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$ ruff --fix --select PIE790 BioSQL/ Bio/ Doc/examples/ Tests/ Scripts/ Found 62 errors (62 fixed, 0 remaining). Then re-ran black.
138 lines
4.3 KiB
Python
138 lines
4.3 KiB
Python
# Copyright 2001 by Brad Chapman. All rights reserved.
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# Copyright 2009 by Peter Cock. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Test for bitmap output via ReportLab (requires an extra dependency).
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The primary purpose of this is to flag if renderPM is missing, but also
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to check Bio.Graphics can make a bitmap (e.g. PNG).
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The example itself is essentially a repeat from test_GraphicsGeneral.py.
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"""
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import os
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import random
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import unittest
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from Bio import MissingExternalDependencyError
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from Bio import MissingPythonDependencyError
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try:
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# Skip the test if reportlab is not installed
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import reportlab as r
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del r
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except Exception:
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raise MissingPythonDependencyError(
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"Install ReportLab if you want to use Bio.Graphics."
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) from None
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try:
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# Skip the test if reportlab is not installed
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from reportlab.graphics import renderPM
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del renderPM
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except Exception:
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raise MissingPythonDependencyError(
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"Install ReportLab's renderPM module if you want to create bitmaps with "
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"Bio.Graphics."
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) from None
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try:
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# Skip the test if PIL is not installed
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# The preferred PIL import has changed over time:
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try:
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from PIL import Image as i
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except ImportError:
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import Image as i
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del i
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except Exception:
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raise MissingPythonDependencyError(
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"Install Pillow or its predecessor PIL (Python Imaging Library) "
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"if you want to create bitmaps with Bio.Graphics."
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) from None
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from reportlab.graphics.renderPM import RenderPMError
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# the stuff we're testing
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from Bio.Graphics.Comparative import ComparativeScatterPlot
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# We're not really using the unittest framework, because we need to
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# raise the dependency error BEFORE the individual tests in order that
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# this be skipped by run_tests.py
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def real_test():
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min_two_d_lists = 1
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max_two_d_lists = 7
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min_num_points = 1
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max_num_points = 500
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min_point_num = 0
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max_point_num = 200
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plot_info = []
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num_two_d_lists = random.randrange(min_two_d_lists, max_two_d_lists)
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for two_d_list in range(num_two_d_lists):
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cur_list = []
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num_points = random.randrange(min_num_points, max_num_points)
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for point in range(num_points):
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x_point = random.randrange(min_point_num, max_point_num)
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y_point = random.randrange(min_point_num, max_point_num)
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cur_list.append((x_point, y_point))
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plot_info.append(cur_list)
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compare_plot = ComparativeScatterPlot("png")
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compare_plot.display_info = plot_info
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output_file = os.path.join(os.getcwd(), "Graphics", "scatter_test.png")
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try:
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compare_plot.draw_to_file(output_file, "Testing Scatter Plots")
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# there is a bug in reportlab which occasionally generates an
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# error here.
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except IndexError:
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pass
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except OSError as err:
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if "encoder zip not available" in str(err):
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raise MissingExternalDependencyError(
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"Check zip encoder installed for PIL and ReportLab renderPM"
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) from None
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else:
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raise
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except RenderPMError as err:
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if str(err).startswith("Can't setFont(") or str(err).startswith(
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"Error in setFont("
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):
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# TODO - can we raise the error BEFORE the unit test function
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# is run? That way it can be skipped in run_tests.py
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raise MissingExternalDependencyError(
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"Check the fonts needed by ReportLab if you want "
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"bitmaps from Bio.Graphics\n" + str(err)
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) from None
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elif str(err).startswith("cannot import desired renderPM backend rlPyCairo"):
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raise MissingExternalDependencyError(
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"Reportlab module rlPyCairo unavailable\n" + str(err)
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) from None
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else:
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raise
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return True
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# Run the actual test BEFORE the unittest stuff gets called
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real_test()
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class ComparativeTest(unittest.TestCase):
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"""Do tests for modules involved with comparing data."""
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def test_simple_scatter_plot(self):
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"""Test creation of a simple PNG scatter plot."""
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# Dummy method to show up via run_tests.py
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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