Code

Add GPs#632

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Merged

tomicapretto merged 70 commits intobambinos:mainbambinos/bambi:mainfrom tomicapretto:gpstomicapretto/bambi:gpsCopy head branch name to clipboardMar 20, 2023

Commits

Commits on Jan 28, 2023

• Use pyproject.toml. Remove unnecesary files. Improve CI workflows

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  2296a0d

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• name change

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• stringify python version

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• Take version from a file. Install optional deps from local as well

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• Changelog.md -> CHANGELOG.md

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• add pydata-sphinx-theme to dependencies

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• try to fix test workflow

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• lint

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• Add 'bash -l {0}' to tests

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• [no ci] update contributing.md

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Commits on Jan 29, 2023

• Plan GPs

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Commits on Jan 30, 2023

• Start implementation

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Commits on Jan 31, 2023

• Start background term

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• first POC

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• update uplanning

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Commits on Feb 2, 2023

• Custom priors

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• bring changes from main

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• more progress

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Commits on Feb 3, 2023

• Write HSGP as a transformation

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Commits on Feb 4, 2023

• [no ci] first model that runs with bambi

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• [no ci] update example

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Commits on Feb 6, 2023

• [no ci] predictions prototype working

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• Add GP example with bambi

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Commits on Feb 7, 2023

• Small tweak to the example

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• Allow more covariance functions and general names

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Commits on Feb 8, 2023

• Handle HSGP > 1D

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• [no ci] docs, comments and ideas

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Commits on Feb 10, 2023

• example changes

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Commits on Feb 11, 2023

• Merge branch 'main' of github.com:bambinos/bambi into gps

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• Store HSGP instance in the Bambi HSGP term

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• add default priors for HSGP

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• [no ci] create test script. I'm just writing ideas for now

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Commits on Feb 13, 2023

• [no ci] rerun with new version of formulae

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  caa7e5b

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• [no ci] add hsgp component to idata when computing predictions. Reproduce some examples

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Commits on Feb 14, 2023

• [no ci] hsgp by categories

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Commits on Feb 17, 2023

• [no ci] latest ideas

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Commits on Feb 20, 2023

• [no ci] update to new API of hsgp

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Commits on Feb 27, 2023

• [no ci] reconciliate shapes for by-group case

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• [no ci] make hsgp more flexible

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• [no ci] Compute 'L' for the most general case

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• [no ci] hsgp is working again after tweaks to allow for groups

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Commits on Feb 28, 2023

• [no ci] 'by' seems to be working!

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Commits on Mar 1, 2023

• [no ci] different covariance function instances by group

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Commits on Mar 2, 2023

• [no ci] hsgp by group seems to be working but prediction problems

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• Predictions by group working

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• It seems the implementation is done

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• lint

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Commits on Mar 6, 2023

• Add support for the 'scale' argument

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• [no ci] scale works more intuitively now

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Commits on Mar 7, 2023

• [no ci] scale and iso available?

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• Many examples using HSGP with 2D data

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Commits on Mar 10, 2023

• [no ci] add HSGP in the model summary and clean notebooks a litle

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• [no ci] docs and more examples

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Commits on Mar 13, 2023

• Add text to the 2-dimensional notebook

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• [no ci] add text to examples

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• [no ci] add final version of examples

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Commits on Mar 14, 2023

• [no ci] add how bambi works notebook

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• [no ci] remove gp_notes.ipynb

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• [no ci] add first set of tests

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• [no ci] transpose coords of hsgp contribution

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• [no ci] add more deep tests

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• [no ci] rerun notebooks

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  7bcfbbb

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• [no ci] fix import in test

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• [no ci] add optional namespace to the model

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• [no ci] extra_namespace is clearer than namespace

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Commits on Mar 20, 2023

• [no ci] revisit notebooks

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• Switch to PyMC dev version

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• Small tweak to test

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• Remove problematic type hints

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• linter

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