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[WIP] v0.11.0 RC#132

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Commits on Sep 6, 2024

• (feat) added auto handling of traditional pin and testing

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• (fix) added handling of default direction

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Commits on Sep 7, 2024

• (fix) changed intermediate files pin->tsv and fixed tests accordingly

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• (chore) formatting on docs and removed T20 from them

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• (chore) upgraded to upstream actions

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• (chore) removed unused dependency in docs

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• (chore) reformatted tests

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Commits on Dec 4, 2024

• Feature/confidence streaming (wfondrie#127)

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• Small changes for FlashLFQ writer (wfondrie#131)

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Commits on Dec 5, 2024

• wip: formatting and rebasing fixes

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• chore: merge main

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• chore: ruff format

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• wip,chore: re-adding flashlfq support

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• ci,fix: fixed confidence out and ci migration

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• format: eof newline

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• wip,fix: progress to re-add flashlfq output

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• chore: uv lock and formatting

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• chore: added pr template

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Commits on Dec 6, 2024

• wip: make brew generic again

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• wip,fix: added deleter to on psm dataset

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Commits on Dec 7, 2024

• feat: re-added flashlfq support

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• chore: linting + formatting

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Commits on Dec 8, 2024

• fix: fixtures and progess in definition of cols

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• test, fix: annotated/commented new fixtures

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• lint: formatting

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• ci: removed fail on codecov fail

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• ci: test speedup replacing RF with dtree

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• ci: attempt to fix test docker build

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Commits on Dec 13, 2024

• refactor: change stats to dataclass

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Commits on Dec 14, 2024

• refactor: extracted output writer factory

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• refactor: extracted level manager in confidence

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• refactor: extracted level writer group

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Commits on Dec 15, 2024

• refactor: extracted more writer builder work to class

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Commits on Dec 16, 2024

• feat: score propagation and unscored confidence

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• feat(confidence): add data reading api

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• feat,experiment: Experimental qvalue-fdr estimation

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Commits on Dec 17, 2024

• chore,docs: updated basic docs to curr api and updated typing

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• chore: updated basic n joint model docs code (md in progress)

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• chore: updated notebook

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Commits on Dec 19, 2024

• chore,confidence: update docstrings

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• chore,qvalue: removed commented out code

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• Merge pull request #2 from jspaezp/chore/fix_confidence_api

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• chore: fixed line length lints in docstrings

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Commits on Dec 20, 2024

• fix,sqlite: fixed path for sqlite writer

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