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 |