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memento#918

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atolopko-czi wants to merge 83 commits intomainchanzuckerberg/cellxgene-census:mainfrom atol/memento/epicchanzuckerberg/cellxgene-census:atol/memento/epicCopy head branch name to clipboard

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Commits on Dec 6, 2023

• Initial revision

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• python compatibility fix

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• doc updates

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Commits on Dec 11, 2023

• estimators cube schema improvements

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• estimators cube schema improvements

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Commits on Dec 14, 2023

• data fixes

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Commits on Dec 15, 2023

• memento cube builder validation

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• simplify joins memento cube builder

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• diff exp fixes

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• parameterize census_fixture.py script

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• Merge branch 'atol/memento/877-cube-schema-updates' into atol/memento/877-cube-schema-updates--simplify-joins

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• cube builder regression test

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• Fix size_factors join

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Commits on Dec 17, 2023

• log estimator computation anomalies as debug level

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• add missing pip requirement to install notes

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• comments

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Commits on Dec 18, 2023

• TODO

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Commits on Dec 19, 2023

• optimize dense data creation

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Commits on Dec 20, 2023

• pandas memory optimization

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Commits on Dec 21, 2023

• remove memento cube data existence checks

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• Write memento cube batches within each child process

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• Use obs.raw_sum instead of computing equivalent value

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• log progress and estimated time to completion

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• suppress numpy/pandas warnings

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Commits on Jan 2, 2024

• add more cube schema tiledb filters

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Commits on Jan 3, 2024

• normalize obs dims into separate array

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• fix overwrite

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• fix diff_expr for new cube structure

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Commits on Jan 4, 2024

• TODOs

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• Merge branch 'atol/memento/879-move-code-to-census-repo' into atol/memento/epic

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• Merge branch 'atol/memento/877-cube-schema-updates' into atol/memento/epic

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• optimize dense_gene_data()

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• Merge branch 'atol/memento/880-cube-builder-optimizations' into atol/memento/epic

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Commits on Jan 5, 2024

• Remove more unused estimators & consolidate post-build

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• remove improper dependency

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• use raw categorical codes in diff_expr cube

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• handle invalid SEM values in the cube

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• fix numpy warning

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Commits on Jan 8, 2024

• parallelize diff expr

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• move n_obs from estimators to obs_groups array

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• fix input check

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Commits on Jan 9, 2024

• diff expr optimizations

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• lint & typing

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• cube validator

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Commits on Jan 10, 2024

• add profiler

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• factor out methods for clearer profiling output

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• factor out methods for clearer profiling output

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Commits on Jan 11, 2024

• replace cProfile with bespoke timing logic

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• Factor out methods for profiling visibility

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• Factor out methods for profiling visibility

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Commits on Jan 12, 2024

• optimizations

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Commits on Jan 14, 2024

• Add polars library for DataFrame manipulation

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Commits on Jan 15, 2024

• polars fix

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• rm timing output

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• fast LR; disable cprofile

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• cli fix

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Commits on Jan 16, 2024

• use float32 in cube; migration scripts; cube query notebook

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• add features_ids.json to cube

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• add requirements.txt

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• update and move adhoc query notebook

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• Merge branch 'atol/memento/epic' into atol/memento/parallelize-diffexpr-profiler-polars

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• rm feature_ids.json creation

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• refactor profiling code; requirements updates

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• rm sklearnex

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Commits on Jan 18, 2024

• Update README.md

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• fix tiledb config option

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• rename "pass" to "step" and renumber

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Commits on Jan 19, 2024

• fix regression test logic

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• fixes & typing

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• replace print with logging

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• update and enable cube builder regression test

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Commits on Jan 20, 2024

• fix design matrix

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Commits on Jan 23, 2024

• TODO, comments

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• Merge remote-tracking branch 'origin/main' into atol/memento/epic

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• lint

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• Merge branch 'atol/memento/epic' of github.com:chanzuckerberg/cellxgene-census into atol/memento/epic

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Commits on Jan 30, 2024

• Merge branch 'main' into atol/memento/epic

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Commits on Feb 1, 2024

• Add vscode launch.json

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• lint

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Commits on Feb 6, 2024

• feat: allow users to select covariates for memento (#963)

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Commits on Feb 7, 2024

• chore: Write unit test for differential expression computation (#976)

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Commits on Mar 12, 2024

• Merge branch 'main' into atol/memento/epic

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Commits on Mar 15, 2024

• Merge branch 'main' into atol/memento/epic

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