minor docs fixes

cboulay · cboulay · commit 791cee10c5e8 · 2025-10-28T19:41:03.000-04:00
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -15,6 +15,7 @@
     "sphinx.ext.duration",
     "sphinx.ext.graphviz",
     "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
     "sphinxext.rediraffe",
     "myst_parser",
     "sphinx_copybutton",
@@ -38,10 +39,10 @@
     "python": ("https://docs.python.org/3/", None),
     "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
-    "ezmsg": ("https://ezmsg.org/ezmsg/", None),
-    "ezmsg.sigproc": ("https://ezmsg.org/ezmsg-sigproc/", None),
-    "ezmsg.learn": ("https://ezmsg.org/ezmsg-learn/", None),
-    "ezmsg.lsl": ("https://ezmsg.org/ezmsg-lsl/", None),
+    "ezmsg": ("https://www.ezmsg.org/ezmsg/", None),
+    "ezmsg.sigproc": ("https://www.ezmsg.org/ezmsg-sigproc/", None),
+    "ezmsg.learn": ("https://www.ezmsg.org/ezmsg-learn/", None),
+    "ezmsg.lsl": ("https://www.ezmsg.org/ezmsg-lsl/", None),
 }
 intersphinx_disabled_domains = ["std"]
 
diff --git a/docs/source/explanations/axisarray.rst b/docs/source/explanations/axisarray.rst
@@ -127,14 +127,12 @@ Calling ``ezmsg.util.messages.axisarray.replace()`` calls the utility function `
 
 If you have concerns over this reduced safety, if you set the environment variable ``EZMSG_DISABLE_FAST_REPLACE=1``, then this imported ``replace`` function will simply be the function ``dataclasses.replace`` defined in the python standard `dataclasses` module. 
 
-.. note:: Use of this purpose-made ``replace`` function is not limited to ``AxisArray`` objects. It can be used to create any dataclass object given an instance of said class, including user-defined dataclasses. An example of this can be seen in the tutorial :ref:`here <processing_data_tutorial>`.
+.. note:: Use of this purpose-made ``replace`` function is not limited to ``AxisArray`` objects. It can be used to create any dataclass object given an instance of said class, including user-defined dataclasses.
 
 |ezmsg_logo_small| See Also
 ********************************
 
-#. :doc:`../reference/API/axisarray`
-
-.. :doc:`../how-tos/axisarray/content-axisarray`
+#. `AxisArray API Reference <https://www.ezmsg.org/ezmsg/reference/API/axisarray.html>`_
 
 .. |ezmsg_logo_small| image:: ../_static/_images/ezmsg_logo.png
   :width: 40
diff --git a/docs/source/explanations/content-explanations.rst b/docs/source/explanations/content-explanations.rst
@@ -3,7 +3,7 @@ What is ezmsg?
 
 .. under construction - Griffin to add content
 
-This section of the documentation aims to provide a comprehensive overview of the `ezmsg` framework from a design and decision-making perspective. These are four "explainer" documents for users to gain an understanding of the major parts of `ezmsg` and why they are implemented the way that they are. This page provides a high-level overview of the framework, its design philosophy, and motivations. The remaining pages delve into the design details of `ezmsg` core components, the in-built message format `AxisArray` and the signal processing tools provided in the `ezmsg-sigproc` extension to `ezmsg` respectively.
+This section of the documentation aims to provide a comprehensive overview of the `ezmsg` framework from a design and decision-making perspective. These explainer documents help users gain an understanding of the major parts of `ezmsg` and why they are implemented the way that they are. This page provides a high-level overview of the framework, its design philosophy, and motivations. The remaining pages delve into the design details of `ezmsg` core components and the in-built message format `AxisArray`.
 
 .. toctree::
     :maxdepth: 1
@@ -28,7 +28,7 @@ Other ways to learn about `ezmsg` include following our :doc:`Tutorial <../tutor
 - **Minimal boilerplate code** required for `ezmsg` components: `ezmsg` is designed to minimize the amount of boilerplate code required to create new components. This allows users to focus on the core functionality of their components rather than getting bogged down in implementation details.
 - Provides an **in-built message format** (`AxisArray`): `AxisArray` is a message format for handling multi-dimensional arrays with labeled axes. It is designed to facilitate the organization, manipulation, and analysis of complex data structures commonly encountered in signal processing and related fields. See :doc:`AxisArray <axisarray>` for more information.
 - Provides a **command line interface**: `ezmsg` includes a command line interface (CLI) that allows users to manage and interact with signal processing pipelines. The CLI provides commands for starting, stopping, and visualising pipelines.
-- Provides fundamental **signal processing units**: through the extension `ezmsg-sigproc`, users of `ezmsg` have access to over 20 in-built signal processing units, that can be used both in an `ezmsg` context as well as outside of it. See :doc:`sigproc <sigproc>` for more information.
+- Provides fundamental **signal processing units**: through the extension `ezmsg-sigproc`, users of `ezmsg` have access to over 20 in-built signal processing units, that can be used both in an `ezmsg` context as well as outside of it. See the `ezmsg-sigproc documentation <https://www.ezmsg.org/ezmsg-sigproc/>`_ for more information.
 - **Extensible** via extensions: `ezmsg` is designed to be extensible, allowing users to create and share custom components and extensions. This extensibility enables users to tailor the framework to their specific needs and contribute to the broader `ezmsg` community. See :doc:`Extensions <../extensions/content-extensions>` for more information.
 - **Open-source**: `ezmsg` is an open-source project, released under the permissive MIT license. This encourages collaboration and contributions from the community, fostering a vibrant ecosystem of users and developers.
 
diff --git a/docs/source/how-tos/basics/install.rst b/docs/source/how-tos/basics/install.rst
@@ -97,7 +97,7 @@ To install an extension, you can use pip:
 
    pip install ezmsg[extension_name]
 
-For more information on available extensions, please refer to the :doc:`Extensions page <../extensions/content-extensions>`.
+For more information on available extensions, please refer to the :doc:`Extensions page <../../extensions/content-extensions>`.
 
 
 .. |ezmsg_logo_small| image:: ../../_static/_images/ezmsg_logo.png
diff --git a/docs/source/how-tos/basics/sandbox.rst b/docs/source/how-tos/basics/sandbox.rst
@@ -19,7 +19,7 @@ The former is explained below.
 |ezmsg_logo_small| The ``run()`` function
 ***********************************************************
 
-In order to run the ezmsg pipeline in any mode, your script must contain a call to ``ezmsg.core.run()``. You can consult the API reference for :doc:`run() here <../../reference/API/entrypoint>`.
+In order to run the ezmsg pipeline in any mode, your script must contain a call to ``ezmsg.core.run()``. You can consult the `API reference for run() <https://www.ezmsg.org/ezmsg/reference/API/entrypoint.html>`_.
 
 At minimum, you need to provide the components and connections of your pipeline to the ``run()`` function.
 
diff --git a/docs/source/reference/content-reference.rst b/docs/source/reference/content-reference.rst
@@ -6,10 +6,10 @@ API Documentation
 
 For detailed API documentation, please visit the individual package documentation sites:
 
-* `ezmsg Core API <https://ezmsg.org/ezmsg/reference/content-reference.html>`_ - Core ezmsg API reference
-* `ezmsg-sigproc API <https://ezmsg.org/ezmsg-sigproc/>`_ - Signal processing extensions
-* `ezmsg-lsl API <https://ezmsg.org/ezmsg-lsl/>`_ - Lab Streaming Layer integration
-* `ezmsg-learn API <https://ezmsg.org/ezmsg-learn/>`_ - Machine learning extensions
+* `ezmsg Core API <https://www.ezmsg.org/ezmsg/reference/content-reference.html>`_ - Core ezmsg API reference
+* `ezmsg-sigproc API <https://www.ezmsg.org/ezmsg-sigproc/>`_ - Signal processing extensions
+* `ezmsg-lsl API <https://www.ezmsg.org/ezmsg-lsl/>`_ - Lab Streaming Layer integration
+* `ezmsg-learn API <https://www.ezmsg.org/ezmsg-learn/>`_ - Machine learning extensions
 
 See :doc:`../extensions/content-extensions` for a complete list of available extensions.
 
diff --git a/docs/source/tutorials/content-tutorials.rst b/docs/source/tutorials/content-tutorials.rst
@@ -16,7 +16,6 @@ For more in-depth documentation of the code, please refer to the :doc:`reference
     start
     pipeline
     run
-    signalprocessing
 
 .. |ezmsg_logo_small| image:: ../_static/_images/ezmsg_logo.png
   :width: 40
diff --git a/docs/source/tutorials/run.rst b/docs/source/tutorials/run.rst
@@ -92,7 +92,7 @@ The alternative, if you want the graphserver to use a particular address, is to
 1. set the ``EZMSG_GRAPH_SERVER`` environment variable before running your script.
 2. start an ezmsg instance from the command line with the `serve` or `start` commands, which will allow you to specify the address and port.
 
-.. note:: For a deeper dive into the backend of ezmsg, please refer to the :doc:`../explanations/ezmsg` section. Here you will find more information about the ezmsg graphserver, how it works, and how to configure it.
+.. note:: For a deeper dive into the backend of ezmsg, please refer to the :doc:`../explanations/ezmsg-design` section. Here you will find more information about the ezmsg graphserver, how it works, and how to configure it.
 
 
 |ezmsg_logo_small| Run the pipeline using the command line
@@ -183,9 +183,9 @@ then ezmsg will output a **Graphviz** representation of the pipeline to the term
 
 .. note:: The really long numerical node identifiers are simply randomly generated unique identifiers for each connection point (since the names may be the same like `INPUT_SIGNAL`). These identifiers have no special meaning.
 
-.. warning:: This command and the ones described in the :ref:`mermaid-section` section below will only output the pipeline graph if the ezmsg system is running and has a pipeline connected to it. If you run this command when the pipeline is finished or not running, you will not get any output. Our example is so simple that it will finish very quickly, so in order to visualise the graph maybe change the `iterations` in the `CountSettings` to a larger number, e.g. 100000, so that you have time to run the command and see the output.
+.. warning:: This command and the ones described in the :ref:`mermaid-section-tutorial` section below will only output the pipeline graph if the ezmsg system is running and has a pipeline connected to it. If you run this command when the pipeline is finished or not running, you will not get any output. Our example is so simple that it will finish very quickly, so in order to visualise the graph maybe change the `iterations` in the `CountSettings` to a larger number, e.g. 100000, so that you have time to run the command and see the output.
 
-.. _mermaid-section:
+.. _mermaid-section-tutorial:
 
 Mermaid visualisation
 ===========================
diff --git a/docs/source/tutorials/start.rst b/docs/source/tutorials/start.rst
@@ -53,7 +53,7 @@ To install the ezmsg framework, you can use pip in your terminal:
 
    pip install ezmsg
 
-Once installed, you can start using ezmsg in your projects. You can skip straight to the section on :ref:`updating-ezmsg`.
+Once installed, you can start using ezmsg in your projects. You can skip straight to the section on :ref:`updating-ezmsg-tutorial`.
 
 From source (using git)
 ==========================
@@ -127,7 +127,7 @@ Running the tests ensures everything is working correctly.
 
   python -m pytest -v tests
 
-.. _updating-ezmsg:
+.. _updating-ezmsg-tutorial:
 
 |ezmsg_logo_small| How to update ezmsg
 ***************************************
