reflectivity · alexhroom · Feb 10, 2025 · Feb 10, 2025 · Feb 21, 2025
diff --git a/docs/api/modules.rst b/docs/api/modules.rst
@@ -0,0 +1,7 @@
+orsopy
+======
+
+.. toctree::
+   :maxdepth: 1
+
+   orsopy
diff --git a/docs/api/orsopy.fileio.rst b/docs/api/orsopy.fileio.rst
@@ -0,0 +1,58 @@
+orsopy.fileio package
+=====================
+
+.. automodule:: orsopy.fileio
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+orsopy.fileio.base module
+-------------------------
+
+.. automodule:: orsopy.fileio.base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.fileio.data\_source module
+---------------------------------
+
+.. automodule:: orsopy.fileio.data_source
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.fileio.model\_language module
+------------------------------------
+
+.. automodule:: orsopy.fileio.model_language
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.fileio.orso module
+-------------------------
+
+.. automodule:: orsopy.fileio.orso
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.fileio.reduction module
+------------------------------
+
+.. automodule:: orsopy.fileio.reduction
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.fileio.typing\_backport module
+-------------------------------------
+
+.. automodule:: orsopy.fileio.typing_backport
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/orsopy.rst b/docs/api/orsopy.rst
@@ -0,0 +1,36 @@
+orsopy package
+==============
+
+.. automodule:: orsopy
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 1
+
+   orsopy.fileio
+   orsopy.slddb
+   orsopy.utils
+
+Submodules
+----------
+
+orsopy.orb2ort module
+---------------------
+
+.. automodule:: orsopy.orb2ort
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.ort2orb module
+---------------------
+
+.. automodule:: orsopy.ort2orb
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/orsopy.slddb.element_table.rst b/docs/api/orsopy.slddb.element_table.rst
@@ -0,0 +1,66 @@
+orsopy.slddb.element\_table package
+===================================
+
+.. automodule:: orsopy.slddb.element_table
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+orsopy.slddb.element\_table.element module
+------------------------------------------
+
+.. automodule:: orsopy.slddb.element_table.element
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.element\_table.masses module
+-----------------------------------------
+
+.. automodule:: orsopy.slddb.element_table.masses
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.element\_table.nabs\_geant4 module
+-----------------------------------------------
+
+.. automodule:: orsopy.slddb.element_table.nabs_geant4
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.element\_table.nlengths module
+-------------------------------------------
+
+.. automodule:: orsopy.slddb.element_table.nlengths
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.element\_table.nlengths\_pt module
+-----------------------------------------------
+
+.. automodule:: orsopy.slddb.element_table.nlengths_pt
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.element\_table.xray\_henke module
+----------------------------------------------
+
+.. automodule:: orsopy.slddb.element_table.xray_henke
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.element\_table.xray\_nist module
+---------------------------------------------
+
+.. automodule:: orsopy.slddb.element_table.xray_nist
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/orsopy.slddb.rst b/docs/api/orsopy.slddb.rst
@@ -0,0 +1,82 @@
+orsopy.slddb package
+====================
+
+.. automodule:: orsopy.slddb
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 1
+
+   orsopy.slddb.element_table
+
+Submodules
+----------
+
+orsopy.slddb.comparators module
+-------------------------------
+
+.. automodule:: orsopy.slddb.comparators
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.constants module
+-----------------------------
+
+.. automodule:: orsopy.slddb.constants
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.converters module
+------------------------------
+
+.. automodule:: orsopy.slddb.converters
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.database module
+----------------------------
+
+.. automodule:: orsopy.slddb.database
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.dbconfig module
+----------------------------
+
+.. automodule:: orsopy.slddb.dbconfig
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.importers module
+-----------------------------
+
+.. automodule:: orsopy.slddb.importers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.material module
+----------------------------
+
+.. automodule:: orsopy.slddb.material
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.slddb.webapi module
+--------------------------
+
+.. automodule:: orsopy.slddb.webapi
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/orsopy.utils.rst b/docs/api/orsopy.utils.rst
@@ -0,0 +1,34 @@
+orsopy.utils package
+====================
+
+.. automodule:: orsopy.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+orsopy.utils.chemical\_formula module
+-------------------------------------
+
+.. automodule:: orsopy.utils.chemical_formula
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.utils.density\_resolver module
+-------------------------------------
+
+.. automodule:: orsopy.utils.density_resolver
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+orsopy.utils.resolver\_slddb module
+-----------------------------------
+
+.. automodule:: orsopy.utils.resolver_slddb
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/index.rst b/docs/index.rst
@@ -6,7 +6,7 @@
 
    installation
    usage
-   modules
+   Reference <api/orsopy>
    contributing
    authors
    history

diff --git a/docs/modules.rst b/docs/modules.rst
diff --git a/docs/orsopy.fileio.base.rst b/docs/orsopy.fileio.base.rst
diff --git a/docs/orsopy.fileio.data_source.rst b/docs/orsopy.fileio.data_source.rst
diff --git a/docs/orsopy.fileio.orso.rst b/docs/orsopy.fileio.orso.rst
diff --git a/docs/orsopy.fileio.reduction.rst b/docs/orsopy.fileio.reduction.rst
diff --git a/orsopy/fileio/__init__.py b/orsopy/fileio/__init__.py
@@ -1,5 +1,8 @@
 """
-Implementation of the Orso class that defined the header.
+The role of the :py:mod:`fileio` module is to enable the creation of and parsing from ORSO reduced data files.
+All public classes and functions in the :py:mod:`fileio` module are available directly from :py:mod:`fileio` without needing to specify a particular submodule.
+
+The ORSO file format specification is available `here <https://www.reflectometry.org/advanced_and_expert_level/file_format>`_.
 """
 
 from .base import (Column, ComplexValue, ErrorColumn, File, Header, Person, Value, ValueRange, ValueVector,

diff --git a/requirements_dev.txt b/requirements_dev.txt
@@ -3,6 +3,7 @@ wheel>=0.33.6
 flake8>=3.7.8
 coverage>=4.5.4
 Sphinx>=1.8.5
+sphinx-rtd-theme
 twine>=1.14.0
 numpy>=1.19.0
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,7 +6,7 @@ @@
        installation
        usage
-       modules
+       Reference <api/orsopy>
        contributing
        authors
        history
@@ Expand Down @@