Moved doc theme

.github/workflows/deploy_ghpages.yml

@@ -26,14 +26,15 @@ jobs:
     - name: Install dependencies
       run: |
            python -m pip install --upgrade pip
-           python -m pip install pydata-sphinx-theme==0.7.1
+           python -m pip install furo
            python -m pip install numpydoc
            python -m pip install sphinx-gallery==0.9.0
            python -m pip install sphinxcontrib-httpdomain
            python -m pip install sphinxcontrib-ghcontributors
            python -m pip install sphinx-issues
            python -m pip install sphinx-copybutton  
-           python -m pip install sphinx==4.2
+           python -m pip install sphinx
+           python -m pip install sphinx-design
            sudo apt install texlive-extra-utils
            sudo apt-get install texlive-latex-extra
            python -m pip install .

.github/workflows/docs_PR.yml

@@ -30,14 +30,15 @@ jobs:
     - name: Install dependencies
       run: |
            python -m pip install --upgrade pip
-           python -m pip install pydata-sphinx-theme==0.7.1
+           python -m pip install furo
            python -m pip install numpydoc
            python -m pip install sphinx-gallery==0.9.0
            python -m pip install sphinxcontrib-httpdomain
            python -m pip install sphinxcontrib-ghcontributors
-           python -m pip install sphinx-copybutton  
            python -m pip install sphinx-issues
-           python -m pip install sphinx==4.2
+           python -m pip install sphinx-copybutton  
+           python -m pip install sphinx
+           python -m pip install sphinx-design
            sudo apt install texlive-extra-utils
            sudo apt-get install texlive-latex-extra
            python -m pip install .

.github/workflows/examples_PR.yml

@@ -30,14 +30,15 @@ jobs:
     - name: Install dependencies
       run: |
            python -m pip install --upgrade pip
-           python -m pip install pydata-sphinx-theme
+           python -m pip install furo
            python -m pip install numpydoc
            python -m pip install sphinx-gallery
            python -m pip install sphinxcontrib-httpdomain
            python -m pip install sphinxcontrib-ghcontributors
-           python -m pip install sphinx-copybutton  
            python -m pip install sphinx-issues
+           python -m pip install sphinx-copybutton  
            python -m pip install sphinx
+           python -m pip install sphinx-design
            sudo apt install texlive-extra-utils
            sudo apt-get install texlive-latex-extra
            python -m pip install .

deerlab/bg_models.py

@@ -129,7 +129,7 @@ def _hom3d(t,conc,lam):
 The expression for this model is
 
 .. math::
-   B(t) = \mathrm{exp}\left(-\ii\frac{8\pi}{9\sqrt{3}}(\sqrt{3} + \mathrm{ln}(2-\sqrt{3}))\lambda c_s D |t|\right)`
+   B(t) = \mathrm{exp}\left(i \frac{8\pi}{9\sqrt{3}}(\sqrt{3} + \mathrm{ln}(2-\sqrt{3}))\lambda c_s D t\right)
 
 where `c_s` is the spin concentration (entered in spins/m\ :sup:`3` into this expression) and D is the dipolar constant
 
@@ -220,7 +220,7 @@ def _hom3dex(t,conc,rex,lam):
 
 The expression for this model is
 
-.. math:: B(t) = \exp \Bigg(- \ii c_\mathrm{s}\lambda_k \bigg( V_\mathrm{ex} \mathrm{Im}\{\mathcal{K}_0(t, R_\mathrm{ex})\} + \mathcal{I}_\mathrm{C}(t) \bigg) 
+.. math:: B(t) = \exp \Bigg(- i c_\mathrm{s}\lambda_k \bigg( V_\mathrm{ex} \mathrm{Im}\{\mathcal{K}_0(t, R_\mathrm{ex})\} + \mathcal{I}_\mathrm{C}(t) \bigg) 
 
 where `\mathcal{I}_\mathrm{C}(t)` is an integral without analytical form given by 
 

deerlab/dipolarbackground.py

@@ -42,20 +42,20 @@ def dipolarbackground(t, pathways, basis):
 
     pathways : list of dictionaries  or ``None``, optional
         List of dipolar pathways. 
-        :raw-html:`<br /><br />`
+
         For *two-spin dipolar interactions*, each pathway is defined as a dictionary containing the pathway's amplitude :math:`\lambda_k` (``'amp'``), 
         refocusing time :math:`t_{\mathrm{ref},k}` (``'reftime'``) in microseconds, and (sub)harmonic :math:`\delta_k` (``'harmonic'``).
         For example, for a one-dimensional experiment ``{'amp:'lambda, 'reftime':tref, 'harmonic':delta}`` or ``{'amp:'lambda, 'reftime':tref}``. If ``'harmonic'`` is not
         specified, it is assumed to be 1 (modulated). For an unmodulated pathway, specify only the amplitude, i.e. ``{'amp':Lambda0}``.
-        :raw-html:`<br /><br />`
+
         For *multi-dimensional experiments*, the pathway refocusing times \mathbf{\t}_{\mathrm{ref},k}` and harmonics `\mathbf{\delta}_k` 
         along the different dimensions must be specified as a list, e.g. for a pathway in a two-dimensional experiment 
         ``{'amp:'lambda, 'reftime':[tref1,tref2], 'harmonic':[delta1,delta2]}``
-        :raw-html:`<br /><br />`
+        `
         For *three-spin interactions*, each pathway is defined as a dictionary containing the pathway's amplitude :math:`\lambda_k` (``'amp'``),
         a tuple of refocusing times :math:`t_{\mathrm{ref},k,q}` (``'reftime'``), and a tuple of (sub)harmonics :math:`\delta_{k,q}` (``'harmonic'``). 
         For example, for a one-dimensional experiment ``{'amp:'lambda, 'reftime':(tref1,tref2,tref3), 'harmonic':(delta1,delta2,delta3)}``. 
-        :raw-html:`<br /><br />`
+
         If neither ``pathways`` or ``mod`` are specified (or set to ``None``), ``pathways=[{'amp':1,'reftime':0}]`` is used as the default.
 
     basis : callable or array_like or ``None``, optional

deerlab/dipolarkernel.py

@@ -89,20 +89,20 @@ def dipolarkernel(t, r, *, pathways=None, mod=None, bg=None, method='fresnel', e
 
     pathways : list of dictionaries  or ``None``, optional
         List of dipolar pathways. 
-        :raw-html:`<br /><br />`
+
         For *two-spin dipolar interactions*, each pathway is defined as a dictionary containing the pathway's amplitude :math:`\lambda_k` (``'amp'``), 
         refocusing time :math:`t_{\mathrm{ref},k}` (``'reftime'``) in microseconds, and (sub)harmonic :math:`\delta_k` (``'harmonic'``).
         For example, for a one-dimensional experiment ``{'amp:'lambda, 'reftime':tref, 'harmonic':delta}`` or ``{'amp:'lambda, 'reftime':tref}``. If ``'harmonic'`` is not
         specified, it is assumed to be 1 (modulated). For an unmodulated pathway, specify only the amplitude, i.e. ``{'amp':Lambda0}``.
-        :raw-html:`<br /><br />`
+
         For *multi-dimensional experiments*, the pathway refocusing times \mathbf{\t}_{\mathrm{ref},k}` and harmonics `\mathbf{\delta}_k` 
         along the different dimensions must be specified as a list, e.g. for a pathway in a two-dimensional experiment 
         ``{'amp:'lambda, 'reftime':[tref1,tref2], 'harmonic':[delta1,delta2]}``
-        :raw-html:`<br /><br />`
+
         For *three-spin interactions*, each pathway is defined as a dictionary containing the pathway's amplitude :math:`\lambda_k` (``'amp'``),
         a tuple of refocusing times :math:`t_{\mathrm{ref},k,q}` (``'reftime'``), and a tuple of (sub)harmonics :math:`\delta_{k,q}` (``'harmonic'``). 
         For example, for a one-dimensional experiment ``{'amp:'lambda, 'reftime':(tref1,tref2,tref3), 'harmonic':(delta1,delta2,delta3)}``. 
-        :raw-html:`<br /><br />`
+
         If neither ``pathways`` or ``mod`` are specified (or set to ``None``), ``pathways=[{'amp':1,'reftime':0}]`` is used as the default.
 
     mod : scalar  or ``None``, optional

deerlab/utils.py

@@ -331,7 +331,7 @@ def der_snr(y):
     """
     DER-SNR noise estimation 
 
-    Estimate the noise level using the DER_SNR method [1]_.
+    Estimate the noise level using the DER_SNR method [1].
 
     Parameters
     ----------

docsrc/README.md

@@ -12,14 +12,15 @@ In order to compile the documentation the following steps must be followed:
 
 3) Install Sphinx and Sphinx extensions
 
-        pip install sphinx==4.2
-        pip install pydata-sphinx-theme==0.7.1
+        pip install sphinx
+        pip install furo
         pip install sphinxcontrib-httpdomain
         pip install sphinx-gallery
         pip install sphinxcontrib-ghcontributors
         pip install sphinx-issues
         pip install sphinx-copybutton 
         pip install numpydoc
+        pip install sphinx-design
 
 5) Download and install [dvisvgm](https://dvisvgm.de/Downloads/).