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Refactoring code and storing configs #15

Merged
merged 12 commits into from
Oct 10, 2023
Merged

Refactoring code and storing configs #15

merged 12 commits into from
Oct 10, 2023

Commits on Oct 10, 2023

  1. MAINT: make sure to commit after Genome.add_records()

    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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  2. ENH: added CompressedGenome.add_compressed_records() 

    [NEW] provide sequences already compressed to this method
    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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  3. MAINT: tweaks to CompressedGenome related code 

    [CHANGED] renamed _to_bytes() to _str_to_bytes() and renamed
    _from_bytes() to _bytes_to_str()

[CHANGED] _compress and _decompress to public names compress_it,
    decompress_it

[CHANGED] the CompressedGenome.add_records() now calls the new
    add_compressed_records() method.
    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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  4. MAINT: refactor installing genome seqs 

    [CHANGED] now use the CompressedGenome class
    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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  5. ENH: save resolved config file into staging directory 

    [NEW] added _config.DOWNLOADED_CONFIG_NAME constant

[NEW] add Config.to_dict(), Config.write() methods. The latter
    uses the to_dict() method, and writes an ini file to
    self.staging_path / DOWNLOADED_CONFIG_NAME
    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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  6. ENH: write the fully resolved config during download

    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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  7. MAINT: install now only uses download dir

    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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  8. MAINT: updated API on HomologyDb

    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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  9. API: change genome names to end with db

    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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  10. API: renamed files for consistency 

    [CHANGED] all modules containing db classes have db at end
    of filename and names start with _
    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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  11. MAINT: code tidy

    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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  12. MAINT: remove unused import

    @GavinHuttley
    GavinHuttley committed Oct 10, 2023
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