Move and reorganize setup dict out of AnnData into Manager #1285
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adamgayoso
reviewed
Dec 9, 2021
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| adata = self._validate_anndata(adata) | ||
| batch = self.get_from_registry(adata, _CONSTANTS.BATCH_KEY).ravel() | ||
| cats = adata.uns["_scvi"]["categorical_mappings"]["_scvi_batch"]["mapping"] |
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no I haven't moved all these references yet, I'm planning on doing that in chunks
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| warnings.warn( | ||
| "Is adata.obs['{}'] continuous? SCVI doesn't support continuous obs yet." | ||
| ) |
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this could probably be changed as well
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should it be removed?
adamgayoso
requested changes
Dec 9, 2021
justjhong
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Jan 16, 2022
* new base field API for setup dict * adapt manager to new registry * backwards compatibility implementation * train works * adapt get_from_registry function * simplify needs transfer logic, working test_scvi * change _REGISTRY_KEYS back to _CONSTANTS * address comments, fix compat test * codacy
justjhong
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that referenced
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Feb 2, 2022
* new base field API for setup dict * adapt manager to new registry * backwards compatibility implementation * train works * adapt get_from_registry function * simplify needs transfer logic, working test_scvi * change _REGISTRY_KEYS back to _CONSTANTS * address comments, fix compat test * codacy
justjhong
added a commit
that referenced
this pull request
Feb 5, 2022
* placeholder release notes for base * AnnData Manager refactor (#1238) * move anndata file into anndata subfolder * mock out anndata manager and fields for categorical obs fields only * add layerfield * fix imports * fix imports in models * add temporary test and fix bugs in manager code * manager store on model class, refactor what needs to be defined for a model * clean up some existing code * restructure fields file, clean up more view anndata setup code, add more skeleton * add transfer_field for obs and layer fields * naive implementation of transfer_setup in anndata manager * implement backwards compat with setup dict on load * add docstrings to all new methods * address comments: change to registry_key, change fields to set in manager * add tests for transfer and manager from setup * remove anndata_fields method * address pr comment * Implement NonCategoricalJointObsField (#1247) * implement continuous obsm field * make class specific to joint obs fields * make fields public * address comments * faster concat by subsetting obs * Implement CategoricalJointObsField (#1248) * add categorical joint obs field * fix _make_obsm_categorical * add line in test * address pr comment * Pass manager to data loader (#1280) * pass manager to data loader * address comment * Move and reorganize setup dict out of AnnData into Manager (#1285) * new base field API for setup dict * adapt manager to new registry * backwards compatibility implementation * train works * adapt get_from_registry function * simplify needs transfer logic, working test_scvi * change _REGISTRY_KEYS back to _CONSTANTS * address comments, fix compat test * codacy * Add anndata registration classes to developer API (#1292) * add anndata registration classes to developer API * move manager to anndata submodule to fix docs * Save/Load with saved setup inputs (#1294) * skeleton for new save load, missing field logic * save load with saved setup inputs * add docstring for setup_inputs * codacy * fix documentation * additional pr comments * fix manager imports * Adapt TotalVI to new setup (#1298) * obsm field * adapt totalVI to new setup * fix additional totalvi test * make field registration ordered * fix totalvi protein priors logic * address pr comments * address pr comments * Fix tests for SCVI, TOTALVI, generic AnnData utils (#1299) * adapt totalVI to new setup * fix additional totalvi test * remove run_setup_anndata kwarg, reassign uuid on view copy, fix some tests * remove run_setup_anndata comments * fix transfer anndata test * fix test data format test * fix setup anndata test * fix most pyro tests * fix most scarches tests * remove state dict from field * Adapt all internal models to new setup (#1301) * adapt LDA * adapt linearscvi * remove _get_var_names_from_setup_anndata * adapt peakvi * adapt autozi * adapt scanvi * fix scanvi test * fix totalvi test * fix dataloader tests * fix multiple cov tests * adapt condscvi * adapt destvi * adapt multivi * fix setup compat test * remove get_from_registry util * fix scanvi and peakvi scarches tests * fix backwards compat tests and default missing summary stat in models * address comment * Adapt all external models to new setup (#1302) * adapt cellassign * adapt gimvi * adapt solo model * adapt stereoscope * codacy * rename _CONSTANTS to REGISTRY_KEYS (#1306) * Remove deprecated functions (#1308) * remove unused utils * remove references to removed functions in docs * Cleanup Manager register reference with AttrDict implementation (#1307) * implement attrdict and add it to properties of manager * use attrdict feature model code * address pr comments * codacy * view_anndata_setup new implementation (#1313) * implement attrdict and add it to properties of manager * use attrdict feature model code * address pr comments * view anndata setup implementation * fix bugs and tweak text * Field specific `view_anndata_setup` (#1315) * implement attrdict and add it to properties of manager * use attrdict feature model code * address pr comments * view anndata setup implementation * fix bugs and tweak text * field specific view setup * rich links in docstrings * update get_totalvi_protein_priors code w/ master * Fix docs (#1330) * codacy * address first round of comments * comments in constants file * add view registry tests * fix compat function * Update _layer_field.py * Update _obsm_field.py Co-authored-by: Adam Gayoso <[email protected]>
nrclaudio
pushed a commit
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Jun 21, 2022
* placeholder release notes for base * AnnData Manager refactor (scverse#1238) * move anndata file into anndata subfolder * mock out anndata manager and fields for categorical obs fields only * add layerfield * fix imports * fix imports in models * add temporary test and fix bugs in manager code * manager store on model class, refactor what needs to be defined for a model * clean up some existing code * restructure fields file, clean up more view anndata setup code, add more skeleton * add transfer_field for obs and layer fields * naive implementation of transfer_setup in anndata manager * implement backwards compat with setup dict on load * add docstrings to all new methods * address comments: change to registry_key, change fields to set in manager * add tests for transfer and manager from setup * remove anndata_fields method * address pr comment * Implement NonCategoricalJointObsField (scverse#1247) * implement continuous obsm field * make class specific to joint obs fields * make fields public * address comments * faster concat by subsetting obs * Implement CategoricalJointObsField (scverse#1248) * add categorical joint obs field * fix _make_obsm_categorical * add line in test * address pr comment * Pass manager to data loader (scverse#1280) * pass manager to data loader * address comment * Move and reorganize setup dict out of AnnData into Manager (scverse#1285) * new base field API for setup dict * adapt manager to new registry * backwards compatibility implementation * train works * adapt get_from_registry function * simplify needs transfer logic, working test_scvi * change _REGISTRY_KEYS back to _CONSTANTS * address comments, fix compat test * codacy * Add anndata registration classes to developer API (scverse#1292) * add anndata registration classes to developer API * move manager to anndata submodule to fix docs * Save/Load with saved setup inputs (scverse#1294) * skeleton for new save load, missing field logic * save load with saved setup inputs * add docstring for setup_inputs * codacy * fix documentation * additional pr comments * fix manager imports * Adapt TotalVI to new setup (scverse#1298) * obsm field * adapt totalVI to new setup * fix additional totalvi test * make field registration ordered * fix totalvi protein priors logic * address pr comments * address pr comments * Fix tests for SCVI, TOTALVI, generic AnnData utils (scverse#1299) * adapt totalVI to new setup * fix additional totalvi test * remove run_setup_anndata kwarg, reassign uuid on view copy, fix some tests * remove run_setup_anndata comments * fix transfer anndata test * fix test data format test * fix setup anndata test * fix most pyro tests * fix most scarches tests * remove state dict from field * Adapt all internal models to new setup (scverse#1301) * adapt LDA * adapt linearscvi * remove _get_var_names_from_setup_anndata * adapt peakvi * adapt autozi * adapt scanvi * fix scanvi test * fix totalvi test * fix dataloader tests * fix multiple cov tests * adapt condscvi * adapt destvi * adapt multivi * fix setup compat test * remove get_from_registry util * fix scanvi and peakvi scarches tests * fix backwards compat tests and default missing summary stat in models * address comment * Adapt all external models to new setup (scverse#1302) * adapt cellassign * adapt gimvi * adapt solo model * adapt stereoscope * codacy * rename _CONSTANTS to REGISTRY_KEYS (scverse#1306) * Remove deprecated functions (scverse#1308) * remove unused utils * remove references to removed functions in docs * Cleanup Manager register reference with AttrDict implementation (scverse#1307) * implement attrdict and add it to properties of manager * use attrdict feature model code * address pr comments * codacy * view_anndata_setup new implementation (scverse#1313) * implement attrdict and add it to properties of manager * use attrdict feature model code * address pr comments * view anndata setup implementation * fix bugs and tweak text * Field specific `view_anndata_setup` (scverse#1315) * implement attrdict and add it to properties of manager * use attrdict feature model code * address pr comments * view anndata setup implementation * fix bugs and tweak text * field specific view setup * rich links in docstrings * update get_totalvi_protein_priors code w/ master * Fix docs (scverse#1330) * codacy * address first round of comments * comments in constants file * add view registry tests * fix compat function * Update _layer_field.py * Update _obsm_field.py Co-authored-by: Adam Gayoso <[email protected]>
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