From 2a3a284cb4d90fce845dc7cc2769949fc6e784bf Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Thu, 28 Sep 2023 19:33:47 -0700 Subject: [PATCH] cleanup and comment plot tests --- tests/test_sourmash.py | 62 +++++++++++++++++++++++++----------------- 1 file changed, 37 insertions(+), 25 deletions(-) diff --git a/tests/test_sourmash.py b/tests/test_sourmash.py index 353837076e..3d49ad745b 100644 --- a/tests/test_sourmash.py +++ b/tests/test_sourmash.py @@ -838,8 +838,10 @@ def test_do_plot_comparison(runtmp): assert os.path.exists(c.output("cmp.matrix.png")) -@utils.in_tempdir -def test_do_plot_comparison_2(c): +def test_do_plot_comparison_2_pdf(runtmp): + # test plot --pdf + c = runtmp + testdata1 = utils.get_test_data('short.fa') testdata2 = utils.get_test_data('short2.fa') c.run_sourmash('sketch', 'translate', '-p', 'k=31,num=500', testdata1, testdata2) @@ -851,8 +853,10 @@ def test_do_plot_comparison_2(c): assert os.path.exists(c.output("cmp.matrix.pdf")) -@utils.in_tempdir -def test_do_plot_comparison_3(c): +def test_do_plot_comparison_3(runtmp): + # test plot --labels + c = runtmp + testdata1 = utils.get_test_data('short.fa') testdata2 = utils.get_test_data('short2.fa') c.run_sourmash('sketch', 'translate', '-p', 'k=31,num=500', testdata1, testdata2) @@ -865,8 +869,10 @@ def test_do_plot_comparison_3(c): assert os.path.exists(c.output("cmp.matrix.png")) -@utils.in_tempdir -def test_do_plot_comparison_4_output_dir(c): +def test_do_plot_comparison_4_output_dir(runtmp): + # test plot --output-dir + c = runtmp + output_dir = c.output('xyz_test') testdata1 = utils.get_test_data('short.fa') @@ -881,8 +887,10 @@ def test_do_plot_comparison_4_output_dir(c): assert os.path.exists(os.path.join(output_dir, "cmp.matrix.png")) -@utils.in_tempdir -def test_do_plot_comparison_5_force(c): +def test_do_plot_comparison_5_force(runtmp): + # test -f to force display of something that's not a distance matrix + c = runtmp + D = numpy.zeros([2, 2]) D[0, 0] = 5 with open(c.output('cmp'), 'wb') as fp: @@ -896,8 +904,10 @@ def test_do_plot_comparison_5_force(c): assert c.last_result.status == 0 -@utils.in_tempdir -def test_do_plot_comparison_4_fail_not_distance(c): +def test_do_plot_comparison_4_fail_not_distance(runtmp): + # plot should fail when not a distance matrix + c = runtmp + D = numpy.zeros([2, 2]) D[0, 0] = 5 with open(c.output('cmp'), 'wb') as fp: @@ -914,31 +924,33 @@ def test_do_plot_comparison_4_fail_not_distance(c): def test_plot_override_labeltext(runtmp): - testdata1 = utils.get_test_data('genome-s10.fa.gz.sig') - testdata2 = utils.get_test_data('genome-s11.fa.gz.sig') - testdata3 = utils.get_test_data('genome-s12.fa.gz.sig') - testdata4 = utils.get_test_data('genome-s10+s11.sig') + # test overriding labeltext + testdata1 = utils.get_test_data('genome-s10.fa.gz.sig') + testdata2 = utils.get_test_data('genome-s11.fa.gz.sig') + testdata3 = utils.get_test_data('genome-s12.fa.gz.sig') + testdata4 = utils.get_test_data('genome-s10+s11.sig') - runtmp.run_sourmash('compare', testdata1, testdata2, testdata3, testdata4, '-o', 'cmp', '-k', '21', '--dna') + runtmp.run_sourmash('compare', testdata1, testdata2, testdata3, testdata4, '-o', 'cmp', '-k', '21', '--dna') - with open(runtmp.output('new.labels.txt'), 'wt') as fp: - fp.write('a\nb\nc\nd\n') + with open(runtmp.output('new.labels.txt'), 'wt') as fp: + fp.write('a\nb\nc\nd\n') - runtmp.sourmash('plot', 'cmp', '--labeltext', 'new.labels.txt') + runtmp.sourmash('plot', 'cmp', '--labeltext', 'new.labels.txt') - print(runtmp.last_result.out) + print(runtmp.last_result.out) - assert 'loading labels from new.labels.txt' in runtmp.last_result.err + assert 'loading labels from new.labels.txt' in runtmp.last_result.err - expected = """\ + expected = """\ 0\ta 1\tb 2\tc 3\td""" - assert expected in runtmp.last_result.out + assert expected in runtmp.last_result.out def test_plot_override_labeltext_fail(runtmp): + # test failed override of labeltext testdata1 = utils.get_test_data('genome-s10.fa.gz.sig') testdata2 = utils.get_test_data('genome-s11.fa.gz.sig') testdata3 = utils.get_test_data('genome-s12.fa.gz.sig') @@ -960,7 +972,7 @@ def test_plot_override_labeltext_fail(runtmp): def test_plot_reordered_labels_csv(runtmp): - # test 'plot --csv' + # test 'plot --csv' & correct ordering of labels c = runtmp ss2 = utils.get_test_data('2.fa.sig') @@ -970,8 +982,6 @@ def test_plot_reordered_labels_csv(runtmp): c.run_sourmash('compare', '-k', '31', '-o', 'cmp', ss2, ss47, ss63) c.run_sourmash('plot', 'cmp', '--csv', 'neworder.csv') - print(open(c.output('neworder.csv'), 'rt').read()) - with open(c.output('neworder.csv'), newline="") as fp: r = csv.DictReader(fp) @@ -1008,6 +1018,7 @@ def test_plot_reordered_labels_csv_gz(runtmp): def test_plot_subsample_1(runtmp): + # test plotting with --subsample testdata1 = utils.get_test_data('genome-s10.fa.gz.sig') testdata2 = utils.get_test_data('genome-s11.fa.gz.sig') testdata3 = utils.get_test_data('genome-s12.fa.gz.sig') @@ -1027,6 +1038,7 @@ def test_plot_subsample_1(runtmp): def test_plot_subsample_2(runtmp): + # test plotting --subsample with --subsample-seed testdata1 = utils.get_test_data('genome-s10.fa.gz.sig') testdata2 = utils.get_test_data('genome-s11.fa.gz.sig') testdata3 = utils.get_test_data('genome-s12.fa.gz.sig')