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KANBAN-504 seq retrieval #2

Merged
merged 32 commits into from
Mar 14, 2024
Merged

KANBAN-504 seq retrieval #2

merged 32 commits into from
Mar 14, 2024

Commits on Mar 6, 2024

  1. Built basic framework for seq retrieval component

    @mluypaert
    mluypaert committed Mar 6, 2024
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Commits on Mar 7, 2024

  1. Updated input params to match single sequence retrieval and added inp… 

    …ut validation
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    mluypaert committed Mar 7, 2024
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  2. Added code for basic (+ strand) seq retrieval

    @mluypaert
    mluypaert committed Mar 7, 2024
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  3. Refactored faidx to enable more broad seq functions import

    @mluypaert
    mluypaert committed Mar 7, 2024
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  4. Added support for correct negative strand sequence retrieval (and cha… 

    …ining)
    @mluypaert
    mluypaert committed Mar 7, 2024
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  5. Added additional python pysam and biopython package installation depe… 

    …ndencies
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    mluypaert committed Mar 7, 2024
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Commits on Mar 8, 2024

  1. Updated fasta_file option to support remote URLs

    @mluypaert
    mluypaert committed Mar 8, 2024
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  2. Added Make targets for easy python dependency installation

    @mluypaert
    mluypaert committed Mar 8, 2024
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  3. Sorted python requirements alphabetically

    @mluypaert
    mluypaert committed Mar 8, 2024
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  4. Minor docstring update

    @mluypaert
    mluypaert committed Mar 8, 2024
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  5. Added option to reuse local cache

    @mluypaert
    mluypaert committed Mar 8, 2024
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  6. Prevent reads of partial streamed file after interrupts

    @mluypaert
    mluypaert committed Mar 8, 2024
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Commits on Mar 11, 2024

  1. Refactor to improve code readability

    @mluypaert
    mluypaert committed Mar 11, 2024
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  2. Minor refactor to improve code readability

    @mluypaert
    mluypaert committed Mar 11, 2024
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Commits on Mar 12, 2024

  1. Unused import cleanup

    @mluypaert
    mluypaert committed Mar 12, 2024
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  2. Added framework for PR validation through GH actions

    @mluypaert
    mluypaert committed Mar 12, 2024
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  3. Added python type testing + included in PR validation

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    mluypaert committed Mar 12, 2024
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  4. Python type checking bugfix

    @mluypaert
    mluypaert committed Mar 12, 2024
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  5. Added main app dependencies as dependency for type testing

    @mluypaert
    mluypaert committed Mar 12, 2024
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  6. Fixed typing errors reported by mypy

    @mluypaert
    mluypaert committed Mar 12, 2024
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  7. Updated GH actions runner to current Ubuntu LTS (22.04)

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    mluypaert committed Mar 12, 2024
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  8. GH actions checkout version bump (to deprecate node.js v16 usage)

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    mluypaert committed Mar 12, 2024
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  9. Added vscode configs to gitignore

    @mluypaert
    mluypaert committed Mar 12, 2024
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  10. Added output typing for all methods and functions

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    mluypaert committed Mar 12, 2024
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  11. Bugfix for seqRegion sorting in chain_seq_region_seqs() function

    @mluypaert
    mluypaert committed Mar 12, 2024
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  12. Additional main functions arguments and output typing

    @mluypaert
    mluypaert committed Mar 12, 2024
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Commits on Mar 13, 2024

  1. Added typing guidelines to README

    @mluypaert
    mluypaert committed Mar 13, 2024
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  2. Comply with google-style docstring documentation 

    This enables relevant IDE tooltip hints in VS Code (and presumably other IDEs) and thus more efficient coding.
    @mluypaert
    mluypaert committed Mar 13, 2024
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  3. Added sequence length assertion to SeqRegion class

    @mluypaert
    mluypaert committed Mar 13, 2024
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Commits on Mar 14, 2024

  1. Improved readability of typing + add typing for click values

    @mluypaert
    mluypaert committed Mar 14, 2024
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  2. Moved tests files and configs to more standard path

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    mluypaert committed Mar 14, 2024
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  3. Added flake8 style check and made code compliant

    @mluypaert
    mluypaert committed Mar 14, 2024
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