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Packageify & Migrate to Py3#17

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crimBubble merged 74 commits intoflexidot-bio:masterflexidot-bio/flexidot:masterfrom

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May 19, 2025

Commits

Commits on Dec 12, 2024

• rm old releases

  

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• create changelog

  

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• rm old changelog

  

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• init env yaml

  

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• init pyproject toml

  

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• update image paths

  

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• mv docs

  

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• mv images to docs

  

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• mv images to docs

  

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• mv old docs

  

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• mv test data to tests

  

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• add init

  

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• migrate main module to py3

  

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Commits on Dec 17, 2024

• Ignore dynamic _version

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• Limit to Py 3.12.8 until next Biopython release

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• Manage build with Hatch

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• pytest config

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• Update for new args

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• init automated pytest action

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• init auto ruff formatting

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• Archived code for testing

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• update commands

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• init empty test file

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• use logging module

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• Attempt to modularize

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• Fix non-LF line endings on test data

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• New entry point and arg handling!

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• Style fixes by Ruff

  

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• archive unreleased flexidot v2.0.1

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• Add plotting module

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• rm current release link

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• rm bool arg logging

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• Fix unicode str encoding and rm logging bool arg

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Commits on Jan 6, 2025

• Add TODO notes

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• linting

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Commits on Jan 8, 2025

• direct test if true

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• simplify example cases

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• increase log source detail

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• Add arg summary + rm timers

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• rm erroneous logging arg

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• Add input check functions

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• rm time track

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• Fix colormap selection bugs

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Commits on Jan 13, 2025

• mv argparser to utils

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• mv parser + user to set max_n

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• clean prints

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• add max_n report

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• Improve error handling when loading or combining fasta input

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• streamline match finding, fix double counting on self-self

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• basic kmer matching tests

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• test set for TIR plotting

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• change max_n defaults

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• time track returns delta

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• fix norev

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• Add gap

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• update logging in read_seq

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• Standardise logging

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• Tidy up logging

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• cleanup temp degap or concat fasta files

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• seq for test: multi file input, gap, skip N, and ambiguity

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• unused test file

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• rename test data

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• init concat check

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• fix msg fmt

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• Validate all examples

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• Add example data files

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• link to testing data

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• Style fixes by Ruff

  

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• Add note only_vs_first_seq

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• v2.0.0 changelog draft entry

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• Check outdir exists

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• Add outdir opt

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• Add citation message on completion.

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Commits on Apr 14, 2025

• rm % in arg description

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