Missed running black on test files

docs/conf.py

@@ -17,11 +17,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'pandas-genomics'
-copyright = '2020, John McGuigan'
-author = 'John McGuigan'
+project = "pandas-genomics"
+copyright = "2020, John McGuigan"
+author = "John McGuigan"
 
 import pandas_genomics
+
 # The short X.Y version.
 version = pandas_genomics.__version__
 # The full version, including alpha/beta/rc tags.
@@ -34,15 +35,15 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.githubpages',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.viewcode',
-    'IPython.sphinxext.ipython_directive',
-    'IPython.sphinxext.ipython_console_highlighting',
-    'numpydoc',
-    'sphinx_copybutton'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "IPython.sphinxext.ipython_directive",
+    "IPython.sphinxext.ipython_console_highlighting",
+    "numpydoc",
+    "sphinx_copybutton",
 ]
 
 # Configuration options for plot_directive. See:
@@ -55,41 +56,42 @@
 numpydoc_show_class_members = False
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 
 # -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 import sphinx_rtd_theme
+
 html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-html_logo = '_static/logo.png'
+html_logo = "_static/logo.png"
 html_theme_options = {
-    'logo_only': True,
+    "logo_only": True,
 }
 
 # Custom sidebar templates, must be a dictionary that maps document names
@@ -98,8 +100,8 @@
 # This is required for the alabaster theme
 # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
 html_sidebars = {
-    '**': [
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
+    "**": [
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
     ]
 }

tests/genotype_array/conftest.py

@@ -69,7 +69,9 @@ def all_boolean_reductions(request):
 # Implement the required fixtures
 @pytest.fixture
 def dtype():
-    variant = Variant(chromosome='chr1', position=123456, id='rs12345', ref='A', alt=['T', 'G'])
+    variant = Variant(
+        chromosome="chr1", position=123456, id="rs12345", ref="A", alt=["T", "G"]
+    )
     return GenotypeDtype(variant=variant)
 
 
@@ -79,11 +81,15 @@ def data():
     * data[0] and data[1] should both be non missing
     * data[0] and data[1] should not be equal
     """
-    alleles = ['A', 'T', 'G']
-    variant = Variant(chromosome='chr1', position=123456, id='rs12345', ref='A', alt=['T', 'G'])
-    genotypes = [variant.make_genotype('A', 'T'), variant.make_genotype('T', 'T')]
+    alleles = ["A", "T", "G"]
+    variant = Variant(
+        chromosome="chr1", position=123456, id="rs12345", ref="A", alt=["T", "G"]
+    )
+    genotypes = [variant.make_genotype("A", "T"), variant.make_genotype("T", "T")]
     for i in range(98):
-        genotypes.append(variant.make_genotype(random.choice(alleles), random.choice(alleles)))
+        genotypes.append(
+            variant.make_genotype(random.choice(alleles), random.choice(alleles))
+        )
     return GenotypeArray(values=genotypes)
 
 
@@ -97,8 +103,10 @@ def data_for_twos():
 @pytest.fixture
 def data_missing():
     """Length-2 array with [NA, Valid]"""
-    variant = Variant(chromosome='chr1', position=123456, id='rs12345', ref='A', alt=['T', 'G'])
-    genotypes = [variant.make_genotype(), variant.make_genotype('T', 'T')]
+    variant = Variant(
+        chromosome="chr1", position=123456, id="rs12345", ref="A", alt=["T", "G"]
+    )
+    genotypes = [variant.make_genotype(), variant.make_genotype("T", "T")]
     return GenotypeArray(values=genotypes)
 
 
@@ -108,10 +116,12 @@ def data_for_sorting():
     This should be three items [B, C, A] with
     A < B < C
     """
-    variant = Variant(chromosome='chr1', position=123456, id='rs12345', ref='A', alt=['T', 'G'])
-    a = variant.make_genotype('A', 'A')
-    b = variant.make_genotype('A', 'T')
-    c = variant.make_genotype('T', 'T')
+    variant = Variant(
+        chromosome="chr1", position=123456, id="rs12345", ref="A", alt=["T", "G"]
+    )
+    a = variant.make_genotype("A", "A")
+    b = variant.make_genotype("A", "T")
+    c = variant.make_genotype("T", "T")
     return GenotypeArray(values=[b, c, a])
 
 
@@ -121,9 +131,11 @@ def data_missing_for_sorting():
     This should be three items [B, NA, A] with
     A < B and NA missing.
     """
-    variant = Variant(chromosome='chr1', position=123456, id='rs12345', ref='A', alt=['T', 'G'])
-    a = variant.make_genotype('A', 'A')
-    b = variant.make_genotype('A', 'T')
+    variant = Variant(
+        chromosome="chr1", position=123456, id="rs12345", ref="A", alt=["T", "G"]
+    )
+    a = variant.make_genotype("A", "A")
+    b = variant.make_genotype("A", "T")
     na = variant.make_genotype()
     return GenotypeArray(values=[b, na, a])
 
@@ -141,7 +153,9 @@ def na_cmp():
 @pytest.fixture
 def na_value():
     """The scalar missing value for this type. Default 'None'"""
-    variant = Variant(chromosome='chr1', position=123456, id='rs12345', ref='A', alt=['T', 'G'])
+    variant = Variant(
+        chromosome="chr1", position=123456, id="rs12345", ref="A", alt=["T", "G"]
+    )
     return variant.make_genotype()
 
 
@@ -151,10 +165,12 @@ def data_for_grouping():
     Expected to be like [B, B, NA, NA, A, A, B, C]
     Where A < B < C and NA is missing
     """
-    variant = Variant(chromosome='chr1', position=123456, id='rs12345', ref='A', alt=['T', 'G'])
-    a = variant.make_genotype('A', 'A')
-    b = variant.make_genotype('A', 'T')
-    c = variant.make_genotype('T', 'T')
+    variant = Variant(
+        chromosome="chr1", position=123456, id="rs12345", ref="A", alt=["T", "G"]
+    )
+    a = variant.make_genotype("A", "A")
+    b = variant.make_genotype("A", "T")
+    c = variant.make_genotype("T", "T")
     na = variant.make_genotype()
     return GenotypeArray([b, b, na, na, a, a, b, c])
 
@@ -165,9 +181,11 @@ def data_for_encoding():
     Contains one alt allele.
     Variants are Homozygouse Ref, Heterozygous, Homozygous Alt, and Missing
     """
-    variant = Variant(chromosome='chr1', position=123456, id='rs12345', ref='A', alt=['T'])
-    a = variant.make_genotype('A', 'A')
-    b = variant.make_genotype('A', 'T')
-    c = variant.make_genotype('T', 'T')
+    variant = Variant(
+        chromosome="chr1", position=123456, id="rs12345", ref="A", alt=["T"]
+    )
+    a = variant.make_genotype("A", "A")
+    b = variant.make_genotype("A", "T")
+    c = variant.make_genotype("T", "T")
     na = variant.make_genotype()
     return GenotypeArray([a, b, c, na])

tests/genotype_array/test_ExtensionArray.py

@@ -35,7 +35,6 @@ class TestParsing(base.BaseParsingTests):
 
 
 class TestMethods(base.BaseMethodsTests):
-
     def test_combine_add(self, data_repeated):
         """Addition of Genotypes isn't valid"""
         pass
@@ -65,6 +64,7 @@ class TestComparisonOps(base.BaseComparisonOpsTests):
 class TestOpsUtil(base.BaseOpsUtil):
     pass
 
+
 # No way to invert a genotype
 # class TestUnaryOps(base.BaseUnaryOpsTests):
 #     pass

tests/genotype_array/test_GenotypeArray.py

@@ -14,43 +14,53 @@ def test_encoding_extra_alt(data):
 
 def test_encoding_additive(data_for_encoding):
     # Test arrays directly
-    expected = pd.array([0, 1, 2, None], dtype='UInt8')
+    expected = pd.array([0, 1, 2, None], dtype="UInt8")
     result = data_for_encoding.encode_additive()
     assert_extension_array_equal(result, expected)
     # Test using series accessor
-    expected = pd.Series(result, name=f"{data_for_encoding.variant.id}_{data_for_encoding.variant.alt}")
+    expected = pd.Series(
+        result, name=f"{data_for_encoding.variant.id}_{data_for_encoding.variant.alt}"
+    )
     result_series = pd.Series(data_for_encoding).genotype.encode_additive()
     assert_series_equal(result_series, expected)
 
 
 def test_encoding_dominant(data_for_encoding):
     # Test arrays directly
-    expected = pd.array([0, 1, 1, None], dtype='UInt8')
+    expected = pd.array([0, 1, 1, None], dtype="UInt8")
     result = data_for_encoding.encode_dominant()
     assert_extension_array_equal(result, expected)
     # Test using series accessor
-    expected = pd.Series(result, name=f"{data_for_encoding.variant.id}_{data_for_encoding.variant.alt}")
+    expected = pd.Series(
+        result, name=f"{data_for_encoding.variant.id}_{data_for_encoding.variant.alt}"
+    )
     result_series = pd.Series(data_for_encoding).genotype.encode_dominant()
     assert_series_equal(result_series, expected)
 
 
 def test_encoding_recessive(data_for_encoding):
     # Test arrays directly
-    expected = pd.array([0, 0, 1, None], dtype='UInt8')
+    expected = pd.array([0, 0, 1, None], dtype="UInt8")
     result = data_for_encoding.encode_recessive()
     assert_extension_array_equal(result, expected)
     # Test using series accessor
-    expected = pd.Series(result, name=f"{data_for_encoding.variant.id}_{data_for_encoding.variant.alt}")
+    expected = pd.Series(
+        result, name=f"{data_for_encoding.variant.id}_{data_for_encoding.variant.alt}"
+    )
     result_series = pd.Series(data_for_encoding).genotype.encode_recessive()
     assert_series_equal(result_series, expected)
 
 
 def test_encoding_codominant(data_for_encoding):
     # Test arrays directly
-    expected = pd.Categorical(["Ref", "Het", "Hom", None], categories=["Ref", "Het", "Hom"], ordered=True)
+    expected = pd.Categorical(
+        ["Ref", "Het", "Hom", None], categories=["Ref", "Het", "Hom"], ordered=True
+    )
     result = data_for_encoding.encode_codominant()
     assert_extension_array_equal(result, expected)
     # Test using series accessor
-    expected = pd.Series(result, name=f"{data_for_encoding.variant.id}_{data_for_encoding.variant.alt}")
+    expected = pd.Series(
+        result, name=f"{data_for_encoding.variant.id}_{data_for_encoding.variant.alt}"
+    )
     result_series = pd.Series(data_for_encoding).genotype.encode_codominant()
     assert_series_equal(result_series, expected)

tests/io/conftest.py

@@ -45,6 +45,7 @@ def vcf_test():
         pytest.skip("VCF IO requires HTSLIB, which isn't easy to install on Windows")
     # Run otherwise
     import cyvcf2
+
     VCF_DIR = Path(cyvcf2.__file__).parent / "tests"
     vcf_filename = VCF_DIR / "test.vcf.gz"
     result = io.from_vcf(vcf_filename)

tests/scalars/test_variant.py

@@ -2,5 +2,5 @@
 
 
 def test_create_variant():
-    variant = Variant('12', 112161652, 'rs12462', ref='C', alt=['T'])
+    variant = Variant("12", 112161652, "rs12462", ref="C", alt=["T"])
     print(variant)