This PR adds two main things to GPy:
- to- and from-dict functions for the kernels listed belop
- a fix for the appveyor CI
Please see the squashed commit messages listed below.
Authors: @gehbiszumeis @ppk42 respectively
Reviewer: @ekalosak
---
* new: added to_dict() method to Coregionalize kernel class
* new: added to_dict() method to MixedNoise likelihood class
* fix: made Y_metadata dict content serializable
* fix: typo
* added additional needed parameters to to_dict() method for Coregionalize kernel + added _build_from_input dict method
* new: added possibility to build MixedNoise likelihood from input_dict
* Y_metadata conversion from serializable to np.array when loading from dict
* fix: rework Y_metadata part for compatibility with unittests !minor
* conda cleanup in appveyors pipeline
* conda clean up after conda update
* conda clean before conda update
* try pinning packages for conda
* revert all conda changes
* conda clean all (not only packages)
* use conda update anaconda
* pin conda package
* pin conda package
* try installing charset-normalizer beforehand
* try to get from conda-forge
* revert all conda changes
* Try to fix the conda update challange.
See: https://community.intel.com/t5/Intel-Distribution-for-Python/Conda-update-Conda-fails/td-p/1126174
It is just a try for a different context/(conda version).
* Still fixing build error on appveyor
I also use a newer miniconda version for greater python versions.
* Update appveyor.yml
Thinking it over it decided to use miniconda38 for all python versions unless python 3.5.
* revert miniconda versioning changes
* adjust GPy version in appveyor.yml
* 1st attempt bring the appveyor build to life again
* #955 fixing ci build on appveyor
After bringing the miniconda env to work again, the wrong matplotlib version was used. This commit should fix that.
* #955 Fix CI build
Freezing numpy and scipy was a bad idea.
I freeze matplotlib dependend on the python version only.
* add: built_from_dict method for White Kernel
Co-authored-by: Peter Paul Kiefer <ppk42@users.noreply.github.com>
Co-authored-by: Peter Paul Kiefer <dafisppk@gmail.com>
* 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>
