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First pass at modular DataPipeline #1

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First pass at modular DataPipeline #1

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Commits on Aug 2, 2021

  1. Fix a few typos. 

    PiperOrigin-RevId: 388172326
Change-Id: I11d9e498c226cd752947feb51b7d1eb343b4d7ab
    @Augustin-Zidek @copybara-github
    Augustin-Zidek authored and copybara-github committed Aug 2, 2021
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  2. Add a direct link to PDB70 2020-05-13. 

    PiperOrigin-RevId: 388195957
Change-Id: Id22b96c964a82e3450a5f457d8facd1e85b1e86a
    @Augustin-Zidek @copybara-github
    Augustin-Zidek authored and copybara-github committed Aug 2, 2021
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Commits on Aug 12, 2021

  1. Remove a redundant space. 

    PiperOrigin-RevId: 390355132
Change-Id: I920a80db674541af41ee83ef3d5bd5255c782ee9
    @Augustin-Zidek @copybara-github
    Augustin-Zidek authored and copybara-github committed Aug 12, 2021
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Commits on Aug 13, 2021

  1. Set versions of libraries AlphaFold Colab notebook depends on. 

    PiperOrigin-RevId: 390553964
Change-Id: Ia5bc6e12ab3f1a7827b7d914c93f6990a1139780
    @Augustin-Zidek @copybara-github
    Augustin-Zidek authored and copybara-github committed Aug 13, 2021
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  2. Use pLDDT in the B-factor column of the output PDBs. 

    PiperOrigin-RevId: 390566020
Change-Id: I3fafbe8246d0a5ad018f0398b39bf7dacee00468
    @Augustin-Zidek @copybara-github
    Augustin-Zidek authored and copybara-github committed Aug 13, 2021
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Commits on Aug 18, 2021

  1. git co c2bc13b .gitignore

    Ethan Ho committed Aug 18, 2021
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  2. cp alphafold/data/pipeline.py

    Ethan Ho committed Aug 18, 2021
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  3. Halfway through refactor as a dataclass

    Ethan Ho committed Aug 18, 2021
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  4. Finish process refactor

    Ethan Ho committed Aug 18, 2021
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  5. Entrypoint script uses ModularDataPipeline

    Ethan Ho committed Aug 18, 2021
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  6. git co c2bc13b job.slurm

    Ethan Ho committed Aug 18, 2021
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  7. Fix syntax errors

    Ethan Ho committed Aug 18, 2021
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  8. Move cli interface to dedicated submodule

    Ethan Ho committed Aug 18, 2021
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  9. Add afpipeline as console_script

    Ethan Ho committed Aug 18, 2021
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  10. Minimal click CLI

    Ethan Ho committed Aug 18, 2021
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  11. Sets are not hashable

    Ethan Ho committed Aug 18, 2021
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  12. hhsearch hits cached as ASCII

    Ethan Ho committed Aug 18, 2021
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  13. Click command for jackhmmer_mgnify

    Ethan Ho committed Aug 18, 2021
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Commits on Aug 19, 2021

  1. Working cache

    Ethan Ho committed Aug 19, 2021
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  2. Change console script to af2

    Ethan Ho committed Aug 19, 2021
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  3. Interface tweaks

    Ethan Ho committed Aug 19, 2021
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Commits on Aug 20, 2021

  1. Properly order kwarg keys

    Ethan Ho committed Aug 20, 2021
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  2. Expose cache directory as env var

    Ethan Ho committed Aug 20, 2021
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  3. cache_to_pckl in its own module

    Ethan Ho committed Aug 20, 2021
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Commits on Aug 23, 2021

  1. Catch NoneType kwargs

    Ethan Ho committed Aug 23, 2021
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  2. Logging for click CLI commands

    Ethan Ho committed Aug 23, 2021
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