Merge branch 'master' into 0.8.X

# Conflicts:
#	upsetplot/__init__.py

.github/workflows/lint.yml

@@ -0,0 +1,20 @@
+name: Lintbb
+on: [push]
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+        - uses: actions/checkout@v4
+        - name: Set up Python
+          uses: actions/setup-python@v4
+          with:
+            python-version: '3.x'
+        - name: Install dependencies
+          run: |
+            python -m pip install --upgrade pip
+            pip install .
+        - name: Lint with Ruff
+          run: |
+            pip install ruff
+            ruff --output-format=github .
+          continue-on-error: true

.github/workflows/test.yml

@@ -0,0 +1,29 @@
+name: Build
+on: [push]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        conda-deps:
+          - python=3.6 pandas=1.0 matplotlib=2.1.2 numpy=1.17
+          - pandas matplotlib numpy
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+      - name: conda debug info
+        shell: bash -el {0}
+        run: conda info -a
+      - name: install
+        shell: bash -el {0}
+        run: |
+          conda install pytest pytest-cov coveralls ${{ matrix.conda-deps }}
+          python setup.py install
+          cp ci/matplotlibrc matplotlibrc
+      - name: test
+        shell: bash -el {0}
+        run: pytest
+      - name: Coveralls
+        uses: coverallsapp/github-action@v2

.gitignore

@@ -20,6 +20,7 @@
 .ipynb_checkpoints
 .tags
 .cache/
+.direnv/
 
 # Compiled source #
 ###################
@@ -84,3 +85,4 @@ Thumbs.db
 *.cpp
 
 .pytest_cache
+.envrc

CHANGELOG.rst

@@ -10,6 +10,8 @@ What's new in version 0.8
 - Added `subsets` attribute to QueryResult. (:issue:`198`)
 - Fixed a bug where more than 64 categories could result in an error. (:issue:`193`)
 
+Patch release 0.8.1 handles deprecations in dependencies.
+
 What's new in version 0.7
 -------------------------
 

LICENSE

@@ -1,6 +1,6 @@
 New BSD License
 
-Copyright (c) 2018 Joel Nothman.
+Copyright (c) 2018-2023 Joel Nothman.
 All rights reserved.
 
 

README.rst

@@ -164,10 +164,10 @@ References
     :alt: Latest version on PyPi
     :target: https://badge.fury.io/py/UpSetPlot
 
-.. |build| image:: https://travis-ci.org/jnothman/UpSetPlot.svg?branch=master
-    :alt: Travis CI build status
+.. |build| image:: https://github.com/jnothman/upsetplot/actions/workflows/test.yml/badge.svg
+    :alt: Github Workflows CI build status
     :scale: 100%
-    :target: https://travis-ci.org/jnothman/UpSetPlot
+    :target: https://github.com/jnothman/UpSetPlot/actions/workflows/test.yml
 
 .. |issues| image:: https://img.shields.io/github/issues/jnothman/UpSetPlot.svg
     :alt: Issue tracker

doc/conf.py

@@ -67,7 +67,7 @@
 
 # General information about the project.
 project = u'upsetplot'
-copyright = u'2018-2022, Joel Nothman'
+copyright = u'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

setup.py

@@ -19,8 +19,7 @@ def setup_package():
               version=version,
               packages=["upsetplot"],
               license='BSD-3-Clause',
-              setup_requires=['pytest-runner'],
-              tests_require=['pytest>=2.7', 'pytest-cov<2.6'],
+              extras_require={'testing': ['pytest>=2.7', 'pytest-cov<2.6']},
               # TODO: check versions
               install_requires=['pandas>=0.23', 'matplotlib>=2.0'])
     finally:

upsetplot/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.8.0'
+__version__ = '0.8.2'
 
 import os
 

upsetplot/plotting.py

@@ -656,7 +656,10 @@ def plot_matrix(self, ax):
                          "linewidth": "linewidths",
                          "linestyle": "linestyles",
                          "hatch": "hatch"}
-        styles = pd.DataFrame(styles).reindex(columns=style_columns.keys())
+        styles = (pd.DataFrame(styles)
+                  .reindex(columns=style_columns.keys())
+                  .astype({"facecolor": 'O',
+                           "edgecolor": 'O', "linewidth": float, "linestyle": 'O', "hatch": 'O'}))
         styles["linewidth"].fillna(1, inplace=True)
         styles["facecolor"].fillna(self._facecolor, inplace=True)
         styles["edgecolor"].fillna(styles["facecolor"], inplace=True)

upsetplot/tests/test_data.py

@@ -3,7 +3,7 @@
 import pandas as pd
 import numpy as np
 from distutils.version import LooseVersion
-from pandas.util.testing import (assert_series_equal, assert_frame_equal,
+from pandas.testing import (assert_series_equal, assert_frame_equal,
                                  assert_index_equal)
 from upsetplot import (from_memberships, from_contents, from_indicators,
                        generate_data)
@@ -111,7 +111,8 @@ def test_from_contents_vs_memberships(data, typ, id_column):
     assert_series_equal(baseline[id_column].reset_index(drop=True),
                         pd.Series(['aa', 'bb', 'cc', 'dd', 'ee', 'ff'],
                                   name=id_column))
-    assert_frame_equal(baseline.drop([id_column], axis=1), expected)
+    baseline_without_id = baseline.drop([id_column], axis=1)
+    assert_frame_equal(baseline_without_id, expected, check_column_type=baseline_without_id.shape[1] > 0)
 
 
 def test_from_contents(typ=set, id_column='id'):

upsetplot/tests/test_reformat.py

@@ -1,6 +1,6 @@
 import pytest
 import pandas as pd
-from pandas.util.testing import assert_series_equal, assert_frame_equal
+from pandas.testing import assert_series_equal, assert_frame_equal
 
 from upsetplot import generate_counts, generate_samples
 from upsetplot import query

upsetplot/tests/test_upsetplot.py

@@ -2,7 +2,7 @@
 import itertools
 
 import pytest
-from pandas.util.testing import (
+from pandas.testing import (
     assert_series_equal, assert_frame_equal, assert_index_equal)
 from numpy.testing import assert_array_equal
 import pandas as pd