msaexplorer.cli

 1"""
 2A script to provide minimal argument parsing for displaying the version or
 3launching the MSAexplorer app. Not needed for usage as a python module.
 4
 5This module defines functions to parse command-line arguments and either display
 6the version information or start the MSAexplorer application. It primarily serves
 7as an entry point for launching the application or retrieving its version.
 8"""
 9
10import sys
11import argparse
12from msaexplorer import __version__
13
14
15def parse_args(sysargs):
16    """
17    Minimal argument parser for displaying the version or launching the app.
18    """
19    parser = argparse.ArgumentParser(
20        description='The MSAexplorer app is an interactive visualization tool designed for exploring multiple sequence alignments (MSAs).',
21        usage='''\tmsaexplorer --run --port (optional) --host (optional)'''
22    )
23
24    parser.add_argument(
25         '--run',
26        action='store_true',
27        help='Start the MSAexplorer app'
28    )
29
30    parser.add_argument(
31        '--host',
32        type=str,
33        default='127.0.0.1',
34        metavar='ip',
35        help='The address that the app should listen on. Defaults to 127.0.0.1'
36    )
37
38    parser.add_argument(
39        '--port',
40        type=int,
41        default=8080,
42        metavar='port',
43        help='The port that the app should listen on. Set to 0 to use a random port. Defaults to 8080.'
44    )
45
46    parser.add_argument(
47        '--version',
48        action='version',
49        version=f'MSAexplorer {__version__}'
50    )
51
52    if not sysargs:
53        parser.print_help()
54        sys.exit(0)
55
56    return parser.parse_args(sysargs)
57
58
59def main(sysargs=sys.argv[1:]):
60    args = parse_args(sysargs)
61
62    if args.run:
63        try:
64            from shiny import run_app
65            from shiny import App
66            from app_src.shiny_user_interface import shiny_ui
67            from app_src.shiny_server import server
68            from importlib.resources import files
69        except ImportError:
70            sys.exit(
71                "Please install the MSAexplorer front end app via 'pip install msaexplorer[app]' or 'pip install msaexplorer[app-plus]'."
72            )
73
74        css_path = files("app_src").joinpath("www/css/styles.css")
75        js_path = files("app_src").joinpath("www/js/helper_functions.js")
76        img_path = files("app_src").joinpath("www/img")
77        # same code as in root/app.py
78        run_app(
79            app=App(
80                shiny_ui(
81                    css_file=css_path,
82                    js_file=js_path
83                ),
84                server,
85                static_assets={'/img': str(img_path)}
86            ),
87            port=args.port,
88            host=args.host
89        )
90
91
92if __name__ == "__main__":
93    main()