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Release v0.1.0 #21

Merged
merged 91 commits into from
Feb 29, 2024
Merged

Release v0.1.0 #21

merged 91 commits into from
Feb 29, 2024

Commits on Oct 5, 2023

  1. fixed typos, requirements and tests

    @khoroshevskyi
    khoroshevskyi committed Oct 5, 2023
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Commits on Oct 17, 2023

  1. Fixed incorrect md5sum of bed files

    @khoroshevskyi
    khoroshevskyi committed Oct 17, 2023
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Commits on Oct 19, 2023

  1. Fixed #19

    @khoroshevskyi
    khoroshevskyi committed Oct 19, 2023
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Commits on Oct 27, 2023

  1. ignore test outputs

    @nsheff
    nsheff committed Oct 27, 2023
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  2. simplify test docker instructions

    @nsheff
    nsheff committed Oct 27, 2023
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  3. remove dockerfile (not needed)

    @nsheff
    nsheff committed Oct 27, 2023
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Commits on Oct 30, 2023

  1. Fixed tests and updated bed hashing

    @khoroshevskyi
    khoroshevskyi committed Oct 30, 2023
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Commits on Nov 1, 2023

  1. Fixed #20

    @khoroshevskyi
    khoroshevskyi committed Nov 1, 2023
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Commits on Nov 20, 2023

  1. Fixed errors in pipeline due to bbclient and qdrant update

    @khoroshevskyi
    khoroshevskyi committed Nov 20, 2023
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Commits on Nov 27, 2023

  1. 1. Fixed bedbuncher and bedstut 

    2. Added uploading with pep
    @khoroshevskyi
    khoroshevskyi committed Nov 27, 2023
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  2. Fixed insert cli

    @khoroshevskyi
    khoroshevskyi committed Nov 27, 2023
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  3. Updated initiation of bbconf object (initiaded once for insert option)

    @khoroshevskyi
    khoroshevskyi committed Nov 27, 2023
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Commits on Nov 28, 2023

  1. Unified pipeline Manager

    @khoroshevskyi
    khoroshevskyi committed Nov 28, 2023
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  2. added s3 uploading

    @khoroshevskyi
    khoroshevskyi committed Nov 28, 2023
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  3. fixed bedbuncher bbc

    @khoroshevskyi
    khoroshevskyi committed Nov 28, 2023
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  4. updated dependencies

    @khoroshevskyi
    khoroshevskyi committed Nov 28, 2023
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Commits on Nov 30, 2023

  1. pipeline manager improvments

    @khoroshevskyi
    khoroshevskyi committed Nov 30, 2023
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Commits on Dec 7, 2023

  1. fixed #25

    @khoroshevskyi
    khoroshevskyi committed Dec 7, 2023
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  2. narrowpeak spec fix

    @khoroshevskyi
    khoroshevskyi committed Dec 7, 2023
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  3. Added uploading to s3 to bedstat

    @khoroshevskyi
    khoroshevskyi committed Dec 7, 2023
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Commits on Dec 11, 2023

  1. Updated documentation

    @khoroshevskyi
    khoroshevskyi committed Dec 11, 2023
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Commits on Jan 2, 2024

  1. Updated requirements

    @khoroshevskyi
    khoroshevskyi committed Jan 2, 2024
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Commits on Jan 9, 2024

  1. Update README.md 

    Correct typos
    @donaldcampbelljr
    donaldcampbelljr authored Jan 9, 2024
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Commits on Jan 29, 2024

  1. Update bedboss/__init__.py

    @donaldcampbelljr
    donaldcampbelljr authored Jan 29, 2024
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  2. update pre-commit to use black instead of ruff

    @donaldcampbelljr
    donaldcampbelljr committed Jan 29, 2024
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  3. remove ruff comments, update repo url

    @donaldcampbelljr
    donaldcampbelljr committed Jan 29, 2024
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  4. try again based on black's own documentation

    @donaldcampbelljr
    donaldcampbelljr committed Jan 29, 2024
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  5. lint

    @donaldcampbelljr
    donaldcampbelljr committed Jan 29, 2024
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  6. update doc strings

    @donaldcampbelljr
    donaldcampbelljr committed Jan 29, 2024
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  7. remove unused code

    @donaldcampbelljr
    donaldcampbelljr committed Jan 29, 2024
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  8. add consistency to naming

    @donaldcampbelljr
    donaldcampbelljr committed Jan 29, 2024
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  9. change f to file for readability

    @donaldcampbelljr
    donaldcampbelljr committed Jan 29, 2024
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  10. update qdrant index doc strings

    @donaldcampbelljr
    donaldcampbelljr committed Jan 29, 2024
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Commits on Jan 30, 2024

  1. add func upload_pephub for uploading BED metadata 

    #31
    @donaldcampbelljr
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Commits on Jan 31, 2024

  1. Changed arguments based on newest version of PEPHubClient().sample.cr… 

    …eate

#31
    @donaldcampbelljr
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  2. Add Sample attributes to other_metadata when uploading to pephub 

    #31
    @donaldcampbelljr
    donaldcampbelljr committed Jan 31, 2024
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Commits on Feb 1, 2024

  1. add upload_pephub cli argument 

    #31
    @donaldcampbelljr
    donaldcampbelljr committed Feb 1, 2024
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  2. Fix parsed_pep_list to parsed_pep_dict 

    #31
    @donaldcampbelljr
    donaldcampbelljr committed Feb 1, 2024
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Commits on Feb 9, 2024

  1. Initial work on bedclassifier for https://github.com/databio/bedbase/… 

    …issues/55
    @donaldcampbelljr
    donaldcampbelljr committed Feb 9, 2024
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Commits on Feb 12, 2024

  1. Handle .gz files, add basic test https://github.com/databio/bedbase/i… 

    …ssues/55
    @donaldcampbelljr
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  2. Add reporting results via pm.report_result, use nrows for performance… 

    … increase #34
    @donaldcampbelljr
    donaldcampbelljr committed Feb 12, 2024
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  3. Merge pull request #33 from databio/dev_phc_bed_Metadata 

    Allow uploading meta data from input pep to an output pep via registry path
    @khoroshevskyi
    khoroshevskyi authored Feb 12, 2024
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Commits on Feb 13, 2024

  1. Add error handling when reading csv, defualt to "unknown_bedtype" #34

    @donaldcampbelljr
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  2. Add better exception handling and allowing for integer/float chromoso… 

    …mes in column 0 #34
    @donaldcampbelljr
    donaldcampbelljr committed Feb 13, 2024
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  3. Fix returns, and grouped exceptions

    @donaldcampbelljr
    donaldcampbelljr committed Feb 13, 2024
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  4. work on metadata and cleaning

    @khoroshevskyi
    khoroshevskyi committed Feb 13, 2024
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  5. add clarity to errors

    @donaldcampbelljr
    donaldcampbelljr committed Feb 13, 2024
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  6. skip first rows of bed file if they are not in column format

    @donaldcampbelljr
    donaldcampbelljr committed Feb 13, 2024
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  7. add simple narrowPeak and broadPeak logic for classification

    @donaldcampbelljr
    donaldcampbelljr committed Feb 13, 2024
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  8. remove unused code

    @donaldcampbelljr
    donaldcampbelljr committed Feb 13, 2024
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  9. comment out manual test

    @donaldcampbelljr
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Commits on Feb 14, 2024

  1. comment out main call for manual test, add pytest skipping for tests

    @donaldcampbelljr
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  2. add returning tuple when classifying, e.g. (f"bed{bedtype}+{n}", "bro… 

    …adpeak")
    @donaldcampbelljr
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  3. Merge pull request #35 from databio/dev_assign_bed_format 

    Add Bed Classifier
    @khoroshevskyi
    khoroshevskyi authored Feb 14, 2024
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Commits on Feb 15, 2024

  1. big refactoring

    @khoroshevskyi
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  2. fix error with reporting tuples

    @donaldcampbelljr
    donaldcampbelljr committed Feb 15, 2024
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  3. adjust broadpeak/narrowpeak logic

    @donaldcampbelljr
    donaldcampbelljr committed Feb 15, 2024
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  4. added model of output metadata

    @khoroshevskyi
    khoroshevskyi committed Feb 15, 2024
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Commits on Feb 16, 2024

  1. allow BedClassifier to handle returned None from get_bed_type

    @donaldcampbelljr
    donaldcampbelljr committed Feb 16, 2024
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  2. get_bed_type always returns a tuple

    @donaldcampbelljr
    donaldcampbelljr committed Feb 16, 2024
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  3. for bed type catch all return bed type instead of "unknown_bedtype"

    @donaldcampbelljr
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  4. Added pipeline stop if necessary

    @khoroshevskyi
    khoroshevskyi committed Feb 16, 2024
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  5. Fixed #30

    @khoroshevskyi
    khoroshevskyi committed Feb 16, 2024
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Commits on Feb 20, 2024

  1. add more logic for catching narrowpeak and broadpeak files that are n… 

    …ot named as such #34
    @donaldcampbelljr
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Commits on Feb 21, 2024

  1. Add simple tests #34

    @donaldcampbelljr
    donaldcampbelljr committed Feb 21, 2024
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  2. Use all, fix column out of range error #34

    @donaldcampbelljr
    donaldcampbelljr committed Feb 21, 2024
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  3. Fixed bedmaker bed format

    @khoroshevskyi
    khoroshevskyi committed Feb 21, 2024
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  4. Merge pull request #39 from databio/dev_update_bed_classifier 

    Update bed classifier
    @khoroshevskyi
    khoroshevskyi authored Feb 21, 2024
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  5. Fixed bedmaker bed format

    @khoroshevskyi
    khoroshevskyi committed Feb 21, 2024
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  6. moved uploading to db from stats to bedboss

    @khoroshevskyi
    khoroshevskyi committed Feb 21, 2024
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  7. fixed tests

    @khoroshevskyi
    khoroshevskyi committed Feb 21, 2024
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  8. updated models

    @khoroshevskyi
    khoroshevskyi committed Feb 21, 2024
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  9. updated metadata model

    @khoroshevskyi
    khoroshevskyi committed Feb 21, 2024
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  10. updated phc logger

    @khoroshevskyi
    khoroshevskyi committed Feb 21, 2024
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  11. Merge pull request #40 from databio/restructuring 

    Restructuring
    @khoroshevskyi
    khoroshevskyi authored Feb 21, 2024
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Commits on Feb 22, 2024

  1. Fixed #41

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  2. Fixed #42

    @khoroshevskyi
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  3. Fixed #32

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    khoroshevskyi committed Feb 22, 2024
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  4. fixed bedsets

    @khoroshevskyi
    khoroshevskyi committed Feb 22, 2024
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  5. fixed bedsets 2

    @khoroshevskyi
    khoroshevskyi committed Feb 22, 2024
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Commits on Feb 26, 2024

  1. added requirement test to cli

    @khoroshevskyi
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  2. Merge pull request #44 from databio/restructuring 

    Restructuring
    @khoroshevskyi
    khoroshevskyi authored Feb 26, 2024
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  3. updated docs

    @khoroshevskyi
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  4. Merge branch 'restructuring' into dev

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  5. updated docs

    @khoroshevskyi
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  6. Updated usage

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  7. Updated README

    @khoroshevskyi
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Commits on Feb 27, 2024

  1. Updated README

    @khoroshevskyi
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  2. Updated README

    @khoroshevskyi
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Commits on Feb 29, 2024

  1. Updated installation

    @khoroshevskyi
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  2. Updated requirements

    @khoroshevskyi
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