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21 April 2024, 10:16:19 UTC
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Revision Author Date Message Commit Date
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
34e3f45 Thomas Wiecki 17 November 2016, 15:04:41 UTC MAINT Convert some examples to new sample() api. Adapt tests. 17 November 2016, 15:04:41 UTC
b91d3be Thomas Wiecki 17 November 2016, 13:32:00 UTC Merge pull request #1528 from taku-y/fix_sbtrans Fix stickbreaking transform dtype 17 November 2016, 13:32:00 UTC
34a8bd4 taku-y 17 November 2016, 10:48:17 UTC Fix stickbreaking transform dtype 17 November 2016, 10:48:17 UTC
85e0f9d Thomas Wiecki 16 November 2016, 09:46:05 UTC REF Make all_continuous() a general purpose function. 16 November 2016, 09:46:05 UTC
4d53a36 Thomas Wiecki 16 November 2016, 09:37:51 UTC WIP Perform initializing inside of sample instead of adding new sample_init() as per @fonnesbeck suggestion. 16 November 2016, 09:37:51 UTC
e3c8b63 Thomas Wiecki 11 November 2016, 15:04:26 UTC DOC Add better docs and add advi_map. 16 November 2016, 07:17:36 UTC
85b46f6 Thomas Wiecki 11 November 2016, 10:51:57 UTC MAINT Remove Metropolis init as it does not seem to work well. 16 November 2016, 07:17:36 UTC
dc203d9 Thomas Wiecki 11 November 2016, 08:33:23 UTC DOC Convert more NBs to use sample_init(). 16 November 2016, 07:17:36 UTC
77b67d0 Thomas Wiecki 11 November 2016, 06:20:15 UTC ENH Add sample_init() function and update examples. 16 November 2016, 07:17:36 UTC
1770be2 Thomas Wiecki 11 November 2016, 06:12:57 UTC ENH Infer variable names directly from model in covariance estimation from trace. 16 November 2016, 07:17:36 UTC
25939fd Chris Fonnesbeck 15 November 2016, 18:57:10 UTC Merge branch 'constant' of github.com:pymc-devs/pymc3 into constant 15 November 2016, 18:57:10 UTC
ba872ea Chris Fonnesbeck 15 November 2016, 18:56:51 UTC Remove Constant step method test 15 November 2016, 18:56:51 UTC
a61cf73 Chris Fonnesbeck 15 November 2016, 18:55:18 UTC Removed Constant step method 15 November 2016, 18:55:18 UTC
4f54823 Thomas Wiecki 14 November 2016, 20:41:46 UTC ENH: Add Dockerfile for development inside a container (#1527) * Add Dockerfile for development inside a container * Use /Users/austin for portability * Put Dockerfile with scripts * Add script for starting development Docker container * Really add script this time * Modify options to create_testenv.sh * Shift while parsing arguments * Update dockerfile to run test suite * Add documentation for docker * Typo 14 November 2016, 20:41:46 UTC
7367f20 colin 14 November 2016, 20:39:54 UTC Typo 14 November 2016, 20:39:54 UTC
d8800bf colin 13 November 2016, 00:01:34 UTC Add documentation for docker 13 November 2016, 18:38:58 UTC
75dac62 colin 13 November 2016, 00:01:14 UTC Update dockerfile to run test suite 13 November 2016, 18:38:58 UTC
08fbeeb AustinRochford 01 November 2016, 00:44:48 UTC Shift while parsing arguments 13 November 2016, 18:38:58 UTC
9d38375 AustinRochford 01 November 2016, 00:08:01 UTC Modify options to create_testenv.sh 13 November 2016, 18:38:58 UTC
c489ea6 AustinRochford 23 October 2016, 22:10:35 UTC Really add script this time 13 November 2016, 18:38:58 UTC
655a4db AustinRochford 23 October 2016, 21:37:43 UTC Add script for starting development Docker container 13 November 2016, 18:38:58 UTC
f60492c AustinRochford 23 October 2016, 15:46:01 UTC Put Dockerfile with scripts 13 November 2016, 18:38:58 UTC
3180376 AustinRochford 23 October 2016, 15:45:37 UTC Use /Users/austin for portability 13 November 2016, 18:38:58 UTC
231e30f AustinRochford 23 October 2016, 13:09:05 UTC Add Dockerfile for development inside a container 13 November 2016, 18:38:58 UTC
082c982 Thomas Wiecki 12 November 2016, 13:40:11 UTC Nuts speed up ~1.5x (#1522) * PERF Make NUTS 1.5x faster by moving E0 calculation outside of buildtree inner loop. * STY Refactor creation of functions. * DOC Adapt doc-string. * STY Pep8. * STY Only return scalar * DOC Typo * MAINT Move theano.tensor to tt. Remove obsolete p0 and q0 args from build_tree. 12 November 2016, 13:40:11 UTC
5716806 Chris Fonnesbeck 03 November 2016, 03:19:14 UTC Renamed ConstantDist to Constant 12 November 2016, 10:08:00 UTC
0d5f292 Maxim 12 November 2016, 09:31:01 UTC MAINT glm fixes and refactoring (#1513) * Fixed a bug when it is not possible to run more than one glm models in a model * names are as were in previous versions by default * Added glm.from_xy constructor * Fixed confusing docstrings * Refactored Code 12 November 2016, 09:31:01 UTC
3f300e9 Osvaldo Martin 12 November 2016, 08:40:18 UTC change circular transform from ElemwiseTransform to Transform. add circular domain for vonmises tests (#1520) 12 November 2016, 08:40:18 UTC
ebf26d5 colin 10 November 2016, 01:35:06 UTC Remove `verbose` argument 10 November 2016, 13:42:41 UTC
c04da31 Colin 09 November 2016, 16:42:06 UTC Merge pull request #1516 from pymc-devs/transform_verbosity Changed verbosity threshold for variable transformation 09 November 2016, 16:42:06 UTC
1f5480f Chris Fonnesbeck 09 November 2016, 15:39:16 UTC Used logging.debug instead of verbosity level 09 November 2016, 15:39:16 UTC
4ca4ef9 Chris Fonnesbeck 09 November 2016, 15:26:45 UTC Changed verbosity threshold for variable transformation 09 November 2016, 15:26:45 UTC
af2dcb2 Chris Fonnesbeck 08 November 2016, 21:53:34 UTC Merge branch 'constant' of github.com:pymc-devs/pymc3 into constant 08 November 2016, 21:53:34 UTC
fff053f Chris Fonnesbeck 03 November 2016, 03:19:14 UTC Renamed ConstantDist to Constant 08 November 2016, 21:53:23 UTC
51f196d Colin 08 November 2016, 07:23:44 UTC Accept `extent` as kwarg to kde_plot (#1509) 08 November 2016, 07:23:44 UTC
1e8549e Thomas Wiecki 08 November 2016, 06:29:20 UTC Merge pull request #1508 from ColCarroll/unpin Unpin theano 08 November 2016, 06:29:20 UTC
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