Reimplement click options as argparse arguments

src/hermes/cli.py

@@ -8,161 +8,52 @@
 """
 This module provides the main entry point for the HERMES command line application.
 """
-import logging
-import typing as t
 import pathlib
-from importlib import metadata
+import argparse
 
-from hermes import config
-from hermes.commands import workflow
-from hermes.config import configure, init_logging
 
-
-def log_header(header, summary=None):
-    _log = config.getLogger('cli')
-
-    dist = metadata.distribution('hermes')
-    meta = dist.metadata
-
-    if header is None:
-        title = f"{dist.name} workflow ({dist.version})"
-
-        _log.info(title)
-        _log.info("=" * len(title))
-        _log.info('')
-
-        if 'Summary' in meta:
-            _log.info('%s', meta['Summary'])
-            _log.info('')
-
-    else:
-        _log.info("%s", header)
-        if summary:
-            _log.info("%s", summary)
-            _log.info('')
-
-
-class WorkflowCommand(click.Group):
-    """
-    Custom multi-command that implements
-
-    - sub-commands in a fixed order,
-    - automatic call of sub-commands, and
-    - filtering of commands to be executed.
-    """
-
-    def __init__(self, *args, **kwargs) -> None:
-        self._command_order = []
-        super().__init__(*args, **kwargs)
-
-    def add_command(self, cmd: click.Command, name: t.Optional[str] = None) -> None:
-        """
-        Overridden to ensure the order of commands is retained.
-        """
-
-        cmd_name = name or cmd.name
-        if cmd_name not in self.commands:
-            self._command_order.append(cmd_name)
-        super().add_command(cmd, name)
-
-    def list_commands(self, ctx: click.Context) -> t.List[str]:
-        """
-        Overridden to return commands in fixed order.
-        """
-
-        return self._command_order
-
-    def invoke(self, ctx: click.Context) -> t.Any:
-        """
-        Invoke all sub-commands in a given order.
-
-        If there is a flag in `ctx.params` with the name of a sub-command that evaluates to `False`,
-        the command is not invoked.
-
-        :param ctx: Context for the command.
-        """
-
-        # Get the user provided working dir from the --path option or default to current working directory.
-        working_path = ctx.params.get('path').absolute()
-
-        configure(ctx.params.get('config').absolute(), working_path)
-        init_logging()
-        log_header(None)
-
-        audit_log = logging.getLogger('audit')
-        audit_log.info("# Running Hermes")
-        audit_log.info("Running Hermes command line in: %s", working_path)
-        audit_log.debug("")
-        audit_log.debug("Invoked `%s` with", ctx.invoked_subcommand or self.name)
-        audit_log.debug("")
-        for k, v in ctx.params.items():
-            audit_log.debug("`--%s`", k)
-            audit_log.debug(":   `%s`", v)
-            audit_log.debug("")
-
-        if ctx.protected_args:
-            return super().invoke(ctx)
-
-        # The following code is largely copied from the base implementation that can be found in
-        # click.core.MultiCommand.
-
-        def _process_result(value: t.Any) -> t.Any:
-            if self._result_callback is not None:
-                value = ctx.invoke(self._result_callback, value, **ctx.params)
-            return value
-
-        args = [*ctx.protected_args, *ctx.args]
-        ctx.args = []
-        ctx.protected_args = []
-
-        with ctx:
-            contexts = []
-            for cmd_name in self.list_commands(ctx):
-                if not ctx.params.get(cmd_name, True):
-                    continue
-
-                cmd = self.get_command(ctx, cmd_name)
-                sub_ctx = cmd.make_context(
-                    cmd_name,
-                    args,
-                    parent=ctx,
-                    allow_extra_args=True,
-                    allow_interspersed_args=False
-                )
-                contexts.append(sub_ctx)
-                args, sub_ctx.args = sub_ctx.args, []
-
-            rv = []
-            for sub_ctx in contexts:
-                with sub_ctx:
-                    rv.append(sub_ctx.command.invoke(sub_ctx))
-            return _process_result(rv)
-
-
-@click.group(cls=WorkflowCommand, invoke_without_command=True)
-@click.option(
-    "--config", default=pathlib.Path('hermes.toml'),
-    help="Configuration file in TOML format", type=pathlib.Path
-)
-@click.option("--curate", is_flag=True, default=False)
-@click.option("--deposit", is_flag=True, default=False)
-@click.option("--postprocess", is_flag=True, default=False)
-@click.option("--clean", is_flag=True, default=False)
-@click.option('--path', default=pathlib.Path('./'), help='Working path', type=pathlib.Path)
-@click.pass_context
-def main(ctx: click.Context, *args, **kwargs) -> None:
+def main(*args, **kwargs) -> None:
     """
     HERMES
 
     This command runs the HERMES workflow or parts of it.
     """
-
-    pass
-
-
-main.add_command(workflow.clean)
-main.add_command(workflow.harvest)
-main.add_command(workflow.process)
-main.add_command(workflow.curate)
-main.add_command(workflow.deposit)
-main.add_command(workflow.postprocess)
+    parser = argparse.ArgumentParser(
+        prog="hermes",
+        description="This command runs the HERMES workflow or parts of it.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    parser.add_argument(
+        "--config",
+        default=pathlib.Path("hermes.toml"),
+        help="Configuration file in TOML format",
+        type=pathlib.Path,
+    )
+    parser.add_argument(
+        "--curate",
+        action="store_true",
+        default=False,
+        help="Run the 'curate' workflow step",
+    )
+    parser.add_argument(
+        "--deposit",
+        action="store_true",
+        default=False,
+        help="Run the 'deposit' workflow step",
+    )
+    parser.add_argument(
+        "--postprocess",
+        action="store_true",
+        default=False,
+        help="Run the 'postprocess' workflow step",
+    )
+    parser.add_argument(
+        "--clean",
+        action="store_true",
+        default=False,
+        help="Remove cached data",
+    )
+    parser.add_argument(
+        "--path", default=pathlib.Path("./"), help="Working path", type=pathlib.Path
+    )
+    args = parser.parse_args()