{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":176723021,"defaultBranch":"master","name":"PBjam","ownerLogin":"grd349","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2019-03-20T11:54:52.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/14784265?v=4","public":true,"private":false,"isOrgOwned":false},"refInfo":{"name":"","listCacheKey":"v0:1726049765.0","currentOid":""},"activityList":{"items":[{"before":null,"after":"8607282706c5edb9d029bff153f0a3420e160742","ref":"refs/heads/dev","pushedAt":"2024-09-11T10:16:05.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"nielsenmb","name":"Martin Nielsen","path":"/nielsenmb","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/18048879?s=80&v=4"},"commit":{"message":"PBjam 2.0 update (#276)\n\n* move more IO stuff from star to IO.py\r\n\r\n* add smry stats func\r\n\r\n* adding result parser\r\n\r\n* move background to separate module\r\n\r\n* initial jaxxed peakbag version needs bkg removal\r\n\r\n* mv harvey func\r\n\r\n* peakbag should take snr\r\n\r\n* switch meanbkg to unpacked sample dict\r\n\r\n* peakbag should now be running???\r\n\r\n* Addin echelle from DHey anb WBall\r\n\r\n* cleanup notebooks\r\n\r\n* integrating echelle from DHey and Wball\r\n\r\n* echelle integration\r\n\r\n* fix for outputpath\r\n\r\n* star class __call__ now working nothing fancy though\r\n\r\n* star example\r\n\r\n* fix for empty prior selection\r\n\r\n* p_L and p_D now correctly log parameters\r\n\r\n* SG examples\r\n\r\n* Notebooks with SG\r\n\r\n* bla\r\n\r\n* added DPi0 for RGs and cleaned prior sample a bit\r\n\r\n* moving prior data\r\n\r\n* echelle should now work\r\n\r\n* rename star module to core, is this really necessary?\r\n\r\n* updated to DPi0 for high numax\r\n\r\n* changed init so plotting can see module attributes\r\n\r\n* rename peakbag module to peakbagging\r\n\r\n* fix plotting for peakbagging\r\n\r\n* tweak\r\n\r\n* a few SG examples\r\n\r\n* more examples\r\n\r\n* example\r\n\r\n* gridy\r\n\r\n* bla\r\n\r\n* bla\r\n\r\n* Best results on SG so far\r\n\r\n* bad\r\n\r\n* OK\r\n\r\n* OK\r\n\r\n* smryStats now array not tuple cause it was annoying\r\n\r\n* prior update\r\n\r\n* prior update\r\n\r\n* latest\r\n\r\n* nan notebook\r\n\r\n* prior update function fix for harvey exponents\r\n\r\n* Example of nan values\r\n\r\n* include median example\r\n\r\n* new notebook\r\n\r\n* bla\r\n\r\n* fix for nan frequencies\r\n\r\n* checking DR and cleanup\r\n\r\n* testing\r\n\r\n* add latentcorner with priors\r\n\r\n* nevermind fix didnt work\r\n\r\n* added initial live points to get around nans\r\n\r\n* upped resolution in ppf, got rid of gridding\r\n\r\n* cleanup\r\n\r\n* cleanup\r\n\r\n* plotting thing doesnt work correctly, need fix\r\n\r\n* widening linewidths\r\n\r\n* Increasing resolution on interpolation\r\n\r\n* Tweaking echelles\r\n\r\n* adding u1, u2 and envelope rotation\r\n\r\n* envelope rotation implimented\r\n\r\n* remove symmetrize and standard angle they are not needed\r\n\r\n* Dpi0 in Ms to Dpi1 in s\r\n\r\n* variables tweak\r\n\r\n* bla\r\n\r\n* notebooks\r\n\r\n* bli\r\n\r\n* docstring updates\r\n\r\n* docstrings\r\n\r\n* if for echelle on modeID before and after __call__\r\n\r\n* docstrings\r\n\r\n* add mode visibilities due to inclination\r\n\r\n* add l=2 splitting\r\n\r\n* adding plotting options\r\n\r\n* reorganizing peakbag to match layout for modeID\r\n\r\n* simplified notebook\r\n\r\n* updated notebooks\r\n\r\n* adding g-modes to echelle prior plot\r\n\r\n* updated notebook\r\n\r\n* wonky\r\n\r\n* updated notebook\r\n\r\n* updated notebook\r\n\r\n* slight refactoring for speed??\r\n\r\n* label tweak\r\n\r\n* adding storage option\r\n\r\n* updated notebook\r\n\r\n* fix for output\r\n\r\n* updated notebook\r\n\r\n* adding radial orders to g-modes in echelle\r\n\r\n* updated notebooks\r\n\r\n* peakbag is now working(ish)\r\n\r\n* adding plotting functions for peakbag\r\n\r\n* example with peakbag\r\n\r\n* d02 fix\r\n\r\n* adding randint, might be useful\r\n\r\n* added prior corner to plotting\r\n\r\n* cleanup\r\n\r\n* plotting echelle for peakbag\r\n\r\n* including extended epsilon_g\r\n\r\n* N for spectrum fitting moved up\r\n\r\n* adjust freq prior to allow higher uncertainty from asypeakbag\r\n\r\n* mode frequency selection now allows for l20 only\r\n\r\n* adding model frequency error, should probably rename\r\n\r\n* attempt at adding l=2,0 model only\r\n\r\n* Fix P0 to 0, should this be a free variable?\r\n\r\n* adding model frequency error handling\r\n\r\n* examples using model frequency error\r\n\r\n* adding optional dnu and numax to echelle\r\n\r\n* cleanup\r\n\r\n* adding fudge to the mix\r\n\r\n* fix for unhandled stage argument\r\n\r\n* fix for downloadDir\r\n\r\n* fix for plotting with freq fudge\r\n\r\n* fix for corner\r\n\r\n* added a short sleep\r\n\r\n* added more possible fudge frequencies\r\n\r\n* move use_cached higher\r\n\r\n* fix for fudge frequency trimming\r\n\r\n* moving dynesty sampling to jar\r\n\r\n* fac and logfac fix\r\n\r\n* removed self.V20, not needed?\r\n\r\n* split l20 and l1 model estimation\r\n\r\n* adding parseSamples as separate functions for the different models\r\n\r\n* adding merger function for results dicts\r\n\r\n* removed alpha reduced range for N_g\r\n\r\n* adding SGs to prior\r\n\r\n* replace general eig function, use smaller N_g set\r\n\r\n* fix for Peakbag prior plotting\r\n\r\n* new eig function\r\n\r\n* trying to speedup pairmodel a bit\r\n\r\n* attempt at faster eig function\r\n\r\n* prior fix for DPi0 -> DPi1\r\n\r\n* removing fudge for N_g == 0, should fix d01 prob\r\n\r\n* tidy up\r\n\r\n* clean up\r\n\r\n* modify frequency range settings for l20 and l1 models\r\n\r\n* fix for DPi0 -> DPi1, this time for real\r\n\r\n* adding DR back into l1 model\r\n\r\n* bla\r\n\r\n* tweaks\r\n\r\n* more g-modes and wider fudge\r\n\r\n* split Npca and PCAdims into two\r\n\r\n* split mix and nonmixed models\r\n\r\n* variable name changes to be more general\r\n\r\n* variable name change to be more general\r\n\r\n* include l1 non mixed model\r\n\r\n* outputting logz now\r\n\r\n* work on mix/asy selection, not complete\r\n\r\n* findNearest now provides some helpful feedback\r\n\r\n* parsing samples show now work with asy and mix\r\n\r\n* fixes for asy/mixed split testing\r\n\r\n* adjusting nan fractions\r\n\r\n* adding numpyro peakbag, not working\r\n\r\n* spectrum chunking\r\n\r\n* inserted minimum sample checks\r\n\r\n* set up envelope slice sampling\r\n\r\n* echelles now handle sliced spectra\r\n\r\n* store unweighted and weights\r\n\r\n* reenable unsmoothed plot\r\n\r\n* ordering args\r\n\r\n* switch priors on rotation/inc to uniform\r\n\r\n* added some exceptions\r\n\r\n* mod height prior and switch to nusini\r\n\r\n* getting rid of partials slowly\r\n\r\n* adjusting prior selection\r\n\r\n* fix for badPrior flag\r\n\r\n* fix for plotting\r\n\r\n* more live points for the mixed model\r\n\r\n* adding exception for bad mixed prior\r\n\r\n* moving badMixPrior flag from DR to Mixl1 class\r\n\r\n* fix for nu0_p frequencies passed to l1 model\r\n\r\n* priors on spectrum\r\n\r\n* simplifying rejection of prior\r\n\r\n* fiddling with plots\r\n\r\n* working example\r\n\r\n* modify DR selection\r\n\r\n* k-means slicing\r\n\r\n* cleanup\r\n\r\n* update trapz update for newer jax\r\n\r\n* adding RGB l1 model\r\n\r\n* cleanup and work on RGB model\r\n\r\n* adding general funcs to jar\r\n\r\n* fix for truncsine.logpdf\r\n\r\n* simplify variable selection\r\n\r\n* adding joint rotation inclincation thing to peakbag\r\n\r\n* moving variable definitions to separate file\r\n\r\n* remove numpyro\r\n\r\n* KIC TIC begone\r\n\r\n* renaming class for consistency\r\n\r\n* removing some unnecessary jits\r\n\r\n* refactoring for consistency between models\r\n\r\n* the l1models are now the users choice\r\n\r\n* cleanup\r\n\r\n* adding median model\r\n\r\n* rename for consistency\r\n\r\n* cleanup\r\n\r\n* update to plotting posteriors and priors\r\n\r\n* switching to p_L and p_D instead of u1 and u2\r\n\r\n* change p_L0 and p_D0 to p_L and p_D\r\n\r\n* added reference corner plot method to plotting\r\n\r\n* cleanup\r\n\r\n* cleanup\r\n\r\n* moved session to core\r\n\r\n* moved session to core and cleanup in star\r\n\r\n* tidying up\r\n\r\n* standardaizing bits\r\n\r\n* cleanup in modeID\r\n\r\n* cleanup\r\n\r\n* variable name fix\r\n\r\n* fix for rotAsym\r\n\r\n* cleanup\r\n\r\n* fix for manually defining priors and a few other tweaks\r\n\r\n* fix for merging results\r\n\r\n* fix for recording results\r\n\r\n* plotting tweaks should be faster now\r\n\r\n* Cleaning up the notebook\r\n\r\n* small fixes\r\n\r\n* adjusting prior numax dnu d01 slightly\r\n\r\n* adding slurm stuff\r\n\r\n* scipy update fix\r\n\r\n* adding emcee\r\n\r\n* setting some default values\r\n\r\n* fix for simpsons\r\n\r\n* fix for plotting\r\n\r\n* docstrings\r\n\r\n* doc strings\r\n\r\n* docstrings\r\n\r\n* docstrings and cleanup\r\n\r\n* typos\r\n\r\n* Modify to allow for different sampler types\r\n\r\n* naming cleanup\r\n\r\n* naming cleanup\r\n\r\n* adding emcee as an optional sampler\r\n\r\n* naming cleanup\r\n\r\n* unnecessary\r\n\r\n* doc strings complete\r\n\r\n* doc strings complete\r\n\r\n* cleanup\r\n\r\n* tweaks for emcee sampling\r\n\r\n* fix for plotting when l1 has fewer samples\r\n\r\n* restoring prior, still needs some tweaks\r\n\r\n* tutorial updates\r\n\r\n---------\r\n\r\nCo-authored-by: Guy <grd34@gmail.com>","shortMessageHtmlLink":"PBjam 2.0 update (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2505579836\" data-permission-text=\"Title is private\" data-url=\"https://github.com/grd349/PBjam/issues/276\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/grd349/PBjam/pull/276/hovercard\" href=\"https://github.com/grd349/PBjam/pull/276\">#276</a>)"}},{"before":"f69abf1694e255fb47f18fd690bf39e839ceb837","after":null,"ref":"refs/heads/dev","pushedAt":"2024-09-11T10:15:37.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"nielsenmb","name":"Martin Nielsen","path":"/nielsenmb","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/18048879?s=80&v=4"}},{"before":"c1c49ea186eb61bfee88910476029cb45b60de38","after":"ebcdb380bd196362497b441f19da3e589012332a","ref":"refs/heads/teaching","pushedAt":"2024-09-11T09:53:35.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"nielsenmb","name":"Martin Nielsen","path":"/nielsenmb","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/18048879?s=80&v=4"},"commit":{"message":"Update README.rst","shortMessageHtmlLink":"Update 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peakbag should take snr\r\n\r\n* switch meanbkg to unpacked sample dict\r\n\r\n* peakbag should now be running???\r\n\r\n* Addin echelle from DHey anb WBall\r\n\r\n* cleanup notebooks\r\n\r\n* integrating echelle from DHey and Wball\r\n\r\n* echelle integration\r\n\r\n* fix for outputpath\r\n\r\n* star class __call__ now working nothing fancy though\r\n\r\n* star example\r\n\r\n* fix for empty prior selection\r\n\r\n* p_L and p_D now correctly log parameters\r\n\r\n* SG examples\r\n\r\n* Notebooks with SG\r\n\r\n* bla\r\n\r\n* added DPi0 for RGs and cleaned prior sample a bit\r\n\r\n* moving prior data\r\n\r\n* echelle should now work\r\n\r\n* rename star module to core, is this really necessary?\r\n\r\n* updated to DPi0 for high numax\r\n\r\n* changed init so plotting can see module attributes\r\n\r\n* rename peakbag module to peakbagging\r\n\r\n* fix plotting for peakbagging\r\n\r\n* tweak\r\n\r\n* a few SG examples\r\n\r\n* more examples\r\n\r\n* example\r\n\r\n* gridy\r\n\r\n* bla\r\n\r\n* bla\r\n\r\n* Best results on SG so far\r\n\r\n* bad\r\n\r\n* OK\r\n\r\n* OK\r\n\r\n* smryStats now array not tuple cause it was annoying\r\n\r\n* prior update\r\n\r\n* prior update\r\n\r\n* latest\r\n\r\n* nan notebook\r\n\r\n* prior update function fix for harvey exponents\r\n\r\n* Example of nan values\r\n\r\n* include median example\r\n\r\n* new notebook\r\n\r\n* bla\r\n\r\n* fix for nan frequencies\r\n\r\n* checking DR and cleanup\r\n\r\n* testing\r\n\r\n* add latentcorner with priors\r\n\r\n* nevermind fix didnt work\r\n\r\n* added initial live points to get around nans\r\n\r\n* upped resolution in ppf, got rid of gridding\r\n\r\n* cleanup\r\n\r\n* cleanup\r\n\r\n* plotting thing doesnt work correctly, need fix\r\n\r\n* widening linewidths\r\n\r\n* Increasing resolution on interpolation\r\n\r\n* Tweaking echelles\r\n\r\n* adding u1, u2 and envelope rotation\r\n\r\n* envelope rotation implimented\r\n\r\n* remove symmetrize and standard angle they are not needed\r\n\r\n* Dpi0 in Ms to Dpi1 in s\r\n\r\n* variables tweak\r\n\r\n* bla\r\n\r\n* notebooks\r\n\r\n* bli\r\n\r\n* docstring updates\r\n\r\n* docstrings\r\n\r\n* if for echelle on modeID before and after __call__\r\n\r\n* docstrings\r\n\r\n* add mode visibilities due to inclination\r\n\r\n* add l=2 splitting\r\n\r\n* adding plotting options\r\n\r\n* reorganizing peakbag to match layout for modeID\r\n\r\n* simplified notebook\r\n\r\n* updated notebooks\r\n\r\n* adding g-modes to echelle prior plot\r\n\r\n* updated notebook\r\n\r\n* wonky\r\n\r\n* updated notebook\r\n\r\n* updated notebook\r\n\r\n* slight refactoring for speed??\r\n\r\n* label tweak\r\n\r\n* adding storage option\r\n\r\n* updated notebook\r\n\r\n* fix for output\r\n\r\n* updated notebook\r\n\r\n* adding radial orders to g-modes in echelle\r\n\r\n* updated notebooks\r\n\r\n* peakbag is now working(ish)\r\n\r\n* adding plotting functions for peakbag\r\n\r\n* example with peakbag\r\n\r\n* d02 fix\r\n\r\n* adding randint, might be useful\r\n\r\n* added prior corner to plotting\r\n\r\n* cleanup\r\n\r\n* plotting echelle for peakbag\r\n\r\n* including extended epsilon_g\r\n\r\n* N for spectrum fitting moved up\r\n\r\n* adjust freq prior to allow higher uncertainty from asypeakbag\r\n\r\n* mode frequency selection now allows for l20 only\r\n\r\n* adding model frequency error, should probably rename\r\n\r\n* attempt at adding l=2,0 model only\r\n\r\n* Fix P0 to 0, should this be a free variable?\r\n\r\n* adding model frequency error handling\r\n\r\n* examples using model frequency error\r\n\r\n* adding optional dnu and numax to echelle\r\n\r\n* cleanup\r\n\r\n* adding fudge to the mix\r\n\r\n* fix for unhandled stage argument\r\n\r\n* fix for downloadDir\r\n\r\n* fix for plotting with freq fudge\r\n\r\n* fix for corner\r\n\r\n* added a short sleep\r\n\r\n* added more possible fudge frequencies\r\n\r\n* move use_cached higher\r\n\r\n* fix for fudge frequency trimming\r\n\r\n* moving dynesty sampling to jar\r\n\r\n* fac and logfac fix\r\n\r\n* removed self.V20, not needed?\r\n\r\n* split l20 and l1 model estimation\r\n\r\n* adding parseSamples as separate functions for the different models\r\n\r\n* adding merger function for results dicts\r\n\r\n* removed alpha reduced range for N_g\r\n\r\n* adding SGs to prior\r\n\r\n* replace general eig function, use smaller N_g set\r\n\r\n* fix for Peakbag prior plotting\r\n\r\n* new eig function\r\n\r\n* trying to speedup pairmodel a bit\r\n\r\n* attempt at faster eig function\r\n\r\n* prior fix for DPi0 -> DPi1\r\n\r\n* removing fudge for N_g == 0, should fix d01 prob\r\n\r\n* tidy up\r\n\r\n* clean up\r\n\r\n* modify frequency range settings for l20 and l1 models\r\n\r\n* fix for DPi0 -> DPi1, this time for real\r\n\r\n* adding DR back into l1 model\r\n\r\n* bla\r\n\r\n* tweaks\r\n\r\n* more g-modes and wider fudge\r\n\r\n* split Npca and PCAdims into two\r\n\r\n* split mix and nonmixed models\r\n\r\n* variable name changes to be more general\r\n\r\n* variable name change to be more general\r\n\r\n* include l1 non mixed model\r\n\r\n* outputting logz now\r\n\r\n* work on mix/asy selection, not complete\r\n\r\n* findNearest now provides some helpful feedback\r\n\r\n* parsing samples show now work with asy and mix\r\n\r\n* fixes for asy/mixed split testing\r\n\r\n* adjusting nan fractions\r\n\r\n* adding numpyro peakbag, not working\r\n\r\n* spectrum chunking\r\n\r\n* inserted minimum sample checks\r\n\r\n* set up envelope slice sampling\r\n\r\n* echelles now handle sliced spectra\r\n\r\n* store unweighted and weights\r\n\r\n* reenable unsmoothed plot\r\n\r\n* ordering args\r\n\r\n* switch priors on rotation/inc to uniform\r\n\r\n* added some exceptions\r\n\r\n* mod height prior and switch to nusini\r\n\r\n* getting rid of partials slowly\r\n\r\n* adjusting prior selection\r\n\r\n* fix for badPrior flag\r\n\r\n* fix for plotting\r\n\r\n* more live points for the mixed model\r\n\r\n* adding exception for bad mixed prior\r\n\r\n* moving badMixPrior flag from DR to Mixl1 class\r\n\r\n* fix for nu0_p frequencies passed to l1 model\r\n\r\n* priors on spectrum\r\n\r\n* simplifying rejection of prior\r\n\r\n* fiddling with plots\r\n\r\n* working example\r\n\r\n* modify DR selection\r\n\r\n* k-means slicing\r\n\r\n* cleanup\r\n\r\n* update trapz update for newer jax\r\n\r\n* adding RGB l1 model\r\n\r\n* cleanup and work on RGB model\r\n\r\n* adding general funcs to jar\r\n\r\n* fix for truncsine.logpdf\r\n\r\n* simplify variable selection\r\n\r\n* adding joint rotation inclincation thing to peakbag\r\n\r\n* moving variable definitions to separate file\r\n\r\n* remove numpyro\r\n\r\n* KIC TIC begone\r\n\r\n* renaming class for consistency\r\n\r\n* removing some unnecessary jits\r\n\r\n* refactoring for consistency between models\r\n\r\n* the l1models are now the users choice\r\n\r\n* cleanup\r\n\r\n* adding median model\r\n\r\n* rename for consistency\r\n\r\n* cleanup\r\n\r\n* update to plotting 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