cli documentation

docs/cli/functions.md

@@ -0,0 +1,16 @@
+# Functions
+
+`laue-dials` contains the following command-line utilities for processing Laue diffraction data:
+
+```{eval-rst}
+.. toctree::
+   :maxdepth: 1
+
+   initial_solution
+   sequence_to_stills
+   optimize_indexing
+   refine
+   predict
+   integrate
+
+```

docs/cli/initial_solution.rst

@@ -0,0 +1,24 @@
+.. _initial_solution:
+
+laue_dials.initial_solution
+================
+
+Introduction
+------------
+
+.. python_string:: laue_dials.command_line.initial_solution.help_message
+
+Basic parameters
+----------------
+
+.. phil:: laue_dials.command_line.initial_solution.working_phil
+   :expert-level: 0
+   :attributes-level: 0
+
+
+Full parameter definitions
+--------------------------
+
+.. phil:: laue_dials.command_line.initial_solution.working_phil
+   :expert-level: 2
+   :attributes-level: 2

docs/cli/integrate.rst

@@ -0,0 +1,24 @@
+.. _integrate:
+
+laue_dials.integrate
+================
+
+Introduction
+------------
+
+.. python_string:: laue_dials.command_line.integrate.help_message
+
+Basic parameters
+----------------
+
+.. phil:: laue_dials.command_line.integrate.working_phil
+   :expert-level: 0
+   :attributes-level: 0
+
+
+Full parameter definitions
+--------------------------
+
+.. phil:: laue_dials.command_line.integrate.working_phil
+   :expert-level: 2
+   :attributes-level: 2

docs/cli/optimize_indexing.rst

@@ -0,0 +1,24 @@
+.. _optimize_indexing:
+
+laue_dials.optimize_indexing
+================
+
+Introduction
+------------
+
+.. python_string:: laue_dials.command_line.optimize_indexing.help_message
+
+Basic parameters
+----------------
+
+.. phil:: laue_dials.command_line.optimize_indexing.working_phil
+   :expert-level: 0
+   :attributes-level: 0
+
+
+Full parameter definitions
+--------------------------
+
+.. phil:: laue_dials.command_line.optimize_indexing.working_phil
+   :expert-level: 2
+   :attributes-level: 2

docs/cli/predict.rst

@@ -0,0 +1,24 @@
+.. _predict:
+
+laue_dials.predict
+================
+
+Introduction
+------------
+
+.. python_string:: laue_dials.command_line.predict.help_message
+
+Basic parameters
+----------------
+
+.. phil:: laue_dials.command_line.predict.working_phil
+   :expert-level: 0
+   :attributes-level: 0
+
+
+Full parameter definitions
+--------------------------
+
+.. phil:: laue_dials.command_line.predict.working_phil
+   :expert-level: 2
+   :attributes-level: 2

docs/cli/refine.rst

@@ -0,0 +1,24 @@
+.. _refine:
+
+laue_dials.refine
+================
+
+Introduction
+------------
+
+.. python_string:: laue_dials.command_line.refine.help_message
+
+Basic parameters
+----------------
+
+.. phil:: laue_dials.command_line.refine.working_phil
+   :expert-level: 0
+   :attributes-level: 0
+
+
+Full parameter definitions
+--------------------------
+
+.. phil:: laue_dials.command_line.refine.working_phil
+   :expert-level: 2
+   :attributes-level: 2

docs/cli/sequence_to_stills.rst

@@ -0,0 +1,25 @@
+.. _sequence_to_stills:
+
+laue_dials.sequence_to_stills
+================
+
+.. Introduction
+.. ------------
+
+.. .. python_string:: laue_dials.command_line.sequence_to_stills.help_message
+
+Basic parameters
+----------------
+
+.. phil:: laue_dials.command_line.sequence_to_stills.phil_scope
+   :expert-level: 0
+   :attributes-level: 0
+
+
+Full parameter definitions
+--------------------------
+
+.. phil:: laue_dials.command_line.sequence_to_stills.phil_scope
+   :expert-level: 2
+   :attributes-level: 2
+

docs/conf.py

@@ -72,6 +72,11 @@
     "sphinx.ext.ifconfig",
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
+    "myst_parser",
+    "sphinxcontrib.autoprogram",
+    "sphinx_rtd_theme",
+    "libtbx.sphinx.phil",
+    "libtbx.sphinx.python_string",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -160,12 +165,14 @@
 # documentation.
 html_theme_options = {"sidebar_width": "300px", "page_width": "1200px"}
 
+html_favicon = "images/rs-favicon_32x32.png"
+
 # Add any paths that contain custom themes here, relative to this directory.
 # html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-# html_title = None
+html_title = "laue-dials"
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 # html_short_title = None

docs/index.rst

@@ -1,40 +1,18 @@
-==========
-laue_dials
-==========
-
-This is the documentation of **laue_dials**.
-
-.. note::
-
-    This is the main page of your project's `Sphinx`_ documentation.
-    It is formatted in `reStructuredText`_. Add additional pages
-    by creating rst-files in ``docs`` and adding them to the `toctree`_ below.
-    Use then `references`_ in order to link them from this page, e.g.
-    :ref:`authors` and :ref:`changes`.
-
-    It is also possible to refer to the documentation of other Python packages
-    with the `Python domain syntax`_. By default you can reference the
-    documentation of `Sphinx`_, `Python`_, `NumPy`_, `SciPy`_, `matplotlib`_,
-    `Pandas`_, `Scikit-Learn`_. You can add more by extending the
-    ``intersphinx_mapping`` in your Sphinx's ``conf.py``.
-
-    The pretty useful extension `autodoc`_ is activated by default and lets
-    you include documentation from docstrings. Docstrings can be written in
-    `Google style`_ (recommended!), `NumPy style`_ and `classical style`_.
 
+.. include:: ../README.rst
 
 Contents
 ========
 
 .. toctree::
    :maxdepth: 2
 
-   Overview <readme>
    Contributions & Help <contributing>
    License <license>
    Authors <authors>
    Changelog <changelog>
-   Module Reference <api/modules>
+   Command-Line Reference <cli/functions>
+   Full API Reference <api/modules>
 
 
 Indices and tables