Re-ran sphinx-apidoc, fixed sphix compile warnings.

docs/analysis.rst

@@ -12,6 +12,7 @@ Analyze output with ``mpetplot.py``. Pass the output data directory, then use th
 1.  Analyze output with plots using ``mpetplot.py``. Pass output data directory, then use ``-pt [plottype]`` with one (or more) of the plot types listed below. Default is ``v``.
     - e.g., voltage plot: ``mpetplot.py sim_output -pt v``
     - other options (``full``, ``c``, ``a`` indicate full cell, cathode, and anode):
+
    #. ``v`` or ``vt`` -- voltage vs filling fraction or vs time
    #. ``curr`` -- current vs time
    #. ``elytec{f}`` -- electrolyte concentration (movie) or final snapshot with f
@@ -23,6 +24,7 @@ Analyze output with ``mpetplot.py``. Pass the output data directory, then use th
    #. ``cbarLine_{c,a}`` -- average concentration in each particle of electrode
    #. ``bulkp_{c,a}`` -- macroscopic electrode solid phase potential (movie)
    #. ``cbar_{full,c,a}`` -- average solid concentrations as changing colors (movie)
+
     - There are two options for the color map type that is used: ``smooth`` or ``discrete``. This can be set with the ``-c`` option, e.g., ``mpetplot.py sim_output -pt cbar_full -c discrete``. The default value is ``discrete``.
     - When using the ``smooth`` color map option, the colors are selected from colormao_custom.npz, which includes three options (``GnYlRd_1``, ``GnYlRd_2``, and ``GnYlRd_3``) that can be selected with the ``st`` option, e.g., ``mpetplot.py sim_output -pt cbar_full -c discrete -st GnYlRd_1``. The default value is ``GnYlRd_3``.
 

docs/dashboard.rst

@@ -1,5 +1,5 @@
 Comparison of different models using Dash
 =========================================
-You can compare the result of different models using the dashboard build with `Dash <https://dash.plotly.com>`_. To create the dashboard, run the ``mpet_plot_app.py`` script (located in the bin folder) and use the ``-d`` argument to provide a directory with model outputs to include the dashbaord. Each model output should be located in a subfolder of the provided directory. For example, to compare the results of all models saved in subfolders of the folder ``history``, run the command:
+You can compare the result of different models using the dashboard build with `Dash <https://dash.plotly.com>`__. To create the dashboard, run the ``mpet_plot_app.py`` script (located in the bin folder) and use the ``-d`` argument to provide a directory with model outputs to include the dashbaord. Each model output should be located in a subfolder of the provided directory. For example, to compare the results of all models saved in subfolders of the folder ``history``, run the command:
 ``bin/mpet_plot_app.py -d history``. It will try to open the dashbaord in your web browser, where the different models can be identified based on their subfolder name.
-Running this script requires the following packages to be installed: `dash <https://pypi.org/project/dash/>`_ and `dash_bootstrap_components <https://pypi.org/project/dash-bootstrap-components/>`_.
+Running this script requires the following packages to be installed: `dash <https://pypi.org/project/dash/>`__ and `dash_bootstrap_components <https://pypi.org/project/dash-bootstrap-components/>`_.

docs/index.rst

@@ -27,7 +27,7 @@ Welcome to MPET's documentation!
    :maxdepth: 1
    :caption: API:
 
-   source/mpet.rst
+   source/modules.rst
 
 
 Indices and tables

docs/source/mpet.config.rst

@@ -0,0 +1,53 @@
+mpet.config package
+===================
+
+Submodules
+----------
+
+mpet.config.configuration module
+--------------------------------
+
+.. automodule:: mpet.config.configuration
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.config.constants module
+----------------------------
+
+.. automodule:: mpet.config.constants
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.config.derived\_values module
+----------------------------------
+
+.. automodule:: mpet.config.derived_values
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.config.parameterset module
+-------------------------------
+
+.. automodule:: mpet.config.parameterset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.config.schemas module
+--------------------------
+
+.. automodule:: mpet.config.schemas
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mpet.config
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/mpet.electrode.diffusion.rst

@@ -0,0 +1,37 @@
+mpet.electrode.diffusion package
+================================
+
+Submodules
+----------
+
+mpet.electrode.diffusion.NMC532\_Colclasure20 module
+----------------------------------------------------
+
+.. automodule:: mpet.electrode.diffusion.NMC532_Colclasure20
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.diffusion.constant module
+----------------------------------------
+
+.. automodule:: mpet.electrode.diffusion.constant
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.diffusion.lattice module
+---------------------------------------
+
+.. automodule:: mpet.electrode.diffusion.lattice
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mpet.electrode.diffusion
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/mpet.electrode.materials.rst

@@ -0,0 +1,189 @@
+mpet.electrode.materials package
+================================
+
+Submodules
+----------
+
+mpet.electrode.materials.LTO module
+-----------------------------------
+
+.. automodule:: mpet.electrode.materials.LTO
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiC6 module
+------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiC6
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiC6\_1param module
+--------------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiC6_1param
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiC6\_2step\_ss module
+-----------------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiC6_2step_ss
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiC6\_Colclasure\_1506T module
+-------------------------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiC6_Colclasure_1506T
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiC6\_LIONSIMBA module
+-----------------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiC6_LIONSIMBA
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiC6\_coke\_ss module
+----------------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiC6_coke_ss
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiC6\_coke\_ss2 module
+-----------------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiC6_coke_ss2
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiC6\_ss module
+----------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiC6_ss
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiC6\_ss2 module
+-----------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiC6_ss2
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiCoO2\_LIONSIMBA module
+-------------------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiCoO2_LIONSIMBA
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiFePO4 module
+---------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiFePO4
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiMn2O4\_ss module
+-------------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiMn2O4_ss
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.LiMn2O4\_ss2 module
+--------------------------------------------
+
+.. automodule:: mpet.electrode.materials.LiMn2O4_ss2
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.Li\_ss module
+--------------------------------------
+
+.. automodule:: mpet.electrode.materials.Li_ss
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.NCA\_ss1 module
+----------------------------------------
+
+.. automodule:: mpet.electrode.materials.NCA_ss1
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.NCA\_ss2 module
+----------------------------------------
+
+.. automodule:: mpet.electrode.materials.NCA_ss2
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.NMC532\_Colclasure20 module
+----------------------------------------------------
+
+.. automodule:: mpet.electrode.materials.NMC532_Colclasure20
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.testIS\_ss module
+------------------------------------------
+
+.. automodule:: mpet.electrode.materials.testIS_ss
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.testRS module
+--------------------------------------
+
+.. automodule:: mpet.electrode.materials.testRS
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.testRS\_ps module
+------------------------------------------
+
+.. automodule:: mpet.electrode.materials.testRS_ps
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mpet.electrode.materials.testRS\_ss module
+------------------------------------------
+
+.. automodule:: mpet.electrode.materials.testRS_ss
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mpet.electrode.materials
+   :members:
+   :undoc-members:
+   :show-inheritance: