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Merge Staging for release of 2.4.0#584

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pchaumeil merged 27 commits intomasterEcogenomics/GTDBTk:masterfrom stagingEcogenomics/GTDBTk:stagingCopy head branch name to clipboardApr 24, 2024

+1,129-538

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Commits on Nov 23, 2023

• fix: Skip empty files for the sketch step

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Commits on Dec 10, 2023

• setup.py: use ~= to constrain major version

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Commits on Mar 18, 2024

• Merge pull request #577 from Ecogenomics/master

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Commits on Mar 19, 2024

• feat(migrating to skani): create a skani class and rename all vairables to skani

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• feat(finish modifying all classes for skani):

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Commits on Mar 26, 2024

• feat(rewrite documentation for skani, modify dockerfile):

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Commits on Mar 27, 2024

• build(docker): Update docker for Skani

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Commits on Mar 28, 2024

• docs(rewrite documentation to use skani):

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Commits on Apr 1, 2024

• docs(update changelogs):

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• Merge pull request #565 from Artoria2e5/patch-1

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Commits on Apr 2, 2024

• feat(af divided by 100, skani doesnt return ani with 0 anymore):

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Commits on Apr 4, 2024

• fix(we sort only by af and not ani/af):

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• Merge pull request #579 from Ecogenomics/skani_branch

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Commits on Apr 8, 2024

• fix(fixing of issue #573):

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Commits on Apr 10, 2024

• Merge pull request #580 from Ecogenomics/issue573

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• feat(change in summary file):

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• docs(improve documentation for --genes flag): related to #571

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• Merge pull request #581 from Ecogenomics/rename_summary_fields

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Commits on Apr 11, 2024

• feat(fix of #576):

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• Merge pull request #582 from Ecogenomics/issue576

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Commits on Apr 16, 2024

• docs(update doco for R220):

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• refactor(updating random.sample to avoid deprecation):

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Commits on Apr 17, 2024

• feat(update setup.py):

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• feat(update version):

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Commits on Apr 23, 2024

• docs(Update docs):

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Commits on Apr 24, 2024

• Merge branch 'staging' into issue540

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• feat(fix merging with 540):

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