DO NOT MERGE {main-> niehs} #4
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…L_dataviz Starting Merge for SL's final commit
merge current ToxicR with SL_dataviz#
Merging stuff for simulations
* begin work * fix install issues * add makefile tests * remove report info * add cache restore * add pycpp * update wheels * ci changes * updates? * fix tests? * debugging * rewrite tests from debugging * move things to setup.py> * Revert "move things to setup.py>" * simplify package for proper wheels? * remove pythonpath * Revert "remove pythonpath" * Revert "simplify package for proper wheels?" * Revert "Revert "move things to setup.py>"" * Revert "move things to setup.py>" * Revert "rewrite tests from debugging" * Revert "debugging" * fix wheel generation? * wheel cleanup? * cleanup and final tests * change when actions are executed * final cleanup of makefile * Update README.md
* build updates * Added debug output for continous_analysis struct * more edits * remove debug * remove more cout * add strip to libDRBMD.so to reduce filesize * remove custom gsl * update * update dockerfile * update build * updates * fix path * updates * updates gitlab ci * fix path * python 3.11 and remove hard-coded environments * fix missing $ * fix final copy? * remove old types --------- Co-authored-by: Cody Simmons <[email protected]>
* cmake build 1st draft * clean up for linux build process * Added Windows build commands * updates for python builds and versions * python version bump; start actions work * updates from CI * cleanup for pull request. changed python module name. * updated tests to remove version assert * run `make format` --------- Co-authored-by: Andy Shapiro <[email protected]>
* cmake build 1st draft * clean up for linux build process * Added Windows build commands * updates for python builds and versions * python version bump; start actions work * updates from CI * cleanup for pull request. changed python module name. * updated tests to remove version assert * run `make format` * add build/dist commands on windows * switch to ruff * remove setuptools.cfg * remove old zip_safe --------- Co-authored-by: Cody Simmons <[email protected]>
* setup workspace * sudo * again * again * fix parens * gsl? * change dir * config * ? * another * ?? * d * remove override * let cmake do its thing * nlopt * add eigen * cpp * add manual trigger
* basic struct to pybind11 * First draft of python compatible structs * Finished single dicho analysis
* basic struct to pybind11 * First draft of python compatible structs * Finished single dicho analysis * Completed DichoMA * cleaned up print statements
* model src and test cpp * added python hooks for continuous models
* updated dicho structs * updated dichoMA structs * updated cont structs * Updated python struct wrappers. Fixed memory leak in continuous models * added BMD print statements and reformatted py scripts * added bypass of format print statement rule
* updated dicho structs * updated dichoMA structs * updated cont structs * Updated python struct wrappers. Fixed memory leak in continuous models * 1st stage of mscombo stub * code cleanup * completed multitumor stub * added nested model stubs * updated format for python script * more lint fixes
* updated dicho structs * updated dichoMA structs * updated cont structs * Updated python struct wrappers. Fixed memory leak in continuous models * 1st stage of mscombo stub * code cleanup * completed multitumor stub * added nested model stubs * updated format for python script * more lint fixes * forgot to add python scripts
* Fix for confidence level bug * code cleanup
* fixed continuous individual data runs * Fixed bug in isIncreasing parameter * added default missing values for BMD, BMDL, and BMDU
* finished BMD calcs * 1st stage of mscombo development * intermediate commit for mscombo calculates BMD, but not BMDL or BMDU * added handling of removed datasets * debug attempt * added combo loglike calc * updated bmdl & bmdu methods * Added slopeFactor * bug fix for windows compilation * removed unused prG and prB in struct. * bug fix for previous commit
* finished BMD calcs * 1st stage of mscombo development * intermediate commit for mscombo calculates BMD, but not BMDL or BMDU * added handling of removed datasets * debug attempt * added combo loglike calc * updated bmdl & bmdu methods * Added slopeFactor * bug fix for windows compilation * removed unused prG and prB in struct. * bug fix for previous commit * fixed bmdl/bmdu multitumor convergence. Fixed cmake build files. * Added multitumor selection routines * Added setSlopeFactor methods * completed beta version of multitumor model code * Addressed comments in PR
* here * setup paths * check eigen env * gsl? * use built-in? * again! * install nlopt? * try cmake command * install gsl * set some envs * add eigen * split up deps * updates * update path * get both * more updates * try conda gsl? * try? * enviro variables * more enviro * progress * conda? * continue * do again * test * pathfinding * use conda? * more updates * conda env list * ls some things * add path variable? * add msbuild tools * fix version? * try cloning gsl instead of anaconda * change dir to search for each library * remove versions * go back to debug gsl * fix path * fix gsl build * try to cache eigen/nlopt/gsl * adjust syntax * try fixing syntax again * try different syntax again * revert to earlier method/fix typo * get rid of .. in dependency dir * set dirs even when cache is hit * continue testing * save pybmds linux wheel * add back enviro settings --------- Co-authored-by: munnsmunns <[email protected]>
* add notes describing type annotation creation * update python package libraries * add stubfile generation to build commands and wheel
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Closing; not updated since July 2022 |
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