Merge branch 'master' into upload-release-to-pypi

.github/workflows/lint.yml

@@ -1,4 +1,4 @@
-name: Lintbb
+name: Lint
 on: [push]
 jobs:
   lint:
@@ -17,4 +17,5 @@ jobs:
           run: |
             pip install ruff
             ruff --output-format=github .
-          continue-on-error: true
+        - name: Check format with ruff
+          run: ruff format --check

conftest.py

@@ -5,6 +5,7 @@
 
 def pytest_runtest_setup(item):
     if isinstance(item, DoctestItem):
-        if sys.version_info.major < 3 or (sys.version_info.major == 3
-                                          and sys.version_info.minor < 6):
-            pytest.skip('Doctests are disabled in Python < 3.6')
+        if sys.version_info.major < 3 or (
+            sys.version_info.major == 3 and sys.version_info.minor < 6
+        ):
+            pytest.skip("Doctests are disabled in Python < 3.6")

doc/conf.py

@@ -17,11 +17,11 @@
 import re
 
 # project root
-sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath(".."))
 
 import matplotlib  # noqa
 
-matplotlib.use('agg')
+matplotlib.use("agg")
 
 import sphinx_rtd_theme  # noqa
 from upsetplot import __version__ as release  # noqa
@@ -40,42 +40,42 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx_gallery.gen_gallery',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'numpydoc',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'sphinx_issues',
-    'nbsphinx',
+    "sphinx_gallery.gen_gallery",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "numpydoc",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx_issues",
+    "nbsphinx",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'upsetplot'
-copyright = u'2018-2023, Joel Nothman'
+project = "upsetplot"
+copyright = "2018-2023, Joel Nothman"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
 
-version = re.match(r'^\d+(\.\d+)*', release).group()
+version = re.match(r"^\d+(\.\d+)*", release).group()
 
 # version = upsetplot.__version__
 # The full version, including alpha/beta/rc tags.
@@ -93,11 +93,11 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ["_build"]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-default_role = 'any'
+default_role = "any"
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
 # add_function_parentheses = True
@@ -111,7 +111,7 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -124,7 +124,7 @@
 
 # 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"
 
 # 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
@@ -153,7 +153,7 @@
 # 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"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -202,18 +202,16 @@
 # html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'project-templatedoc'
+htmlhelp_basename = "project-templatedoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     # 'preamble': '',
 }
@@ -222,8 +220,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    ('index', 'upsetplot.tex', u'upsetplot Documentation',
-     u'Joel Nothman', 'manual'),
+    ("index", "upsetplot.tex", "upsetplot Documentation", "Joel Nothman", "manual"),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -261,24 +258,24 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    'python': ('http://docs.python.org/', None),
-    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
-    'matplotlib': ('https://matplotlib.org/', None),
-    'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
+    "python": ("http://docs.python.org/", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy/", None),
+    "matplotlib": ("https://matplotlib.org/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
 }
 
 
 # Config for sphinx_issues
 
-issues_uri = 'https://github.com/jnothman/upsetplot/issues/{issue}'
-issues_github_path = 'jnothman/upsetplot'
-issues_user_uri = 'https://github.com/{user}'
+issues_uri = "https://github.com/jnothman/upsetplot/issues/{issue}"
+issues_github_path = "jnothman/upsetplot"
+issues_user_uri = "https://github.com/{user}"
 
 
 sphinx_gallery_conf = {
     # path to your examples scripts
-    'examples_dirs': '../examples',
+    "examples_dirs": "../examples",
     # path where to save gallery generated examples
-    'gallery_dirs': 'auto_examples',
-    'backreferences_dir': '_modules',
+    "gallery_dirs": "auto_examples",
+    "backreferences_dir": "_modules",
 }

examples/plot_diabetes.py

@@ -31,18 +31,18 @@
 diabetes_df = pd.DataFrame(diabetes.data, columns=diabetes.feature_names)
 
 # Get five features most correlated with median house value
-correls = diabetes_df.corrwith(pd.Series(diabetes.target),
-                               method='spearman').sort_values()
+correls = diabetes_df.corrwith(
+    pd.Series(diabetes.target), method="spearman"
+).sort_values()
 top_features = correls.index[-5:]
 
 # Get a binary indicator of whether each top feature is above average
 diabetes_above_avg = diabetes_df > diabetes_df.median(axis=0)
 diabetes_above_avg = diabetes_above_avg[top_features]
-diabetes_above_avg = diabetes_above_avg.rename(columns=lambda x: x + '>')
+diabetes_above_avg = diabetes_above_avg.rename(columns=lambda x: x + ">")
 
 # Make this indicator mask an index of diabetes_df
-diabetes_df = pd.concat([diabetes_df, diabetes_above_avg],
-                        axis=1)
+diabetes_df = pd.concat([diabetes_df, diabetes_above_avg], axis=1)
 diabetes_df = diabetes_df.set_index(list(diabetes_above_avg.columns))
 
 # Also give us access to the target (median house value)
@@ -51,10 +51,10 @@
 ##########################################################################
 
 # UpSet plot it!
-upset = UpSet(diabetes_df, subset_size='count', intersection_plot_elements=3)
-upset.add_catplot(value='progression', kind='strip', color='blue')
+upset = UpSet(diabetes_df, subset_size="count", intersection_plot_elements=3)
+upset.add_catplot(value="progression", kind="strip", color="blue")
 print(diabetes_df)
-upset.add_catplot(value='bmi', kind='strip', color='black')
+upset.add_catplot(value="bmi", kind="strip", color="black")
 upset.plot()
 plt.title("UpSet with catplots, for orientation='horizontal'")
 plt.show()
@@ -63,10 +63,14 @@
 
 # And again in vertical orientation
 
-upset = UpSet(diabetes_df, subset_size='count', intersection_plot_elements=3,
-              orientation='vertical')
-upset.add_catplot(value='progression', kind='strip', color='blue')
-upset.add_catplot(value='bmi', kind='strip', color='black')
+upset = UpSet(
+    diabetes_df,
+    subset_size="count",
+    intersection_plot_elements=3,
+    orientation="vertical",
+)
+upset.add_catplot(value="progression", kind="strip", color="blue")
+upset.add_catplot(value="bmi", kind="strip", color="black")
 upset.plot()
 plt.title("UpSet with catplots, for orientation='vertical'")
 plt.show()

examples/plot_discrete.py

@@ -11,24 +11,28 @@
 from matplotlib import pyplot as plt
 from matplotlib import cm
 
-TITANIC_URL = 'https://raw.githubusercontent.com/datasciencedojo/datasets/master/titanic.csv'  # noqa
+TITANIC_URL = (
+    "https://raw.githubusercontent.com/datasciencedojo/datasets/master/titanic.csv"  # noqa
+)
 df = pd.read_csv(TITANIC_URL)
 # Show UpSet on survival and first classs
 df = df.set_index(df.Survived == 1).set_index(df.Pclass == 1, append=True)
 
-upset = UpSet(df,
-              intersection_plot_elements=0)  # disable the default bar chart
-upset.add_stacked_bars(by="Sex", colors=cm.Pastel1,
-                       title="Count by gender", elements=10)
+upset = UpSet(df, intersection_plot_elements=0)  # disable the default bar chart
+upset.add_stacked_bars(
+    by="Sex", colors=cm.Pastel1, title="Count by gender", elements=10
+)
 upset.plot()
 plt.suptitle("Gender for first class and survival on Titanic")
 plt.show()
 
 
-upset = UpSet(df, show_counts=True, orientation="vertical",
-              intersection_plot_elements=0)
-upset.add_stacked_bars(by="Sex", colors=cm.Pastel1,
-                       title="Count by gender", elements=10)
+upset = UpSet(
+    df, show_counts=True, orientation="vertical", intersection_plot_elements=0
+)
+upset.add_stacked_bars(
+    by="Sex", colors=cm.Pastel1, title="Count by gender", elements=10
+)
 upset.plot()
 plt.suptitle("Same, but vertical, with counts shown")
 plt.show()

examples/plot_generated.py

@@ -15,29 +15,29 @@
 ##########################################################################
 
 plot(example)
-plt.suptitle('Ordered by degree')
+plt.suptitle("Ordered by degree")
 plt.show()
 
 ##########################################################################
 
-plot(example, sort_by='cardinality')
-plt.suptitle('Ordered by cardinality')
+plot(example, sort_by="cardinality")
+plt.suptitle("Ordered by cardinality")
 plt.show()
 
 ##########################################################################
 
-plot(example, show_counts='{:d}')
-plt.suptitle('With counts shown')
+plot(example, show_counts="{:d}")
+plt.suptitle("With counts shown")
 plt.show()
 
 ##########################################################################
 
-plot(example, show_counts='%d', show_percentages=True)
-plt.suptitle('With counts and % shown')
+plot(example, show_counts="%d", show_percentages=True)
+plt.suptitle("With counts and % shown")
 plt.show()
 
 ##########################################################################
 
 plot(example, show_percentages="{:.2%}")
-plt.suptitle('With fraction shown in custom format')
+plt.suptitle("With fraction shown in custom format")
 plt.show()

examples/plot_hide.py

@@ -13,29 +13,29 @@
 example = generate_counts()
 
 plot(example, show_counts=True)
-plt.suptitle('Nothing hidden')
+plt.suptitle("Nothing hidden")
 plt.show()
 
 ##########################################################################
 
 plot(example, show_counts=True, min_subset_size=100)
-plt.suptitle('Small subsets hidden')
+plt.suptitle("Small subsets hidden")
 plt.show()
 
 ##########################################################################
 
 plot(example, show_counts=True, max_subset_size=500)
-plt.suptitle('Large subsets hidden')
+plt.suptitle("Large subsets hidden")
 plt.show()
 
 ##########################################################################
 
 plot(example, show_counts=True, min_degree=2)
-plt.suptitle('Degree <2 hidden')
+plt.suptitle("Degree <2 hidden")
 plt.show()
 
 ##########################################################################
 
 plot(example, show_counts=True, max_degree=2)
-plt.suptitle('Degree >2 hidden')
+plt.suptitle("Degree >2 hidden")
 plt.show()