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November 2022 clean up megathread #93
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f507997 Initial REVERT: 2fb6ac5 Codespaces configuration. REVERT: c1ca09a Fix up the tutorial. REVERT: b7b296c Fix up the tutorial. REVERT: a86baa3 Default version in setup.py (#26) REVERT: 596ef53 Add back alex's changes to setup REVERT: 1386c12 Fix build system to be editable and add more dependencies REVERT: f9190a6 James.yang/vscode fix (#130) REVERT: 63846ba Update imprint pre-commit config. REVERT: 9a2ecca Merge commit 'af593cc95bc17078757774e4605588373b420e31' REVERT: cbd80b8 Create LICENSE REVERT: 10a90ec Update README.md REVERT: 0407c45 Tbt/add tutorial back (#129) REVERT: 20b8129 Add the tutorial back into the imprint repo. REVERT: a354160 Update README.md REVERT: 2443d2a Conditional INLA, gauss-hermite. REVERT: 1666644 Add thesis link REVERT: 3b2c96c reorder python imports. REVERT: e3fde11 Environment set up. CI. REVERT: f813308 Fixing the CI failure. (#128) REVERT: 0faf2aa Fix pre-commit failures. REVERT: b4d926e Notes on today, fixing the imprint CI failure. REVERT: 4c30bba Research folder. REVERT: 279e568 Research folder. REVERT: 3edfe1d Responsive plotting (#127) REVERT: 23ea4fd Responsive plotting (#127) REVERT: 13a1cd4 Adapting FastINLA to work for a variety of basket trials including survival analysis. (#123) REVERT: cf13926 Adapting FastINLA to work for a variety of basket trials including survival analysis. (#123) REVERT: 75c6cf7 Add back fast math routines (#126) REVERT: 8ec57b7 Add back fast math routines (#126) REVERT: 10ba41c Fully revert performance changes (#125) REVERT: 1d29ca2 Fully revert performance changes (#125) REVERT: 747d848 Revert some performance changes (#124) REVERT: 6ca99e2 Revert some performance changes (#124) REVERT: 2b41a4a Merge branch 'tbt/vscode_config' REVERT: e7db4e6 Merge branch 'tbt/vscode_config' REVERT: 6a86ad2 Upgraded vscode config. REVERT: 01932df Upgraded vscode config. REVERT: 9653991 Add slack alerting for CI pipeline (#120) REVERT: e113636 Add slack alerting for CI pipeline (#120) REVERT: 2bbc28a Small bug fixes for main branch. (#122) REVERT: 9f450ad Small bug fixes for main branch. (#122) REVERT: 37aa0c9 We become imprint. (#112) REVERT: 7014de8 We become imprint. (#112) REVERT: 706901a Additional optimizations for Jax Fast INLA (#111) REVERT: 1125c49 Additional optimizations for Jax Fast INLA (#111) REVERT: 662ae4a A Python Grid (#105) REVERT: 72a448e A Python Grid (#105) REVERT: a0e87cb Remove obsolete Python dependency management (#110) REVERT: 4e95f8d Remove obsolete Python dependency management (#110) REVERT: 14e4923 Update obsolete Github links (#109) REVERT: 40b9d9e Update obsolete Github links (#109) REVERT: 8f91d9c Add CI badge to README (#108) REVERT: 25f2ffe Add CI badge to README (#108) REVERT: 1dae617 Run INLA in 32-bit floating point (#106) REVERT: f63b569 Run INLA in 32-bit floating point (#106) REVERT: c8d3c54 Add CI caching for Conda, Bazel, Pre-commit (#107) REVERT: 6ce8096 Add CI caching for Conda, Bazel, Pre-commit (#107) REVERT: 3ff9393 Implementing a fixed N upper bound calculation in Python (#104) REVERT: ee78c14 Implementing a fixed N upper bound calculation in Python (#104) REVERT: ffa8a59 GridRange.is_regular was incorrect for tiles that had intersections but were pruned (#101) REVERT: 29ac69a GridRange.is_regular was incorrect for tiles that had intersections but were pruned (#101) REVERT: e858feb Exact binomial type I error for Berry. (#95) REVERT: 40ced7d Exact binomial type I error for Berry. (#95) REVERT: 183d284 Better readme installation instructions. A tutorial running a 3D basket trial. (#96) REVERT: 475d8a8 Better readme installation instructions. A tutorial running a 3D basket trial. (#96) REVERT: a367bd1 Fix for HyperPlane.intersect. (#100) REVERT: 2d24a96 Fix for HyperPlane.intersect. (#100) REVERT: ec37f47 Optimize typeI error with gradient ascent to find the worst grid points. (#94) REVERT: 4058c75 Optimize typeI error with gradient ascent to find the worst grid points. (#94) REVERT: ea2ced9 Final Berry notebooks and examples (#93) REVERT: 3fae2fb Final Berry notebooks and examples (#93) REVERT: c5e817e Update README.md REVERT: d0c7210 Update README.md REVERT: 5e6b168 Make colorscale configurable through UI (#92) REVERT: 5938716 Make colorscale configurable through UI (#92) REVERT: ff7ae76 Update README.md REVERT: 28512e5 Update README.md REVERT: 5ca3d2c Update README.md REVERT: 081e97e Update README.md REVERT: 6c08499 Running Berry/INLA accumulation. (#91) REVERT: 76004b3 Running Berry/INLA accumulation. (#91) REVERT: 608216f Merge pull request #90 from Confirm-Solutions/james.yang/python-models REVERT: fcf2571 Merge pull request #90 from Confirm-Solutions/james.yang/python-models REVERT: 6c92ad5 Make example smaller REVERT: b594f95 Make example smaller REVERT: c0a74c5 Revert back to numpy version REVERT: 0fa053c Revert back to numpy version REVERT: ab9680c Add jax version REVERT: 414ba87 Add jax version REVERT: 502762a Remove print REVERT: a34cb76 Remove print REVERT: 8accb2e Fix structure and get simple gaussian model from python workin REVERT: fd26349 Fix structure and get simple gaussian model from python workin REVERT: 0c0647b Add trampoline functionality and small test REVERT: 99eb755 Add trampoline functionality and small test REVERT: a3cd67b Add back export for std::mt19937 REVERT: befb51a Add back export for std::mt19937 REVERT: c8d5a8f Simplify generation of bazelrc (#88) REVERT: 70e31a4 Simplify generation of bazelrc (#88) REVERT: a43c92e Add thompson model (#86) REVERT: f3e7d61 Add thompson model (#86) REVERT: aaee63a Merge pull request #85 from mikesklar/tbt/build_quick_fix REVERT: 4f7f26c Merge pull request #85 from mikesklar/tbt/build_quick_fix REVERT: edff4ca OpenMP linker flag for Mac. Add clangxx to environment.yml REVERT: cfa86be OpenMP linker flag for Mac. Add clangxx to environment.yml REVERT: da74604 Merge pull request #83 from mikesklar/tbt/conda REVERT: 1c9f0aa Merge pull request #83 from mikesklar/tbt/conda REVERT: 3ceb7af Readme updates: installing conda, clarifying clang/gcc usage. REVERT: 9a81474 Readme updates: installing conda, clarifying clang/gcc usage. REVERT: d1e7bd0 Implement inference caching (#79) REVERT: 1b8f2bb Implement inference caching (#79) REVERT: 2134058 clang-format 13.0.1 is now standard. REVERT: f7177d3 clang-format 13.0.1 is now standard. REVERT: bf76aa5 clang-format 13.0.1 is now standard. REVERT: fbbc60e clang-format 13.0.1 is now standard. REVERT: fe82eaa try pinning clang and clang-format. REVERT: 1f1dbd8 try pinning clang and clang-format. REVERT: 4d75efb Check CI clang-format version and location. REVERT: 1d98560 Check CI clang-format version and location. REVERT: 29d5c7a Fix pre-commit failures from before. REVERT: edfd2cd Fix pre-commit failures from before. REVERT: a2082ac Don't install bazel from conda. REVERT: 7b44836 Don't install bazel from conda. REVERT: 46af945 Setting up conda-centric dev environment. REVERT: 35d947c Setting up conda-centric dev environment. REVERT: 30da8b3 Make default build options work for Mac and Linux (#78) REVERT: 42a40ba Make default build options work for Mac and Linux (#78) REVERT: baa6c9a Kill boost dependency (#77) REVERT: 90b3343 Kill boost dependency (#77) REVERT: dd56149 Fix MCMC parallel evaluation (#76) REVERT: 7183528 Fix MCMC parallel evaluation (#76) REVERT: 3992dba Merge branch 'main' of https://github.com/mikesklar/kevlar into main REVERT: befa822 Merge branch 'main' of https://github.com/mikesklar/kevlar into main REVERT: 890384c Finish docs for grid-range REVERT: 1813b65 Finish docs for grid-range REVERT: 77560cc Update Python README REVERT: 07ea72c Update Python README REVERT: 96a82de Kevlar Refactor (#59) REVERT: 540fbb9 Kevlar Refactor (#59) REVERT: 792b098 Pre-commit and a very simple CI pipeline (#74) REVERT: 09ca99e Pre-commit and a very simple CI pipeline (#74) REVERT: 8a46096 Add direct bayes full grid benchmark (#63) REVERT: 525bca7 Add direct bayes full grid benchmark (#63) REVERT: b6158e7 Merge pull request #68 from mikesklar/berry REVERT: a2e5881 Merge pull request #68 from mikesklar/berry REVERT: 195104f Merge branch 'main' into berry REVERT: 61d9593 Merge branch 'main' into berry REVERT: e214ab4 Alex suggested changes. REVERT: 625a519 Alex suggested changes. REVERT: b2b702f Fast inla. REVERT: df6e0fe Fast inla. REVERT: a653241 Revert "cholesky version of c++ inla. not faster." REVERT: 4fafb7e Revert "cholesky version of c++ inla. not faster." REVERT: 17287fb cholesky version of c++ inla. not faster. REVERT: 457f19b cholesky version of c++ inla. not faster. REVERT: 87d45ce Fast c++ version, faster JAX version. REVERT: 7cd976b Fast c++ version, faster JAX version. REVERT: 6f5b8d7 Playing around with Jax optimizations. REVERT: c8b4c24 Playing around with Jax optimizations. REVERT: 168458c Fast JAX implementation. Using vmap productively. REVERT: 10ce1fc Fast JAX implementation. Using vmap productively. REVERT: b5e39ea Merge pull request #67 from mikesklar/const2 REVERT: 4b96f49 Merge pull request #67 from mikesklar/const2 REVERT: 8d075ba A few berry improvements REVERT: e773c6c A few berry improvements REVERT: 3401cf9 Merge pull request #66 from mikesklar/berry REVERT: 8d338f0 Merge pull request #66 from mikesklar/berry REVERT: d9a6849 Alex's comments lead to better code. REVERT: 5d2ff5e Alex's comments lead to better code. REVERT: f376a68 Jupytext notebooks to markdown. REVERT: ee08728 Jupytext notebooks to markdown. REVERT: fec420d Fast INLA. REVERT: 380c510 Fast INLA. REVERT: c44a909 restore direct_bayes folder. REVERT: 7f8ee57 restore direct_bayes folder. REVERT: 4b4ec71 Lots of comparison between INLA methods. REVERT: a8f97cc Lots of comparison between INLA methods. REVERT: 4bc824e numpyro MCMC working! REVERT: 596fc7b numpyro MCMC working! REVERT: 034cf40 Berry Figure 2 with quadrature REVERT: 0c1ae09 Berry Figure 2 with quadrature REVERT: 9cee20d Modifying Berry figures so that we can make plots with the exact integrator. Computing CDF from exact integrator. REVERT: 658d039 Modifying Berry figures so that we can make plots with the exact integrator. Computing CDF from exact integrator. REVERT: 9e52736 Improved exact integrator. REVERT: 87f0bcb Improved exact integrator. REVERT: ef6ca5d Berry with analytical mu integration is working nicely. REVERT: b1d6261 Berry with analytical mu integration is working nicely. REVERT: 3dcba48 INLA is correctly modified for p1 theta offset. REVERT: 08d23af INLA is correctly modified for p1 theta offset. REVERT: a696be4 Dirty bayes is correctly modified for p1 theta offset. REVERT: aba8cab Dirty bayes is correctly modified for p1 theta offset. REVERT: 74c31b3 Crap, the theta parameterization from Berry is the right one to use... REVERT: ae2755e Crap, the theta parameterization from Berry is the right one to use... REVERT: 2e83def Working on one parameter Berry INLA. REVERT: f772145 Working on one parameter Berry INLA. REVERT: 1e53769 Massively simplified the berry_dirty notebook. REVERT: d2ff89e Massively simplified the berry_dirty notebook. REVERT: 6637d50 Add QuadRule structure. REVERT: b8a83fd Add QuadRule structure. REVERT: bc7c638 log_gauss_rule, run black/isort on research/berry folder. REVERT: 8588e91 log_gauss_rule, run black/isort on research/berry folder. REVERT: a58656b strip notebooks. REVERT: 163d127 strip notebooks. REVERT: f7ed040 Merge branch 'main' of github.com:mikesklar/kevlar into berry REVERT: 9b561a1 Merge branch 'main' of github.com:mikesklar/kevlar into berry REVERT: 4d0757f Reorganizing to split out the berry work from the preliminary INLA exploration that is a little crusty. REVERT: 3800f42 Reorganizing to split out the berry work from the preliminary INLA exploration that is a little crusty. REVERT: aeec5cb Exploring DB vs. INLA issues. REVERT: 732769f Exploring DB vs. INLA issues. REVERT: bd80a65 Replace quadpy with numpy and clear notebook output (#65) REVERT: f157635 Replace quadpy with numpy and clear notebook output (#65) REVERT: 979c492 Kevlar integration (#61) REVERT: 0f0ae91 Kevlar integration (#61) REVERT: 286cae6 Compute sigma instead of sigma2 in DB Berry replication. REVERT: 915b93d Compute sigma instead of sigma2 in DB Berry replication. REVERT: 2934747 Compute sigma instead of sigma2 in DB Berry replication. REVERT: 93dae31 Compute sigma instead of sigma2 in DB Berry replication. REVERT: 7726bcb Ben's INLA notebooks (#60) REVERT: cb4e23d Ben's INLA notebooks (#60) REVERT: 347691c Replace direct bayes choleskey with faster sherman-morrison (#56) REVERT: 363d552 Replace direct bayes choleskey with faster sherman-morrison (#56) REVERT: 50efcda Spring cleaning (#55) REVERT: efeef7d Spring cleaning (#55) REVERT: d6de183 Direct Bayes Kevlar integration (#31) REVERT: 3340a3b Direct Bayes Kevlar integration (#31) REVERT: 4425987 Fix openmp not being used issue (#52) REVERT: 181d5d6 Fix openmp not being used issue (#52) REVERT: 34551d7 Fix Python build rules (#51) REVERT: ef52e65 Fix Python build rules (#51) REVERT: 533cf76 Bazel Mac build fix (#50) REVERT: 1f5c192 Bazel Mac build fix (#50) REVERT: 1da0c31 Build Python package with Bazel (#46) REVERT: 33902a6 Build Python package with Bazel (#46) REVERT: b3942ea Support Linux GCC, Linux Clang, and Mac Homebrew Clang builds (#45) REVERT: debfdf7 Support Linux GCC, Linux Clang, and Mac Homebrew Clang builds (#45) REVERT: 6233086 Prelminaries for Direct Bayes (#42) REVERT: 58e43e8 Prelminaries for Direct Bayes (#42) REVERT: cd35dbd Update all READMEs (#40) REVERT: 59b1f3a Update all READMEs (#40) REVERT: 7cac6ca Fix sign warnings REVERT: 8b45f49 Fix sign warnings REVERT: 402a17a Fix path grabbing once again REVERT: fb56c82 Fix path grabbing once again REVERT: 720e3d8 Add external to path REVERT: 3f0404b Add external to path REVERT: 4b312a3 Merge branch 'main' of https://github.com/mikesklar/kevlar into main REVERT: 44f869d Merge branch 'main' of https://github.com/mikesklar/kevlar into main REVERT: b315078 Add a more general way to add bazel deps REVERT: 3b94819 Add a more general way to add bazel deps REVERT: ee93c25 Update c++ engine source (#39) REVERT: 17c8d61 Update c++ engine source (#39) REVERT: 7c339a7 Clean R Legacy and Revamp build system (#38) REVERT: 745b9e3 Clean R Legacy and Revamp build system (#38) REVERT: 0c3b069 Add binomial fit benchmark (#34) REVERT: cf41d43 Add binomial fit benchmark (#34) REVERT: dfeb5ec 0th Order Upper Bound Fix (#33) REVERT: 3b65233 0th Order Upper Bound Fix (#33) REVERT: cab7a49 Add dirty multilevel python and R examples (#20) REVERT: cb93daf Add dirty multilevel python and R examples (#20) REVERT: 18ed8eb Generalized Upper Bound (#32) REVERT: c18d1fb Generalized Upper Bound (#32) REVERT: 3630ddd Don't reload test data on plot state change (#29) REVERT: fc26117 Don't reload test data on plot state change (#29) REVERT: 1e2fda8 Update generalized upper-bound writeup (#28) REVERT: 96d599c Update generalized upper-bound writeup (#28) REVERT: 4ac1667 James.yang/examples csv (#27) REVERT: 4aa8325 James.yang/examples csv (#27) REVERT: 07b9de9 Clang-format everything (#25) REVERT: 46c128e Clang-format everything (#25) REVERT: ac66eca Direct bayes (#19) REVERT: d977e78 Direct bayes (#19) REVERT: b627d65 Kevlar revamp!! (#21) REVERT: 46125f4 Kevlar revamp!! (#21) REVERT: 97882fe Merge pull request #18 from mikesklar/scatter REVERT: 67b9c31 Merge pull request #18 from mikesklar/scatter REVERT: 21e7e1a Add basic React rendering test REVERT: 5a3a055 Add basic React rendering test REVERT: 965ebc9 Merge pull request #17 from mikesklar/scatter REVERT: 688129f Merge pull request #17 from mikesklar/scatter REVERT: cb7a56a Add file upload buttons for custom data REVERT: fcc2cc4 Add file upload buttons for custom data REVERT: ff3439a Merge pull request #12 from mikesklar/scatter REVERT: f83435d Merge pull request #12 from mikesklar/scatter REVERT: 0ac2d45 Add legend labels to scatter plot REVERT: 89e5576 Add legend labels to scatter plot REVERT: b1c5922 Merge pull request #9 from mikesklar/scatter REVERT: 08bfb68 Merge pull request #9 from mikesklar/scatter REVERT: 43e1105 Add layer subvisualization REVERT: bbba082 Add layer subvisualization REVERT: b2a590d Merge pull request #7 from mikesklar/scatter REVERT: df96e44 Merge pull request #7 from mikesklar/scatter REVERT: 7ca10e4 Allow choosing between scatter and surface plots REVERT: 1aa7f04 Allow choosing between scatter and surface plots REVERT: aaa9c88 Merge pull request #5 from mikesklar/const2 REVERT: 4e209fc Merge pull request #5 from mikesklar/const2 REVERT: 8a01923 Update kevlar flowcharts REVERT: dc10f22 Update kevlar flowcharts REVERT: b832f19 Update flowchart with clearer vis subgraph REVERT: f719197 Update flowchart with clearer vis subgraph REVERT: 2218d46 Add initial web frontend REVERT: 32fa045 Add initial web frontend REVERT: 887654c Modify slight comment change on diagram REVERT: e678a6b Modify slight comment change on diagram REVERT: 07a2467 Add framework_flowchart.md REVERT: 6fbe5b7 Add framework_flowchart.md REVERT: 4c15174 Fix compilation bugs REVERT: 4c3a939 Fix compilation bugs REVERT: 946f0fe Fix all R examples that were using incorrect grid radius REVERT: f4a0aed Fix all R examples that were using incorrect grid radius REVERT: 2430627 Refactor CRTP base to just free function and add lots of comments REVERT: 7126e66 Refactor CRTP base to just free function and add lots of comments REVERT: eea5572 Add exponential and start adagrid stuff REVERT: e4c7447 Add exponential and start adagrid stuff REVERT: f3cbc70 Add exponential dist with log rank + example REVERT: 96a6ee6 Add exponential dist with log rank + example REVERT: f1232dc Add Rcpp header REVERT: 2d1cbd7 Add Rcpp header REVERT: 940268b Add fixes to bckt, and export new version with hypos REVERT: f84be87 Add fixes to bckt, and export new version with hypos REVERT: 47aa629 Work in progress REVERT: b82fd87 Work in progress REVERT: f19d6a6 Update README.md REVERT: effeb0b Update README.md REVERT: 57c7f9d Add generalizations REVERT: 5c1b778 Add generalizations REVERT: 6128fe8 Combine and ignore bckt REVERT: 97463f3 Combine and ignore bckt REVERT: a5af985 Add refactor changes with range style REVERT: fad4329 Add refactor changes with range style REVERT: ea1b429 Fix build issues on Mac REVERT: add7e65 Fix build issues on Mac REVERT: fef1fde Fix example REVERT: 8f9c8d7 Fix example REVERT: 9aa608e Make R pkg out of C++ engine and fix bugs with grid epsilon, and make R example work REVERT: b56fdb7 Make R pkg out of C++ engine and fix bugs with grid epsilon, and make R example work REVERT: 7f40dbf Change updates to naive averaging, add hardware information (not used currently but may be useful later), and start serialize process) REVERT: 39ddc28 Add README REVERT: b540f2b Fix tests and headers to work on MSVC REVERT: 200b865 Add progress bar and integrated into tune REVERT: 4f31819 Finish optimizing and refactoring for bckt model REVERT: b0206a5 Add a period in README lol REVERT: ade88ed Add R version of binomial control 2 treatment example REVERT: 9738bcb Move cpp stuff into kevlar dir REVERT: 0e7944a Ignore binaries, pdf, data, etc. REVERT: f132059 Add legacy R code REVERT: eb7f19e Add cpp version of thompson sampling for binomial example with benchmark REVERT: a5f989e Initial commit git-subtree-dir: imprint git-subtree-split: f50799766f3146cdd244b151e9ed2759cb353022
tbenthompson
added a commit
that referenced
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Dec 17, 2022
* Move imprint v1 to research folder. * Keep the frontend and the Berry tutorial. Archive research folder. * Remove references to pyimprint. * Move imprint to imprint repo. * imprint and confirm tests passing. * Fixing up the basket trial example. * Git leaks, separate linting workflow. * Fix lint workflow. * Set up Go for gitleaks. * Fix eligible test failure. * Separate pre-commit install vs run. * ZTest and Fisher exact tutorials. * ZTest and Fisher exact tutorials. * Add links to imprint readme for tutorials. * Squashed 'imprint/' changes from 2fb6ac5..f507997 f507997 Initial REVERT: 2fb6ac5 Codespaces configuration. REVERT: c1ca09a Fix up the tutorial. REVERT: b7b296c Fix up the tutorial. REVERT: a86baa3 Default version in setup.py (#26) REVERT: 596ef53 Add back alex's changes to setup REVERT: 1386c12 Fix build system to be editable and add more dependencies REVERT: f9190a6 James.yang/vscode fix (#130) REVERT: 63846ba Update imprint pre-commit config. REVERT: 9a2ecca Merge commit 'af593cc95bc17078757774e4605588373b420e31' REVERT: cbd80b8 Create LICENSE REVERT: 10a90ec Update README.md REVERT: 0407c45 Tbt/add tutorial back (#129) REVERT: 20b8129 Add the tutorial back into the imprint repo. REVERT: a354160 Update README.md REVERT: 2443d2a Conditional INLA, gauss-hermite. REVERT: 1666644 Add thesis link REVERT: 3b2c96c reorder python imports. REVERT: e3fde11 Environment set up. CI. REVERT: f813308 Fixing the CI failure. (#128) REVERT: 0faf2aa Fix pre-commit failures. REVERT: b4d926e Notes on today, fixing the imprint CI failure. REVERT: 4c30bba Research folder. REVERT: 279e568 Research folder. REVERT: 3edfe1d Responsive plotting (#127) REVERT: 23ea4fd Responsive plotting (#127) REVERT: 13a1cd4 Adapting FastINLA to work for a variety of basket trials including survival analysis. (#123) REVERT: cf13926 Adapting FastINLA to work for a variety of basket trials including survival analysis. (#123) REVERT: 75c6cf7 Add back fast math routines (#126) REVERT: 8ec57b7 Add back fast math routines (#126) REVERT: 10ba41c Fully revert performance changes (#125) REVERT: 1d29ca2 Fully revert performance changes (#125) REVERT: 747d848 Revert some performance changes (#124) REVERT: 6ca99e2 Revert some performance changes (#124) REVERT: 2b41a4a Merge branch 'tbt/vscode_config' REVERT: e7db4e6 Merge branch 'tbt/vscode_config' REVERT: 6a86ad2 Upgraded vscode config. REVERT: 01932df Upgraded vscode config. REVERT: 9653991 Add slack alerting for CI pipeline (#120) REVERT: e113636 Add slack alerting for CI pipeline (#120) REVERT: 2bbc28a Small bug fixes for main branch. (#122) REVERT: 9f450ad Small bug fixes for main branch. (#122) REVERT: 37aa0c9 We become imprint. (#112) REVERT: 7014de8 We become imprint. (#112) REVERT: 706901a Additional optimizations for Jax Fast INLA (#111) REVERT: 1125c49 Additional optimizations for Jax Fast INLA (#111) REVERT: 662ae4a A Python Grid (#105) REVERT: 72a448e A Python Grid (#105) REVERT: a0e87cb Remove obsolete Python dependency management (#110) REVERT: 4e95f8d Remove obsolete Python dependency management (#110) REVERT: 14e4923 Update obsolete Github links (#109) REVERT: 40b9d9e Update obsolete Github links (#109) REVERT: 8f91d9c Add CI badge to README (#108) REVERT: 25f2ffe Add CI badge to README (#108) REVERT: 1dae617 Run INLA in 32-bit floating point (#106) REVERT: f63b569 Run INLA in 32-bit floating point (#106) REVERT: c8d3c54 Add CI caching for Conda, Bazel, Pre-commit (#107) REVERT: 6ce8096 Add CI caching for Conda, Bazel, Pre-commit (#107) REVERT: 3ff9393 Implementing a fixed N upper bound calculation in Python (#104) REVERT: ee78c14 Implementing a fixed N upper bound calculation in Python (#104) REVERT: ffa8a59 GridRange.is_regular was incorrect for tiles that had intersections but were pruned (#101) REVERT: 29ac69a GridRange.is_regular was incorrect for tiles that had intersections but were pruned (#101) REVERT: e858feb Exact binomial type I error for Berry. (#95) REVERT: 40ced7d Exact binomial type I error for Berry. (#95) REVERT: 183d284 Better readme installation instructions. A tutorial running a 3D basket trial. (#96) REVERT: 475d8a8 Better readme installation instructions. A tutorial running a 3D basket trial. (#96) REVERT: a367bd1 Fix for HyperPlane.intersect. (#100) REVERT: 2d24a96 Fix for HyperPlane.intersect. (#100) REVERT: ec37f47 Optimize typeI error with gradient ascent to find the worst grid points. (#94) REVERT: 4058c75 Optimize typeI error with gradient ascent to find the worst grid points. (#94) REVERT: ea2ced9 Final Berry notebooks and examples (#93) REVERT: 3fae2fb Final Berry notebooks and examples (#93) REVERT: c5e817e Update README.md REVERT: d0c7210 Update README.md REVERT: 5e6b168 Make colorscale configurable through UI (#92) REVERT: 5938716 Make colorscale configurable through UI (#92) REVERT: ff7ae76 Update README.md REVERT: 28512e5 Update README.md REVERT: 5ca3d2c Update README.md REVERT: 081e97e Update README.md REVERT: 6c08499 Running Berry/INLA accumulation. (#91) REVERT: 76004b3 Running Berry/INLA accumulation. (#91) REVERT: 608216f Merge pull request #90 from Confirm-Solutions/james.yang/python-models REVERT: fcf2571 Merge pull request #90 from Confirm-Solutions/james.yang/python-models REVERT: 6c92ad5 Make example smaller REVERT: b594f95 Make example smaller REVERT: c0a74c5 Revert back to numpy version REVERT: 0fa053c Revert back to numpy version REVERT: ab9680c Add jax version REVERT: 414ba87 Add jax version REVERT: 502762a Remove print REVERT: a34cb76 Remove print REVERT: 8accb2e Fix structure and get simple gaussian model from python workin REVERT: fd26349 Fix structure and get simple gaussian model from python workin REVERT: 0c0647b Add trampoline functionality and small test REVERT: 99eb755 Add trampoline functionality and small test REVERT: a3cd67b Add back export for std::mt19937 REVERT: befb51a Add back export for std::mt19937 REVERT: c8d5a8f Simplify generation of bazelrc (#88) REVERT: 70e31a4 Simplify generation of bazelrc (#88) REVERT: a43c92e Add thompson model (#86) REVERT: f3e7d61 Add thompson model (#86) REVERT: aaee63a Merge pull request #85 from mikesklar/tbt/build_quick_fix REVERT: 4f7f26c Merge pull request #85 from mikesklar/tbt/build_quick_fix REVERT: edff4ca OpenMP linker flag for Mac. Add clangxx to environment.yml REVERT: cfa86be OpenMP linker flag for Mac. Add clangxx to environment.yml REVERT: da74604 Merge pull request #83 from mikesklar/tbt/conda REVERT: 1c9f0aa Merge pull request #83 from mikesklar/tbt/conda REVERT: 3ceb7af Readme updates: installing conda, clarifying clang/gcc usage. REVERT: 9a81474 Readme updates: installing conda, clarifying clang/gcc usage. REVERT: d1e7bd0 Implement inference caching (#79) REVERT: 1b8f2bb Implement inference caching (#79) REVERT: 2134058 clang-format 13.0.1 is now standard. REVERT: f7177d3 clang-format 13.0.1 is now standard. REVERT: bf76aa5 clang-format 13.0.1 is now standard. REVERT: fbbc60e clang-format 13.0.1 is now standard. REVERT: fe82eaa try pinning clang and clang-format. REVERT: 1f1dbd8 try pinning clang and clang-format. REVERT: 4d75efb Check CI clang-format version and location. REVERT: 1d98560 Check CI clang-format version and location. REVERT: 29d5c7a Fix pre-commit failures from before. REVERT: edfd2cd Fix pre-commit failures from before. REVERT: a2082ac Don't install bazel from conda. REVERT: 7b44836 Don't install bazel from conda. REVERT: 46af945 Setting up conda-centric dev environment. REVERT: 35d947c Setting up conda-centric dev environment. REVERT: 30da8b3 Make default build options work for Mac and Linux (#78) REVERT: 42a40ba Make default build options work for Mac and Linux (#78) REVERT: baa6c9a Kill boost dependency (#77) REVERT: 90b3343 Kill boost dependency (#77) REVERT: dd56149 Fix MCMC parallel evaluation (#76) REVERT: 7183528 Fix MCMC parallel evaluation (#76) REVERT: 3992dba Merge branch 'main' of https://github.com/mikesklar/kevlar into main REVERT: befa822 Merge branch 'main' of https://github.com/mikesklar/kevlar into main REVERT: 890384c Finish docs for grid-range REVERT: 1813b65 Finish docs for grid-range REVERT: 77560cc Update Python README REVERT: 07ea72c Update Python README REVERT: 96a82de Kevlar Refactor (#59) REVERT: 540fbb9 Kevlar Refactor (#59) REVERT: 792b098 Pre-commit and a very simple CI pipeline (#74) REVERT: 09ca99e Pre-commit and a very simple CI pipeline (#74) REVERT: 8a46096 Add direct bayes full grid benchmark (#63) REVERT: 525bca7 Add direct bayes full grid benchmark (#63) REVERT: b6158e7 Merge pull request #68 from mikesklar/berry REVERT: a2e5881 Merge pull request #68 from mikesklar/berry REVERT: 195104f Merge branch 'main' into berry REVERT: 61d9593 Merge branch 'main' into berry REVERT: e214ab4 Alex suggested changes. REVERT: 625a519 Alex suggested changes. REVERT: b2b702f Fast inla. REVERT: df6e0fe Fast inla. REVERT: a653241 Revert "cholesky version of c++ inla. not faster." REVERT: 4fafb7e Revert "cholesky version of c++ inla. not faster." REVERT: 17287fb cholesky version of c++ inla. not faster. REVERT: 457f19b cholesky version of c++ inla. not faster. REVERT: 87d45ce Fast c++ version, faster JAX version. REVERT: 7cd976b Fast c++ version, faster JAX version. REVERT: 6f5b8d7 Playing around with Jax optimizations. REVERT: c8b4c24 Playing around with Jax optimizations. REVERT: 168458c Fast JAX implementation. Using vmap productively. REVERT: 10ce1fc Fast JAX implementation. Using vmap productively. REVERT: b5e39ea Merge pull request #67 from mikesklar/const2 REVERT: 4b96f49 Merge pull request #67 from mikesklar/const2 REVERT: 8d075ba A few berry improvements REVERT: e773c6c A few berry improvements REVERT: 3401cf9 Merge pull request #66 from mikesklar/berry REVERT: 8d338f0 Merge pull request #66 from mikesklar/berry REVERT: d9a6849 Alex's comments lead to better code. REVERT: 5d2ff5e Alex's comments lead to better code. REVERT: f376a68 Jupytext notebooks to markdown. REVERT: ee08728 Jupytext notebooks to markdown. REVERT: fec420d Fast INLA. REVERT: 380c510 Fast INLA. REVERT: c44a909 restore direct_bayes folder. REVERT: 7f8ee57 restore direct_bayes folder. REVERT: 4b4ec71 Lots of comparison between INLA methods. REVERT: a8f97cc Lots of comparison between INLA methods. REVERT: 4bc824e numpyro MCMC working! REVERT: 596fc7b numpyro MCMC working! REVERT: 034cf40 Berry Figure 2 with quadrature REVERT: 0c1ae09 Berry Figure 2 with quadrature REVERT: 9cee20d Modifying Berry figures so that we can make plots with the exact integrator. Computing CDF from exact integrator. REVERT: 658d039 Modifying Berry figures so that we can make plots with the exact integrator. Computing CDF from exact integrator. REVERT: 9e52736 Improved exact integrator. REVERT: 87f0bcb Improved exact integrator. REVERT: ef6ca5d Berry with analytical mu integration is working nicely. REVERT: b1d6261 Berry with analytical mu integration is working nicely. REVERT: 3dcba48 INLA is correctly modified for p1 theta offset. REVERT: 08d23af INLA is correctly modified for p1 theta offset. REVERT: a696be4 Dirty bayes is correctly modified for p1 theta offset. REVERT: aba8cab Dirty bayes is correctly modified for p1 theta offset. REVERT: 74c31b3 Crap, the theta parameterization from Berry is the right one to use... REVERT: ae2755e Crap, the theta parameterization from Berry is the right one to use... REVERT: 2e83def Working on one parameter Berry INLA. REVERT: f772145 Working on one parameter Berry INLA. REVERT: 1e53769 Massively simplified the berry_dirty notebook. REVERT: d2ff89e Massively simplified the berry_dirty notebook. REVERT: 6637d50 Add QuadRule structure. REVERT: b8a83fd Add QuadRule structure. REVERT: bc7c638 log_gauss_rule, run black/isort on research/berry folder. REVERT: 8588e91 log_gauss_rule, run black/isort on research/berry folder. REVERT: a58656b strip notebooks. REVERT: 163d127 strip notebooks. REVERT: f7ed040 Merge branch 'main' of github.com:mikesklar/kevlar into berry REVERT: 9b561a1 Merge branch 'main' of github.com:mikesklar/kevlar into berry REVERT: 4d0757f Reorganizing to split out the berry work from the preliminary INLA exploration that is a little crusty. REVERT: 3800f42 Reorganizing to split out the berry work from the preliminary INLA exploration that is a little crusty. REVERT: aeec5cb Exploring DB vs. INLA issues. REVERT: 732769f Exploring DB vs. INLA issues. REVERT: bd80a65 Replace quadpy with numpy and clear notebook output (#65) REVERT: f157635 Replace quadpy with numpy and clear notebook output (#65) REVERT: 979c492 Kevlar integration (#61) REVERT: 0f0ae91 Kevlar integration (#61) REVERT: 286cae6 Compute sigma instead of sigma2 in DB Berry replication. REVERT: 915b93d Compute sigma instead of sigma2 in DB Berry replication. REVERT: 2934747 Compute sigma instead of sigma2 in DB Berry replication. REVERT: 93dae31 Compute sigma instead of sigma2 in DB Berry replication. REVERT: 7726bcb Ben's INLA notebooks (#60) REVERT: cb4e23d Ben's INLA notebooks (#60) REVERT: 347691c Replace direct bayes choleskey with faster sherman-morrison (#56) REVERT: 363d552 Replace direct bayes choleskey with faster sherman-morrison (#56) REVERT: 50efcda Spring cleaning (#55) REVERT: efeef7d Spring cleaning (#55) REVERT: d6de183 Direct Bayes Kevlar integration (#31) REVERT: 3340a3b Direct Bayes Kevlar integration (#31) REVERT: 4425987 Fix openmp not being used issue (#52) REVERT: 181d5d6 Fix openmp not being used issue (#52) REVERT: 34551d7 Fix Python build rules (#51) REVERT: ef52e65 Fix Python build rules (#51) REVERT: 533cf76 Bazel Mac build fix (#50) REVERT: 1f5c192 Bazel Mac build fix (#50) REVERT: 1da0c31 Build Python package with Bazel (#46) REVERT: 33902a6 Build Python package with Bazel (#46) REVERT: b3942ea Support Linux GCC, Linux Clang, and Mac Homebrew Clang builds (#45) REVERT: debfdf7 Support Linux GCC, Linux Clang, and Mac Homebrew Clang builds (#45) REVERT: 6233086 Prelminaries for Direct Bayes (#42) REVERT: 58e43e8 Prelminaries for Direct Bayes (#42) REVERT: cd35dbd Update all READMEs (#40) REVERT: 59b1f3a Update all READMEs (#40) REVERT: 7cac6ca Fix sign warnings REVERT: 8b45f49 Fix sign warnings REVERT: 402a17a Fix path grabbing once again REVERT: fb56c82 Fix path grabbing once again REVERT: 720e3d8 Add external to path REVERT: 3f0404b Add external to path REVERT: 4b312a3 Merge branch 'main' of https://github.com/mikesklar/kevlar into main REVERT: 44f869d Merge branch 'main' of https://github.com/mikesklar/kevlar into main REVERT: b315078 Add a more general way to add bazel deps REVERT: 3b94819 Add a more general way to add bazel deps REVERT: ee93c25 Update c++ engine source (#39) REVERT: 17c8d61 Update c++ engine source (#39) REVERT: 7c339a7 Clean R Legacy and Revamp build system (#38) REVERT: 745b9e3 Clean R Legacy and Revamp build system (#38) REVERT: 0c3b069 Add binomial fit benchmark (#34) REVERT: cf41d43 Add binomial fit benchmark (#34) REVERT: dfeb5ec 0th Order Upper Bound Fix (#33) REVERT: 3b65233 0th Order Upper Bound Fix (#33) REVERT: cab7a49 Add dirty multilevel python and R examples (#20) REVERT: cb93daf Add dirty multilevel python and R examples (#20) REVERT: 18ed8eb Generalized Upper Bound (#32) REVERT: c18d1fb Generalized Upper Bound (#32) REVERT: 3630ddd Don't reload test data on plot state change (#29) REVERT: fc26117 Don't reload test data on plot state change (#29) REVERT: 1e2fda8 Update generalized upper-bound writeup (#28) REVERT: 96d599c Update generalized upper-bound writeup (#28) REVERT: 4ac1667 James.yang/examples csv (#27) REVERT: 4aa8325 James.yang/examples csv (#27) REVERT: 07b9de9 Clang-format everything (#25) REVERT: 46c128e Clang-format everything (#25) REVERT: ac66eca Direct bayes (#19) REVERT: d977e78 Direct bayes (#19) REVERT: b627d65 Kevlar revamp!! (#21) REVERT: 46125f4 Kevlar revamp!! (#21) REVERT: 97882fe Merge pull request #18 from mikesklar/scatter REVERT: 67b9c31 Merge pull request #18 from mikesklar/scatter REVERT: 21e7e1a Add basic React rendering test REVERT: 5a3a055 Add basic React rendering test REVERT: 965ebc9 Merge pull request #17 from mikesklar/scatter REVERT: 688129f Merge pull request #17 from mikesklar/scatter REVERT: cb7a56a Add file upload buttons for custom data REVERT: fcc2cc4 Add file upload buttons for custom data REVERT: ff3439a Merge pull request #12 from mikesklar/scatter REVERT: f83435d Merge pull request #12 from mikesklar/scatter REVERT: 0ac2d45 Add legend labels to scatter plot REVERT: 89e5576 Add legend labels to scatter plot REVERT: b1c5922 Merge pull request #9 from mikesklar/scatter REVERT: 08bfb68 Merge pull request #9 from mikesklar/scatter REVERT: 43e1105 Add layer subvisualization REVERT: bbba082 Add layer subvisualization REVERT: b2a590d Merge pull request #7 from mikesklar/scatter REVERT: df96e44 Merge pull request #7 from mikesklar/scatter REVERT: 7ca10e4 Allow choosing between scatter and surface plots REVERT: 1aa7f04 Allow choosing between scatter and surface plots REVERT: aaa9c88 Merge pull request #5 from mikesklar/const2 REVERT: 4e209fc Merge pull request #5 from mikesklar/const2 REVERT: 8a01923 Update kevlar flowcharts REVERT: dc10f22 Update kevlar flowcharts REVERT: b832f19 Update flowchart with clearer vis subgraph REVERT: f719197 Update flowchart with clearer vis subgraph REVERT: 2218d46 Add initial web frontend REVERT: 32fa045 Add initial web frontend REVERT: 887654c Modify slight comment change on diagram REVERT: e678a6b Modify slight comment change on diagram REVERT: 07a2467 Add framework_flowchart.md REVERT: 6fbe5b7 Add framework_flowchart.md REVERT: 4c15174 Fix compilation bugs REVERT: 4c3a939 Fix compilation bugs REVERT: 946f0fe Fix all R examples that were using incorrect grid radius REVERT: f4a0aed Fix all R examples that were using incorrect grid radius REVERT: 2430627 Refactor CRTP base to just free function and add lots of comments REVERT: 7126e66 Refactor CRTP base to just free function and add lots of comments REVERT: eea5572 Add exponential and start adagrid stuff REVERT: e4c7447 Add exponential and start adagrid stuff REVERT: f3cbc70 Add exponential dist with log rank + example REVERT: 96a6ee6 Add exponential dist with log rank + example REVERT: f1232dc Add Rcpp header REVERT: 2d1cbd7 Add Rcpp header REVERT: 940268b Add fixes to bckt, and export new version with hypos REVERT: f84be87 Add fixes to bckt, and export new version with hypos REVERT: 47aa629 Work in progress REVERT: b82fd87 Work in progress REVERT: f19d6a6 Update README.md REVERT: effeb0b Update README.md REVERT: 57c7f9d Add generalizations REVERT: 5c1b778 Add generalizations REVERT: 6128fe8 Combine and ignore bckt REVERT: 97463f3 Combine and ignore bckt REVERT: a5af985 Add refactor changes with range style REVERT: fad4329 Add refactor changes with range style REVERT: ea1b429 Fix build issues on Mac REVERT: add7e65 Fix build issues on Mac REVERT: fef1fde Fix example REVERT: 8f9c8d7 Fix example REVERT: 9aa608e Make R pkg out of C++ engine and fix bugs with grid epsilon, and make R example work REVERT: b56fdb7 Make R pkg out of C++ engine and fix bugs with grid epsilon, and make R example work REVERT: 7f40dbf Change updates to naive averaging, add hardware information (not used currently but may be useful later), and start serialize process) REVERT: 39ddc28 Add README REVERT: b540f2b Fix tests and headers to work on MSVC REVERT: 200b865 Add progress bar and integrated into tune REVERT: 4f31819 Finish optimizing and refactoring for bckt model REVERT: b0206a5 Add a period in README lol REVERT: ade88ed Add R version of binomial control 2 treatment example REVERT: 9738bcb Move cpp stuff into kevlar dir REVERT: 0e7944a Ignore binaries, pdf, data, etc. REVERT: f132059 Add legacy R code REVERT: eb7f19e Add cpp version of thompson sampling for binomial example with benchmark REVERT: a5f989e Initial commit git-subtree-dir: imprint git-subtree-split: f50799766f3146cdd244b151e9ed2759cb353022
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Planning for after the paper is submitted...
Other issues that discuss "clean up" type tasks:
Done:
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