adjusted README, gave up on import, added badge

Author: AndrewGibbs

.github/workflows/docs.yml

@@ -5,8 +5,8 @@ on:
   push:
     branches:
       - '**'
-    # paths:
-    # - docs/guide/**
+    paths:
+    - docs/guide/**
 
 # This job installs dependencies, builds the book, and pushes it to `gh-pages`
 jobs:

.github/workflows/draft-pdf.yml

@@ -11,12 +11,12 @@ jobs:
         uses: openjournals/openjournals-draft-action@master
         with:
           journal: joss
-          paper-path: documents/joss_paper/paper.md
+          paper-path: docs/joss_paper/paper.md
       - name: Upload
         uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled
           # PDF. Note, this should be the same directory as the input
           # paper.md
-          path: documents/joss_paper/paper.pdf
+          path: docs/joss_paper/paper.pdf

README.md

@@ -5,9 +5,20 @@
 [![status](https://joss.theoj.org/papers/851d659a3a85536bfc6b86de45a1641d/status.svg)](https://joss.theoj.org/papers/851d659a3a85536bfc6b86de45a1641d)
 [![CI](https://github.com/AndrewGibbs/PathFinder/actions/workflows/ubuntu.yml/badge.svg)](https://github.com/AndrewGibbs/PathFinder/actions/workflows/ubuntu.yml//badge.svg)
 [![CI](https://github.com/AndrewGibbs/PathFinder/actions/workflows/windows.yml/badge.svg)](https://github.com/AndrewGibbs/PathFinder/actions/workflows/windows.yml//badge.svg)
+[![Documentation Status](https://img.shields.io/badge/docs-published-success)](https://andrewgibbs.github.io/PathFinder/)
 
 
-```{include} docs/intro_insert.md
+PathFinder is a Matlab/Octave toolbox for the numerical evaluation of highly oscillatory integrals. Specifically, PathFinder can efficiently evaluate integrals of the form
+
+$$
+I = \int_{a}^b f(z)\exp(\mathrm{i}\omega g(z)) \mathrm{d}z
+$$
+
+where $g$ is a polynomial, $f$ is entire (analytic everywhere in $\mathbb{C}$), $\omega>0$ is a frequency parameter, and the endpoints $a$ and $b$ may be finite or infinite. Further, it is assumed that $I$ is a convergent integral and that $|f(z)|$ grows sub-exponentially as $|z|\to\infty$.
+
+PathFinder is based on steepest descent contour deformation, but it can be easily used without a deep understanding of the underlying mathematics; it is sufficient to understand the conditions in the previous paragraph.
+
+For information about installation, syntax and how to contribute, please refer to [the full documentation](https://andrewgibbs.github.io/PathFinder/).
 
 ## Acknowledgments
 

docs/guide/intro.md

@@ -1,7 +1,11 @@
-# PathfFinder Documentation
+# PathFinder Documentation
 
-```{include} ../intro_insert.md
+PathFinder is a Matlab/Octave toolbox for the numerical evaluation of highly oscillatory integrals. Specifically, PathFinder can efficiently evaluate integrals of the form
 
+$$
+I = \int_{a}^b f(z)\exp(\mathrm{i}\omega g(z)) \mathrm{d}z
+$$
 
-```{tableofcontents}
-```
+where $g$ is a polynomial, $f$ is entire (analytic everywhere in $\mathbb{C}$), $\omega>0$ is a frequency parameter, and the endpoints $a$ and $b$ may be finite or infinite. Further, it is assumed that $I$ is a convergent integral and that $|f(z)|$ grows sub-exponentially as $|z|\to\infty$.
+
+PathFinder is based on steepest descent contour deformation, but it can be easily used without a deep understanding of the underlying mathematics; it is sufficient to understand the conditions in the previous paragraph. This document intends to provide a full explanation of **how to use PathFinder**. For a full explanation of the underlying mathematics, the interested reader is referred to {cite:p}`PFpaper`.

docs/guide/theory/rootfinding.md

@@ -1,6 +1,6 @@
 # Construction of Coefficients for Polynomial Root-finding Problems in PathFinder
 
-### Outline
+## Outline
 In the original paper about the PathFinder algorithm In the paper {cite:p}`PFpaper`, the derivations of some root-finding procedures were deemed too trivial to include. Unfortunately, these derivations are not trivial enough to explain within the code's comments, so full details are given here for anyone interested in fully understanding the algorithm/code.
 
 Following the notation of {cite:p}`PFpaper`, we write the polynomial phase function as
@@ -11,7 +11,7 @@ $$
 
 We use $\xi$ to denote the center of a complex ball, which is *usually* a stationary point.
 
-### Finding the Intersection of Rays with the Boundary of the Non-oscillatory Region
+## Finding the Intersection of Rays with the Boundary of the Non-oscillatory Region
 In section 2.2 of the paper {cite:p}`PFpaper`, we discuss the procedure for choosing the balls around the stationary points. This can be broken down into several smaller root-finding problems of the following form: Given $\theta$ and $\xi$, find $r>0$ such that
 
 $$
@@ -57,7 +57,7 @@ $$ b_j=\sum_{\ell=0}^{j}a_\ell\overline{a}_{j-\ell}, \text{ for } j=1,\ldots,2J.
 
 By default, in PathFinder a Mex routine `getRGivenTheta_mex` is used to find the roots of $G$. The relevant subroutine is `get_r_given_theta`, in the C header file `get_r.h`. Here the coefficients $a_k$ and $\overline{a_k}$ are represented by arrays `a` and `a_`, respectively. The coefficients vector $b_j$ is represented by the array `coeffs`. When Mex is not used, the Matlab file `getRGivenTheta.m` is used to achieve the same result.
 
-### Finding the Exits on the Circumference of the Ball
+## Finding the Exits on the Circumference of the Ball
 Section 2.3 of the PathFinder paper {cite:p}`PFpaper`mentions that the exits are determined using a trigonometric root-finding procedure. The radius $r$ of the ball is fixed, and we are looking for local maxima (in $\theta$) of $\Im g(\xi+r\mathrm{e}^{\mathrm{i} \theta})$. The approach is to represent $\Im g(\xi+r\mathrm{e}^{\mathrm{i} \theta})$ exactly in terms of a finite-dimensional Fourier basis.
 
 First, construct the trigonometric polynomial in $\theta$ from (2):

docs/guide/usage/advanced.md

@@ -2,7 +2,7 @@
 
 ## Adjustable parameters
 
-The optional inputs `'plot'`, `'plot graph'` and `'infcontour'` are just three of many adjustable parameters. In fact, all of the algorithm parameters defined in [1, Table 4.1](#references) can be easily modified, if the user wishes to do so. Here is a list of adjustable parameters - each can be adjusted by adding the optional input as a text string, followed by the new value.
+The optional inputs `'plot'`, `'plot graph'` and `'infcontour'` are just three of many adjustable parameters. In fact, all of the algorithm parameters defined in {cite:p}`PFpaper` can be easily modified, if the user wishes to do so. Here is a list of adjustable parameters - each can be adjusted by adding the optional input as a text string, followed by the new value.
 
 |  Parameter |  Meaning |  Default | 
 |---|---|---|