Restructure a bit to make this work

src/sim_recon/__init__.py

@@ -1,4 +1,10 @@
-from .main import sim_reconstruct, sim_psf_to_otf
 from .info import __version__
 
-__all__ = ("__version__", "sim_reconstruct", "sim_psf_to_otf")
+__all__ = [
+    __version__,
+]
+
+if __name__ == "__main__":
+    from .main import sim_reconstruct, sim_psf_to_otf
+
+    __all__.append(sim_reconstruct, sim_psf_to_otf)

src/sim_recon/cli/otf.py

@@ -1,12 +1,12 @@
 import logging
 
 from ..main import sim_psf_to_otf
-from .parsing import parse_otf_args
+from .parsing.otf import parse_args
 from ..progress import set_use_tqdm
 
 
 def main() -> None:
-    namespace, otf_kwargs = parse_otf_args()
+    namespace, otf_kwargs = parse_args()
 
     set_use_tqdm(namespace.use_tqdm)
 

src/sim_recon/cli/otf_view.py

@@ -1,12 +1,12 @@
 import logging
 
 from ..otf_view import plot_otfs
-from .parsing import parse_otf_view_args
+from .parsing.otf_view import parse_args
 from ..progress import set_use_tqdm
 
 
 def main():
-    namespace = parse_otf_view_args()
+    namespace = parse_args()
 
     set_use_tqdm(namespace.use_tqdm)
 

src/sim_recon/cli/parsing/otf.py

@@ -0,0 +1,95 @@
+from __future__ import annotations
+import argparse
+from typing import TYPE_CHECKING
+
+from ...settings.formatting import OTF_FORMATTERS
+from .shared import (
+    add_general_args,
+    add_override_args_from_formatters,
+    add_help,
+    handle_required,
+)
+
+if TYPE_CHECKING:
+    from typing import Any
+    from collections.abc import Sequence
+
+__all__ = ("parse_args",)
+
+
+def parse_args(
+    args: Sequence[str] | None = None,
+) -> tuple[argparse.Namespace, dict[str, Any]]:
+    parser = argparse.ArgumentParser(
+        prog="sim-otf",
+        description="SIM PSFs to OTFs",
+        add_help=False,
+    )
+    parser.add_argument(
+        "-c",
+        "--config-path",
+        dest="config_path",
+        help="Path to the root config that specifies the paths to the OTFs and the other configs",
+    )
+    parser.add_argument(
+        "-p",
+        "--psf",
+        dest="psf_paths",
+        nargs="+",
+        help="Paths to PSF files to be reconstructed (multiple paths can be given)",
+    )
+    parser.add_argument(
+        "-o",
+        "--output-directory",
+        default=None,
+        help="If specified, the output directory that the OTFs will be saved in, otherwise each OTF will be saved in the same directory as its PSF",
+    )
+    parser.add_argument(
+        "--overwrite",
+        action="store_true",
+        help="If specified, files will be overwritten if they already exist (unique filenames will be used otherwise)",
+    )
+    parser.add_argument(
+        "--no-cleanup",
+        dest="cleanup",
+        action="store_false",
+        help="If specified, files created during the OTF creation process will not be cleaned up",
+    )
+    parser.add_argument(
+        "--shape",
+        dest="xy_shape",
+        default=None,
+        nargs=2,
+        type=int,
+        help="Takes 2 integers (X Y), specifying the shape to crop PSFs to before converting (powers of 2 are fastest)",
+    )
+
+    add_general_args(parser)
+
+    namespace, unknown = parser.parse_known_args(args)
+
+    add_override_args_from_formatters(parser, OTF_FORMATTERS)
+
+    add_help(parser)
+
+    override_namespace = parser.parse_args(unknown)
+
+    handle_required(
+        parser,
+        namespace,
+        ("-c/--config-path", "config_path"),
+        ("-p/--psf", "psf_paths"),
+    )
+
+    non_override_dests = vars(namespace).keys()
+    otf_kwargs = {
+        k: v
+        for k, v in vars(override_namespace).items()
+        if v is not None and k not in non_override_dests
+    }
+
+    return namespace, otf_kwargs
+
+
+if __name__ == "__main__":
+    parse_args()