add installation config

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

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='[email protected]',

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"):