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Issue 373 #375

Merged
merged 33 commits into from
Jan 20, 2022
Merged

Issue 373 #375

merged 33 commits into from
Jan 20, 2022

Commits on Jan 19, 2022

  1. update Makefile and requirements.txt 

    Unpinned SQLAlchemy so that Python 3.9 can be used.
Updated makefile to use -o and --run_id arguments in new CLI.
    @widdowquinn
    widdowquinn committed Jan 19, 2022
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  2. Add multiprocessing support to pyani plot

    @baileythegreen @widdowquinn
    baileythegreen authored and widdowquinn committed Jan 19, 2022
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  3. Revert "Parser choices"

    @baileythegreen @widdowquinn
    baileythegreen authored and widdowquinn committed Jan 19, 2022
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  4. Add parser option to override matrix labels

    @baileythegreen @widdowquinn
    baileythegreen authored and widdowquinn committed Jan 19, 2022
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  5. Ensure genomes are sorted

    @baileythegreen @widdowquinn
    baileythegreen authored and widdowquinn committed Jan 19, 2022
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  6. Fix genome sorting

    @baileythegreen @widdowquinn
    baileythegreen authored and widdowquinn committed Jan 19, 2022
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  7. Change nargs for pyani plot 

    This should not ever have more than one value as files will just be
overwritten.
    @baileythegreen @widdowquinn
    baileythegreen authored and widdowquinn committed Jan 19, 2022
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  8. Add docs/subcmd_plot.rst

    @baileythegreen @widdowquinn
    baileythegreen authored and widdowquinn committed Jan 19, 2022
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  9. Add docs/subcmd_report.rst 

    I am less familiar with how this should work, and therefore this file
probably requires more scrutiny.
    @baileythegreen @widdowquinn
    baileythegreen authored and widdowquinn committed Jan 19, 2022
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  10. Remove references to ANIm from ANIb documentation

    @baileythegreen @widdowquinn
    baileythegreen authored and widdowquinn committed Jan 19, 2022
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  11. Add test for NUCmer version parsing regex

    @baileythegreen @widdowquinn
    baileythegreen authored and widdowquinn committed Jan 19, 2022
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  12. tidy test_mummer_single long filenames

    @widdowquinn
    widdowquinn committed Jan 19, 2022
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  13. update test_anim.py to use pandas.testing

    @widdowquinn
    widdowquinn committed Jan 19, 2022
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  14. update test_anim.py to use keywords for .sort_index()

    @widdowquinn
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  15. remove unused import, unnecessary parentheses

    @widdowquinn
    widdowquinn committed Jan 19, 2022
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  16. restore changes to ANIb docs

    @widdowquinn
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  17. restored changes to docs for subcmd_plot

    @widdowquinn
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  18. restore changes to docs for subcmd_report

    @widdowquinn
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  19. restore changes to subcmd_plot.py

    @widdowquinn
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  20. restore changes to subcmd_report.py

    @widdowquinn
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  21. restore changes to plot_parser.py and subcmd_anim.py

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  22. allow exception to report an identifier rather than an error

    @widdowquinn
    widdowquinn committed Jan 19, 2022
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  23. update Makefile for new report CLI

    @widdowquinn
    widdowquinn committed Jan 19, 2022
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  24. bring plotting up to date with master

    @widdowquinn
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  25. bring ANIm up to date with master

    @widdowquinn
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  26. bring tests up to date with master

    @widdowquinn
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Commits on Jan 20, 2022

  1. fix to resolve pandas deprecation warning

    @widdowquinn
    widdowquinn committed Jan 20, 2022
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  2. fix to avoid pandas future deprecation, and remove unused imports

    @widdowquinn
    widdowquinn committed Jan 20, 2022
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  3. suppress non-relevant scipy cluster warning about distance matrices

    @widdowquinn
    widdowquinn committed Jan 20, 2022
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  4. make warning filter more precise

    @widdowquinn
    widdowquinn committed Jan 20, 2022
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  5. suppress warning about SQL JOIN statements arising from pandas

    @widdowquinn
    widdowquinn committed Jan 20, 2022
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  6. suppress pandas/SQL SAWarnings about Cartesian joins

    @widdowquinn
    widdowquinn committed Jan 20, 2022
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  7. make plt.close() consistent across all plots 

    This is functionally useless, I think.
    @widdowquinn
    widdowquinn committed Jan 20, 2022
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