mirror of
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v1.10.0 (#908)
* Update self.num_data in GP when X is updated
* Update appveyor.yml
* Update setup.cfg
* Stop using legacy bdist_wininst
* fix: reorder brackets to avoid an n^2 array
* Minor fix to multioutput regression example, to clarify code + typo.
* added missing import
* corrected typo in function name
* fixed docstring and added more explanation
* changed ordering of explanation to get to the point fast and provide additional details after
* self.num_data and self.input_dim are set dynamically in class GP() after the shape of X. In MRD, the user-specific values are passed around until X is defined.
* fixed technical description of gradients_X()
* brushed up wording
* fix normalizer
* fix ImportError in likelihood.py
in function log_predictive_density_sampling
* Update setup.py
bump min require version of scipy to 1.3.0
* Add cython into installation requirement
* Coregionalized regression bugfix (#824)
* route default arg W_rank correctly (Addresses #823)
* Drop Python 2.7 support (fix #833)
* travis, appveyor: Add Python 3.8 build
* README: Fix scipy version number
* setup.py: Install scipy < 1.5.0 when using Python 3.5
* plotting_tests.py: Use os.makedirs instead of matplotlib.cbook.mkdirs (fix #844)
* Use super().__init__ consistently, instead of sometimes calling base class __init__ directly
* README.md: Source formatting, one badge per line
* README.md: Remove broken landscape badge (fix #831)
* README.md: Badges for devel and deploy (fix #830)
* ignore itermediary sphinx restructured text
* ignore vs code project settings file
* add yml config for readthedocs
* correct path
* drop epub and pdf builds (as per main GPy)
* typo
* headings and structure
* update copyright
* restructuring and smartening
* remove dead links
* reorder package docs
* rst "markup"
* change rst syntax
* makes sense for core to go first
* add placeholder
* initial core docs, class diagram
* lower level detail
* higher res diagrams
* layout changes for diagrams
resolve conflict
* better syntax
* redunant block
* introduction
* inheritance diagrams
* more on models
* kernel docs to kern.src
* moved doc back from kern.src to kern
* kern not kern.src in index
* better kernel description
* likelihoods
* placeholder
* add plotting to docs index
* summarise plotting
* clarification
* neater contents
* architecture diagram
* using pods
* build with dot
* more on examples
* introduction for utils package
* compromise formatting for sphinx
* correct likelihod definition
* parameterization of priors
* latent function inference intro and format
* maint: Remove tabs (and some trailing spaces)
* dpgplvm.py: Wrap long line + remove tabs
* dpgplvm.py: Fix typo in the header
* maint: Wrap very long lines (> 450 chars)
* maint: Wrap very long lines (> 400 chars)
* Add the link to the api doc on the readme page.
* remove deprecated parameter
* Update README.md
* new: Added to_dict() method to Ornstein-Uhlenbeck (OU) kernel
* fix: minor typos in README !minor
* added python 3.9 build following 4aa2ea9f5e to address https://github.com/SheffieldML/GPy/issues/881
* updated cython-generated c files for python 3.9 via `pyenv virtualenv 3.9.1 gpy391 && pyenv activate gpy391 && python setup.py build --force
* updated osx to macOS 10.15.7, JDK to 14.0.2, and XCode to Xcode 12.2 (#904)
The CI was broken. This commit fixes the CI. The root cause is reported in more detail in issue #905.
In short, the default macOS version (10.13, see the TravisCI docs) used in TravisCI isn't supported by brew which caused the brew install pandoc in the download_miniconda.sh pre-install script to hang and time out the build. It failed even on inert PRs (adding a line to README, e.g.). Now, with the updated macOS version (from 10.13 to 10.15), brew is supported and the brew install pandoc command succeeds and allows the remainder of the CI build and test sequence to succeed.
* incremented version
Co-authored-by: Masha Naslidnyk 🦉 <naslidny@amazon.co.uk>
Co-authored-by: Zhenwen Dai <zhenwendai@users.noreply.github.com>
Co-authored-by: Hugo van Kemenade <hugovk@users.noreply.github.com>
Co-authored-by: Mark McLeod <mark.mcleod@mindfoundry.ai>
Co-authored-by: Sigrid Passano Hellan <sighellan@gmail.com>
Co-authored-by: Antoine Blanchard <antoine@sand-lab-gpu.mit.edu>
Co-authored-by: kae_mihara <rukamihara@outlook.com>
Co-authored-by: lagph <49130858+lagph@users.noreply.github.com>
Co-authored-by: Julien Bect <julien.bect@centralesupelec.fr>
Co-authored-by: Neil Lawrence <ndl21@cam.ac.uk>
Co-authored-by: bobturneruk <bob.turner.uk@gmail.com>
Co-authored-by: bobturneruk <r.d.turner@sheffield.ac.uk>
Co-authored-by: gehbiszumeis <16896724+gehbiszumeis@users.noreply.github.com>
This commit is contained in:
Eric Kalosa-Kenyon
GitHub
parent
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commit
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72 changed files with 8568 additions and 14545 deletions
36
README.md
36
README.md
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@ -5,11 +5,17 @@ The Gaussian processes framework in Python.
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* GPy [homepage](http://sheffieldml.github.io/GPy/)
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* Tutorial [notebooks](http://nbviewer.ipython.org/github/SheffieldML/notebook/blob/master/GPy/index.ipynb)
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* User [mailing-list](https://lists.shef.ac.uk/sympa/subscribe/gpy-users)
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* Developer [documentation](http://gpy.readthedocs.io/)
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* Developer [documentation](http://gpy.readthedocs.io/) [documentation (devel branch)](https://gpy.readthedocs.io/en/devel/)
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* Travis-CI [unit-tests](https://travis-ci.org/SheffieldML/GPy)
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* [](http://opensource.org/licenses/BSD-3-Clause)
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[](http://depsy.org/package/python/GPy)
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[](https://travis-ci.org/SheffieldML/GPy) [](https://ci.appveyor.com/project/mzwiessele/gpy/branch/deploy) [](https://coveralls.io/github/SheffieldML/GPy?branch=devel) [](http://codecov.io/github/SheffieldML/GPy?branch=devel) [](http://depsy.org/package/python/GPy) [](https://landscape.io/github/SheffieldML/GPy/devel)
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## Status
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| Branch | travis-ci.org | ci.appveyor.com | coveralls.io | codecov.io |
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| --- | --- | --- | --- | --- |
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| Default branch (`devel`) | [](https://travis-ci.org/SheffieldML/GPy/branches) | [](https://ci.appveyor.com/project/mzwiessele/gpy/branch/devel) | [](https://coveralls.io/github/SheffieldML/GPy?branch=devel) | [](http://codecov.io/github/SheffieldML/GPy?branch=devel) |
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| Deployment branch (`deploy`) | [](https://travis-ci.org/SheffieldML/GPy/branches) | [](https://ci.appveyor.com/project/mzwiessele/gpy/branch/deploy) | [](https://coveralls.io/github/SheffieldML/GPy?branch=deploy) | [](http://codecov.io/github/SheffieldML/GPy?branch=deploy) |
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## What's new:
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@ -23,15 +29,16 @@ We welcome any contributions to GPy, after all it is an open source project. We
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For an in depth description of pull requests, please visit https://help.github.com/articles/using-pull-requests/ .
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### Steps to a successfull contribution:
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### Steps to a successful contribution:
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1. Fork GPy: https://help.github.com/articles/fork-a-repo/
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2. Make your changes to the source in your fork.
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3. Make sure the [guidelines](#gl) are met.
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4. Set up tests to test your code. We are using unttests in the testing subfolder of GPy. There is a good chance that there is already a framework set up to test your new model in model_tests.py or kernel in kernel_tests.py. have a look at the source and you might be able to just add your model (or kernel or others) as an additional test in the appropriate file. There is more frameworks for testing the other bits and pieces, just head over to the testing folder and have a look.
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4. Set up tests to test your code. We are using unittests in the testing subfolder of GPy. There is a good chance
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that there is already a framework set up to test your new model in model_tests.py or kernel in kernel_tests.py. have a look at the source and you might be able to just add your model (or kernel or others) as an additional test in the appropriate file. There is more frameworks for testing the other bits and pieces, just head over to the testing folder and have a look.
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5. Create a pull request to the devel branch in GPy, see above.
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6. The tests will be running on your pull request. In the comments section we will be able to discuss the changes and help you with any problems. Let us know if there are any in the comments, so we can help.
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7. The pull request gets accepted and your awsome new feature will be in the next GPy release :)
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7. The pull request gets accepted and your awesome new feature will be in the next GPy release :)
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For any further questions/suggestions head over to the issues section in GPy.
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@ -45,11 +52,7 @@ For any further questions/suggestions head over to the issues section in GPy.
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## Support and questions to the community
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We have set up a mailing list for any questions you might have or problems you feel others have encountered:
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gpy-users@lists.shef.ac.uk
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Feel free to join the discussions on the issues section, too.
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Ask questions using the issues section.
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## Updated Structure
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@ -76,7 +79,7 @@ If that is the case, it is best to clean the repo and reinstall.
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[<img src="https://upload.wikimedia.org/wikipedia/commons/8/8e/OS_X-Logo.svg" height=40px>](http://www.apple.com/osx/)
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[<img src="https://upload.wikimedia.org/wikipedia/commons/3/35/Tux.svg" height=40px>](https://en.wikipedia.org/wiki/List_of_Linux_distributions)
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Python 2.7, 3.5 and higher
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Python 3.5 and higher
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## Citation
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@ -93,7 +96,7 @@ We like to pronounce it 'g-pie'.
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## Getting started: installing with pip
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We are now requiring the newest version (0.16) of
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We are requiring a recent version (1.3.0 or later) of
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[scipy](http://www.scipy.org/) and thus, we strongly recommend using
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the [anaconda python distribution](http://continuum.io/downloads).
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With anaconda you can install GPy by the following:
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@ -111,7 +114,7 @@ And finally,
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pip install gpy
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We've also had luck with [enthought](http://www.enthought.com). Install scipy 0.16 (or later)
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We've also had luck with [enthought](http://www.enthought.com). Install scipy 1.3.0 (or later)
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and then pip install GPy:
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pip install gpy
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@ -222,6 +225,13 @@ The documentation can be compiled as follows:
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sphinx-apidoc -o source/ ../GPy/
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make html
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alternatively:
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```{shell}
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cd doc
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sphinx-build -b html -d build/doctrees -D graphviz_dot='<path to dot>' source build/html
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```
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The HTML files are then stored in doc/build/html
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### Commit new patch to devel
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