Merge branch 'master' into issue-845-bokeh

Author: jonbrenas

tests/integration/test_adar1.py

@@ -1,7 +1,4 @@
-import pytest
-
-from malariagen_data import Adar1, Region
-from malariagen_data.util import _locate_region, _resolve_region
+from malariagen_data import Adar1
 
 
 def setup_adar1(url="simplecache::gs://vo_adar_release_master_us_central1/", **kwargs):
@@ -18,60 +15,60 @@ def setup_adar1(url="simplecache::gs://vo_adar_release_master_us_central1/", **k
     return Adar1(url, **kwargs)
 
 
-def test_repr():
-    adar1 = setup_adar1(check_location=True)
-    assert isinstance(adar1, Adar1)
-    r = repr(adar1)
-    assert isinstance(r, str)
+# def test_repr():
+#    adar1 = setup_adar1(check_location=True)
+#    assert isinstance(adar1, Adar1)
+#    assert isinstance(r, str)
+#    r = repr(adar1)
 
 
-@pytest.mark.parametrize(
-    "region_raw",
-    [
-        "2",
-        "gene-LOC125950257",
-        "2:4871446-4871535",
-        "2:2,630,355-2,633,221",
-        Region("2", 4871446, 4871535),
-    ],
-)
-def test_locate_region(region_raw):
-    # TODO Migrate this test.
-    adar1 = setup_adar1()
-    gene_annotation = adar1.geneset(attributes=["ID"])
-    region = _resolve_region(adar1, region_raw)
-    pos = adar1.snp_sites(region=region.contig, field="POS")
-    # Used by some code that has not been added yet
-    # ref = adar1.snp_sites(region=region.contig, field="REF")
-    loc_region = _locate_region(region, pos)
+# @pytest.mark.parametrize(
+#    "region_raw",
+#    [
+#        "2",
+#        "gene-LOC125950257",
+#        "2:4871446-4871535",
+#        "2:2,630,355-2,633,221",
+#        Region("2", 4871446, 4871535),
+#    ],
+# )
+# def test_locate_region(region_raw):
+#    # TODO Migrate this test.
+#    adar1 = setup_adar1()
+#    gene_annotation = adar1.geneset(attributes=["ID"])
+#    region = _resolve_region(adar1, region_raw)
+#    pos = adar1.snp_sites(region=region.contig, field="POS")
+#    # Used by some code that has not been added yet
+#    # ref = adar1.snp_sites(region=region.contig, field="REF")
+#    loc_region = _locate_region(region, pos)
 
-    # check types
-    assert isinstance(loc_region, slice)
-    assert isinstance(region, Region)
+# check types
+#    assert isinstance(loc_region, slice)
+#    assert isinstance(region, Region)
 
-    # check Region with contig
-    if region_raw == "2":
-        assert region.contig == "2"
-        assert region.start is None
-        assert region.end is None
+# check Region with contig
+#    if region_raw == "2":
+#        assert region.contig == "2"
+#        assert region.start is None
+#        assert region.end is None
 
-    # check that Region goes through unchanged
-    if isinstance(region_raw, Region):
-        assert region == region_raw
+# check that Region goes through unchanged
+#    if isinstance(region_raw, Region):
+#        assert region == region_raw
 
-    # check that gene name matches coordinates from the geneset and matches gene sequence
-    if region_raw == "gene-LOC125950257":
-        gene = gene_annotation.query("ID == 'gene-LOC125950257'").squeeze()
-        assert region == Region(gene.contig, gene.start, gene.end)
-        assert pos[loc_region][0] == gene.start
-        assert pos[loc_region][-1] == gene.end
-        # To be checked
-        # assert (
-        #    ref[loc_region][:5].compute() == np.array(["T", "T", "G", "T", "T"])
-        # ).all()
+# check that gene name matches coordinates from the geneset and matches gene sequence
+#    if region_raw == "gene-LOC125950257":
+#        gene = gene_annotation.query("ID == 'gene-LOC125950257'").squeeze()
+#        assert region == Region(gene.contig, gene.start, gene.end)
+#        assert pos[loc_region][0] == gene.start
+#        assert pos[loc_region][-1] == gene.end
+# To be checked
+# assert (
+#    ref[loc_region][:5].compute() == np.array(["T", "T", "G", "T", "T"])
+# ).all()
 
-    # check string parsing
-    if region_raw == "2:4871446-4871535":
-        assert region == Region("2", 4871446, 4871535)
-    if region_raw == "2:2,630,355-2,633,221":
-        assert region == Region("2", 2630355, 2633221)
+# check string parsing
+#    if region_raw == "2:4871446-4871535":
+#        assert region == Region("2", 4871446, 4871535)
+#    if region_raw == "2:2,630,355-2,633,221":
+#        assert region == Region("2", 2630355, 2633221)