From c0b37088bd1c2a52056e7f65af158efaa8f22ade Mon Sep 17 00:00:00 2001 From: Cunliang Geng Date: Fri, 31 May 2024 17:33:12 +0200 Subject: [PATCH] remove useless unit tests --- tests/unit/scoring/test_metcalf_scoring.py | 7 +----- tests/unit/scoring/test_nplinker_scoring.py | 27 --------------------- 2 files changed, 1 insertion(+), 33 deletions(-) diff --git a/tests/unit/scoring/test_metcalf_scoring.py b/tests/unit/scoring/test_metcalf_scoring.py index 74cdd93f..b1cf4c7a 100644 --- a/tests/unit/scoring/test_metcalf_scoring.py +++ b/tests/unit/scoring/test_metcalf_scoring.py @@ -129,11 +129,7 @@ def test_setup_load_cache(mc, npl): def test_calc_score_raw_score(mc): - """Test `calc_score` method for `raw_score_spec_gcf` and `raw_score_mf_gcf`. - - The expected values are calculated manually by using values from `test_init` - of `test_data_links.py` and the default scoring weights. - """ + """Test `calc_score` method for `raw_score_spec_gcf` and `raw_score_mf_gcf`.""" # link type = 'spec-gcf' mc.calc_score(link_type="spec-gcf") assert_frame_equal( @@ -185,7 +181,6 @@ def test_get_links_gcf_standardised_false(mc, gcfs, spectra, mfs): assert len(links) == 3 assert {i.gcf_id for i in links.keys()} == {"gcf1", "gcf2", "gcf3"} assert isinstance(links[gcfs[0]][spectra[0]], ObjectLink) - # expected values are from `test_get_links_gcf` of test_link_finder.py assert links[gcfs[0]][spectra[0]].data(mc) == 12 assert links[gcfs[1]][spectra[0]].data(mc) == -9 assert links[gcfs[2]][spectra[0]].data(mc) == 11 diff --git a/tests/unit/scoring/test_nplinker_scoring.py b/tests/unit/scoring/test_nplinker_scoring.py index 8062cd75..7464eef7 100644 --- a/tests/unit/scoring/test_nplinker_scoring.py +++ b/tests/unit/scoring/test_nplinker_scoring.py @@ -4,9 +4,6 @@ from nplinker.scoring import ObjectLink -pytestmark = pytest.mark.skip(reason="Skipping all tests in this file temporarily for dev") - - def test_get_links_gcf_standardised_false(npl, mc, gcfs, spectra, mfs, strains_list): """Test `get_links` method when input is GCF objects and `standardised` is False.""" # test raw scores (no standardisation) @@ -20,20 +17,12 @@ def test_get_links_gcf_standardised_false(npl, mc, gcfs, spectra, mfs, strains_l assert len(links) == 3 assert {i.gcf_id for i in links.keys()} == {"gcf1", "gcf2", "gcf3"} assert isinstance(links[gcfs[0]][spectra[0]], ObjectLink) - # expected values are from `test_get_links_gcf` of test_link_finder.py assert links[gcfs[0]][spectra[0]].data(mc) == 12 assert links[gcfs[1]][spectra[0]].data(mc) == -9 assert links[gcfs[2]][spectra[0]].data(mc) == 11 assert links[gcfs[0]][mfs[0]].data(mc) == 12 assert links[gcfs[1]][mfs[1]].data(mc) == 12 assert links[gcfs[2]][mfs[2]].data(mc) == 21 - # expected values are from `test_get_common_strains_spec` of test_data_links.py - assert links[gcfs[0]][spectra[0]].common_strains == [strains_list[0]] - assert links[gcfs[1]][spectra[0]].common_strains == [] - assert links[gcfs[2]][spectra[0]].common_strains == [strains_list[0]] - assert links[gcfs[0]][mfs[0]].common_strains == [strains_list[0]] - assert links[gcfs[1]][mfs[1]].common_strains == [strains_list[1]] - assert set(links[gcfs[2]][mfs[2]].common_strains) == set(strains_list[0:2]) # when test cutoff is 0, i.e. taking scores >= 0 mc.cutoff = 0 @@ -49,12 +38,6 @@ def test_get_links_gcf_standardised_false(npl, mc, gcfs, spectra, mfs, strains_l assert links[gcfs[0]][mfs[0]].data(mc) == 12 assert links[gcfs[1]][mfs[1]].data(mc) == 12 assert links[gcfs[2]][mfs[2]].data(mc) == 21 - # test shared strains - assert links[gcfs[0]][spectra[0]].common_strains == [strains_list[0]] - assert links[gcfs[2]][spectra[0]].common_strains == [strains_list[0]] - assert links[gcfs[0]][mfs[0]].common_strains == [strains_list[0]] - assert links[gcfs[1]][mfs[1]].common_strains == [strains_list[1]] - assert set(links[gcfs[2]][mfs[2]].common_strains) == set(strains_list[0:2]) @pytest.mark.skip(reason="To add after refactoring relevant code.") @@ -78,9 +61,6 @@ def test_get_links_spec_standardised_false(npl, mc, gcfs, spectra, strains_list) assert links[spectra[0]][gcfs[0]].data(mc) == 12 assert links[spectra[0]][gcfs[1]].data(mc) == -9 assert links[spectra[0]][gcfs[2]].data(mc) == 11 - assert links[spectra[0]][gcfs[0]].common_strains == [strains_list[0]] - assert links[spectra[0]][gcfs[1]].common_strains == [] - assert links[spectra[0]][gcfs[2]].common_strains == [strains_list[0]] mc.cutoff = 0 links = npl.get_links(list(spectra), mc, and_mode=True) @@ -92,8 +72,6 @@ def test_get_links_spec_standardised_false(npl, mc, gcfs, spectra, strains_list) assert links[spectra[0]][gcfs[0]].data(mc) == 12 assert links[spectra[0]].get(gcfs[1]) is None assert links[spectra[0]][gcfs[2]].data(mc) == 11 - assert links[spectra[0]][gcfs[0]].common_strains == [strains_list[0]] - assert links[spectra[0]][gcfs[2]].common_strains == [strains_list[0]] @pytest.mark.skip(reason="To add after refactoring relevant code.") @@ -117,9 +95,6 @@ def test_get_links_mf_standardised_false(npl, mc, gcfs, mfs, strains_list): assert links[mfs[0]][gcfs[0]].data(mc) == 12 assert links[mfs[0]][gcfs[1]].data(mc) == -9 assert links[mfs[0]][gcfs[2]].data(mc) == 11 - assert links[mfs[0]][gcfs[0]].common_strains == [strains_list[0]] - assert links[mfs[0]][gcfs[1]].common_strains == [] - assert links[mfs[0]][gcfs[2]].common_strains == [strains_list[0]] mc.cutoff = 0 links = npl.get_links(list(mfs), mc, and_mode=True) @@ -131,8 +106,6 @@ def test_get_links_mf_standardised_false(npl, mc, gcfs, mfs, strains_list): assert links[mfs[0]][gcfs[0]].data(mc) == 12 assert links[mfs[0]].get(gcfs[1]) is None assert links[mfs[0]][gcfs[2]].data(mc) == 11 - assert links[mfs[0]][gcfs[0]].common_strains == [strains_list[0]] - assert links[mfs[0]][gcfs[2]].common_strains == [strains_list[0]] @pytest.mark.skip(reason="To add after refactoring relevant code.")