Merge in main #346
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Merge in main #346
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Abstract integrator
Add integrator/likelihoods doc
Integration testing added
* Interrogater added * Interrogater added * Final cleanup * Cleanup deps * Update .gitignore Signed-off-by: Thomas Pinder <tompinder@live.co.uk> --------- Signed-off-by: Thomas Pinder <tompinder@live.co.uk>
* decouple kernel init and computations * pass all tests * update docstrings * make angry bear happy * add missing docstring
Updated documentation for contributing to reflect the change to using Poetry for dependency management. Also added the command for manually running the pre-commit hook to the documentation. Also fixed a few broken links and typos I had encountered.
Added suggestion to use Conda miniforge for users wishing to run GPJax on Apple Silicon. Co-authored-by: Thomas Pinder <tompinder@live.co.uk> Signed-off-by: Thomas Christie <thomashamish@hotmail.com>
Update contribution documentation
Main change is to add a notebook introducing the concept of a kernel for those new to Gaussian processes. This focuses on mathematical intuition and introduces useful concepts such as covariance matrices and positive-definiteness. Also noted that the README file for writing documentation hadn't been updated since switching to using MkDocs, so updated it to reflect these changes. Also found that the relative path to the style file for the notebooks caused issues when running the `poetry run mkdocs serve` command. Now instead of using a relative path to the style file, we point to the URL of the style file directly. I have copied the style file into the `_static` directory, and a future PR will point to this URL instead. Finally made a few other minor edits: - Updated docstring for the periodic kernel as it was incomplete. - Made some minor fixes to a few other docstrings I found flaws in.
Added an extra section to the kernel introduction notebook detailing how one can create new kernels by adding/multiplying two existing kernels. Also added an example using the Mauna Loa CO2 dataset. Also renamed the original 'kernels.py' notebook to 'constructing_new_kernels.py' and edited references to this notebook.
Add introductory kernel notebook and change style file path in notebooks
Added introduction to Bayesian optimisation notebook. Also fixed some links which had broken after renaming the old kernels notebook in a previous PR.
Added `sudo apt-get update` command before `sudo apt-get install` as recommended in https://docs.github.com/en/actions/using-github-hosted-runners/customizing-github-hosted-runners in order to mitigate package installation failures.
Incorporated feedback into BO notebook and added link to BO notebook from project README.
Add BO notebook
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Merge in latest commits from main.