implementing Variant.__repr__

[chriscrsmith]

Description

Returning a string representation of the raw data for a variant without spewing megabytes of text.

Fixes #2694

Notes:

• If a site has experienced many mutations (as with one of the test cases), the repr() output can be quite large (~6600 characters for one test case). I left this as is for now.
• added a test, checking that len(repr(variant)) < 10000
• I didn't add anything to the docs yet

PR Checklist:

• Tests that fully cover new/changed functionality.
• Documentation including tutorial content if appropriate.
• Changelogs, if there are API changes.

[codecov]

Codecov Report

Merging #2695 (5daf0af) into main (ba5d66a) will decrease coverage by 13.14%.
The diff coverage is 33.33%.

❗ Current head 5daf0af differs from pull request most recent head d7dd944. Consider uploading reports for the commit d7dd944 to get more accurate results

@@             Coverage Diff             @@
##             main    #2695       +/-   ##
===========================================
- Coverage   94.00%   80.86%   -13.14%     
===========================================
  Files          29       29               
  Lines       28070    27782      -288     
  Branches     1585     1312      -273     
===========================================
- Hits        26386    22465     -3921     
- Misses       1648     5221     +3573     
- Partials       36       96       +60     

Flag	Coverage Δ
c-tests	92.26% <ø> (ø)
lwt-tests	89.05% <ø> (ø)
python-c-tests	71.17% <33.33%> (-0.01%)	⬇️
python-tests	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
python/tskit/genotypes.py	31.63% <33.33%> (-67.42%)	⬇️
python/tskit/cli.py	0.00% <0.00%> (-96.95%)	⬇️
python/tskit/vcf.py	7.87% <0.00%> (-90.56%)	⬇️
python/tskit/text_formats.py	9.87% <0.00%> (-90.13%)	⬇️
python/tskit/drawing.py	10.92% <0.00%> (-88.31%)	⬇️
python/tskit/stats.py	12.99% <0.00%> (-85.58%)	⬇️
python/tskit/intervals.py	19.61% <0.00%> (-80.39%)	⬇️
python/tskit/combinatorics.py	41.49% <0.00%> (-57.88%)	⬇️
python/tskit/trees.py	46.20% <0.00%> (-52.57%)	⬇️
... and 4 more

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[jeromekelleher]

Looks great, thanks @chriscrsmith!

Can you paste in an example of what this looks like please?

[benjeffery]

Thanks @chriscrsmith!
Just a couple of minor comments, then it's good to merge.

[chriscrsmith]

Example output:

Variant({'site': Site(id=4, position=97801505.0, ancestral_state='T', mutations=[Mutation(id=4, site=4, node=30647, derived_state='A', parent=-1, metadata={'mutation_list': []}, time=30.135398854734376, edge=93786)], metadata=b''), 'samples': array([ 0, 1, 2, ..., 22855, 22856, 22857], dtype=int32), 'alleles': ('T', 'A'), 'genotypes': array([0, 0, 0, ..., 0, 0, 0], dtype=int32), 'has_missing_data': False, 'isolated_as_missing': 1})

And a longer example, from tests/test_genotypes.py:

Variant({'site': Site(id=0, position=0.0, ancestral_state='C', mutations=[Mutation(id=0, site=0, node=8, derived_state='G', parent=-1, metadata={'foo': 'n_mutations_0'}, time=2667.608851448006, edge=380), Mutation(id=1, site=0, node=217, derived_state='G', parent=-1, metadata={'foo': 'n_mutations_1'}, time=2425.261482015569, edge=371), Mutation(id=2, site=0, node=8, derived_state='T', parent=0, metadata={'foo': 'n_mutations_2'}, time=2244.539354591147, edge=380), Mutation(id=3, site=0, node=8, derived_state='G', parent=2, metadata={'foo': 'n_mutations_3'}, time=1757.3165010264859, edge=380), Mutation(id=4, site=0, node=187, derived_state='C', parent=1, metadata={'foo': 'n_mutations_4'}, time=1722.3181109326438, edge=354), Mutation(id=5, site=0, node=204, derived_state='A', parent=-1, metadata={'foo': 'n_mutations_5'}, time=1582.8304459003948, edge=370), Mutation(id=6, site=0, node=204, derived_state='T', parent=5, metadata={'foo': 'n_mutations_6'}, time=1528.2758355792398, edge=370), Mutation(id=7, site=0, node=62, derived_state='T', parent=4, metadata={'foo': 'n_mutations_7'}, time=1067.4406919914602, edge=236), Mutation(id=8, site=0, node=80, derived_state='C', parent=1, metadata={'foo': 'n_mutations_8'}, time=1067.3525903283573, edge=338), Mutation(id=9, site=0, node=8, derived_state='T', parent=3, metadata={'foo': 'n_mutations_9'}, time=1014.6272474926118, edge=380), Mutation(id=10, site=0, node=78, derived_state='G', parent=4, metadata={'foo': 'n_mutations_10'}, time=814.0050926266172, edge=179), Mutation(id=11, site=0, node=37, derived_state='A', parent=4, metadata={'foo': 'n_mutations_11'}, time=789.2733680668103, edge=294), Mutation(id=12, site=0, node=32, derived_state='T', parent=1, metadata={'foo': 'n_mutations_12'}, time=737.3299514705911, edge=196), Mutation(id=13, site=0, node=78, derived_state='T', parent=10, metadata={'foo': 'n_mutations_13'}, time=723.4207151671163, edge=179), Mutation(id=14, site=0, node=21, derived_state='G', parent=4, metadata={'foo': 'n_mutations_14'}, time=690.0505206401573, edge=208), Mutation(id=15, site=0, node=17, derived_state='C', parent=6, metadata={'foo': 'n_mutations_15'}, time=682.2665224720806, edge=195), Mutation(id=16, site=0, node=37, derived_state='C', parent=11, metadata={'foo': 'n_mutations_16'}, time=669.4367836154175, edge=294), Mutation(id=17, site=0, node=4, derived_state='G', parent=4, metadata={'foo': 'n_mutations_17'}, time=616.446641249868, edge=156), Mutation(id=18, site=0, node=37, derived_state='A', parent=16, metadata={'foo': 'n_mutations_18'}, time=562.246881209518, edge=294), Mutation(id=19, site=0, node=88, derived_state='C', parent=1, metadata={'foo': 'n_mutations_19'}, time=544.0367311716333, edge=103), Mutation(id=20, site=0, node=8, derived_state='G', parent=9, metadata={'foo': 'n_mutations_20'}, time=533.0561026628599, edge=380), Mutation(id=21, site=0, node=13, derived_state='G', parent=6, metadata={'foo': 'n_mutations_21'}, time=522.472812667567, edge=326), Mutation(id=22, site=0, node=7, derived_state='C', parent=1, metadata={'foo': 'n_mutations_22'}, time=498.5647240606464, edge=204), Mutation(id=23, site=0, node=78, derived_state='C', parent=13, metadata={'foo': 'n_mutations_23'}, time=477.9634290872342, edge=179), Mutation(id=24, site=0, node=13, derived_state='T', parent=21, metadata={'foo': 'n_mutations_24'}, time=399.12490967472513, edge=326), Mutation(id=25, site=0, node=70, derived_state='T', parent=4, metadata={'foo': 'n_mutations_25'}, time=393.88467311832983, edge=101), Mutation(id=26, site=0, node=21, derived_state='A', parent=14, metadata={'foo': 'n_mutations_26'}, time=368.75034368650824, edge=208), Mutation(id=27, site=0, node=7, derived_state='T', parent=22, metadata={'foo': 'n_mutations_27'}, time=314.0656767695335, edge=204), Mutation(id=28, site=0, node=32, derived_state='A', parent=12, metadata={'foo': 'n_mutations_28'}, time=286.55445412227243, edge=196), Mutation(id=29, site=0, node=7, derived_state='C', parent=27, metadata={'foo': 'n_mutations_29'}, time=275.8245274129919, edge=204), Mutation(id=30, site=0, node=21, derived_state='C', parent=26, metadata={'foo': 'n_mutations_30'}, time=214.80423590748185, edge=208), Mutation(id=31, site=0, node=7, derived_state='T', parent=29, metadata={'foo': 'n_mutations_31'}, time=196.1373450749133, edge=204), Mutation(id=32, site=0, node=39, derived_state='G', parent=19, metadata={'foo': 'n_mutations_32'}, time=191.19194691507988, edge=87), Mutation(id=33, site=0, node=28, derived_state='G', parent=19, metadata={'foo': 'n_mutations_33'}, time=170.12282642461471, edge=96), Mutation(id=34, site=0, node=28, derived_state='C', parent=33, metadata={'foo': 'n_mutations_34'}, time=159.88367311045664, edge=96), Mutation(id=35, site=0, node=20, derived_state='C', parent=6, metadata={'foo': 'n_mutations_35'}, time=143.67051844412873, edge=122), Mutation(id=36, site=0, node=30, derived_state='G', parent=23, metadata={'foo': 'n_mutations_36'}, time=35.657691380446494, edge=26), Mutation(id=37, site=0, node=28, derived_state='G', parent=34, metadata={'foo': 'n_mutations_37'}, time=32.67691409795943, edge=96), Mutation(id=38, site=0, node=38, derived_state='G', parent=19, metadata={'foo': 'n_mutations_38'}, time=7.570763846286966, edge=86)], metadata={'foo': 'n_sites_0'}), 'samples': array([  1,   3,   5,   7,   9,  11,  13,  15,  17,  19,  21,  23,  25,
        27,  29,  31,  33,  35,  37,  39,  41,  43,  45,  47,  49,  51,
        53,  55,  57,  59,  61,  63,  65,  67,  69,  71,  73,  75,  77,
        79,  81,  83,  85,  87,  89,  91,  93,  95,  97,  99, 101, 103,
       105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129,
       131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155,
       157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181,
       183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207,
       209, 211, 213, 215, 217, 219, 221, 223, 225, 227, 229, 231, 233],
      dtype=int32), 'alleles': ('C', 'G', 'T', 'A', None), 'genotypes': array([ 2,  2,  2,  2,  0,  2,  2,  2,  0,  0,  0,  1,  2,  2,  1,  0,  0,
        2,  3,  1, -1, -1, -1, -1, -1, -1,  0, -1, -1, -1, -1, -1, -1, -1,
       -1, -1, -1, -1, -1, -1, -1,  0, -1, -1, -1,  1,  0,  1, -1, -1,  2,
       -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,  0, -1, -1, -1,
        2, -1, -1, -1, -1, -1, -1, -1,  0, -1, -1, -1, -1, -1, -1, -1,  0,
        0, -1, -1, -1, -1, -1, -1, -1,  0, -1, -1, -1, -1, -1, -1, -1,  2,
       -1, -1,  1, -1, -1,  1,  1, -1, -1, -1,  0, -1, -1, -1, -1],
      dtype=int32), 'has_missing_data': True, 'isolated_as_missing': 1})

[jeromekelleher]

LGTM, thanks @chriscrsmith !

[jeromekelleher]

Can you update the CHANGELOG with your contribution also please @chriscrsmith?

[chriscrsmith]

Can you update the CHANGELOG with your contribution also please @chriscrsmith?

done!

[jeromekelleher]

Great! Just needs commit squash and we're good to merge I think

[chriscrsmith]

done

[benjeffery]

Great, thanks @chriscrsmith. Almost there, just need the changelog in the right place. As we only just released I haven't made a new section yet - sorry!

[chriscrsmith]

Fixed the changelog, and squashed

[benjeffery]

Thanks @chriscrsmith!