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Pytorch refactor#168

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ebolyen wants to merge 28 commits intobiocore:masterbiocore/mmvec:masterfrom Keegan-Evans:pytorch-refactorKeegan-Evans/mmvec:pytorch-refactorCopy head branch name to clipboard

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Commits on Apr 12, 2022

• DRAFT: first draft of model

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Commits on Apr 15, 2022

• REFACTOR: beginning of refactor

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Commits on Apr 18, 2022

• FEAT: forward likelihood now sum(lu, lv, ly)

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Commits on Apr 19, 2022

• DEBUG: first pass package refactoring

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Commits on Apr 27, 2022

• IMP: split ILR and ALR, ALR done to ranks

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• IMP: ALR outputs working

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Commits on Apr 29, 2022

• FEAT: function for ordination created

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Commits on Apr 30, 2022

• FEAT: Produces OrdinationResults

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Commits on May 2, 2022

• IMP: cleanup before working on tests.

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Commits on May 3, 2022

• TEST: test_multimodal runs but fails.

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Commits on May 5, 2022

• checkpoint before cleanup for pr

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• IMP: cleanup refactor examples directory

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• IMP: remove sneaky notebook checkpoints

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• IMP: restore original mmvec/multimodal.py

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• IMP: restore q2 goodies

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• IMP: q2 goodies

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• IMP: add min pytorch version

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• DEBUG: conda-> pip pytorch install name

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• IMP: name tweaks

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Commits on May 6, 2022

• IMP: var renaming and observation based epochs

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Commits on May 19, 2022

• FEAT: plugin-standup

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• Merge branch 'pytorch-refactor' of github.com:Keegan-Evans/mmvec into pytorch-refactor

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• BUG: getting test interface to work after plugin

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Commits on May 25, 2022

• IMP: q2 paired-omics method wired up

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• BUG: fixing index filtering on biom-tables

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• BUG: index dfs based on intersection of indexes

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Commits on Jun 1, 2022

• BUG: paired-omics working now.

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Commits on Jun 3, 2022

• TEST: adding tests for ranks_bare

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