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Cohort Tracker#658

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eroell merged 50 commits intotheislab:maintheislab/ehrapy:mainfrom eroell:pop-logCopy head branch name to clipboardMar 13, 2024

+865-3

Commits

Commits on Feb 12, 2024

• nb with stuff that at least does not just fail

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Commits on Feb 13, 2024

• population logging and tracking first support

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Commits on Feb 14, 2024

• refined and first-line debugged population tracking

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• population to cohort

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• cohort logging with tests

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Commits on Feb 15, 2024

• toy notebook cleaned

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Commits on Feb 29, 2024

• small comments included

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• documentation working somewhat

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Commits on Mar 1, 2024

• remove class in tests

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• move read_csv to fixture

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Commits on Mar 5, 2024

• remove tracking dict, use tableones for tracking instead

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• remove DataFrame as accepted input

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• legend label order matching bar order

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• prepare type detection for alignment, added test

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Commits on Mar 6, 2024

• add ax and remove unused args, return not solved yet

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• tests for plots, move to pyplot for flowchart

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Commits on Mar 9, 2024

• Update ehrapy/tools/cohort_tracking/_cohort_tracker.py

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• Update ehrapy/tools/cohort_tracking/_cohort_tracker.py

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• remove reset, add updated notebook for quick check

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• typehints and review comments

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• remove comment in test

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• tableone to requirements?

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Commits on Mar 12, 2024

• allow typehint union

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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• Fix scanpy pre-release compat

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• Remove anndata warning ignore

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• future import fixed in test conf

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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• track_t1 -> tracked_tables

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Commits on Mar 13, 2024

• updates with better names, label-dicts, better colors, more tests

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• Merge branch 'pop-log' of github.com:eroell/ehrapy into pop-log

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• remove grid lines, add notebook for testimages generation

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• prettier docstring demo

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• Update ehrapy/tools/cohort_tracking/_cohort_tracker.py

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• Update ehrapy/tools/cohort_tracking/_cohort_tracker.py

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• Update ehrapy/tools/cohort_tracking/_cohort_tracker.py

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• Update ehrapy/tools/cohort_tracking/_cohort_tracker.py

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• Update ehrapy/tools/cohort_tracking/_cohort_tracker.py

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• remove old comments, better variable names, simplify adata check

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• Merge branch 'pop-log' of github.com:eroell/ehrapy into pop-log

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• fix two doc typos

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• Merge branch 'main' of github.com:eroell/ehrapy

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• Merge branch 'main' into pop-log

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• identical Returns field

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