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[ENH] turn
--action into subcommands (#215)
* speed up CLI and pin docker dependencies * add more flake8 * update CLI * split parser and cli * use sub commands * fix doc * fix imports * update linting * fixes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix * fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix * fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,19 +1,15 @@ | ||
| [flake8] | ||
| max-line-length = 90 | ||
| count = True | ||
| show-source = True | ||
| statistics = True | ||
| exclude = | ||
| *build | ||
| .git | ||
| __pycache__ | ||
| tests/* | ||
| _version.py | ||
| versioneer.py | ||
| tests_.*.py | ||
| version.*.py | ||
| setup.py | ||
| max-complexity = 10 | ||
| ignore = D100, D103, W503 | ||
| per-file-ignores = | ||
| setup.py:E121 | ||
| max-line-length = 90 | ||
| max_complexity = 15 | ||
| max_function_length = 150 | ||
| max_parameters_amount = 15 | ||
| max_returns_amount = 5 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| """Define the command line interface.""" | ||
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| from __future__ import annotations | ||
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| import sys | ||
| from typing import Any | ||
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| from rich_argparse import RichHelpFormatter | ||
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| from bidsmreye._parsers import common_parser, download_parser | ||
| from bidsmreye.bidsmreye import bidsmreye | ||
| from bidsmreye.defaults import default_log_level, log_levels | ||
| from bidsmreye.download import download | ||
| from bidsmreye.logging import bidsmreye_log | ||
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| log = bidsmreye_log(name="bidsmreye") | ||
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| def cli(argv: Any = sys.argv) -> None: | ||
| """Run the bids app. | ||
| :param argv: _description_, defaults to sys.argv | ||
| :type argv: _type_, optional | ||
| """ | ||
| parser = common_parser(formatter_class=RichHelpFormatter) | ||
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| args = parser.parse_args(argv[1:]) | ||
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| log.debug(f"args:\n{args}") | ||
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| # TODO integrate as part of base config | ||
| # https://stackoverflow.com/a/53293042/14223310 | ||
| log_level = log_levels().index(default_log_level()) | ||
| # For each "-v" flag, adjust the logging verbosity accordingly | ||
| # making sure to clamp off the value from 0 to 4, inclusive of both | ||
| for adjustment in args.log_level or (): | ||
| log_level = min(len(log_levels()) - 1, max(log_level + adjustment, 0)) | ||
| log_level_name = log_levels()[log_level] | ||
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| model_weights_file = None | ||
| if getattr(args, "model", None) is not None: | ||
| model_weights_file = str(getattr(args, "model")) | ||
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| bidsmreye( | ||
| bids_dir=args.bids_dir[0], | ||
| output_dir=args.output_dir[0], | ||
| analysis_level=args.analysis_level[0], | ||
| action=args.command, | ||
| participant_label=args.participant_label or None, | ||
| space=args.space or None, | ||
| task=args.task or None, | ||
| run=args.run or None, | ||
| debug=args.debug, | ||
| model_weights_file=model_weights_file, | ||
| reset_database=args.reset_database, | ||
| bids_filter_file=args.bids_filter_file, | ||
| non_linear_coreg=bool(getattr(args, "non_linear_coreg", False)), | ||
| log_level_name=log_level_name, | ||
| ) | ||
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| def cli_download(argv: Any = sys.argv) -> None: | ||
| """Download the models from OSF. | ||
| :return: _description_ | ||
| :rtype: _type_ | ||
| """ | ||
| parser = download_parser(formatter_class=RichHelpFormatter) | ||
| args = parser.parse_args(argv[1:]) | ||
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| download(model_name=args.model_name, output_dir=args.output_dir) |
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