diff --git a/plotsr/scripts/plotsr.py b/plotsr/scripts/plotsr.py index e15403f..131e3dd 100644 --- a/plotsr/scripts/plotsr.py +++ b/plotsr/scripts/plotsr.py @@ -288,7 +288,7 @@ def plotsr(args): logger.info('Finished') # END -def main(cmd): +def main(): from matplotlib.rcsetup import non_interactive_bk as bklist parser = argparse.ArgumentParser("Plotting structural rearrangements between genomes", formatter_class=argparse.ArgumentDefaultsHelpFormatter) other = parser._action_groups.pop() @@ -331,7 +331,7 @@ def main(cmd): parser._action_groups.append(other) # args = parser.parse_args([]) # TODO: Delete this line - args = parser.parse_args(cmd) + args = parser.parse_args() # args = parser.parse_args('--sr col_lersyri.out --sr ler_cvisyri.out --sr cvi_erisyri.out --sr eri_shasyri.out --sr sha_kyosyri.out --sr kyo_an1syri.out --sr an1_c24syri.out --genomes genomes.txt --chr Chr3 -S 1 -o ampril_col0_chr3.png -W 5 -H 3 -f 8 --cfg base.cfg'.split()) plotsr(args) # END diff --git a/setup.py b/setup.py index efee412..cf7fbc5 100644 --- a/setup.py +++ b/setup.py @@ -1,9 +1,9 @@ from setuptools import setup, Extension -from plotsr import __version__ +# from plotsr import __version__ setup( name="plotsr", - version='{}'.format(__version__), + # version='{}'.format(__version__), description='Package to plot structural annotations between multiple genomes', author='Manish Goel', author_email='mnshgl0110@gmail.com', diff --git a/test/pytest.py b/test/pytest.py index c7ffbcc..04df478 100644 --- a/test/pytest.py +++ b/test/pytest.py @@ -24,7 +24,6 @@ def test_pdf_out(self): command = f'plotsr --sr syri.out --genomes genomes.txt -o {output}'.split() p = Popen(command, stdout=PIPE, stderr=PIPE) out = p.communicate() - print(out) assert os.path.isfile(output) os.remove(output) for f in glob(f"*log"):