Code

Jr dev#11

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Merged

mattheww95 merged 55 commits intodevphac-nml/locidex:devfrom jr_devphac-nml/locidex:jr_devCopy head branch name to clipboardMay 2, 2024

Commits

Commits on Mar 20, 2024

• Merge pull request #3 from phac-nml/dev

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  ChristyPeterson

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• Merge pull request #4 from phac-nml/dev

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  ChristyPeterson

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Commits on Mar 21, 2024

• Word smithing introduction

  jrober84

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• Word smithing introduction

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Commits on Mar 26, 2024

• corrected behaviour of extract for overlaping loci

  jrober84

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Commits on Mar 27, 2024

• added new report mode

  jrober84

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Commits on Apr 4, 2024

• Update version.py

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  mattheww95

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Commits on Apr 11, 2024

• corrected paralog handelling

  jrober84

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• paralog work

  jrober84

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• removed testing code

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Commits on Apr 12, 2024

• updated paralog handelling

  jrober84

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Commits on Apr 15, 2024

• added int stop filter

  jrober84

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• added int stop filter

  jrober84

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Commits on Apr 17, 2024

• updated report description

  jrober84

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Commits on Apr 21, 2024

• Merge branch 'tests' of https://github.com/phac-nml/locidex into tests

  jrober84

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Commits on Apr 22, 2024

• updated report format to include db info and sequence data

  jrober84

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• updated report to use the same template as search module

  jrober84

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• updated report to use the same template as search module

  jrober84

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• added in seq_data

  jrober84

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• merge updated template and connection to new report format

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• merge included mafft alignment and production of concatenated alignment

  jrober84

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• added missing input file protection

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• added db_version validation

  jrober84

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• updated search to use manifest, created manifest module

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• removed print

  jrober84

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Commits on Apr 23, 2024

• removed blank space

  jrober84

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• added manifest module

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• removed print

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• changed date format

  jrober84

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• updated db config to respect which db type is enabled

  jrober84

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• corrected path issue with output seq_store

  jrober84

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• removed print

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Commits on Apr 25, 2024

• updated test_db.py tests to pass

  mattheww95

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• updated manifest tests

  mattheww95

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Commits on Apr 29, 2024

• updated db config to dataclass

  mattheww95

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• Added refactor for database config class

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Commits on Apr 30, 2024

• refactored merge module

  mattheww95

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• refactored manifest module

  mattheww95

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• refactored manifest module and tests

  mattheww95

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• refactored manifest module and tests

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  mattheww95

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• updated manifest to allow for multiple versions of different dbs

  mattheww95

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• updated extract, build, search classes

  mattheww95

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• updated tests

  mattheww95

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• fixed merge conflicts

  mattheww95

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• updated tests and and search workflow

  mattheww95

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• updated test data for workflows

  mattheww95

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• updated multi db selection for data using a manifest

  mattheww95

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Commits on May 2, 2024

• added complete workflow tests and updated CI Scripts

  mattheww95

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• updated CI

  mattheww95

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• updated CI

  mattheww95

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• Added pytest-workflow to CI

  mattheww95

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• Added pytest-workflow to CI

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• Added pytest-workflow to CI

  mattheww95

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• altered CI workflow due to tmp dir issues

  mattheww95

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• updated manifest test to remove dependency on order

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