Require the arguments to the CLI

Author: Benjamin-Lee

CAI/cli.py

@@ -4,13 +4,14 @@
 from .CAI import CAI
 
 @click.command()
-@click.option("-s", "--sequence", type=click.Path(exists=True, dir_okay=False), help="The sequence to calculate the CAI for.")
-@click.option("-r", "--reference", type=click.Path(exists=True, dir_okay=False), help="The reference sequences to calculate CAI against.")
+@click.option("-s", "--sequence", type=click.Path(exists=True, dir_okay=False), help="The sequence to calculate the CAI for.", required=True)
+@click.option("-r", "--reference", type=click.Path(exists=True, dir_okay=False), help="The reference sequences to calculate CAI against.", required=True)
 @click.option("-g", "--genetic-code", type=int, default=11, help="The genetic code to use. Defaults to 11.")
 def cli(reference, sequence, genetic_code):
     sequence = SeqIO.read(sequence, "fasta").seq
     reference = [str(x.seq) for x in SeqIO.parse(reference, "fasta")]
     print(CAI(sequence, reference=reference, genetic_code=genetic_code))
 
+
 if __name__ == '__main__':
     cli()

setup.py

@@ -9,7 +9,7 @@
 setup(
     name='CAI',
     packages=["CAI"],
-    version='1.0.1',
+    version='1.0.2',
     description='Python implementation of codon adaptation index',
     long_description=long_description,
     author='Benjamin Lee',
@@ -18,7 +18,7 @@
     classifiers=["Intended Audience :: Science/Research",
                  "Topic :: Scientific/Engineering :: Bio-Informatics",
                  "Programming Language :: Python"],
-    install_requires=['scipy', 'biopython', 'click'],
+    install_requires=['scipy', 'biopython', 'click>=7'],
     tests_require=["pytest"],
     setup_requires=['pytest-runner'],
     license="MIT",