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21 April 2024, 10:16:19 UTC
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Revision Author Date Message Commit Date
40ccb10 Chris Fonnesbeck 09 January 2017, 14:08:10 UTC Merge pull request #1647 from pymc-devs/v3.0_release REL Update version to 3.0. 09 January 2017, 14:08:10 UTC
5b6bb33 Thomas Wiecki 09 January 2017, 11:41:53 UTC BLD Remove Python 3.6 compatibility. 09 January 2017, 11:41:53 UTC
36457cb Thomas Wiecki 09 January 2017, 11:00:22 UTC DOC Update date. Split up authos and outside contributors. 09 January 2017, 11:00:22 UTC
69b9461 Chris Fonnesbeck 09 January 2017, 03:49:16 UTC Merge pull request #1637 from pymc-devs/sqlite_record_indent Revert indentation in sqlite.record and clarify syntax 09 January 2017, 03:49:16 UTC
4953515 Osvaldo Martin 06 January 2017, 20:53:21 UTC auto-scale the max value of y when njobs > 1 (#1648) 08 January 2017, 20:47:50 UTC
7c8cd15 Christopher Fonnesbeck 02 January 2017, 04:32:08 UTC Reverted c0351c19 and clarified reference to varnames element 08 January 2017, 20:47:50 UTC
6d02627 Osvaldo Martin 06 January 2017, 20:53:21 UTC auto-scale the max value of y when njobs > 1 (#1648) 06 January 2017, 20:53:21 UTC
5740e84 Colin 06 January 2017, 20:16:31 UTC Add Colin's email 06 January 2017, 20:16:31 UTC
832ad65 Thomas Wiecki 06 January 2017, 12:22:31 UTC DOC Update release notes. 06 January 2017, 12:22:31 UTC
4f6bdf6 Thomas Wiecki 06 January 2017, 12:16:55 UTC REL Update version to 3.0. 06 January 2017, 12:16:55 UTC
2394fac Osvaldo Martin 06 January 2017, 10:38:39 UTC add varnames argument for consintency (#1641) * add varnames argument for consintency * do not pass flat_names argument (or varnames) 06 January 2017, 10:38:39 UTC
19fcf4b Thomas Wiecki 05 January 2017, 20:29:40 UTC Merge pull request #1645 from aloctavodia/init_sampling use tranformed variables as starting points 05 January 2017, 20:29:40 UTC
88125bc aloctavodia 05 January 2017, 15:07:48 UTC use tranformed variables as starting points 05 January 2017, 15:07:48 UTC
704a897 Thomas Wiecki 03 January 2017, 12:04:46 UTC Merge pull request #1639 from pymc-devs/adding_book DOCS: Adding Osvaldo Martin book 03 January 2017, 12:04:46 UTC
270f42a springcoil 03 January 2017, 09:48:29 UTC DOCS: Adding Osvaldo Martin book 03 January 2017, 09:48:29 UTC
0bc5f8f Thomas Wiecki 02 January 2017, 13:10:23 UTC Merge pull request #1623 from huynhnguyen/master fix issue with advi when running on GPU 02 January 2017, 13:10:23 UTC
cad8ec2 Peadar Coyle 02 January 2017, 00:28:08 UTC Merging (#1635) 02 January 2017, 00:28:08 UTC
cc57a0c Chris Fonnesbeck 01 January 2017, 23:17:42 UTC Removed doc from packages list (#1634) 01 January 2017, 23:17:42 UTC
4079f6e Chris Fonnesbeck 01 January 2017, 23:03:29 UTC Fixed indentation in record (#1632) 01 January 2017, 23:03:29 UTC
581b704 Chris Fonnesbeck 01 January 2017, 20:09:27 UTC Merge pull request #1630 from pymc-devs/rc5 REL: Incrementing to release candidate 5 01 January 2017, 20:09:27 UTC
87ae225 springcoil 01 January 2017, 16:31:15 UTC REL: Incrementing to release candidate 5 01 January 2017, 16:31:15 UTC
5376771 huynhnguyen 01 January 2017, 06:18:14 UTC avdi: change cast type to theano standard type 01 January 2017, 06:18:14 UTC
f20aca4 Osvaldo Martin 31 December 2016, 22:35:01 UTC add jitter to fast_kde (#1629) * add jitter to fast_kde, prevents errors when input values are all the same * remove unnecessary print 31 December 2016, 22:35:01 UTC
ca7f68d Peadar Coyle 31 December 2016, 19:23:39 UTC Sampling Output checks and Normality tests to check for bugs (#1618) * Fixing up tests Updating tests Updating tests again Added in one test for each sampler Updating tests Sampling errors Trying this commit Removing parameterized nose tests as they didn't work with the model context Moving asserts and removing arguments which are unnecessary - removing requirements.txt reference to nose_parameterized Changing shape Removing unnecessary test, and checking they run locally * TST Improve test. * TST Add thinning. 31 December 2016, 19:23:39 UTC
f450940 Chris Fonnesbeck 31 December 2016, 14:30:22 UTC Updates to README (#1626) 31 December 2016, 14:30:22 UTC
f222ffd huynhnguyen 29 December 2016, 06:05:11 UTC fix issue with advi when running on GPU 29 December 2016, 06:05:11 UTC
ab437e4 Colin 19 December 2016, 23:34:14 UTC Bounded now works with array bounds (#1604) * Bounded now works with array bounds * Bound is now a function returning a type 19 December 2016, 23:34:14 UTC
d9e57e8 John Salvatier 19 December 2016, 21:28:29 UTC Merge pull request #1596 from pymc-devs/fix_bounds2 Make bound broadcast again. 19 December 2016, 21:28:29 UTC
6c7f127 Thomas Wiecki 19 December 2016, 21:25:22 UTC MAINT Remove double import of bound. 19 December 2016, 21:25:22 UTC
1b01b53 Thomas Wiecki 19 December 2016, 15:54:03 UTC MAINT Instead of separate functions, add broadcast kwarg and make it be used by multivariate distributions. 19 December 2016, 18:51:28 UTC
ed89f10 Thomas Wiecki 13 December 2016, 17:01:53 UTC BUG Wrong search/replace. 19 December 2016, 16:02:27 UTC
59f68c3 Thomas Wiecki 13 December 2016, 16:49:22 UTC Make all univariate distributions use bound_elemwise. Addd tests. 19 December 2016, 16:02:27 UTC
1ad526a Thomas Wiecki 13 December 2016, 08:16:57 UTC MAINT Add back bound_elemwise. Port DiscreteUniform and Uniform to use it. 19 December 2016, 16:02:27 UTC
1a1a36e Colin 17 December 2016, 18:06:39 UTC Merge pull request #1609 from ColCarroll/make_scripts_executable Adds executable mode to `start_container.sh` 17 December 2016, 18:06:39 UTC
466b38b colin 16 December 2016, 21:08:04 UTC Adds executable mode to `start_container.sh` 16 December 2016, 21:08:04 UTC
628cb52 Colin 16 December 2016, 20:51:45 UTC Merge pull request #1608 from tyarkoni/fix-batches Dynamically set number of batches to appropriate value 16 December 2016, 20:51:45 UTC
c378850 tyarkoni 16 December 2016, 19:01:14 UTC dynamically sets batches to min(n_samples, 100); closes #1606 16 December 2016, 19:01:14 UTC
7584b3b Maxim Kochurov 13 December 2016, 19:42:54 UTC Merge pull request #1599 from Spaak/master replacing mutable default value with None 13 December 2016, 19:42:54 UTC
cfa709a Eelke Spaak 13 December 2016, 16:31:53 UTC replacing mutable default value with None 13 December 2016, 16:31:53 UTC
5be027f Colin 11 December 2016, 04:25:55 UTC Merge pull request #1592 from ColCarroll/fix_travis_build Actually build on miniconda with python2.7 11 December 2016, 04:25:55 UTC
7b23fb5 colin 11 December 2016, 03:53:36 UTC Fix for py2/py3 11 December 2016, 03:53:36 UTC
0150b75 colin 11 December 2016, 01:49:55 UTC Fix python2 build errors 11 December 2016, 01:49:55 UTC
e7dc271 colin 11 December 2016, 00:40:17 UTC Actually build on miniconda with python2.7 11 December 2016, 00:44:21 UTC
60c7209 Thomas Wiecki 10 December 2016, 12:26:33 UTC DOC Add list of software using and papers citing PyMC3. (#1588) * DOC Add list of software using and papers citing PyMC3. * DOC Add BEAT package. 10 December 2016, 12:26:33 UTC
ab51b6a Thomas Wiecki 09 December 2016, 07:34:02 UTC Merge pull request #1586 from aloctavodia/master traceplot: auto-scale the max value of y 09 December 2016, 07:34:02 UTC
c8fdf88 aloctavodia 09 December 2016, 02:00:39 UTC traceplot: auto-scale the max value of y 09 December 2016, 02:00:39 UTC
1a83358 Thomas Wiecki 08 December 2016, 17:05:16 UTC TST Remove stray debug print. 08 December 2016, 17:05:16 UTC
9b380da Thomas Wiecki 08 December 2016, 16:59:51 UTC Merge pull request #1582 from pymc-devs/fix_scaling Fix NUTS scaling bounds #1581 08 December 2016, 16:59:51 UTC
74db63b Thomas Wiecki 08 December 2016, 16:16:28 UTC TST Update Hamiltonian and NUTS samples. 08 December 2016, 16:16:28 UTC
84d3b06 Thomas Wiecki 08 December 2016, 11:57:33 UTC BUG 362c8ee introduced a bug by switching the bounds of the scaling matrix. The bounds 1e-3 are also too stringent for some data types, like returns. This thus adjusts bounds to 1e-8 instead of 1e-3. 08 December 2016, 11:57:33 UTC
2d632de Thomas Wiecki 07 December 2016, 08:25:21 UTC DOC Improve axes doc string in response to #1577. 07 December 2016, 08:25:21 UTC
784a773 Thomas Wiecki 06 December 2016, 13:57:20 UTC DOC Add Probabilistic ML to summary. 06 December 2016, 13:57:20 UTC
2edbe6c Colin 03 December 2016, 18:29:35 UTC Add mkl-service to build (#1572) 03 December 2016, 18:29:35 UTC
493d281 Thomas Wiecki 02 December 2016, 06:35:57 UTC DOC Add baseball model. 02 December 2016, 06:35:57 UTC
67c1cd0 Colin 02 December 2016, 06:32:21 UTC Add test to warn for algorithmic changes (#1570) 02 December 2016, 06:32:21 UTC
bdd1dc3 Chris Fonnesbeck 01 December 2016, 22:45:24 UTC Incremented release version to 3.0.4c4 01 December 2016, 22:45:24 UTC
bbb4d57 Chris Fonnesbeck 01 December 2016, 08:06:27 UTC Tweaked the BEST notebook (#1568) 01 December 2016, 08:06:27 UTC
010de60 Chris Fonnesbeck 01 December 2016, 02:06:34 UTC Merge pull request #1546 from usptact/master Adding hierarhical partial pooling example 01 December 2016, 02:06:34 UTC
aab8625 usptact 01 December 2016, 00:09:01 UTC Adding v2 of the hierarchical partial pooling notebook credits: Chris Fonnesback 01 December 2016, 00:09:01 UTC
a54a53e Osvaldo Martin 30 November 2016, 20:18:14 UTC Kde boundaries (#1567) * use a fft-based kde instead of scipy.gaussian_kde * fix typo 30 November 2016, 20:18:14 UTC
68e53eb Yves Delley 30 November 2016, 10:15:45 UTC BUG placed context stack inside thread-local data space (#1555) * placed context stack inside thread-local data space * fixed thread-local context manager, and added a regression test * fixed docstring of #1552 regression test 30 November 2016, 10:15:45 UTC
8a6d87e Thomas Wiecki 29 November 2016, 16:30:01 UTC Revert "ENH Add burn and thin kwargs to sample." (#1564) 29 November 2016, 16:30:01 UTC
1c9adc6 Thomas Wiecki 29 November 2016, 10:30:52 UTC MAINT Re-enable trust_input. 29 November 2016, 10:30:52 UTC
a7410c2 notoraptor 29 November 2016, 10:29:33 UTC Fix the TypeError issue #994 on Windows. (#1550) * Suggestion to fix the TypeError issue #994 on Windows. Errors occurs because some ndarrays with dtype=int32 are passed to the function delta_logp which expects ndarrays with dtype=int64 as inputs. Inputs are casted with `ndarray.astype(int)`, but on Windows, the Python 'int' type is treated as a 32-bit integer by NumPy. I suggest to remove the line with `f.trust_input = True` to ensure that Theano always checks the inputs and casts it if necessary and when possible. This fix resolves the issue on my computer: ``` Python version: 2.7.12 |Continuum Analytics, Inc.| (default, Jun 29 2016, 11:07:13) [MSC v.1500 64 bit (AMD64)] OS version: Windows-8.1-6.3.9600 ``` * Discrete super-class raises TypeError if dtype != 'int64'. Arguments for delta_logp in Metropolis.astep() are now casted to 'int64' when Metropolis handles a discrete model. 29 November 2016, 10:29:33 UTC
f61d8cd Thomas Wiecki 29 November 2016, 10:09:32 UTC ENH Add burn and thin kwargs to sample. (#1562) * ENH Add burn and thin kwargs to sample. * MAINT Move new thin and burn behind start kwarg. Make test use kwargs. 29 November 2016, 10:09:32 UTC
2caa005 Yves Delley 28 November 2016, 21:46:40 UTC Fix #895: Bug pickling model instances (#1560) * added regression test for #895 * fixes #895 28 November 2016, 21:46:40 UTC
c0cc253 Thomas Wiecki 28 November 2016, 04:36:13 UTC BUG Convert mean and mode to tensors before applying theano indexing. 28 November 2016, 04:36:13 UTC
8a59d87 Chris Fonnesbeck 28 November 2016, 04:20:11 UTC DOC tidy notebooks (#1535) * Removed discrete_find_MAP.ipynb Cleanup of several notebooks Additional cleanup of notebooks Cleanup of additional notebooks Removed discrete_find_MAP.ipynb Cleanup of several notebooks Additional cleanup of notebooks Cleanup of additional notebooks WIP: Notebooks updated rugby analytics * Removed discrete_find_MAP.ipynb * Removed discrete_find_MAP.ipynb Cleanup of several notebooks Additional cleanup of notebooks Cleanup of additional notebooks Removed discrete_find_MAP.ipynb Cleanup of several notebooks Additional cleanup of notebooks Cleanup of additional notebooks WIP: Notebooks updated rugby analytics * Cleanup of several notebooks * Additional cleanup of notebooks * Cleanup of additional notebooks * More cleaned up notebooks (including divergent LKJ) * Removed discrete_find_MAP.ipynb Cleanup of several notebooks Additional cleanup of notebooks Cleanup of additional notebooks Removed discrete_find_MAP.ipynb Cleanup of several notebooks Additional cleanup of notebooks Cleanup of additional notebooks WIP: Notebooks updated rugby analytics * Cleanup of several notebooks * More cleaned up notebooks (including divergent LKJ) * DOC Rename pmf example. * DOC Remove glm-logistic as it timeouts on reading data. * DOC Revert LKJ model use Metropolis sampler as NUTS runs into non-singular errors. * DOC Remove NUTS scaling NB as it stops running and is mostly obsolete now that we auto-init in this manner. * DOC Change some samplers in model selection NB to make it faster. * DOC Change getting started guide to use auto-init and auto-assigned samplers. * DOC Remove link to paper as it's out-of-date. 28 November 2016, 04:20:11 UTC
9543afc Mehmet Ozan Kabak 28 November 2016, 04:19:01 UTC Fixed bug in WAIC and LOO computation, also switched to SciPy's (#1557) logsumexp function for better numerical stability. 28 November 2016, 04:19:01 UTC
50d0e02 Yves Delley 26 November 2016, 16:45:10 UTC fix computation of test-values when distribution parameters are given by a theano TensorConstant (#1554) 26 November 2016, 16:45:10 UTC
8db9069 Vladislavs Dovgalecs 26 November 2016, 03:30:03 UTC Adding notebook on Hierarchical Partial Pooling 26 November 2016, 03:30:03 UTC
0bdff96 Thomas Wiecki 25 November 2016, 15:26:35 UTC Do not compute gradient in find_MAP() if it's not required. (#1551) * ENH Do not compute gradient in find_MAP() if it's not required. Closes #639. * MAINT Remove unused Poisson import. * BUG Add missing allfinite() call. Refactor model to models.py * TST Missed import. 25 November 2016, 15:26:35 UTC
818e4cd Thomas Wiecki 24 November 2016, 13:56:14 UTC Merge pull request #1548 from Spaak/master some small changes to make advi respect theano.config.floatX 24 November 2016, 13:56:14 UTC
39c3281 Eelke Spaak 24 November 2016, 11:57:29 UTC some small changes to make advi respect theano.config.floatX and improve GPU compatibility 24 November 2016, 11:57:29 UTC
df93e9d Thomas Wiecki 23 November 2016, 15:58:23 UTC MAINT Forward *kwargs to init_nuts to NUTS. 23 November 2016, 16:01:39 UTC
7cc7668 usptact 22 November 2016, 21:22:27 UTC Adding hierarhical partial pooling example Credits: http://mc-stan.org/documentation/case-studies/pool-binary-trials.html 22 November 2016, 21:22:27 UTC
808d7dd griosd 22 November 2016, 20:32:44 UTC Update text.py (#1545) 22 November 2016, 20:32:44 UTC
57b6f13 Chris Fonnesbeck 22 November 2016, 18:55:31 UTC Merge pull request #1543 from pymc-devs/reduce_advi_n_init MAINT Reduce number of n_init advi steps. Closes #1540. 22 November 2016, 18:55:31 UTC
47dd7d7 Thomas Wiecki 21 November 2016, 08:34:18 UTC MAINT Reduce number of n_init advi steps. Closes #1540. 21 November 2016, 08:34:18 UTC
27f663d Thomas Wiecki 21 November 2016, 08:25:44 UTC Merge pull request #1542 from ColCarroll/scientific_notation ADVI uses scientific notation for greater than 5 digits. 21 November 2016, 08:25:44 UTC
e672ee9 colin 21 November 2016, 03:48:24 UTC ADVI uses scientific notation for greater than 5 digits. 21 November 2016, 03:48:24 UTC
ff28eff Chris Fonnesbeck 20 November 2016, 22:28:07 UTC Removed tutorial.ipynb -- seems redundant in the presence of getting_started.ipynb 20 November 2016, 22:28:07 UTC
00eb604 Austin Rochford 20 November 2016, 20:00:33 UTC Merge pull request #1539 from AustinRochford/example-dp-marginal-mixture Use marginalized mixture classes for DP example 20 November 2016, 20:00:33 UTC
2e4e842 AustinRochford 20 November 2016, 19:23:57 UTC Use marginalized mixture classes for DP example 20 November 2016, 19:23:57 UTC
296ed60 Austin Rochford 20 November 2016, 18:29:55 UTC Merge pull request #1538 from springcoil/docker DOCS: Clarified the developing in docker part of CONTRIBUTING.md 20 November 2016, 18:29:55 UTC
806ad51 springcoil 20 November 2016, 18:10:39 UTC DOCS: Clarified the developing in docker part of Contributing 20 November 2016, 18:10:39 UTC
08556d7 Thomas Wiecki 20 November 2016, 14:19:22 UTC Merge pull request #1537 from ColCarroll/rm_hierarchical Just remove hierarchical test 20 November 2016, 14:19:22 UTC
83a638f colin 19 November 2016, 17:40:42 UTC Just remove hierarchical test 19 November 2016, 17:40:42 UTC
b233972 Thomas Wiecki 19 November 2016, 14:34:20 UTC DOC Add math to docs. Fix other doc string problems. 19 November 2016, 14:34:32 UTC
fffd959 Chris Fonnesbeck 18 November 2016, 16:29:21 UTC Merge pull request #1495 from pymc-devs/constant Renamed ConstantDist to Constant 18 November 2016, 16:29:21 UTC
976393b Thomas Wiecki 18 November 2016, 15:43:02 UTC Merge pull request #1533 from AustinRochford/advi-init-remove-sample_vp-progress Remove sample_vp progressbar for ADVI initialization 18 November 2016, 15:43:02 UTC
a70689e Chris Fonnesbeck 18 November 2016, 15:27:55 UTC Merge branch 'constant' of github.com:pymc-devs/pymc3 into constant 18 November 2016, 15:27:55 UTC
bd80b46 Chris Fonnesbeck 15 November 2016, 18:56:51 UTC Remove Constant step method test 18 November 2016, 15:27:40 UTC
93bd8e3 Chris Fonnesbeck 15 November 2016, 18:55:18 UTC Removed Constant step method 18 November 2016, 15:27:40 UTC
45720d2 Chris Fonnesbeck 03 November 2016, 03:19:14 UTC Renamed ConstantDist to Constant 18 November 2016, 15:27:40 UTC
71be307 AustinRochford 18 November 2016, 14:57:59 UTC Remove sample_vp progressbar for ADVI initialization 18 November 2016, 14:57:59 UTC
d57000d Thomas Wiecki 18 November 2016, 14:11:30 UTC DOC Add None option for NUTS intialization. 18 November 2016, 14:11:30 UTC
dbf0654 Thomas Wiecki 18 November 2016, 13:59:18 UTC ENH Add ADVI initializing for continuous models sampled using NUTS. 18 November 2016, 13:59:18 UTC
ad7dc8a Chris Fonnesbeck 18 November 2016, 10:21:34 UTC Replaced fixed kappa with passed value (#1531) 18 November 2016, 10:21:34 UTC
59f500c Thomas Wiecki 18 November 2016, 08:33:20 UTC TST Fix Rhat bad test by changing seed and starting point. 18 November 2016, 08:33:20 UTC
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