>See More</b></summary>

* 38c96f502c99785550489d261ac74a3d4bf19ddf Fixes RSS tests
* 2818b256a9edf049914a2a0943d1f2db52f42af6 Fixes RSS tests
* 08b5f33f821a270361aeb8666be4dc7b95572dd8 Fixes AKMCS tests
* 80c3b0333143025d4a5adcbdd6e080d79d2b3e07 Removes old kriging files
* 1bfec7cc798be3cbbcf077def0064f924aae462a Merge pull request 192 from SURGroup/bugfix/nataf_stability
* 293f374e5516a96ead5309a0c93c4dec05e5ce92 Test fix
* e1cee93b4b965766baf84adae2d22f2dbf8f0382 Fixes matplotlib 3d projection issue
* 10a38229207b0d579b7453e0ed5a6ab469e356c3 Fixes matplotlib 3d projection issue
* 5a9c338aea3695e0488288981b9fe069c1dec1f3 Fixes Nataf Stability issue by adding an n_gauss_points optional parameter to distortion_z2x function

This list of changes was [auto generated](https://dev.azure.com/UQpy/UQpy/_build/results?buildId=937&view=logs).</details>

Changes:

* 2f16b1aa8999dd3bfc93cdd9378484cd1af35ea5 Merge pull request 190 from SURGroup/Development
* 0c523f12417851bf2f7f13eb737bee8178fe9903 Merge branch 'master' into Development
* 5dba9deac0e4807f0018583db9a0fa59c7dfa3ac Merge pull request 189 from SURGroup/feature/new_sensitivities
* bba0a67f2fbb8f094e3e2dcc6c56238d6c25361d Revert "Delete src/UQpy/surrogates/kriging directory"
* a79da949517463543e37d532a3e84fb9fe6cd52b Delete src/UQpy/surrogates/kriging directory
* 066e5a35ebef50dfcb4ca86bc9192bda2c7e4e07 Update README.rst
* b82e53ee96030c234bf8fb599e6ea94435d41070 Very minor updates to the documentation for Chatterjee Sensitivity documentation
* ec2f910a4418efa32b4911b599d13d867d10279d Fixes failing Sobol Sensitivity tests
* bc15e7f02aff2579f576659666c6c75c46f28f4b Documentation fixes due to class and attribute renaming
* 7f3a9dc33d5cc16b9abe439fffea8c7fa31658b1 Fixes failing examples due to changed naming conventions
<details><summary><b>See More</b></summary>

* 0b0ee2f75f0197c67db2d265dfaa0cbc2d4c6aca Fixes failing tests after changing naming conventions
* 813ae54e75164b74317695aeba218fe949b537dd Naming fixes
* 02bbff761057c637862ccee41116169885a926aa Minor example fixes
* f4e2bb31b6231c94e2db597a3f553c5847766f2a Merge pull request 186 from Uncertainty-Group-Braunschweig/Development
* e57f82dcdb2089869e7d942670733577378344d7 Described why SA outputs are different
* ee1d892118a4a594a99519afd071497b4275f46c Minor changes in documentation
* af5e2a57643d0fed0317a997daa41eee1330c167 Minor fixes to docstring
* 786c6e58b3ec37913ea2a9b6f84e2a149c86b44b Changed a_values in Sobol func
* dfa17e9390bffd59958716b29a03f1edebbdc2b8 Added convergence study
* 08d9180144873404704e3f9f2d13990fdaeb4428 Minor fix
* 7da93b1420e584141685a62df3e958199c02b8ee Added a basic comparison of sensitivity indices
* 624c37325e6f7ff9bf90047562e571f27d183152 Fixed minor typo
* 0216941dad7ea51c8fd057c91b99f223a94f613b Added type hints to PostProcess module
* 564086bc89d8e1e81505509c3f697819bc91f9ea Added plots in Chatterjee index examples
* ef52484b831764408d5cbeffb21eaa748f3a6e71 Added plots in CVM index examples
* bb14e82c39af7f845df2c37d94f99687fb6728f9 Added plots in Generalised Sobol examples
* d11e3955b0fc75166a39f6e87698a2e281304504 Added plots in Sobol examples
* 08d954fcaed264a414c5f946d9788ac0145c374a Added PostProcess module for sensitivity indices.
* dd6393f5155fafffdb5f2337090ac97bd5e22a40 Added references to bibliography for Sobol
* 168f7d3e389ce93de2fcdd2ea8927603d00c8deb Added references to bibliography for GSI
* e3f0d7a6661af28d59c9c2ed5a5abf265f17f37d Added references to bibliography for CVM
* f3b59350063dd7a2c9809e265efddc4108bc76bb Added references to bibliography for Chatterjee
* caffb2d07770a4c295e94b525bcb27a956bb3f32 Changed variable name: CI -> confidence interval
* d78b28ba8da7405d111d2715a459c694aa023697 Changed variable name: CI -> confidence interval
* e0ad8da9db9eb20330f53ffc8b3cb4139ebcdc37 Changed baseclass module names to CamelCase
* bfa2c53e0b7252f84d2841c33652618d79e064a0 Changed Sobol module name to CamelCase
* f9eec9ac7896b0e50999b7f11a469ad51fb5b27a Changed GSI module name to CamelCase
* 78ba451e7c00db6b6e1ac6320428230a2f870df1 Changed CVM module name to CamelCase
* 4ceb33c9193e56c3637057fd403022d07202d6a4 Changed Chatterjee module name to CamelCase
* aff7d0965a335b342a367f5eadcd48ca1f5fdcd8 Added Type Hints to baseclass modules
* 13d229e128489f550f5baa9ede391dd60256aa83 Added Type Hints to Sobol module
* 9fcda77409fc41079c95ddf697253c716d420a0c Added Type Hints to GSI module
* 358440614de4d3fb4b42de178b8c5965ef89dd0e Added Type Hints to CVM module
* df66e93ce4abf2cd10189f39ac0ed9d554312a11 Added Type Hints to Chatterjee module
* 12a5b8252676f4bd3ec1bd3641a63a4b358a1d58 Added NumpyIntArray to support int arrays as input
* d842ec67457ba1cc49df0eb005af160b7e2809f4 Improved documentation Sobol indices
* 26d27db486b26b21315aef003763408329994bd0 Merge pull request 1 from SURGroup/Development
* d48552cddd22fc0181baa1135e83fba27c920873 Improved documentation GeneralisedSobol indices
* 86dcd1aacc8a40869247f2866cde36814f25cf77 Improved documentation for CramervonMises indices
* 21c02896e2ca5947470f95dc160bb2ca82e7ee85 Improved documentation for Chatterjee indices
* f15c7bb4cb6f88b1311698b3f1180806cdb0d67b Added examples generalised sobol sensitivity
* 29b47271e500ed76dfbab00156831536957be1d0 Add unit tests for generalised sobol sensitivity
* 3da45cf5af9360c8dfb7756500000269d0cdd1f2 Added documentation for generalised sobol indices
* 1e6118f00155192508aedf0e12cf0df126cff5d4 Added generalised sobol sensitivity
* e181e738dfe4c441cb917a67e2b6c2736e7b2f0f Add unit tests for Chatterjee sensitivity
* e4407c667e188acbaa0fe1af97727f3df95f1f18 Added examples Chatterjee sensitivity
* 0b5a6662be6e673ff2ffd34807f1cb8afa3f5f53 Added documentation Chatterjee sensitivity
* c86aea248903b03f72c0b918556d911b13ab3f41 Minor docstring fix
* 92a724c1efd93d2af33233fd5491afc3b773ab21 Added Chatterjee sensitivity index
* 3f59fd89706be8e48dfdae1d1efef719aaa7f2d4 Changed docstrings to match rtd_theme
* 69ac38aec2546bd9b6afb8b634eb9d5ff4fd6115 Minor fixes in docstrings
* 852be9d3f41a0815be3d831088c21579ca76fb04 Rearranged order in index
* 8ab489215f852ec46de90164ad92bf4281dd39a5 Fixed references in documentation
* 4d4a012828c69713b17dc78fb565a48d12738695 Added examples Cramér-von Mises sensitivity
* 27305fc4ecb3a9342892bc0b88446cf77f970979 Added documentation Cramér-von Mises sensitivity
* f16288d6d537bb96cded08ae98f7a11d3ebb4021 Add unit tests for Cramér-von Mises sensitivity
* 068fde50f05f5084cfee6a33bab741f175637464 Added Cramér-von Mises sensitivity index
* c38b2e6f20013054375cf02568dc7f11446b3c42 Added examples for Sobol indices
* 5de396e2efbeffd97c0f000be6e126bca16fc6c7 Added documentation for Sobol indices
* 23c0607cf9e4e7a625d893e872177dd7e315c595 Formatted conf.py with Black
* 2ae7cebbbd197323f05ec2dcbf34d684d5a8448c Added modules in sensitivity __init__.py
* d2da7d124eb25e04e6aaf69f7fb3c5a182f64f9a Fixed minor typo
* 18ed2f2fe4e6dbb446142c9e8b1255906a382b45 Add unit tests for sobol & sensitivity baseclass
* a0ddbede089ce5fee1bc152640496c66f5949e9c Added sobol sensitivity

This list of changes was [auto generated](https://dev.azure.com/UQpy/UQpy/_build/results?buildId=898&view=logs).</details>

Changes:

* b8bc0706af281d33a956d746663a42d5183b745e Merge pull request 184 from SURGroup/Development
* 836e83c671c7274d6664b4c8ef9fdc1b451c65e2 Merge pull request 185 from SURGroup/feature/DirectoryFix
* 17cc73ef1142c68d3a94ce425eba8fe2d25638a2 Merge remote-tracking branch 'origin/Development' into feature/DirectoryFix
* 019d1cbde5eea3bdce663e61108713aa7d8fdccd Directory fix
* 4333f04bef3a2a381f56d0aa7f1e77df46a37014 Merge pull request 183 from SURGroup/feature/conda_fix
* 6b41d55cff2291322bb1f7d9f166435a4fe9879c Fix for missing beartype package

This list of changes was [auto generated](https://dev.azure.com/UQpy/UQpy/_build/results?buildId=885&view=logs).