Run tests in CI #5
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shapiromatron
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Feb 12, 2024
* attempt to run tests in cicd * add PAT * update coverage reporting * add coverage report to gitignore
shapiromatron
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Feb 13, 2024
* Multitumor and Nested Dichotomous (#264) * troubleshooting * format * trusted host all the things * update documentation * future flag change, rm background, testfix * lint * rm more background, testfix * unused import * testfix rm used for testing * docs * review fixes * formatting * formatting * to remove * remove testing * rm fake failing data * mt breadcrumbs * enable nested dichotomous * run all permutations of lsc/ilc * updates * build basic excel/word reports * ui stubs * litter data & bootstrap * enable nested dichotomous on frontend * sr, ll, chi^2 * model params, misc values matched * combined pvalue, -9999 -> ??? * excel exports * update UI for multitumor degree settings * MT excel exports * sketch placeholders * col headings, isSummary modal jank * more plug n play, formatting * rm t specific, reuse individual * tweak incompatibility, chasing loose ends * summary & parameter settings * add !isSummary * slightly less clonky? * misc cleanup * latest updates * updates from review * checkout `next`; tests will still fail --------- Co-authored-by: Andy Shapiro <[email protected]> * BMDS Desktop settings flag (#261) * sketch is_desktop * notes, add to config test * add further restrictions, override item limit, ui fix * pin pydantic to version 1.10.* series * updates * revise * wrap up desktop * final review --------- Co-authored-by: hausman-gdit <[email protected]> * UI updates for nested dichotomous and multitumor (#265) * set max height for dataset tables * fix layout issues with ND * add ND hover * make dataset y-size resizable * ND model options * ND read only options * add modal outputs * deployment updates * nested logistic UI updaets * complete nested dichotomous modal * fix resizing of dataset table * a few summary table/option updates * dont show multitumor model selection since there's only one * add ms combo summary tables * add CSF to summary table * multitumor updates * individual plot * show all models in result table; highlight selected * add multitumor plot * 4 dose groups * add bottom margin * simplify legend * expand use of TwoColumnTable * 293 mt min max datasets (#266) * increase MT datasets to 10 * decrease MT option set * move logic to store * update contraints on server to relax for desktop --------- Co-authored-by: Andy Shapiro <[email protected]> * Complete nested dichotomous summary table (#267) * wip * improve nested dichotomous table! * switch to ruff format (#271) * update python package versions (#268) * karen dev ev fix, package updates * sync frontend packages too * fix integration tests --------- Co-authored-by: Andy Shapiro <[email protected]> * integration tests - nested dichotomous + multitumor (#269) * basic ND MT test, tweak button language * update test data, R-O sketch * read-only update * misc changes * a few updates * add back change --------- Co-authored-by: Andy Shapiro <[email protected]> * 297 dynamic word export (#270) * change default download options * forgot this * big T little t, set defaults but still wonky model_type reset * oops * a little better * move logic to one location * delete * change default type to continuous --------- Co-authored-by: Andy Shapiro <[email protected]> * update to pydantic v2 (#273) * ran bump, tweaking * err message change, mod deprecated * future test tweak, forgot something, alias not working? * deprecated * more updates * fix tests * add key so that page updates * revert changes --------- Co-authored-by: hausman-gdit <[email protected]> * multitumor display edits (#272) * add residuals to summary table * rename model name * rename model average row * add bmd diamonds to multitumor result * lint * draw csf to bmdl, not bmd * (unrelated) update django version * add slope factor for individual models; see bmds PR 123 * add years context (#274) * remove zenodo.org badge (#278) * 283 polyk data link (#275) * try gitattribute fix before reset * add button for polyk * better * </> --> null * use flex layout for icons; update icon --------- Co-authored-by: Andy Shapiro <[email protected]> * polyk - copy dataset to clipboard for bmds modeling (#276) * add copy to clipboard * basic copied alert * clean up * missed one * missed another one * use ClipobardButton; add on optional click handler * removed store info --------- Co-authored-by: Andy Shapiro <[email protected]> * Add Word and Excel reports to Poly K adjustments (#277) * add download buttons and apis for polyk reports * wip * resketch * update integration with new polyk adjustment type * add tests for all api views * sync w/ latest bmds branch * pass dose_units --------- Co-authored-by: hausman-gdit <[email protected]> * add Desktop mode (#279) * hello desktop * start app * add logging * wip * updates * finish demo * cleanup * start server * start next steps * updates * add bmdsdesktop cli option * hacks for desktop demo * lint * enable wal * update .gitignore * wip - continue * double getter? * demo prep * add a few updates to the desktop * desktop updates * add collections * refactor homepage * updates to desktop * parsimony * add collections * include markdown in bundle * add package versions * fix integration tests * 2, 6 * Revert "2, 6" This reverts commit c8ecff5. * Run tests in CI (#5) * attempt to run tests in cicd * add PAT * update coverage reporting * add coverage report to gitignore * 324 random bootstrap seed (#1) * set seed on dataset select & add options * attempt to run tests in cicd * add PAT * update coverage reporting * add coverage report to gitignore * refactor - only set bootstrap_seed for nested dichotomous --------- Co-authored-by: Andy Shapiro <[email protected]> * 328 improve error message (#4) * set seed on dataset select & add options * basic functionality * move to utils, test, add node * attempt to run tests in cicd * add PAT * update coverage reporting * add coverage report to gitignore * refactor - only set bootstrap_seed for nested dichotomous * refactorings * tweak * standardize server error parsing * remove --------- Co-authored-by: Andy Shapiro <[email protected]> * 321 improve nomenclature for statistical outputs (#2) * 8 * 25a, 26, 30 comment * 27, 29, 33, 34, 35 * 2, 6 * 31 * testfix * rm comment, 31 * 3 note, 2, 5a, 12, 24, rm comment * js eol lf * revert MT * rename percentile to cummulative probability * resize tables as needed * remove change * fix test w/ degree symbol * rename log likelihood globally * fix bug in layout * rename scaled residual * rename DOF to d.f. * change Summary to Modeling Summary * rename "Abs(Residual of interest)" -> "|Residual near BMD|" * rename "Frequentist Model Results" to "Maximum Likelihood Approach Model Results" * title case * add vertical spacing * Change "Confidence Level" to "Confidence Level (one-sided)" globally * add on bound footnote to UI * handle goodness of fit table * use < and > instead of less than and greater than * only show tail probability if hybrid continuous bmr * make format --------- Co-authored-by: Andy Shapiro <[email protected]> * EPA Template CSS updates * fix branch info * pull in content for usepa/hawc * fix animation * add sticky top --------- Co-authored-by: Andy Shapiro <[email protected]>
shapiromatron
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Apr 17, 2024
* Multitumor and Nested Dichotomous (#264) * troubleshooting * format * trusted host all the things * update documentation * future flag change, rm background, testfix * lint * rm more background, testfix * unused import * testfix rm used for testing * docs * review fixes * formatting * formatting * to remove * remove testing * rm fake failing data * mt breadcrumbs * enable nested dichotomous * run all permutations of lsc/ilc * updates * build basic excel/word reports * ui stubs * litter data & bootstrap * enable nested dichotomous on frontend * sr, ll, chi^2 * model params, misc values matched * combined pvalue, -9999 -> ??? * excel exports * update UI for multitumor degree settings * MT excel exports * sketch placeholders * col headings, isSummary modal jank * more plug n play, formatting * rm t specific, reuse individual * tweak incompatibility, chasing loose ends * summary & parameter settings * add !isSummary * slightly less clonky? * misc cleanup * latest updates * updates from review * checkout `next`; tests will still fail --------- Co-authored-by: Andy Shapiro <[email protected]> * BMDS Desktop settings flag (#261) * sketch is_desktop * notes, add to config test * add further restrictions, override item limit, ui fix * pin pydantic to version 1.10.* series * updates * revise * wrap up desktop * final review --------- Co-authored-by: hausman-gdit <[email protected]> * UI updates for nested dichotomous and multitumor (#265) * set max height for dataset tables * fix layout issues with ND * add ND hover * make dataset y-size resizable * ND model options * ND read only options * add modal outputs * deployment updates * nested logistic UI updaets * complete nested dichotomous modal * fix resizing of dataset table * a few summary table/option updates * dont show multitumor model selection since there's only one * add ms combo summary tables * add CSF to summary table * multitumor updates * individual plot * show all models in result table; highlight selected * add multitumor plot * 4 dose groups * add bottom margin * simplify legend * expand use of TwoColumnTable * 293 mt min max datasets (#266) * increase MT datasets to 10 * decrease MT option set * move logic to store * update contraints on server to relax for desktop --------- Co-authored-by: Andy Shapiro <[email protected]> * Complete nested dichotomous summary table (#267) * wip * improve nested dichotomous table! * switch to ruff format (#271) * update python package versions (#268) * karen dev ev fix, package updates * sync frontend packages too * fix integration tests --------- Co-authored-by: Andy Shapiro <[email protected]> * integration tests - nested dichotomous + multitumor (#269) * basic ND MT test, tweak button language * update test data, R-O sketch * read-only update * misc changes * a few updates * add back change --------- Co-authored-by: Andy Shapiro <[email protected]> * 297 dynamic word export (#270) * change default download options * forgot this * big T little t, set defaults but still wonky model_type reset * oops * a little better * move logic to one location * delete * change default type to continuous --------- Co-authored-by: Andy Shapiro <[email protected]> * update to pydantic v2 (#273) * ran bump, tweaking * err message change, mod deprecated * future test tweak, forgot something, alias not working? * deprecated * more updates * fix tests * add key so that page updates * revert changes --------- Co-authored-by: hausman-gdit <[email protected]> * multitumor display edits (#272) * add residuals to summary table * rename model name * rename model average row * add bmd diamonds to multitumor result * lint * draw csf to bmdl, not bmd * (unrelated) update django version * add slope factor for individual models; see bmds PR 123 * add years context (#274) * remove zenodo.org badge (#278) * 283 polyk data link (#275) * try gitattribute fix before reset * add button for polyk * better * </> --> null * use flex layout for icons; update icon --------- Co-authored-by: Andy Shapiro <[email protected]> * polyk - copy dataset to clipboard for bmds modeling (#276) * add copy to clipboard * basic copied alert * clean up * missed one * missed another one * use ClipobardButton; add on optional click handler * removed store info --------- Co-authored-by: Andy Shapiro <[email protected]> * Add Word and Excel reports to Poly K adjustments (#277) * add download buttons and apis for polyk reports * wip * resketch * update integration with new polyk adjustment type * add tests for all api views * sync w/ latest bmds branch * pass dose_units --------- Co-authored-by: hausman-gdit <[email protected]> * add Desktop mode (#279) * hello desktop * start app * add logging * wip * updates * finish demo * cleanup * start server * start next steps * updates * add bmdsdesktop cli option * hacks for desktop demo * lint * enable wal * update .gitignore * wip - continue * double getter? * demo prep * add a few updates to the desktop * desktop updates * add collections * refactor homepage * updates to desktop * parsimony * add collections * include markdown in bundle * add package versions * fix integration tests * 2, 6 * Revert "2, 6" This reverts commit c8ecff5. * basic config tab, styling, and notes * rename, styling, more sketch * tweaks * reclass, style, notes * meat&potatoes * stub check for updates * Run tests in CI (#5) * attempt to run tests in cicd * add PAT * update coverage reporting * add coverage report to gitignore * 324 random bootstrap seed (#1) * set seed on dataset select & add options * attempt to run tests in cicd * add PAT * update coverage reporting * add coverage report to gitignore * refactor - only set bootstrap_seed for nested dichotomous --------- Co-authored-by: Andy Shapiro <[email protected]> * stub & notes * works better, fiddly db selection * minor cleanup * cleanup/naming/test stub * oops * ah ha! * naming update, req update, tab test * notes, refine validator w/ btn * use settings & notes * change css, format/validation tweaks * rm 'btn' from content switch id * quick code scan * fix merge conflicts? * add newline * version bump * fix tab selection after textual update --------- Co-authored-by: Andy Shapiro <[email protected]>
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Fix github actions so they run in CI.