Merge pull request USNavalResearchLaboratory#89 from MJWeberg/main

Update RTD config

.readthedocs.yaml

@@ -5,6 +5,12 @@
 # Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
@@ -15,7 +21,7 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
+  version: 3.10
   install:
     - method: pip
       path: .

docs/guide/00-quick.rst

@@ -18,7 +18,7 @@ Example call signature,
 
 ::
 
-   read_cube('eis_20190404_131513.data.h5', 195.119)
+   data_cube = read_cube('eis_20190404_131513.data.h5', 195.119)
 
 `~eispac.core.read_cube` typically requires two arguments:
 
@@ -65,15 +65,17 @@ Example call signature,
 
 ::
 
-   read_template('fe_12_195_119.2c.template.h5')
+   tmplt = read_template('fe_12_195_119.2c.template.h5')
 
 `~eispac.core.read_template` is relatively simple. It takes a single argument
 giving the filename of a template file and returns an `~eispac.core.EISFitTemplate`
-class instance containing the the initial fit parameters. Users may view the parameter
-values by using either the ``print_parinfo()`` method or manually inspecting the
-``.template`` attribute. For convenience, there is also a ``central_wave`` attribute
-that contains the mean wavelength value within the template. This can be useful for
-loading the correct spectral window using `~eispac.core.read_cube`.
+class instance containing the the initial fit parameters. You can also load custom 
+templates by first defining a TOML file with your template parameters (see the
+:ref:`Custom Fit Templates <sec-template_toml>`: section for an example TOML
+file). You may print a summary of the template and parameter contraints by typing
+``print(TEMPLATE)``. For convenience, there is also a ``.central_wave`` attribute 
+that contains the mean wavelength value within the template. This can be useful 
+for loading the correct spectral window using `~eispac.core.read_cube`.
 
 fit_spectra
 -----------
@@ -82,7 +84,7 @@ This is the main fitting routine. Example call signature,
 
 ::
 
-   fit_spectra(data_cube, fit_template)
+   fit_results = fit_spectra(data_cube, fit_template)
 
 The simplest way to use `~eispac.core.fit_spectra()` is to give it two arguments:
 
@@ -101,8 +103,8 @@ Alternatively, you may provide the function with individual data arrays like thi
 
 ::
 
-   fit_spectra(inten_arr, template_dict, parinfo=parinfo_dict,
-               wave=wavelength_arr, errs=error_arr)
+   fit_result = fit_spectra(inten_arr, template_dict, parinfo=parinfo_dict,
+                            wave=wavelength_arr, errs=error_arr)
 
 The function will loop over the data according to its dimensionality. 3D data is
 assumed to be a full EIS raster (or a sub region), 2D data is assumed to be a

docs/guide/02-scripts.rst

@@ -68,7 +68,7 @@ EISPAC. If you have a working IDL installation of SolarSoft, the tool will
 attempt to locate a copy of the ``eis_cat.sqlite`` database on your computer.
 Otherwise, the program will try to download the database the first time you
 start the GUI. Please be patient, downloading the full catalog can take a
-minute of two.
+minute or two.
 
 .. figure:: figures/eis_catalog_example.png
    :align: center

docs/guide/04-fitting.rst

@@ -18,9 +18,9 @@ determining an initial guess for each parameter. The next ingredient for
 a fit is the selection of an optimization method. By default, EISPAC
 uses a Python implementation of the well-known IDL method **MPFIT**,
 which solves the non-linear least squares problem using the Levenberg-
-Marquardt algorithm. The Python module, ``mpfit.py``, can be found on
-GitHub [#]_ and is included in EISPAC. Future versions of the code will
-include full support for other fitting packages such as the newer
+Marquardt algorithm. The Python module, ``mpfit.py``, is included in EISPAC 
+and the orginal source code can found on GitHub [#]_. Future versions of 
+of EISPAC may include support for other fitting packages such as the newer
 `astropy.modeling` framework.
 
 Template Files
@@ -197,7 +197,7 @@ number of parameters. Other valid template keys include,
 * **n_gauss** (int) - number of Gaussian components
 * **n_poly** (int) - Number of background polynomial terms. 
   Common values are: 0 (no background), 1 (constant), and 2 (linear).
-* **line_ids** (array_like) - Strings giving the line identification 
+* **line_ids** (array-like) - Strings giving the line identification 
    for each Gaussian component. For example, "Fe XII 195.119". 
    If not specified, placeholder values of "unknown I {INITAL CENTROID VALUE}" 
    will be used.
@@ -210,14 +210,16 @@ in the ``.parinfo`` list of dicts. As such, they must be input as arrays or list
 with the same number of elements as the ``value`` array. 
 
 * **fixed** (0 or 1) - If set to "1", will not fit the parameter and just use initial value instead
-* **limited** (two-element array_like) - If set to "1" in the first/second
+* **limited** (two-element array-like) - If set to "1" in the first/second
   value, will apply and limit to the parameter on the lower/upper side
-* **limits** (two-element array_like) - Values of the limits on the
+* **limits** (two-element array-like) - Values of the limits on the
   lower/upper side. Both "limited" and "limits" must be give together.
 * **tied** (str) - String defining a fixed relationship between this
   parameters one or more others. For example "p[0] / 2" would define
   a parameter to ALWAYS be exactly half the value of the first parameter.
 
+.. _sec-template_toml:
+
 The second method for initializing a custom template is to write a separate 
 TOML-formatted text file with all of the input parameters and then load the 
 custom template file using the `~eispac.core.read_template`. This allows you to 
@@ -366,6 +368,8 @@ of arrays.
    err_int         float64 (128, 32, 2)
    vel             float64 (128, 32, 2)
    err_vel         float64 (128, 32, 2)
+   width           float64 (128, 32, 2)
+   err_width       float64 (128, 32, 2)
    params          float64 (128, 32, 7)
    perror          float64 (128, 32, 7)
    component       int32 (7,)

docs/install.rst

@@ -32,12 +32,14 @@ try installing the required packages individually first.
 
 -  python-dateutil >= 2.8
 
+-  tomli >= 1.1.0 (python < v3.11 only)
+
 .. _sec-install:
 
 Standard Installation
 ---------------------
 
-EISPAC is now available on PyPI. To install, just use the following command,
+EISPAC is available on PyPI. To install, use the following command,
 
 ::