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661 commits

Author SHA1 Message Date
Martin Bubel
8274d02147 fix changes made to initializatino in #1078 2024-07-21 17:00:37 +02:00
Martin Bubel
55bcc27a2e introduce deprecation path to empirical_samples in initialize_latent 2024-07-21 16:16:36 +02:00
Martin Bubel
92fb49d001 update string checks in initialization.py 2024-07-21 16:14:07 +02:00
Martin Bubel
f485af7dcd update config parser due to deprecated function usage 2023-12-02 15:48:47 +01:00
Martin Bubel
65af6ee35e replace np.int by int 2023-10-16 21:20:17 +02:00
Jeremy Sanders
c22b5294bf
Rerun with cython 0.29.35 to fix Python 3.11 compatibility issues (#1020) 2023-09-23 12:59:59 -04:00
Neil Lawrence
714ad858aa Update GPy/util/normalizer.py 2021-05-19 18:52:40 +01:00
Neil Lawrence
5f68d8a7c3 Fix normalizer to catch when output scale is zero. 2021-05-19 18:52:40 +01:00
Neil Lawrence
95426aed34 Fix normalizer to catch when output scale is zero. 2021-05-19 18:52:40 +01:00
Neil Lawrence
943be980d4 Fix normalizer to catch when output scale is zero. 2021-05-19 18:52:40 +01:00
Neil Lawrence
11f806df3f Fix normalizer to catch when output scale is zero. 2021-05-19 18:52:40 +01:00
Eric Kalosa-Kenyon
434e1b0f5e updated cython-generated c files for python 3.9 via `pyenv virtualenv 3.9.1 gpy391 && pyenv activate gpy391 && python setup.py build --force 2021-03-15 21:27:38 +00:00
Julien Bect
44f4739efb maint: Wrap very long lines (> 400 chars) 2020-06-24 16:22:19 +01:00
Neil Lawrence
490c4c73f5
Merge pull request #829 from jbect/init-super 
Use super().__init__ consistently
 2020-06-19 11:16:43 +01:00
bobturneruk
3684e64ac2 introduction for utils package 2020-06-18 14:41:06 +01:00
Julien Bect
5dd81288f2 Use super().__init__ consistently, instead of sometimes calling base class __init__ directly 2020-06-18 15:32:59 +02:00
mzwiessele
22ce7ad207 Merge branch 'feature-multioutput-grad-obs' of git://github.com/esiivola/GPy into esiivola-feature-multioutput-grad-obs 2019-07-22 10:54:28 +01:00
Zhenwen Dai
06acc6a44b
Merge pull request #718 from KOLANICH/patch-1 
Don't import `datasets` by default since it is almost never needed
 2019-04-11 07:58:12 +01:00
Zhenwen Dai
0b8fd0d951
Merge pull request #708 from KOLANICH/cython_code_fix 
Integer division is needed here.
 2019-04-11 07:57:15 +01:00
Alexander Pitchford
08c74e2fce recythonised c files 2019-01-10 12:50:34 +00:00
KOLANICH
b47cc90f95
Don't import datasets by default since it is almost never needed 2019-01-01 21:25:58 +00:00
KOLANICH
900acedea5
Integer division is needed here. 2018-11-08 12:27:47 +00:00
Alexander Pitchford
e30ce11804 np.import_array() added to files where cimport numpy used 2018-10-18 16:39:37 +01:00
Siivola Eero
0b5e8d895e Changed the place of index_to_slices to more logical place 2018-09-05 14:57:16 +03:00
mzwiessele
da82f356a8 Merge branch 'cython-fix' of git://github.com/jayanthkoushik/GPy into jayanthkoushik-cython-fix 2018-09-02 19:10:19 +01:00
Moreno
11aa6ea27b Serialization: Add docstrings 2018-06-07 09:52:13 +01:00
Jayanth Koushik
1aab041885 Fix cython check in linalg 2018-02-15 17:17:25 -05:00
Mark Pullin
ccfcfa1a85 Allow calculation of full predictive covariance matrices with multiple outputs and normalization 2018-02-05 11:21:02 +00:00
Neil Lawrence
87df10707c
Change dtype for Python 3 in robot_wirelss 2017-12-03 09:56:14 -08:00
Jayanth Koushik
928559216c Refactor checking for cython availability 2017-11-16 20:29:49 -05:00
Moreno
0cfd1cdc6e Fix DSYR function (See https://github.com/scipy/scipy/issues/8155) 2017-11-14 00:22:13 +00:00
Jayanth Koushik
a7af12e6ea fix: dev: cython import errors 
This commit fixes issues observed in Windows where some
cython modules are successfully imported, and some are not.
This causes the global config cython.working to be inconsistent,
which causes import errors when unavailable cython modules
are tried to be imported (example
https://github.com/SheffieldML/GPy/issues/266). This commit uses
a separate flag for each module to fix the issue.
 2017-10-23 15:58:17 -04:00
Moreno
e572bfb746 Basic framework for serializing GPy models 2017-09-11 12:18:01 +01:00
Shen
e72f0b6c9b Input warping using Kumar warping 2017-09-08 15:10:40 +02:00
Akash Kumar Dhaka
f0f1a183b0 merging with the gpy devel branch to be in sync with the latest code and make pull request again .. 2017-08-10 11:47:26 +03:00
Akash Kumar Dhaka
ae27e1225d adding file for gaussian-kronrod integration, test cases and calculating gradients of log marginal wrt theta-likelihood params 2017-08-10 11:14:40 +03:00
mzwiessele
000d832830 fix: updated keywords 2017-08-10 11:14:40 +03:00
Moreno
63751de912 Changes in EP/EPDTC to fix numerical issues and increase the flexibility of the inference. 
Changes to avoid numerical issues and improve the performance:
    - Keep value of the EP parameters between calls
    - Enforce positivity of tau_tilde
    - Stable computation of the EP moments for the Bernoulli likelihood
    - Compute marginal in the GP model without directly inverting tau_tilde

    Changes to improve the flexibility:
    - Add parameter for maximum number of iterations
    - Distinguish between alternated/nested mode
    - Distinguish between sequential/parallel updates in EP
 2017-06-01 11:59:04 +03:00
Max Zwiessele
113f84d6a7 cython in linalg 
did set cython to working if linalg_cython was importable.
 2017-06-01 11:59:04 +03:00
Ruben Martinez-Cantin
d288341d55 Fix python 2-3 compatibility 2017-05-16 16:47:43 +02:00
mzwiessele
480aedb74a fix: updated keywords 2017-04-12 11:53:05 +01:00
Zhenwen Dai
2f7ab3f5c7 Merge pull request #492 from pgmoren/devel 
We did some benchmarking on classification. These changes should be fine. Let's merge it in.
 2017-03-27 13:26:27 +01:00
Moreno
0c248e7520 Changes in EP/EPDTC to fix numerical issues and increase the flexibility of the inference. 
Changes to avoid numerical issues and improve the performance:
    - Keep value of the EP parameters between calls
    - Enforce positivity of tau_tilde
    - Stable computation of the EP moments for the Bernoulli likelihood
    - Compute marginal in the GP model without directly inverting tau_tilde

    Changes to improve the flexibility:
    - Add parameter for maximum number of iterations
    - Distinguish between alternated/nested mode
    - Distinguish between sequential/parallel updates in EP
 2017-03-22 13:40:06 +00:00
Max Zwiessele
bc59dc4ee0 cython in linalg 
did set cython to working if linalg_cython was importable.
 2017-03-10 08:05:36 +00:00
Safrone
14046705cf fix: fallback for when no environment variables are set (#467) 
* fix: dev: add or in home directory getting

adds another or when getting the home directory with os.getenv() so that if neither $HOME nor $USERPROFILE environment variable is set, os.path.join() will not fail by getting a None and the config will revert to the default configuration file.

* fix: remove extra statement
 2017-01-09 09:50:29 +00:00
Michael T Smith
826618e143 fix: Bug in dataset (in fn download_url) which wrongly interprets the Content-Length meta data, and just takes first character. 2016-09-09 16:27:08 +01:00
mzwiessele
d343ec8b41 [warped stuff] plotting and normalizer in warped gps 2016-08-17 14:51:29 +01:00
mzwiessele
746d4daae8 [merge] devel 2016-08-16 12:03:45 +01:00
Michael T Smith
bd758ac849 Removing 'threaded' version 2016-08-09 14:54:29 +01:00
Michael T Smith
6f4d03178e Don't use message added to cluster code 2016-08-04 14:47:08 +01:00