RascalSoftware · StephenNneji · Jul 31, 2025 · Jul 30, 2025 · Jul 30, 2025
diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
@@ -36,10 +36,10 @@ jobs:
         python -m pip install --upgrade pip
         if [ ${VERSION} == 'dev' ]; then
           wget https://github.com/RascalSoftware/RAT/releases/download/nightly/Linux.zip
-          pip install RATapi
+          pip install ratapi --upgrade
         else
           wget "https://github.com/RascalSoftware/RAT/releases/download/${VERSION}/Linux.zip"
-          pip install RATapi==${VERSION} || pip install RATapi
+          pip install ratapi==${VERSION} || pip install ratapi --upgrade
         fi
         unzip Linux.zip -d API/
         rm API/utilities/mockFunction.m  # as otherwise the MATLAB reference fails to parse it

diff --git a/.gitignore b/.gitignore
@@ -18,7 +18,7 @@ source/_outputs/
 .envrc
 
 # autogenerated documentation
-source/reference/python/RATapi.*
+source/reference/python/ratapi.*
 source/python_examples/data/
 source/matlab_examples/*.html
 source/python_examples/notebooks/*

diff --git a/source/_ext/snippets.py b/source/_ext/snippets.py
@@ -5,7 +5,7 @@
 
 from docutils import nodes
 
-import RATapi
+import ratapi
 
 from sphinx.application import Sphinx
 from sphinx.util.docutils import SphinxDirective
@@ -44,15 +44,15 @@ def setup(app: Sphinx) -> ExtensionMetadata:
 
     def setup_envs(*ignore):
         """Initialise Python/MATLAB environments."""
-        app.env.snippets_env = {"RAT": RATapi} 
+        app.env.snippets_env = {"RAT": ratapi} 
         app.env.matlab_engine = setup_matlab()
         app.env.matlab_engine.eval(
             "cd('API'); addPaths; cd('..'); ratVars = who;", nargout=0
         )
 
     def clear_envs(*ignore):
         """Clear Python/MATLAB environments from the build environment."""
-        app.env.snippets_env = {"RAT": RATapi}
+        app.env.snippets_env = {"RAT": ratapi}
         app.env.matlab_engine.eval(
             r"clearvars('-except', 'ratVars', ratVars{:});", nargout=0
         )

diff --git a/source/advanced/events.rst b/source/advanced/events.rst
@@ -19,7 +19,7 @@ The example below registers a function to listen for the ``Plot`` event:
 
     .. code-block:: Python
 
-        import RATapi as RAT
+        import ratapi as RAT
         RAT.events.register(RAT.events.EventTypes.Plot, update_plot)      
 
 The event listener function is also shown below, it uses one of the plot functions provided by RAT to display the event data. The plot event data contains the current state of the reflectivity and SLDs, along with a number of other items which is detailed below.
@@ -71,7 +71,7 @@ Register a function as an event listener by providing the event type and the lis
 
     .. code-block:: Python
 
-        import RATapi as RAT
+        import ratapi as RAT
 
         RAT.events.register(RAT.events.EventTypes.Message, handle_event)   # Message Event
         RAT.events.register(RAT.events.EventTypes.Plot, handle_event)      # Plot Event

diff --git a/source/calcTypes/data/domains_example.py b/source/calcTypes/data/domains_example.py
@@ -1,4 +1,4 @@
-import RATapi as RAT
+import ratapi as RAT
 import numpy as np
 
 problem = RAT.Project(calculation='domains')

diff --git a/source/conf.py b/source/conf.py
@@ -29,8 +29,8 @@
                             'Please download and extract the RAT release to the API folder.')
 sys.path.insert(0, matlab_src_dir)
 
-import RATapi
-sys.path.insert(0, os.path.dirname(os.path.abspath(RATapi.__file__)))
+import ratapi
+sys.path.insert(0, os.path.dirname(os.path.abspath(ratapi.__file__)))
 project = 'RAT'
 copyright = u'2022-{}, ISIS Neutron and Muon Source'.format(datetime.date.today().year)
 author = 'Arwel Hughes, Sethu Pastula, Alex Room, Rabiya Farooq, Paul Sharp, Stephen Nneji'
@@ -52,7 +52,7 @@
 templates_path = ['_templates']
 
 # -- Setup example files -----------------------------------------------------
-PYTHON_RAT_RELEASE = metadata.version("RATapi")
+PYTHON_RAT_RELEASE = metadata.version("ratapi")
 
 MATLAB_AVAILABLE = True
 try:
@@ -67,14 +67,14 @@
         zf.extractall()
     print("Copying Jupyter notebooks...")
     for directory in ['normal_reflectivity', 'domains', 'absorption']:
-        for file in Path(f"./python-RAT-{PYTHON_RAT_RELEASE}/RATapi/examples/{directory}/").glob('*'):
+        for file in Path(f"./python-RAT-{PYTHON_RAT_RELEASE}/ratapi/examples/{directory}/").glob('*'):
             shutil.copy(file, "./python_examples/notebooks/")
     if MATLAB_AVAILABLE:  # convert_rascal example requires matlab engine
-        for file in Path(f"./python-RAT-{PYTHON_RAT_RELEASE}/RATapi/examples/convert_rascal_project/").glob('*'):
+        for file in Path(f"./python-RAT-{PYTHON_RAT_RELEASE}/ratapi/examples/convert_rascal_project/").glob('*'):
             shutil.copy(file, "./python_examples/notebooks/")
 
 
-    shutil.copytree(f"./python-RAT-{PYTHON_RAT_RELEASE}/RATapi/examples/data", "./python_examples/data", dirs_exist_ok=True)
+    shutil.copytree(f"./python-RAT-{PYTHON_RAT_RELEASE}/ratapi/examples/data", "./python_examples/data", dirs_exist_ok=True)
 
     shutil.rmtree(f"./python-RAT-{PYTHON_RAT_RELEASE}")
 
@@ -149,7 +149,7 @@
 
     <div class="admonition note">
       This page was generated from the notebook {{ env.docname.split('/')|last|e + '.ipynb' }} found in 
-      <a class="reference external" href="https://github.com/RascalSoftware/python-RAT/blob/"""+PYTHON_RAT_RELEASE+r"""/RATapi/examples/">the Python-RAT repository</a>.
+      <a class="reference external" href="https://github.com/RascalSoftware/python-RAT/blob/"""+PYTHON_RAT_RELEASE+r"""/ratapi/examples/">the Python-RAT repository</a>.
       <a href="{{ env.docname.split('/')|last|e + '.ipynb' }}" class="reference download internal" download>Download notebook</a>.
     </div>
 
@@ -159,7 +159,7 @@
 
     .. code-block:: python
 
-        from RATapi.examples import {{ env.docname.split('/')|last|e }}
+        from ratapi.examples import {{ env.docname.split('/')|last|e }}
         project, results = {{ env.docname.split('/')|last|e }}() 
 
 -------------------------------------------------------------------------------------

diff --git a/source/install.rst b/source/install.rst
@@ -47,15 +47,15 @@ This section provides more detailed information about installing RAT for MATLAB
 
         .. code-block:: console
 
-            pip install RATapi
+            pip install ratapi
 
         ``matlabengine`` is an optional dependency only required for MATLAB related actions such as running MATLAB custom functions and converting RasCAL-1 projects.
         The version of ``matlabengine`` must match the version of MATLAB installed on the computer. For example, if MATLAB 2023a is installed on the computer, 
         ``matlabengine`` can be installed as shown below:
 
         .. code-block:: console
 
-            pip install RATapi[Matlab-2023a]
+            pip install ratapi[Matlab-2023a]
 
         .. note::
 

diff --git a/source/reference/python/classlist.rst b/source/reference/python/classlist.rst
@@ -1,4 +1,4 @@
 ClassList
 ---------
 
-.. autoclass:: RATapi.ClassList
+.. autoclass:: ratapi.ClassList
diff --git a/source/reference/python/controls.rst b/source/reference/python/controls.rst
@@ -5,5 +5,5 @@ The ``Controls`` class details control parameters for the RAT run. Note that man
 specific to certain procedures: the relevant procedure is listed in square brackets before the
 field description.
 
-.. autopydantic_model:: RATapi.Controls
+.. autopydantic_model:: ratapi.Controls
    :members: 
diff --git a/source/reference/python/core.rst b/source/reference/python/core.rst
@@ -4,5 +4,5 @@ RAT Core
 This module contains the `Pybind11 <https://pybind11.readthedocs.io/en/stable/index.html>`_ objects 
 which are used to interface with RAT's C++ code. 
 
-.. automodule:: RATapi.rat_core
+.. automodule:: ratapi.rat_core
    :members:
diff --git a/source/reference/python/enums.rst b/source/reference/python/enums.rst
@@ -1,9 +1,9 @@
 Enums 
 -----
 
-This utility module (found in ``RATapi.utils.enums``) contains the Enum objects
+This utility module (found in ``ratapi.utils.enums``) contains the Enum objects
 which are used under the hood to represent arguments given as string options,
 such as those for control parameters or background types.
 
-.. automodule:: RATapi.utils.enums
+.. automodule:: ratapi.utils.enums
    :members:
diff --git a/source/reference/python/events.rst b/source/reference/python/events.rst
@@ -1,5 +1,5 @@
 Events
 ------
 
-.. automodule:: RATapi.events
+.. automodule:: ratapi.events
    :members:
diff --git a/source/reference/python/examples.rst b/source/reference/python/examples.rst
@@ -1,5 +1,5 @@
 Examples 
 --------
 
-.. automodule:: RATapi.examples
+.. automodule:: ratapi.examples
    :members:
diff --git a/source/reference/python/inputs.rst b/source/reference/python/inputs.rst
@@ -4,5 +4,5 @@ Inputs
 This module contains the objects used to organise input data to RAT to be fed
 into the C++ module.
 
-.. automodule:: RATapi.inputs
+.. automodule:: ratapi.inputs
    :members:
diff --git a/source/reference/python/models.rst b/source/reference/python/models.rst
@@ -1,7 +1,7 @@
 Models
 ------
 
-.. automodule:: RATapi.models
+.. automodule:: ratapi.models
    :members:
    :inherited-members: RATModel
    :exclude-members: RATModel, Signal
diff --git a/source/reference/python/outputs.rst b/source/reference/python/outputs.rst
@@ -4,5 +4,5 @@ Outputs
 This module contains the Results objects and the relevant objects to retrieve
 results data from the C++ module.
 
-.. automodule:: RATapi.outputs
+.. automodule:: ratapi.outputs
    :members:
diff --git a/source/reference/python/plotting.rst b/source/reference/python/plotting.rst
@@ -1,10 +1,10 @@
 Plotting
 --------
 
-Plotting functionality for RAT results objects is available through the ``RATapi.utils.plotting`` module.
+Plotting functionality for RAT results objects is available through the ``ratapi.utils.plotting`` module.
 
 .. note: plot_bayes is currently excluded because its docstring is not valid RST!
 
-.. automodule:: RATapi.utils.plotting
+.. automodule:: ratapi.utils.plotting
    :members:
    :exclude-members: plot_errorbars, plot_ref_sld_helper, assert_bayesian, name_to_index, panel_plot_helper, plot_bayes 
diff --git a/source/reference/python/project.rst b/source/reference/python/project.rst
@@ -1,6 +1,6 @@
 Project
 -------
 
-.. autopydantic_model:: RATapi.Project
+.. autopydantic_model:: ratapi.Project
    :members:
 
diff --git a/source/reference/python/run.rst b/source/reference/python/run.rst
@@ -3,4 +3,4 @@ Run
 
 The core function to run RAT.
 
-.. autofunction:: RATapi.run
+.. autofunction:: ratapi.run
diff --git a/source/reference/python/wrappers.rst b/source/reference/python/wrappers.rst
@@ -4,5 +4,5 @@ Wrappers
 This module contains the wrappers for interfacing with MATLAB custom functions,
 such as those for custom layers models or function backgrounds.
 
-.. automodule:: RATapi.wrappers
+.. automodule:: ratapi.wrappers
    :members:
diff --git a/source/tutorial/controls.rst b/source/tutorial/controls.rst
@@ -137,3 +137,6 @@ See the :ref:`resampling page<resampling>` for more details. In short:
 
 - ``resampleNPoints``: The initial number of domain points (layers) sampled by the algorithm at the start.
 
+``numSimulationPoints``
+^^^^^^^^^^^^^^^^^^^^^^^
+The number of points used for a reflectivity simulation where no data is present.
diff --git a/source/tutorial/introduction.rst b/source/tutorial/introduction.rst
@@ -53,7 +53,7 @@ The code block below shows how to set up each object for each language, as well
 
     .. code-block:: Python
 
-        import RATapi as RAT
+        import ratapi as RAT
 
         # Create project and controls objects
         project = RAT.Project()
@@ -135,7 +135,7 @@ definition and explain what it describes.
 
         .. output:: Python
 
-            import RATapi as RAT
+            import ratapi as RAT
 
             problem = RAT.Project.load("source/tutorial/data/two_contrast_example.json")
             print(problem)

diff --git a/source/tutorial/project.rst b/source/tutorial/project.rst
@@ -853,7 +853,7 @@ and our new dataset appears in the table:
 
             from importlib.resources import files
             import numpy as np
-            data_path =  files("RATapi.examples.data")
+            data_path =  files("ratapi.examples.data")
             myData = np.loadtxt(data_path / 'c_PLP0016596.dat', delimiter=',')
             problem.data.append(name='My new datafile', data=myData)
             print(problem.data)
@@ -953,7 +953,7 @@ To start, we first make an instance of the **Project** class:
 
     .. code-block:: Python
 
-        import RATapi as RAT
+        import ratapi as RAT
         problem = RAT.Project(name='DSPC monolayers')
 
 Then we need to define the parameters we need. We'll do this by making a parameters block, and adding these to the project:

diff --git a/source/utilities/conversionFuncs.rst b/source/utilities/conversionFuncs.rst
@@ -28,7 +28,7 @@ To convert this, simply navigate to the project directory, and run the following
 
     .. code-block:: Python
 
-        from RATapi.utils.convert import r1_to_project_class
+        from ratapi.utils.convert import r1_to_project_class
 
         problem = r1_to_project_class('monolayer_8_contrasts.mat')
 
@@ -45,7 +45,7 @@ This produces a **Project** object containing the R1 project, which can then be
 
     .. code-block:: Python
 
-        import RATapi as RAT
+        import ratapi as RAT
 
         controls = RAT.Controls(procedure='de', parallel='contrasts')
         problem, results = RAT.run(problem, controls)
@@ -83,7 +83,7 @@ It is also possible to do the opposite conversion, and convert any RAT **Project
 
     .. code-block:: Python
 
-        from RATapi.utils.convert import project_class_to_r1
+        from ratapi.utils.convert import project_class_to_r1
 
         project_class_to_r1(problem, "./testProject/myConvertedProject")
Original file line number	Diff line number	Diff line change
Expand Up		@@ -3,4 +3,4 @@ Run

		The core function to run RAT.

		.. autofunction:: RATapi.run
		.. autofunction:: ratapi.run