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Probing ongoing runs #96

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tbenthompson opened this issue Oct 29, 2022 · 2 comments
Open

Probing ongoing runs #96

tbenthompson opened this issue Oct 29, 2022 · 2 comments

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@tbenthompson
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tbenthompson commented Oct 29, 2022 •
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Investigating the state of an ongoing run. It would be good to have a standard starting point for this. Currently, some interesting plots are produced in the inspector.ipynb notebook. This is closely connected to #63

There are two aspects to this:

  1. Reports that are automatically generated during a run. These need to be fairly fast since they'll happen during every iteration (or maybe not every iteration?? also maybe asynchronously so that they can run on the CPU while the GPU is working on the next iteration).
  2. Reports that can be generated from an ongoing run on demand. These can be slower and more involved.

better tools for looking at which tiles are next up:

  • characteristics of the next batch of tiles:
    • small vs large alpha0
    • small vs large sim_sizes
    • ...
  • investigate the ordering from twb_min_lam
    • what are the alpha0 and sim_sizes for tiles in that ordering.
    • next steps up in lambda**
  • where in the ordering the next "important" tiles are.

improvements to status reporting based on:

  • inspector.ipynb
  • inspector2.ipynb
  • the bayes2022_figs and berry figures from paper_figures/
  • the report from adarunner.
@tbenthompson tbenthompson mentioned this issue Oct 29, 2022
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tbenthompson added a commit that referenced this issue Dec 17, 2022
@tbenthompson
Squashed 'imprint/' changes from 2fb6ac5..f507997
50f1e73 
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 this issue Dec 17, 2022
@tbenthompson
Imprint v0.2 (#186)
5685554 
* 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
@tbenthompson
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tbenthompson commented Mar 28, 2023 •
edited
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Could generate an automated jupyter document or markdown document as a report on a job. This could be produced while the job is still running or after it's done.

  • put the template in confirm/adagrid/
  • automatically run the notebook and dump the result wherever is desired.

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There's good work on this in the probe.ipynb notebook for the WD41 run.

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