Use hierarchical logging; fixes #417 #452
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Codecov Report
@@ Coverage Diff @@
## develop #452 +/- ##
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+ Coverage 87.37% 87.43% +0.05%
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Files 103 103
Lines 6147 6151 +4
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+ Hits 5371 5378 +7
+ Misses 776 773 -3
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EmadAlamoudi
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May 14, 2021
* Fix feather (#442) * check feather dep * foggeddaboutdid * adjust alscatispenumnoipa message * make pyarrow optional * add test * fix typo * Add dynamical mode that only waits for relevant particles in redis server (#448) * Add dynamical mode that only waits for relevant particles * Actually check previous iterations, t-> _t * Variable naming * Update requirements * Add logging * Minor change for better logging in same-time conditions * remove accepted from active set * finalize logging * Fix for batching; simplify pyarrow warning * fix stupid missing f-string error (nothing major) * tmp fix sphinx<4.0.0 * test wait for all mode * put synchronized operations under lock to avoid wrong behavior for fast-running simulations * move lock definitions to cmd.py * add n_worker safeguard stopping criterion for server reset * minor final edits * Standardize logging output; fixes #450 (#451) * Use hierarchical logging; fixes #417 (#452) * Standardize logging output; fixes #450 * Use hierarchical logging; fixes #417 * adjust notebook logging * update releasenotes * Add color customization to plot_credible_intervals (#414) * Add color customization to plot_credible_intervals * Add different variables for different colors * Add separate color variables * Improved readability * tox flake fixes * add functions to reweight with opt ESS * Add functions for ESS maximizing reweighting * Update pyabc/sampler/redis_eps/sampler.py Co-authored-by: Yannik Schälte <[email protected]> * Update pyabc/visualization/credible.py Co-authored-by: Yannik Schälte <[email protected]> * Update pyabc/visualization/credible.py Co-authored-by: Yannik Schälte <[email protected]> * Update pyabc/visualization/credible.py Co-authored-by: Yannik Schälte <[email protected]> * Fix rescaling & add analytical solution * Updated structure and added test * Add graph to test * Fix analytical solution * tidy up * tidy up * tidy up * tidy up Co-authored-by: Yannik Schälte <[email protected]> Co-authored-by: yannikschaelte <[email protected]> * Logo to greyscales; fixes #440 (#453) * Add style set to global figure params; fixes #445 (#454) * add style; fixes #445 * fix typo * update version, releasenotes * Shorten datetime log (#456) Co-authored-by: Yannik Schälte <[email protected]> Co-authored-by: yannikschaelte <[email protected]> Co-authored-by: Felipe <[email protected]>
EmadAlamoudi
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May 14, 2021
* Check components in look-ahead mode (#397) * Check components in look-ahead mode * fixup * update releasenotes * Various improvements (#401) * improve noise notebook * rename quickstart -> model_selection * improve run_notebooks * split nb tests * fixup * fixup * time execution * do not run petab nb -- bad idea * fixup * add walltime plots; minor improvements in others * safe-close smc.run; store calibration end * add visualization test * rename redis_server_starter * give ListEpsilon a length attribute * fix docs * fix tests * fix titles * fixup noise nb * add test function docs * Global figure settings; Fix insufficient logging of look-ahead samples (#405) * minor viz updates * improve la eval logging * add global visualization settings * fixup * update and improve nbs * add tests * cosmetics * add figure settings test * update docs for master->main (#406) * update releasenotes -> 0.10.13 * Speed up parameter handling (#387) * tmp * cache indices in normal transition * add performance study * fix flake8 * cont * cont * cont * various fixes * tmp fix pandas * fixup * update to amici 0.11.12 * Restructure tests and docs (#408) * init * fix * fix * fix * restructure * fixup * test * fix * fix * fix swig for python 3.9 * add pre-commit hooks * add hook * fix end of files * mini edit * mini update * add issue templates; simplify contribution docs * remove nb again * nbs to tox * prolong time * fix * fix examples * test * test tmp fix * annotate flake8 * test * stuff * fix * fix redis for later started workers (#410) * Update to python 3.9 (#411) * -> py39 * add outputs * disable redis * test * add dummy * test * test * test * test * Test * unfix all * Add more replicates to performance test due to unstable failures (#412) * Improve PEtab support (#413) * fix wrong log distributions for petab import; add tests * extend test * add ks test * fix petab priors * Add yaml2sbml example; map parameter bounds and names (#416) * Add yaml2sbml example; map parameter bounds and names * fixup2 * remove yaml2sbml until stable * fix LA sampler weighting (#418) * fix la sampler weighting * cosmetics * fixup * Save proposal id; Add migration routines (#419) * fix la sampler weighting * cosmetics * fixup * Save proposal id; Add migration routines * add migration test; add docs * fixup * add env.py * fixup * rm env * fixup n * prettify table name * fix test * fix own review comments * fix failing test * Change default la weight to ess (#421) * change default la weight to ess * fix proposal_id for evaluated particles * fix typo * refactor nr_samples_per_parameter * fixup * fix typos * fix typos * fix weights * Prepare release (#423) * update releasenotes * Update releasenotes.rst * move doc/releasenotes -> CHANGELOG * Update CHANGELOG.rst * test history.particles.proposa_id; pass t=-1 to sampler for calibration (#424) * update releasenotes * Update releasenotes.rst * move doc/releasenotes -> CHANGELOG * test history.particles.proposa_id; pass t=-1 to sampler for calibration * fix typo * fixup * Limit look-ahead sample number in delayed mode (#428) * limit look-ahead sample number in delayed mode * update releasenotes -> 0.10.15 * improve docs * Update GHA CI to recent changes (#435) * limit look-ahead sample number in delayed mode * update releasenotes -> 0.10.15 * test on ubuntu 20.04 * update to r focal, swig 4 * Various: Test webserver, rerun stochastic tests, tidy up package dependencies (#436) * limit look-ahead sample number in delayed mode * update releasenotes -> 0.10.15 * test on ubuntu 20.04 * CI: give petab more time * stuff * stuff * next * add visserver tests; tidy up deps; add flaky * remove simulation files by default after collecting the summary stati… (#434) * remove simulation files by default after collecting the summary statistics * comply with the reviewer comments Co-authored-by: Yannik Schälte <[email protected]> * Fix typo in petab application nb; fixes #433 (#437) * Add description of JupyterHub (#439) * add description of JupyterHub * unify links in brackets * fix typo * Check feather dependency (#441) * check feather dep * foggeddaboutdid * adjust alscatispenumnoipa message * enable having rejected particles at population t=-1 * additional fix * enable the calibration population consider non successful simulation * fix an issue with the related to population t=-1 * Develop (#457) * Fix feather (#442) * check feather dep * foggeddaboutdid * adjust alscatispenumnoipa message * make pyarrow optional * add test * fix typo * Add dynamical mode that only waits for relevant particles in redis server (#448) * Add dynamical mode that only waits for relevant particles * Actually check previous iterations, t-> _t * Variable naming * Update requirements * Add logging * Minor change for better logging in same-time conditions * remove accepted from active set * finalize logging * Fix for batching; simplify pyarrow warning * fix stupid missing f-string error (nothing major) * tmp fix sphinx<4.0.0 * test wait for all mode * put synchronized operations under lock to avoid wrong behavior for fast-running simulations * move lock definitions to cmd.py * add n_worker safeguard stopping criterion for server reset * minor final edits * Standardize logging output; fixes #450 (#451) * Use hierarchical logging; fixes #417 (#452) * Standardize logging output; fixes #450 * Use hierarchical logging; fixes #417 * adjust notebook logging * update releasenotes * Add color customization to plot_credible_intervals (#414) * Add color customization to plot_credible_intervals * Add different variables for different colors * Add separate color variables * Improved readability * tox flake fixes * add functions to reweight with opt ESS * Add functions for ESS maximizing reweighting * Update pyabc/sampler/redis_eps/sampler.py Co-authored-by: Yannik Schälte <[email protected]> * Update pyabc/visualization/credible.py Co-authored-by: Yannik Schälte <[email protected]> * Update pyabc/visualization/credible.py Co-authored-by: Yannik Schälte <[email protected]> * Update pyabc/visualization/credible.py Co-authored-by: Yannik Schälte <[email protected]> * Fix rescaling & add analytical solution * Updated structure and added test * Add graph to test * Fix analytical solution * tidy up * tidy up * tidy up * tidy up Co-authored-by: Yannik Schälte <[email protected]> Co-authored-by: yannikschaelte <[email protected]> * Logo to greyscales; fixes #440 (#453) * Add style set to global figure params; fixes #445 (#454) * add style; fixes #445 * fix typo * update version, releasenotes * Shorten datetime log (#456) Co-authored-by: Yannik Schälte <[email protected]> Co-authored-by: yannikschaelte <[email protected]> Co-authored-by: Felipe <[email protected]> Co-authored-by: Yannik Schälte <[email protected]> Co-authored-by: yannikschaelte <[email protected]> Co-authored-by: Felipe <[email protected]>
EmadAlamoudi
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Jun 30, 2022
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