Add usage page.

Author: tsalo

docs/index.md

@@ -1,4 +1,9 @@
-# ModelArrayIO
-
 ```{include} ../README.md
 ```
+
+```{toctree}
+:maxdepth: 2
+:caption: Usage
+
+usage
+```

docs/usage.rst

@@ -0,0 +1,62 @@
+########################################
+Using ModelArrayIO from the command line
+########################################
+
+
+********
+confixel
+********
+
+.. argparse::
+   :ref: modelarrayio.fixels:get_parser
+   :prog: confixel
+   :func: get_parser
+
+
+********
+convoxel
+********
+
+.. argparse::
+   :ref: modelarrayio.voxels:get_parser
+   :prog: convoxel
+   :func: get_parser
+
+
+********
+concifti
+********
+
+.. argparse::
+   :ref: modelarrayio.cifti:get_parser
+   :prog: concifti
+   :func: get_parser
+
+
+****************
+fixelstats_write
+****************
+
+.. argparse::
+   :ref: modelarrayio.fixels:get_h5_to_fixels_parser
+   :prog: fixelstats_write
+   :func: get_h5_to_fixels_parser
+
+*****************
+volumestats_write
+*****************
+
+.. argparse::
+   :ref: modelarrayio.voxels:get_h5_to_volume_parser
+   :prog: volumestats_write
+   :func: get_h5_to_volume_parser
+
+
+****************
+ciftistats_write
+****************
+
+.. argparse::
+   :ref: modelarrayio.cifti:get_h5_to_ciftis_parser
+   :prog: ciftistats_write
+   :func: get_h5_to_ciftis_parser

pyproject.toml

@@ -103,7 +103,7 @@ exclude = ".*"
 
 [tool.ruff]
 line-length = 99
-src = ["src"]
+src = ["src/modelarrayio"]
 
 [tool.ruff.lint]
 extend-select = [

src/modelarrayio/fixels.py

@@ -328,7 +328,6 @@ def write_storage(
 
 
 def get_parser():
-
     parser = argparse.ArgumentParser(description='Create a hdf5 file of fixel data')
     parser.add_argument('--index-file', '--index_file', help='Index File', required=True)
     parser.add_argument(