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Add pyani compare#364

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baileythegreen wants to merge 73 commits intomasterwiddowquinn/pyani:masterfrom comparewiddowquinn/pyani:compareCopy head branch name to clipboard

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Commits on Oct 8, 2021

• Add files for pyani compare

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Commits on Nov 2, 2021

• Add functions to pyani_orm.py for pyani compare

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• Rename pyani compare parser options

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• Connect pyani compare to pyani

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• Initial code for pyani compare

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• Add missing type hint

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• Correct calculation of Hadamard distances

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Commits on Nov 4, 2021

• Add imports

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• Define convenience structs and plotting method dictionaries

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• Remove scratch notes

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• Rewrite database approach for increased efficiency

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• Add code to loop over run pairs and subset data matrices

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• Add code to calculate difference matrices

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• Add code to get labels

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• Add code to get heatmaps

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Commits on Nov 5, 2021

• Rename convenience struct

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• Merge dictionaries holding difference matrices

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• Rewrite get_heatmap() for looping over output formats

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• Change from itertools.permutations to itertools.combinations

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• Add distribution plotting code

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• Update compare_parser.py

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• Abstract out difference matrix creation

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• Rename RunMetadatato RunData

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• Abstract out label and class acquisition

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• Update comment skeleton

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Commits on Nov 7, 2021

• Remove unnecessary imports

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• Use multiprocessing to parallelise the plots

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Commits on Nov 8, 2021

• Add workers option to compare parser

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• Add scatter plot function

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• Add code for timed tests

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Commits on Nov 10, 2021

• Change parameter values

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• Rearrange imports

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• Add comments and docstrings

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• Update heatmap colourbar end value calculation

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• Merge branch 'master' of https://github.com/widdowquinn/pyani into compare

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• Add mpl scatter command to dictionary

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• Merge branch 'compare' of https://github.com/widdowquinn/pyani into compare

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• Remove timing code

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Commits on Dec 4, 2021

• Replace f-string in logging command

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• Merge branch 'master' of https://github.com/widdowquinn/pyani into compare

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• Replace f-strings in logging statements

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Commits on Dec 5, 2021

• Change compare parser mechanics

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• Fix heatmap title

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• Add Bland-Altman code to sns.__init__.py

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Commits on Dec 6, 2021

• Save output files to a subdirectory

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• Tidy up plot titles

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• Tidy up loose comments, docstrings, imports

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• Add Bland-Altman code to subcmd_compare.py

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Commits on Dec 12, 2021

• Retrieve traceback from multiprocessing workers

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• Move output file naming outside of plotting functions

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• Implement alternative logging for multiprocess workers

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• Clean up comments and docstrings

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• Remove get_info() function from init.py

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• Clean up Bland-Altman code

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• Add mpl Bland-Altman code

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• Resize mpl heatmaps so labels are legible

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• Write out summary files

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• Add type hints

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Commits on Dec 13, 2021

• Add documentation for pyani compare

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Commits on Dec 15, 2021

• Change variable name to avoid conflict with args Namespace

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• Alter logging messages to avoid loop-induced repetition

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• Reset outsubdir to avoid nesting

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• Clean up comments and logging

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• Change file mode

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Commits on Apr 5, 2022

• Make absdiff heatmap colours non-divergent, others centred at zero

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• Specify xlim values for (abs)diff distribution plots

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• Update plot names to reflect direction of comparison

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Commits on May 17, 2022

• Merge branch 'master' into compare

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Commits on May 24, 2022

• Add default centre value to cmap values

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• Add value for centre to missed dictionary entry

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Commits on Jun 16, 2022

• Add additional element to cmap tuples for 'centre'

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• Merge branch 'master' of https://github.com/widdowquinn/pyani into compare

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• Merge branch 'compare' of https://github.com/widdowquinn/pyani into compare

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