Add parquet and sqlite support; add NNLS-based PEP and Q-value calculation#119

Merged

wfondrie merged 269 commits intowfondrie:mainfrom msaid-de:feature/parquet-sqlite-hist-nnls

Sep 6, 2024

+52,946-11,572

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Commits on Feb 23, 2024

Commits on Feb 27, 2024

Feature/improve speed and limit memory (#11 )

sambenfredj
authored and
gessulat
committed
💄 linting (#12 )
gessulat
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Fix bugs (#17 )
gessulat
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fix test model: remove subset_max_train from percolator model (#18 )

sambenfredj
authored and
gessulat
committed
Fix test brew: (#20 )

sambenfredj
authored and
gessulat
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fix test datasets: (#19 )

sambenfredj
authored and
gessulat
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Fix test confidence (#22 )

sambenfredj
authored and
gessulat
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Fix cli tests: (#28 )

sambenfredj
authored and
gessulat
committed
Fix system tests: (#29 )

sambenfredj
authored and
gessulat
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Fix parser pin test: (#30 )

sambenfredj
authored and
gessulat
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Add tests: (#31 )

sambenfredj
authored and
gessulat
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Fix writer tests: (#32 )

sambenfredj
authored and
gessulat
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fix error no psms found during training : if no psms passed the fdr value then raise error that model performed worse (#33 )

sambenfredj
authored and
gessulat
committed
Introduce new executable and bug fixes

sambenfredj
authored and
gessulat
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✨ force ci re-run
gessulat
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💄 lint mokapot
gessulat
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💄 lints tests
gessulat
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💄 fixes format with ruff
gessulat
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💄 fixes format with ruff
gessulat
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💄 make ruff and black happy together
gessulat
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✨ removed deprecated error ignore
gessulat
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Merge branch 'main' into 'feature/sync'
Siegfried Gessulat
committed
Merge branch 'feature/sync' into 'main'

Siegfried Gessulat
authored and
gessulat
committed
Merge branch 'feature/elmars_algorithms' into 'main'
Siegfried Gessulat
committed

Commits on Mar 11, 2024

Commits on Mar 13, 2024

Commits on Mar 14, 2024

Fix cli system and utils tests
ezander
committed

Commits on Mar 15, 2024

Fix unit tests
ezander
committed

Commits on Mar 20, 2024

Merge branch 'fix/nnls_bug2' into 'main'
ezander
committed
Add documentation and test for create_chunks
ezander
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Make cli unit tests for aggregateP2P easier debuggable
ezander
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Improve test for peptide_csv in test_utils
ezander
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Improve and test convert_targets_column function
ezander
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Enable switching in system tests from subprocess to direct calls
ezander
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Fix cli system and utils tests
ezander
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Fix unit tests
ezander
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Merged origin/fix/cleanup into fix/cleanup
ezander
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parquet reader for mokapot
Vishal Sukumar
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merge sort function adapted for parquet
Vishal Sukumar
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brew function adapted for parquet input
Vishal Sukumar
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confidence assignment modified for parquet format
Vishal Sukumar
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merge sort chunk size added as constant
Vishal Sukumar
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update label func modified for parquet
Vishal Sukumar
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main function uses format arg to choose between csv and parquet
Vishal Sukumar
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pyarrow added to dependancies
Vishal Sukumar
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Commits on Mar 21, 2024

Change conversion of target column values
ezander
committed

Commits on Mar 22, 2024

Commits on Mar 26, 2024

refactored unchunked file reader for parquet and csv
Vishal Sukumar
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Merge branch 'feature/parquet_parser' into 'main'
Vishal Sukumar
committed

Commits on Mar 28, 2024

Commits on Apr 1, 2024

Commits on Apr 2, 2024

Merge branch 'revert-3ce5ca1f' into 'main'
Florian Seefried
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Disable parallel unit tests when debugging
ezander
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Merge branch 'fix/cleanup' into 'main'
micgrab
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Commits on Apr 3, 2024

Commits on Apr 4, 2024

Commits on Apr 8, 2024

Commits on Apr 10, 2024

Merge branch 'feature/rollup' into 'main'
Siegfried Gessulat
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squashed sqlite writer branch
micgrab
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failing test fixed
Vishal Sukumar
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unused function get_unique_peptides_from_psms removed
Vishal Sukumar
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Commits on Apr 15, 2024

format interpreted implicitly using filename
Vishal Sukumar
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Confidencewriter class implemented
Vishal Sukumar
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sqlite path changed to Path type
Vishal Sukumar
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perquet module deleted and integrated into read_pin
Vishal Sukumar
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failing tests fixed
Vishal Sukumar
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Commits on Apr 16, 2024

instantiation done before returning object
Vishal Sukumar
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PSM_PEP column name changed to POSTERIOR_ERROR_PROBABILITY
Vishal Sukumar
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Merge branch 'feature/sqlite_write_cherry_picked' into 'main'
Siegfried Gessulat
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Commits on Apr 17, 2024

add pipeline status for main branch
Siegfried Gessulat
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✨ fixes #54
gessulat
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Merge branch 'feature/54-markdown-licenses' into 'main'
Vishal Sukumar
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Do some cosmetics
ezander
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Commits on Apr 18, 2024

Commits on Apr 22, 2024

Separate general tabular data and confidence writer stuff
ezander
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Commits on Apr 23, 2024

Commits on Apr 24, 2024

Add better unit test for (chunked) confidence
ezander
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Make chunked confidence unit test fail with small chunk size
ezander
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Fix confidence chunk size bug
ezander
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test case added for sqlite writer
Vishal Sukumar
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test data added for sqlite writer
Vishal Sukumar
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Add option for suppressing warnings
ezander
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Merge branch 'fix/suppress_warnings' into 'main'
Siegfried Gessulat
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Revert the change in confidence and adapt unit test
ezander
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Merge branch 'fix/chunking' into 'main'
Siegfried Gessulat
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prepare tables sqlite db added as helper func
Vishal Sukumar
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Merge branch 'feature/sqlite_test' into 'main'
Siegfried Gessulat
committed

Commits on Apr 25, 2024

Commits on Apr 26, 2024

Commits on Apr 30, 2024

Commits on May 6, 2024

Add JoinedTabularData and tests
ezander
committed

Commits on May 8, 2024

Commits on May 15, 2024

buffered write for parquet intermediary files implemented
Vishal Sukumar
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tests updated for parquet writing
Vishal Sukumar
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fixed aggregatePsmstoPeptides cli
Vishal Sukumar
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test data structure changed to list of dicts to match merge sort output structure
Vishal Sukumar
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test data updated to be dataframe readable
Vishal Sukumar
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Remove aggregatePsmsToPeptides
ezander
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Commits on May 17, 2024

fixed rollup app for parquets
Vishal Sukumar
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Merge branch 'feature/new_cli' into feature/new_cli_parquet
Vishal Sukumar
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Merge branch 'feature/new_cli_parquet' into 'feature/new_cli'
Vishal Sukumar
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Merge branch 'feature/new_cli' into 'main'
Vishal Sukumar
committed

Commits on May 29, 2024

Unify csv and parquet methods in merge_sort
ezander
committed

Commits on May 30, 2024

Commits on Jun 5, 2024

Merge branch 'fix/merge_sort_problem' into 'main'
tkschmidt
committed

Commits on Jun 14, 2024

Fix problem with type conversions in merge_sort
ezander
committed

Commits on Jun 17, 2024

Merge branch 'fix/fail_on_bad_input' into 'main'
Siegfried Gessulat
committed

Commits on Jun 20, 2024

✨ addresses @jspaezp suggestions from PR wfondrie#119
gessulat
committed

Commits on Jun 21, 2024

✨ addresses review suggestions
gessulat
committed
Merge branch 'feature/parquet-sqlite-hist-nnls-review' into 'feature/parquet-sqlite-hist-nnls'
Siegfried Gessulat
committed

Commits on Jul 8, 2024

(chore) updated cicd,ruff,black and tests (#42 )
jspaezp
authored

Commits on Jul 9, 2024

✨ fix setting scores when training failed
gessulat
committed

Commits on Jul 29, 2024

Commits on Sep 3, 2024

Merge pull request #46 from msaid-de/feature/pin-to-tsv-convert
tkschmidt
authored