Saving progress on documentation

PlanetMag.m

@@ -1,5 +1,5 @@
-function PlanetMag(moonName, era, coordType, CALC_NEW, ALL_MODELS, DO_FFT, DO_MPAUSE, specificModel, ...
-    specificMPmodel, outData, nptsApprox, magPhase)
+function PlanetMag(moonName, era, coordType, CALC_NEW, ALL_MODELS, DO_FFT, DO_MPAUSE, ...
+    specificModel, specificMPmodel, outData, nptsApprox, magPhase)
 % Evaluates planetary magnetic field for a time series at the specified moon location and inverts
 % for the complex amplitudes of oscillation in that moon's frame.
 %
@@ -26,13 +26,20 @@ function PlanetMag(moonName, era, coordType, CALC_NEW, ALL_MODELS, DO_FFT, DO_MP
 % CALC_NEW : bool
 %   Whether to perform calculations or attempt to reload saved data for plotting purposes.
 % ALL_MODELS : bool
+%   Whether to run all implemented model options for the desired body.
 % DO_FFT : bool
+%   Whether to calculate and print an FFT from the time series after performing the inversion.
 % DO_MPAUSE : bool
+%   Whether to include a magnetopause screening current model.
 % specificModel : int
+%   Index number for the magnetospheric model to run. Options depend on the body, and setting to
+%   0 selects the default model. See GetModelOpts for a description of the options.
 % specificMPmodel : int
+%   Index number for the magnetopause model to run if DO_MPAUSE is true. 0 selects the default
+%   model See MpauseFld for a description of the options.
 % outData : char, 1xF
-%   Directory to use for output complex spectrum amplitudes.
-% nptsApprox : int 
+%   Directory to use for output of complex spectrum amplitudes.
+% nptsApprox : int
 %   Desired number of points to use in time series for inversion. A whole number of the period of 
 %   interest (typically synodic period, as it is the strongest oscillation) will ultimately be 
 %   selected, which is why this number is approximate.

docs/conf.py

@@ -33,6 +33,7 @@
 #sys.path.insert(0, _PACKAGE_DIR)
 
 matlab_src_dir = _ROOT_DIR
+matlab_auto_link = 'all'
 
 apidoc_module_dir = _ROOT_DIR
 apidoc_output_dir = 'stubs'

docs/docstringTemplateMatlab.txt

@@ -38,7 +38,7 @@
 % Contact: corey.j.cochrane@jpl.nasa.gov
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-Keep the above informational notice intact, separated by docstring by an empty line, not preceded
+Keep the above informational notice intact, separated from docstring by an empty line, not preceded
 by a %. The informational notice must appear in the first function in each file, AFTER the
 docstring.
 
@@ -52,12 +52,12 @@ where it's required!):
 % Parameters
 % ----------
 % inputName : type, dims
-%     Description.
+%   Description.
 %
 % Returns
 % -------
 % outputName : type, dims
-%     Description.
+%   Description.
 
 % Part of the PlanetMag framework for evaluation and study of planetary magnetic fields.
 % Created by Corey J. Cochrane and Marshall J. Styczinski

docs/functions.rst

@@ -1,3 +1,5 @@
+.. role:: mat:func
+   :class: func
 .. role:: func
    :class: func
 
@@ -10,138 +12,138 @@ Calculation functions
 .. mat:module:: functions
    :noindex:
 
-:func:`MagFldParent`
-++++++++++++++++++++
+:mat:func:`MagFldParent`
+++++++++++++++++++++++++
 
 .. mat:autofunction:: MagFldParent
 
-:func:`KSMagFldJupiter`
-+++++++++++++++++++++++
+:mat:func:`KSMagFldJupiter`
++++++++++++++++++++++++++++
 
 .. mat:autofunction:: KSMagFldJupiter
 
-:func:`MpauseFld`
-+++++++++++++++++
+:mat:func:`MpauseFld`
++++++++++++++++++++++
 
 .. mat:autofunction:: MpauseFld
 
-:func:`MagFldParentSingle`
-++++++++++++++++++++++++++
+:mat:func:`MagFldParentSingle`
+++++++++++++++++++++++++++++++
 
 .. mat:autofunction:: MagFldParentSingle
 
-:func:`LegendreP`
-+++++++++++++++++
+:mat:func:`LegendreP`
++++++++++++++++++++++
 
 .. mat:autofunction:: LegendreP
 
-:func:`LegendreS`
-+++++++++++++++++
+:mat:func:`LegendreS`
++++++++++++++++++++++
 
 .. mat:autofunction:: LegendreS
 
-:func:`dLegendreP`
-++++++++++++++++++
+:mat:func:`dLegendreP`
+++++++++++++++++++++++
 
 .. mat:autofunction:: dLegendreP
 
-:func:`dLegendreS`
-++++++++++++++++++
+:mat:func:`dLegendreS`
+++++++++++++++++++++++
 
 .. mat:autofunction:: dLegendreS
 
-:func:`Bsph2Bxyz`
-+++++++++++++++++
+:mat:func:`Bsph2Bxyz`
++++++++++++++++++++++
 
 .. mat:autofunction:: Bsph2Bxyz
 
-:func:`Bxyz2Bsph`
-+++++++++++++++++
+:mat:func:`Bxyz2Bsph`
++++++++++++++++++++++
 
 .. mat:autofunction:: Bxyz2Bsph
 
-:func:`CalcExcitationsFFT`
-++++++++++++++++++++++++++
+:mat:func:`CalcExcitationsFFT`
+++++++++++++++++++++++++++++++
 
 .. mat:autofunction:: CalcExcitationsFFT
 
-:func:`ConvertSwarmCDF`
-+++++++++++++++++++++++
+:mat:func:`ConvertSwarmCDF`
++++++++++++++++++++++++++++
 
 .. mat:autofunction:: ConvertSwarmCDF
 
-:func:`ExcitationSpectrum`
-++++++++++++++++++++++++++
+:mat:func:`ExcitationSpectrum`
+++++++++++++++++++++++++++++++
 
 .. mat:autofunction:: ExcitationSpectrum
 
-:func:`GetBodyParams`
-+++++++++++++++++++++
+:mat:func:`GetBodyParams`
++++++++++++++++++++++++++
 
 .. mat:autofunction:: GetBodyParams
 
-:func:`GetBplotAndLsq`
-++++++++++++++++++++++
+:mat:func:`GetBplotAndLsq`
+++++++++++++++++++++++++++
 
 .. mat:autofunction:: GetBplotAndLsq
 
-:func:`GetBplotAndLsqMoon`
-++++++++++++++++++++++++++
+:mat:func:`GetBplotAndLsqMoon`
+++++++++++++++++++++++++++++++
 
 .. mat:autofunction:: GetBplotAndLsqMoon
 
-:func:`GetBplotAndLsqNeptune`
-+++++++++++++++++++++++++++++
+:mat:func:`GetBplotAndLsqNeptune`
++++++++++++++++++++++++++++++++++
 
 .. mat:autofunction:: GetBplotAndLsqNeptune
 
-:func:`GetGaussCoeffs`
-++++++++++++++++++++++
+:mat:func:`GetGaussCoeffs`
+++++++++++++++++++++++++++
 
 .. mat:autofunction:: GetGaussCoeffs
 
-:func:`GetModelOpts`
-++++++++++++++++++++
+:mat:func:`GetModelOpts`
+++++++++++++++++++++++++
 
 .. mat:autofunction:: GetModelOpts
 
-:func:`GetMoonDist`
-+++++++++++++++++++
+:mat:func:`GetMoonDist`
++++++++++++++++++++++++
 
 .. mat:autofunction:: GetMoonDist
 
-:func:`GetPosSpice`
-+++++++++++++++++++
+:mat:func:`GetPosSpice`
++++++++++++++++++++++++
 
 .. mat:autofunction:: GetPosSpice
 
-:func:`GetTargetMoonDist`
-+++++++++++++++++++++++++
+:mat:func:`GetTargetMoonDist`
++++++++++++++++++++++++++++++
 
 .. mat:autofunction:: GetTargetMoonDist
 
-:func:`LoadSpice`
-+++++++++++++++++
+:mat:func:`LoadSpice`
++++++++++++++++++++++
 
 .. mat:autofunction:: LoadSpice
 
-:func:`LshellTrace`
-+++++++++++++++++++
+:mat:func:`LshellTrace`
++++++++++++++++++++++++
 
 .. mat:autofunction:: LshellTrace
 
-:func:`PCA_decomposition`
-+++++++++++++++++++++++++
+:mat:func:`PCA_decomposition`
++++++++++++++++++++++++++++++
 
 .. mat:autofunction:: PCA_decomposition
 
-:func:`PlotSpectrum`
-++++++++++++++++++++
+:mat:func:`PlotSpectrum`
+++++++++++++++++++++++++
 
 .. mat:autofunction:: PlotSpectrum
 
-:func:`RotateBspice`
-++++++++++++++++++++
+:mat:func:`RotateBspice`
+++++++++++++++++++++++++
 
 .. mat:autofunction:: RotateBspice
 

docs/primary.rst

@@ -1,39 +1,42 @@
+.. role:: mat:func
+   :class: func
+
 PlanetMag Matlab run scripts
 ============================
 
 .. mat:module:: .
    :noindex:
 
-:func:`PlanetMag`
-+++++++++++++++++
+:mat:func:`PlanetMag`
++++++++++++++++++++++
 
 .. mat:autofunction:: PlanetMag
 
 .. mat:module:: comparison
    :noindex:
 
-:func:`CompareEarModels`
-++++++++++++++++++++++++
+:mat:func:`CompareEarModels`
+++++++++++++++++++++++++++++
 
 .. mat:autofunction:: CompareEarModels
 
-:func:`CompareJupModels`
-++++++++++++++++++++++++
+:mat:func:`CompareJupModels`
+++++++++++++++++++++++++++++
 
 .. mat:autofunction:: CompareJupModels
 
-:func:`CompareSatModels`
-++++++++++++++++++++++++
+:mat:func:`CompareSatModels`
+++++++++++++++++++++++++++++
 
 .. mat:autofunction:: CompareSatModels
 
-:func:`CompareUraModels`
-++++++++++++++++++++++++
+:mat:func:`CompareUraModels`
+++++++++++++++++++++++++++++
 
 .. mat:autofunction:: CompareUraModels
 
-:func:`CompareNepModels`
-++++++++++++++++++++++++
+:mat:func:`CompareNepModels`
+++++++++++++++++++++++++++++
 
 .. mat:autofunction:: CompareNepModels
 

modelCoeffs/coeffsBode1994G.m

@@ -1,8 +1,28 @@
 function Gnm = coeffsBode1994G(alpha)
-    % Calculate magnetopause field coefficients for use with Engle (1992)
-    % method as a function of dipole "precession angle" alpha, as fit by
-    % Bode (1994) -- see https://apps.dtic.mil/sti/pdfs/ADA284857.pdf.
-    % alpha = 0 is when the the dipole nod longitude is at local noon.
+% **Gnm**
+%
+% Calculate magnetopause field coefficients as fit by Bode (1994).
+%
+% For use with Engle (1992) method as a function of dipole "precession angle" alpha for Jupiter
+% See https://apps.dtic.mil/sti/pdfs/ADA284857.pdf.
+%
+% Parameters
+% ----------
+% alpha : double, 1xN
+%   Nod longitude for planetary dipole moment in degrees. This is the angle between the equatorial
+%   projection of the magnetic dipole moment vector and the direction of the Sun.
+%   alpha = 0 is when the the dipole north nod longitude is at local noon.
+%
+% Returns
+% -------
+% outputName : type, dims
+%   Description.
+
+% Part of the PlanetMag framework for evaluation and study of planetary magnetic fields.
+% Created by Corey J. Cochrane and Marshall J. Styczinski
+% Maintained by Marshall J. Styczinski
+% Contact: corey.j.cochrane@jpl.nasa.gov
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
     npts = length(alpha);
     Gnm = zeros(10, 11, npts);