Reorganize Python package (#20)

Author: tsalo

.gitignore

@@ -71,6 +71,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/generated/
 
 # PyBuilder
 target/

docs/_templates/module.rst

@@ -3,38 +3,57 @@
 
 .. automodule:: {{ fullname }}
 
-   {% block functions %}
-   {% if functions %}
-   .. rubric:: Functions
-
-   .. autosummary::
-      :toctree:
-   {% for item in functions %}
-      {{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-
-   {% block classes %}
-   {% if classes %}
-   .. rubric:: Classes
-
-   .. autosummary::
-      :toctree:
-   {% for item in classes %}
-      {{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
-
-   {% block exceptions %}
-   {% if exceptions %}
-   .. rubric:: Exceptions
-
-   .. autosummary::
-      :toctree:
-   {% for item in exceptions %}
-      {{ item }}
-   {%- endfor %}
-   {% endif %}
-   {% endblock %}
+{% if functions or classes or exceptions %}
+.. currentmodule:: {{ fullname }}
+
+{% endif %}
+{%- block functions %}
+{%- if functions %}
+.. rubric:: Functions
+
+.. autosummary::
+   :toctree: .
+{% for item in functions %}
+   {{ item }}
+{%- endfor %}
+
+{% endif %}
+{%- endblock %}
+{%- block classes %}
+{%- if classes %}
+.. rubric:: Classes
+
+.. autosummary::
+   :toctree: .
+{% for item in classes %}
+   {{ item }}
+{%- endfor %}
+
+{% endif %}
+{%- endblock %}
+{%- block exceptions %}
+{%- if exceptions %}
+.. rubric:: Exceptions
+
+.. autosummary::
+   :toctree: .
+{% for item in exceptions %}
+   {{ item }}
+{%- endfor %}
+
+{% endif %}
+{%- endblock %}
+
+{%- block modules %}
+{%- if modules %}
+.. rubric:: Submodules
+
+.. autosummary::
+   :toctree: .
+   :template: module.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{%- endblock %}

docs/api.rst

@@ -18,11 +18,8 @@ API
 .. autosummary::
    :template: module.rst
    :toctree: generated/
+   :recursive:
 
-   cifti
-   fixels
-   voxels
-   h5_storage
-   parser
-   s3_utils
-   tiledb_storage
+   cli
+   storage
+   utils

docs/conf.py

@@ -41,7 +41,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.append(os.path.abspath('sphinxext'))
-sys.path.insert(0, os.path.abspath('../modelarrayio'))
+sys.path.insert(0, os.path.abspath('../src'))
 
 from github_link import make_linkcode_resolve  # noqa: E402
 

docs/usage.rst

@@ -8,7 +8,7 @@ confixel
 ********
 
 .. argparse::
-   :ref: modelarrayio.fixels.get_parser
+   :ref: modelarrayio.cli.fixels_to_h5.get_parser
    :prog: confixel
    :func: get_parser
 
@@ -18,7 +18,7 @@ convoxel
 ********
 
 .. argparse::
-   :ref: modelarrayio.voxels.get_parser
+   :ref: modelarrayio.cli.voxels_to_h5.get_parser
    :prog: convoxel
    :func: get_parser
 
@@ -28,7 +28,7 @@ concifti
 ********
 
 .. argparse::
-   :ref: modelarrayio.cifti.get_parser
+   :ref: modelarrayio.cli.cifti_to_h5.get_parser
    :prog: concifti
    :func: get_parser
 
@@ -38,25 +38,25 @@ fixelstats_write
 ****************
 
 .. argparse::
-   :ref: modelarrayio.fixels.get_h5_to_fixels_parser
+   :ref: modelarrayio.cli.h5_to_fixels.get_parser
    :prog: fixelstats_write
-   :func: get_h5_to_fixels_parser
+   :func: get_parser
 
 *****************
 volumestats_write
 *****************
 
 .. argparse::
-   :ref: modelarrayio.voxels.get_h5_to_volume_parser
+   :ref: modelarrayio.cli.h5_to_voxels.get_parser
    :prog: volumestats_write
-   :func: get_h5_to_volume_parser
+   :func: get_parser
 
 
 ****************
 ciftistats_write
 ****************
 
 .. argparse::
-   :ref: modelarrayio.cifti.get_h5_to_ciftis_parser
+   :ref: modelarrayio.cli.h5_to_cifti.get_parser
    :prog: ciftistats_write
-   :func: get_h5_to_ciftis_parser
+   :func: get_parser

pyproject.toml

@@ -66,12 +66,12 @@ Repository = "https://github.com/PennLINC/ModelArrayIO"
 Documentation = "https://modelarrayio.readthedocs.io"
 
 [project.scripts]
-confixel = "modelarrayio.fixels:main"
-convoxel = "modelarrayio.voxels:main"
-concifti = "modelarrayio.cifti:main"
-fixelstats_write = "modelarrayio.fixels:h5_to_fixels"
-volumestats_write = "modelarrayio.voxels:h5_to_volumes_wrapper"
-ciftistats_write = "modelarrayio.cifti:h5_to_ciftis"
+confixel = "modelarrayio.cli.fixels_to_h5:main"
+convoxel = "modelarrayio.cli.voxels_to_h5:main"
+concifti = "modelarrayio.cli.cifti_to_h5:main"
+fixelstats_write = "modelarrayio.cli.h5_to_fixels:main"
+volumestats_write = "modelarrayio.cli.h5_to_voxels:main"
+ciftistats_write = "modelarrayio.cli.h5_to_cifti:main"
 
 #
 # Hatch
@@ -103,7 +103,7 @@ exclude = ".*"
 
 [tool.ruff]
 line-length = 99
-src = ["src/modelarrayio"]
+src = ["src"]
 
 [tool.ruff.lint]
 extend-select = [

src/modelarrayio/__init__.py

@@ -1,3 +1 @@
-from . import cifti, fixels, voxels
-
-__all__ = ['cifti', 'fixels', 'voxels']
+"""Top-level package for ModelArrayIO."""