smafa 0.8.0

Read aligner for small pre-aligned sequences
Documentation 
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#!/usr/bin/env python3

###############################################################################
#
#    Copyright (C) 2020 Ben Woodcroft
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License
#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
###############################################################################

__author__ = "Ben Woodcroft"
__copyright__ = "Copyright 2023"
__credits__ = ["Ben Woodcroft"]
__license__ = "GPL3"
__maintainer__ = "Ben Woodcroft"
__email__ = "benjwoodcroft near gmail.com"
__status__ = "Development"

import argparse
import logging
import sys
import os

import extern

sys.path = [os.path.join(os.path.dirname(os.path.realpath(__file__)),'..')] + sys.path

if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('--debug', help='output debug information', action="store_true")
    #parent_parser.add_argument('--version', help='output version information and quit',  action='version', version=repeatm.__version__)
    parser.add_argument('--quiet', help='only output errors', action="store_true")

    parser.add_argument('--version', required=True, help='e.g. 0.0.6')

    args = parser.parse_args()

    # Setup logging
    if args.debug:
        loglevel = logging.DEBUG
    elif args.quiet:
        loglevel = logging.ERROR
    else:
        loglevel = logging.INFO
    logging.basicConfig(level=loglevel, format='%(asctime)s %(levelname)s: %(message)s', datefmt='%m/%d/%Y %I:%M:%S %p')

    if args.version.startswith('v'):
        raise Exception("--version shouldn't have a leading 'v'")

    logging.info("Checking for uncommitted code")
    try:
        extern.run('git diff --exit-code')
        extern.run('git diff --exit-code --cached')
    except:
        raise Exception("There appears to be uncommited code changes. Please commit everything first.")

    print("Updating deps ...")
    extern.run('cargo update')

    print("Running tests ...")
    extern.run('cargo test')

    # Get version from Cargo.toml
    with open('Cargo.toml') as f:
        cargo_toml = f.read()
        cargo_toml_version = cargo_toml.split('version = "')[1].split('"')[0]

    if cargo_toml_version != args.version:
        raise Exception("Cargo.toml version ({}) doesn't match --version ({})".format(cargo_toml_version, args.version))

    # print(extern.run('git commit -am "v{}"'.format(args.version)))
    print(extern.run('git tag v{}'.format(args.version)))

    logging.info("Now run cargo publish && git push && git push --tags")