| ae1d40e | Colin | 30 September 2016, 13:27:54 UTC | Use logging instead of print (#1416) | 30 September 2016, 13:27:54 UTC |
| bad2aa6 | Colin | 30 September 2016, 12:54:44 UTC | Merge pull request #1414 from beckermr/neff-bug BUG clip effective sample size at maximum number of samples | 30 September 2016, 12:54:44 UTC |
| 8d84138 | Matthew R. Becker | 29 September 2016, 22:10:33 UTC | BUG clip effective sample size at maximum number of samples | 29 September 2016, 22:10:33 UTC |
| 0a6078f | Colin | 29 September 2016, 07:37:03 UTC | Refactor shape tests into parent class (#1411) | 29 September 2016, 07:37:03 UTC |
| c4030c1 | Colin | 28 September 2016, 18:58:51 UTC | Removed progressbar.py (#1408) | 28 September 2016, 18:58:51 UTC |
| 220643d | Austin Rochford | 28 September 2016, 12:33:58 UTC | Add http to author link to make Github pages happy (#1406) | 28 September 2016, 12:33:58 UTC |
| c29124d | Thomas Wiecki | 28 September 2016, 12:15:33 UTC | DOC Change title of LKJ tutorial. | 28 September 2016, 12:15:33 UTC |
| a827504 | Austin Rochford | 28 September 2016, 12:11:06 UTC | Add LKJ covariance prior example (#1400) * Add LKJ covariance prior example * Change LKJ example to use cov instead of tau * Fix Markdown formatting; add author link | 28 September 2016, 12:11:06 UTC |
| 057dc42 | Taku Yoshioka | 28 September 2016, 11:30:52 UTC | DOC add docstring of advi_minibatch(). (#1403) * DOC add docstring of advi_minibatch(). * Update advi_minibatch.py * Remove white-spaces * Remove white-spaces | 28 September 2016, 11:30:52 UTC |
| 19a4079 | Thomas Wiecki | 28 September 2016, 10:49:38 UTC | DEPR Remove ATMCMC as discussed in #1264. (#1404) | 28 September 2016, 10:49:38 UTC |
| f8e6f96 | Thomas Wiecki | 27 September 2016, 13:33:55 UTC | BLD Use MANIFEST.in file instead of setup.py package_file. | 28 September 2016, 07:30:24 UTC |
| 98889df | colin | 28 September 2016, 00:28:37 UTC | Unskip some tests | 28 September 2016, 07:12:47 UTC |
| 4157f0f | colin | 27 September 2016, 00:06:29 UTC | Only set random seed on purpose in advi | 27 September 2016, 23:51:33 UTC |
| 9bdb5d4 | Thomas Wiecki | 27 September 2016, 21:25:48 UTC | Reverse order of tau and sd in Normal-related likelihoods (#1398) * MAINT Revert order of tau and sd in all Normal likelihoods as well as add cov to multivariate normal. * DOC Update examples to use tau explicitly where it relied on positional arguments before. DOC Add new calling signatures to release notes. | 27 September 2016, 21:25:48 UTC |
| 1043f21 | Chris Fonnesbeck | 27 September 2016, 21:02:59 UTC | Generalized multinomial to accept multiple observations (#1390) * Generalized multinomial to accept multiple observations * Added test for multinomial with multiple observations * Added shape to Multinomial call in test_multinomial_vec * Fix for test failur in multinomial * Fix for test failure in multinomial * Added correct shape to multinomial_vec test * Dialed down assert_equal precision in mutlinomial test | 27 September 2016, 21:02:59 UTC |
| e9ee56a | colin | 26 September 2016, 13:09:51 UTC | Only set random seed on purpose | 26 September 2016, 14:28:18 UTC |
| 0ca78be | marmaduke woodman | 26 September 2016, 13:36:29 UTC | ENH add SDE class (#1269) | 26 September 2016, 13:36:29 UTC |
| fc71f68 | Osvaldo Martin | 26 September 2016, 13:02:59 UTC | add skew-normal distribution and tests (#1392) * add skew-normal distribution and tests * replace the order of tau and sd to make it match the calling signature | 26 September 2016, 13:02:59 UTC |
| 1962645 | Colin | 26 September 2016, 13:02:22 UTC | Actually set random seed on calls to `sample` (#1393) | 26 September 2016, 13:02:22 UTC |
| 30b0c50 | Colin | 26 September 2016, 10:31:08 UTC | Implement iterative NUTS algorithm (#1381) | 26 September 2016, 10:31:08 UTC |
| 85b0843 | Colin | 26 September 2016, 10:29:26 UTC | Remove knownfailure decorator (#1391) | 26 September 2016, 10:29:26 UTC |
| 8e34b01 | Austin Rochford | 24 September 2016, 21:16:49 UTC | ENH Add random_seed keyword argument to sample_ppc (#1389) | 24 September 2016, 21:16:49 UTC |
| 36c478f | Osvaldo Martin | 24 September 2016, 18:11:44 UTC | Plot posterior (#1388) * add plot_posterior to existing tests * add plot_posterior to existing tests | 24 September 2016, 18:11:44 UTC |
| d2528b8 | Osvaldo Martin | 24 September 2016, 17:19:49 UTC | show transformed variables when requested by the user (#1386) * show transformed when requested by the user * add tests plot_transformed and include_transformed | 24 September 2016, 17:19:49 UTC |
| df0a64b | Thomas Wiecki | 24 September 2016, 13:47:15 UTC | DOC Place badges next to each other. | 24 September 2016, 13:47:15 UTC |
| 1b5b037 | Thomas Wiecki | 24 September 2016, 13:45:20 UTC | DOC Fix indentation in readme.rst. | 24 September 2016, 13:45:20 UTC |
| ccb03d6 | Colin | 24 September 2016, 11:02:20 UTC | TST Refactor some examples to run as tests, delete outdated (#1360) | 24 September 2016, 11:02:20 UTC |
| 33ec4c8 | Peadar Coyle | 24 September 2016, 11:00:14 UTC | Adding coveralls badge to the readme.rst (#1384) | 24 September 2016, 11:00:14 UTC |
| c34c6c5 | Colin | 24 September 2016, 09:29:13 UTC | Add coveralls (#1383) | 24 September 2016, 09:29:13 UTC |
| 114675e | Chris Fonnesbeck | 22 September 2016, 13:41:38 UTC | Renamed StudentTpos to HalfStudentT (#1380) * Renamed StudentTpos to HalfStudentT * Fixed typo * Added deprecation warning for StudentTpos | 22 September 2016, 13:41:38 UTC |
| ba09594 | Osvaldo Martin | 21 September 2016, 08:54:57 UTC | hide transformed variable from user (#1367) | 21 September 2016, 08:54:57 UTC |
| aa7cb73 | Colin | 21 September 2016, 08:53:41 UTC | Refactor Slice.astep (#1371) | 21 September 2016, 08:53:41 UTC |
| c147e75 | Chris Fonnesbeck | 21 September 2016, 08:49:18 UTC | Fixed typo in GLM-robust (#1378) | 21 September 2016, 08:49:18 UTC |
| 5317dd4 | Chris Fonnesbeck | 19 September 2016, 14:24:39 UTC | Added examples data subdirectories to package_data (#1375) | 19 September 2016, 14:24:39 UTC |
| be6886d | Colin | 19 September 2016, 04:59:49 UTC | Pin pyqt to version 4 (as matplotlib expects) (#1372) | 19 September 2016, 04:59:49 UTC |
| 4a9de98 | jeti182 | 15 September 2016, 22:15:12 UTC | ENH Added samples per second and remaining time information to progress bar (#1296) * Added samples per second and remaining time information to progress bar * - Changed ETE to ETA in progressbar.py - Removed unnecessary casts progressbar.py - Reduced witdh of progress bar in progressbar.py - Added explanations for SPS and ETA in the docstring of "sample" in sampling.py - Added missing period in the docstring for another parameter * - Fixed typo * Use fromat instead of %.. place holer fromat string. * Update progressbar.py Removed spaces around "=" in keyword arguments * autopep8ed file | 15 September 2016, 22:15:12 UTC |
| f8ae8de | Thomas Wiecki | 15 September 2016, 15:15:47 UTC | Revert "apply transform to a distribution's test value (#1358)" Caused unanticipated problems: #1365 This reverts commit 4312a840cdad6a5708c3d59ffc2c3eb95c3c55be. | 15 September 2016, 15:15:47 UTC |
| 856eee0 | Peadar Coyle | 14 September 2016, 15:33:42 UTC | ENH: Adding an exception to loo (#1364) Updating a fix | 14 September 2016, 15:33:42 UTC |
| 4312a84 | Eelke Spaak | 14 September 2016, 06:34:38 UTC | apply transform to a distribution's test value (#1358) | 14 September 2016, 06:34:38 UTC |
| 2e62ba3 | Chris Fonnesbeck | 14 September 2016, 01:12:44 UTC | Merge pull request #1362 from AustinRochford/advi-remove-std-log-docs ADVI docstring: std is no longer in log space | 14 September 2016, 01:12:44 UTC |
| 286074b | AustinRochford | 13 September 2016, 23:32:51 UTC | ADVI docstring: std is no longer in log space | 13 September 2016, 23:32:51 UTC |
| c4aa3f3 | Byron Smith | 12 September 2016, 21:14:33 UTC | Catch keyboard interrupt during ADVI (#1357) | 12 September 2016, 21:14:33 UTC |
| dc0bc29 | Colin | 12 September 2016, 12:06:04 UTC | TST Sample more normals (#1354) | 12 September 2016, 12:06:04 UTC |
| ac8138a | Colin | 12 September 2016, 08:54:24 UTC | TST Tidy test suite (#1350) | 12 September 2016, 08:54:24 UTC |
| d4c8742 | Colin | 12 September 2016, 08:53:04 UTC | GLM tests probably pass (#1352) | 12 September 2016, 08:53:04 UTC |
| a54438d | Peadar Coyle | 12 September 2016, 08:51:23 UTC | DOC: Updating release notes (#1315) * WIP: Updating release notes * Adding -y to the conda file (#1345) * Edited and updated release notes * Additional edits to release notes * WIP: Updating release notes * Edited and updated release notes * Additional edits to release notes * Removed all of Thomas' email addresses (except one) | 12 September 2016, 08:51:23 UTC |
| 8e9d33e | Colin | 10 September 2016, 16:06:08 UTC | Refactor assign step methods (#1347) * Refactor step tests * Refactor assign_step_methods and test_step | 10 September 2016, 16:06:08 UTC |
| dcfcf65 | Peadar Coyle | 09 September 2016, 09:38:00 UTC | Adding -y to the conda file (#1345) | 09 September 2016, 09:38:00 UTC |
| e9eec9b | Peadar Coyle | 09 September 2016, 09:25:21 UTC | Merge branch 'master' of https://github.com/pymc-devs/pymc3 | 09 September 2016, 09:25:21 UTC |
| d332cc4 | Eoin Hurrell | 08 September 2016, 21:03:23 UTC | Build bugfix: Add another level to doc folder copying in setup (#1343) * Add another level to doc folder copying in setup Package data wasn't copied correctly because of the behaviour of python's glob module, which needed a further '/*' appended to it. This affects docs/source/data/6bb8d06c69c0666e6da14c094d4320d115f1ffc8 which is a directory but isn't processed as such by glob, resulting in a build error. * Update to catch all doc paths in setup Glob doesn't seem to recur as I had previously thought, so my fix is additive and not a replacement for the original glob path. | 08 September 2016, 21:03:23 UTC |
| 415d1a4 | Chris Fonnesbeck | 08 September 2016, 12:37:00 UTC | BLD Added package_data information to setup.py (#1340) * Added package_data information to include non-Python files in source distribution * Removed MANIFEST.in | 08 September 2016, 12:37:00 UTC |
| c7091d0 | Colin | 08 September 2016, 10:19:19 UTC | TST Refactor unittests. Everyone gets a random seed! (#1341) | 08 September 2016, 10:19:19 UTC |
| db58949 | Colin | 08 September 2016, 10:04:29 UTC | TST Bump to python3.5 for testing (#1342) | 08 September 2016, 10:04:29 UTC |
| f723797 | Thomas Wiecki | 08 September 2016, 10:03:37 UTC | BLD Add MANIFEST.in file for requirements and docs. | 08 September 2016, 10:03:37 UTC |
| b5673fe | Thomas Wiecki | 08 September 2016, 09:57:01 UTC | BLD Add requirements.txt file. | 08 September 2016, 09:57:01 UTC |
| 4191964 | Colin | 07 September 2016, 07:17:44 UTC | TST Limit size of Cartesian product to 100, optimize a hot path (#1335) | 07 September 2016, 07:17:44 UTC |
| 872edb1 | Chris Fonnesbeck | 07 September 2016, 06:40:54 UTC | DOC Updated README to reflect release version (#1337) * Updated README to reflect release version * Changed test version from 3.5 to 3.4 | 07 September 2016, 06:40:54 UTC |
| 90a3fbf | Chris Fonnesbeck | 06 September 2016, 19:12:49 UTC | Incremented version to 3.0.rc1 (#1334) * Incremented version to 3.0.rc1 * Updated classifiers in setup.py * Updated maintainer and author details * Added John back in author list | 06 September 2016, 19:12:49 UTC |
| a29f7f1 | Peadar Coyle | 06 September 2016, 10:35:31 UTC | Merge pull request #1331 from pymc-devs/pep8 STY Ran autopep8 on full code-base. | 06 September 2016, 10:35:31 UTC |
| 537cd4a | Peadar Coyle | 06 September 2016, 09:51:34 UTC | Merge branch 'master' of https://github.com/pymc-devs/pymc3 | 06 September 2016, 09:51:34 UTC |
| bad0c86 | Peadar Coyle | 06 September 2016, 09:45:04 UTC | ENH: Test_distributions_random | 06 September 2016, 09:47:10 UTC |
| d092dd8 | Peadar Coyle | 06 September 2016, 09:42:14 UTC | WIP: Attempt to fix the test bug (#1329) | 06 September 2016, 09:42:14 UTC |
| 7a0bdb5 | Thomas Wiecki | 06 September 2016, 09:25:11 UTC | STY Ran autopep8 on full code-base. | 06 September 2016, 09:25:11 UTC |
| 4456a04 | Peadar Coyle | 06 September 2016, 09:13:21 UTC | PEP8: Fixing best.py file (#1324) Fixing best.py errors | 06 September 2016, 09:13:21 UTC |
| d2abb62 | Colin | 06 September 2016, 07:05:48 UTC | STY Refactor test_distributions for style (#1330) | 06 September 2016, 07:05:48 UTC |
| fe5e514 | Peadar Coyle | 06 September 2016, 07:04:03 UTC | DOC Readding the Euroscipy paper to the Readme.rst (#1322) ENH: Fixing up" removing readme | 06 September 2016, 07:04:03 UTC |
| 32e09b3 | Chris Fonnesbeck | 06 September 2016, 07:02:17 UTC | DOC: bugfix and improvement in getting_started notebook (#1327) * Fixes to S&P500 data import in getting_started * Fixes to S&P500 data import in getting_started * DOC Download SPY returns, initialize NUTS with ADVI. * DOC Add tesxt on new depenncy. * Added conditional import for pandas data loader | 06 September 2016, 07:02:17 UTC |
| 380b0c7 | Peadar Coyle | 06 September 2016, 07:01:27 UTC | PEP8: Optimizing imports and improving the PEP8 compliance of GHME (#1328) | 06 September 2016, 07:01:27 UTC |
| 8936438 | Peadar Coyle | 05 September 2016, 22:22:16 UTC | Merge pull request #1317 from ColCarroll/cc/test_diagnostics Refactor tests, fix geweke bug | 05 September 2016, 22:22:16 UTC |
| 48c6e8d | springcoil | 05 September 2016, 21:15:02 UTC | WIP: Attempt to fix the test bug | 05 September 2016, 21:15:17 UTC |
| 6210f22 | Peadar Coyle | 05 September 2016, 20:30:01 UTC | STY PEP8 for math.py (#1326) | 05 September 2016, 20:30:01 UTC |
| fb4a476 | Peadar Coyle | 05 September 2016, 20:29:58 UTC | Merge pull request #1323 from pymc-devs/drop_hierarhical_notebook Dropping hierarchical.ipynb | 05 September 2016, 20:29:58 UTC |
| 53eaac8 | colin | 04 September 2016, 21:45:11 UTC | Refactor tests, fix geweke bug, set random seed | 05 September 2016, 19:53:31 UTC |
| 6fe4aa2 | Chris Fonnesbeck | 05 September 2016, 19:31:38 UTC | Dropping hierarchical.ipynb | 05 September 2016, 19:31:38 UTC |
| d709a70 | Peadar Coyle | 05 September 2016, 19:18:04 UTC | DOC: Adding an arraystep docstring (#1312) Fixes the docstring | 05 September 2016, 19:18:04 UTC |
| aabeabb | Peadar Coyle | 05 September 2016, 18:21:08 UTC | DOC Contributing Guidelines (#1313) * WIP: Contributing guidelines not ready to merge * Fleshed out contribution guidelines | 05 September 2016, 18:21:08 UTC |
| 03cb54c | Peadar Coyle | 05 September 2016, 18:18:20 UTC | Merge pull request #1321 from ColCarroll/cc/test_distributions_random Make pep8 compliant, some refactoring | 05 September 2016, 18:18:20 UTC |
| 0ba4a53 | colin | 05 September 2016, 16:31:38 UTC | Make pep8 compliant, some refactoring | 05 September 2016, 16:31:38 UTC |
| 50070e2 | Chris Fonnesbeck | 03 September 2016, 20:46:02 UTC | Merge pull request #1311 from pymc-devs/ppc DOCS: Updating the ppc file - improving readability | 03 September 2016, 20:46:02 UTC |
| a46d013 | springcoil | 03 September 2016, 17:03:24 UTC | DOCS: Enhancing Posterior Predictive Checks document | 03 September 2016, 17:06:03 UTC |
| a58ff5d | Osvaldo Martin | 02 September 2016, 08:31:38 UTC | ENH add ZINB distribution and test (#1310) | 02 September 2016, 08:31:38 UTC |
| f5ea795 | Hannes Vasyura-Bathke | 01 September 2016, 09:14:04 UTC | BUG correction for progressbar ending with i > iterations (#1309) | 01 September 2016, 09:14:04 UTC |
| 01a7000 | Chris Fonnesbeck | 31 August 2016, 12:45:24 UTC | Re-implemented zero-inflated Poisson to use standard parameterization (#1300) * Re-implemented zero-inflated Poisson to use standard parameterization, rather than using indicators * Fixed typo in latent occupancy * Fix to ZIP test | 31 August 2016, 12:45:24 UTC |
| 2c9fb26 | Chris Fonnesbeck | 25 August 2016, 22:50:05 UTC | Merge pull request #1302 from tyarkoni/string-checking fixes string checking for Python 2/3 compatibility; closes #1301 | 25 August 2016, 22:50:05 UTC |
| 1a78390 | tyarkoni | 25 August 2016, 18:24:04 UTC | moves string_types to vartypes module | 25 August 2016, 18:24:04 UTC |
| 135da45 | tyarkoni | 25 August 2016, 18:08:31 UTC | fixes string checking for Python 2/3 compatibility; closes #1301 | 25 August 2016, 18:08:31 UTC |
| 636bddb | Thomas Wiecki | 19 August 2016, 07:54:30 UTC | Merge pull request #1294 from taku-y/advi_opt ENH Arbitrary optimizer for ADVI | 19 August 2016, 07:54:30 UTC |
| bc38179 | taku-y | 18 August 2016, 12:24:56 UTC | FIX Fix tests for refactoring of advi(). | 18 August 2016, 12:24:56 UTC |
| f34c0b3 | taku-y | 18 August 2016, 12:04:31 UTC | ENH Support arbitrary optimizer. | 18 August 2016, 12:04:31 UTC |
| 641c0f5 | Thomas Wiecki | 17 August 2016, 11:13:24 UTC | ENH Add initialization via testval to WishartBartlett. | 17 August 2016, 11:13:24 UTC |
| a17b9d5 | Byron Smith | 15 August 2016, 15:02:22 UTC | Swap in dx.doi.org "permanent" URLs (#1292) Rather than a proprietary service like bit.ly, explicitly linking to DOIs is less at risk for breakage and abuse. | 15 August 2016, 15:02:22 UTC |
| 5446efe | Colin | 15 August 2016, 14:26:23 UTC | BLD Refactor build (#1290) * Add manifest * Tidy setup.py * Add install miniconda script * Refactoring build * Add debugging messages * Bash is hard * Set python versions correctly * Trying it out * Remove some debug messages * Factor out more test utilities * More nits * Remove changes to manifest and setup for now | 15 August 2016, 14:26:23 UTC |
| c396430 | Thomas Wiecki | 14 August 2016, 19:26:14 UTC | Revert "MAINT Samplers should keep the same dtype as provided by theano. (#1253)" This reverts commit 680a8eb97704150cb4bd49c00c78415448e6efbf. | 14 August 2016, 19:26:14 UTC |
| 786271c | Thomas Wiecki | 13 August 2016, 23:44:55 UTC | Merge pull request #1285 from taku-y/advi_doc DOC Modify docstring in advi(). | 13 August 2016, 23:44:55 UTC |
| 2136347 | taku-y | 12 August 2016, 16:23:38 UTC | Fix typo. | 12 August 2016, 16:39:27 UTC |
| fe566d5 | taku-y | 12 August 2016, 02:46:19 UTC | Modify docstring in advi(). | 12 August 2016, 16:39:27 UTC |
| a53728e | Maxim | 12 August 2016, 10:18:54 UTC | small fix (#1284) This construction could accidentally fail | 12 August 2016, 10:18:54 UTC |
| 923d322 | Jordi Diaz | 12 August 2016, 09:30:10 UTC | ENH Prevent duplicate variable names in model by raising exception at model creation. Fix #1161 (#1286) | 12 August 2016, 09:30:10 UTC |
| 313ad0d | Osvaldo Martin | 11 August 2016, 10:02:22 UTC | ENH Add warning to WAIC for high values of the log predictive densities variance (#1281) | 11 August 2016, 10:02:22 UTC |
| 5d8a8c5 | Osvaldo Martin | 09 August 2016, 19:56:56 UTC | Report loo results in terms of deviance. (#1279) * report loo results in terms of deviance. Optionally report the estimated effective number of parameters * improved docstring | 09 August 2016, 19:56:56 UTC |
