Merge pull request nipreps#1 from eilidhmacnicol/enh/reports_cli_patch

enh: add cli args

nirodents/cli/group_report.py

@@ -1,3 +1,50 @@
-from niworkflows.reports.core import Report
-rodents_path = "/oak/stanford/groups/russpold/data/rodents/derivatives/antsai-yes/ratLCdfMRI_RAS/"
-Report("/home/oesteban/tmp/nirodents/out/", "madeoutuid", reportlets_dir=rodents_path, config="group.yml").generate_report()
+"""Command Line Interface to generate group reports"""
+
+import os
+from pathlib import Path
+
+def get_parser():
+    """Build parser object."""
+    from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
+
+    parser = ArgumentParser(
+        prog="generate_group_report",
+        description="""generate_group_report -- Create group report based on individual reportlets.""",
+        formatter_class=ArgumentDefaultsHelpFormatter,
+    )
+
+    parser.add_argument(
+        "-r", "--reports", type=Path, help="The location of reportlet files.", required=True
+    )
+    parser.add_argument(
+        "-o", "--output", type=Path, help="The output location for report."
+    )
+    parser.add_argument(
+        "-n", "--report-name", help="The output file name."
+    )
+    return parser
+
+def main():
+    """Entry point."""
+    from niworkflows.reports.core import Report
+    opts = get_parser().parse_args()
+    if opts.output is None:
+        opts.output = opts.reports
+    if opts.report_name is None:
+        opts.report_name = 'group_report.html'
+
+    Report(
+        out_dir=opts.output,
+        run_uuid="madeoutuid",
+        reportlets_dir=opts.reports,
+        config="group.yml",
+        out_filename=opts.report_name,
+        ).generate_report()
+
+
+if __name__ == "__main__":
+    raise RuntimeError(
+        """\
+nirodents/cli/group_report.py should not be run directly;
+Please `pip install` nirodents and use the `generate_group_report` command."""
+    )