docs/changes/newsfragments/366.doc

@@ -0,0 +1 @@
+Add documentation on how to make a ``junifer`` plugin by `Synchon Mandal`_

docs/changes/newsfragments/366.feature

@@ -0,0 +1 @@
+Add support for plugins by `Synchon Mandal`_

docs/extending/index.rst

@@ -30,3 +30,4 @@ DataGrabbers, Preprocessors, Markers, etc.,  following the *junifer* way.
    parcellations
    coordinates
    masks
+   plugins

docs/extending/plugins.rst

@@ -0,0 +1,50 @@
+.. include:: ../links.inc
+
+.. _plugins:
+
+Creating a ``junifer`` plugin
+=============================
+
+What is a plugin
+----------------
+
+Plugins are additional components that extend the functionality of ``junifer``.
+Technically, plugins can also be called as extensions, but we clearly differentiate
+them in ``junifer`` as :ref:`extensions<extending_extension>` serve a different
+purpose. ``junifer`` plugins are command line programs which can be used
+independently but also integrates with the core ``junifer`` command line interface
+(CLI) framework.
+
+When a plugin is installed, we basically inject new behaviours into the ``junifer`` CLI
+while promoting modularity and allowing for easier maintenance and updates to the core
+application. A great plugin example is `junifer-data`_ which is well-integrated
+in ``junifer`` to access assets like parcellations, coordinates and masks, but also
+remains modular enough to update its CLI without disturbing that of ``junifer``.
+
+How to make a plugin
+--------------------
+
+A key distinction between a ``junifer`` extension and a ``junifer`` plugin is that a
+plugin will have its own CLI and be a Python package in its own right, for example,
+`junifer-data`_.
+
+The following steps should lead you to make a successful plugin:
+
+#. Create CLI for your plugin. As ``junifer`` uses `click`_ for its CLI, a plugin
+   should be creating its own ``click.Group`` as shown here:
+   `<https://click.palletsprojects.com/en/stable/commands/#commands-and-groups>`_.
+
+#. Integrate the `click`_-based plugin CLI with `setuptools`_ as shown here:
+   `<https://click.palletsprojects.com/en/stable/setuptools/#setuptools-integration>`_.
+
+#. Make sure the plugin CLI independently works as intended.
+
+#. Follow the steps here:
+   `<https://setuptools.pypa.io/en/latest/userguide/entry_point.html#entry-points-for-plugins>`_
+   and make a new entry point with the *name* as the sub-command you want under ``junifer`` command
+   and the *group* as ``"junifer.ext"``. The *name* should refer to the ``click.Group`` of your
+   plugin CLI.
+
+#. After you install your plugin in the same environment as your ``junifer`` installation, you can
+   observe your plugin being added as a new sub-command under ``junifer`` and working exactly as it
+   did independently.

docs/links.inc

@@ -12,6 +12,7 @@
 .. _`AML`: https://www.fz-juelich.de/inm/inm-7/EN/Forschung/Applied%20Machine%20Learning/_node.html
 .. _`INM-7`: https://www.fz-juelich.de/inm/inm-7/EN/Home/home_node.html
 .. _`julearn`: https://juaml.github.io/julearn
+.. _`junifer-data`: https://github.com/juaml/junifer-data-client
 
 .. _`pandas`: https://pandas.pydata.org
 .. _`pandas.DataFrame` : https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html
@@ -24,6 +25,7 @@
 .. _`nipype`: https://nipype.readthedocs.io
 .. _`datalad`: https://datalad.org
 .. _`templateflow`: https://www.templateflow.org
+.. _`click`: https://click.palletsprojects.com/en/stable/
 
 .. _`venv`: https://docs.python.org/3/tutorial/venv.html
 .. _`conda env`: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html
@@ -36,6 +38,7 @@
 .. _`Wikipedia`: https://wikipedia.org
 .. _`YAML`: https://yaml.org
 
+.. _`setuptools`: https://setuptools.pypa.io/en/latest/
 .. _`setuptools_scm`: https://github.com/pypa/setuptools_scm/
 
 .. _`sphinx gallery`: https://sphinx-gallery.github.io/stable/index.html

junifer/cli/__init__.py

@@ -3,7 +3,22 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import sys
+
 import lazy_loader as lazy
 
 
+if sys.version_info < (3, 11):  # pragma: no cover
+    from importlib_metadata import entry_points
+else:
+    from importlib.metadata import entry_points
+
+
 __getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)
+
+
+# Register extensions
+from .cli import cli
+
+for ep in entry_points(group="junifer.ext"):
+    cli.add_command(ep.load(), name=ep.name)

junifer/cli/cli.py

@@ -111,7 +111,9 @@ def _validate_verbose(
     )
 
 
-@click.group()
+@click.group
+@click.version_option()
+@click.help_option()
 def cli() -> None:  # pragma: no cover
     """JUelich NeuroImaging FEature extractoR."""
 

pyproject.toml

@@ -52,7 +52,7 @@ dependencies = [
     "lazy_loader==0.4",
     "importlib_metadata; python_version<'3.9'",
     "looseversion==1.3.0; python_version>='3.12'",
-    "junifer_data==1.2.0",
+    "junifer_data==1.3.0",
 ]
 dynamic = ["version"]