tidy up after updating nbdev

_docs/callbacks.html

@@ -301,7 +301,7 @@ <h3 class="anchored" data-anchor-id="shortepochcallback">ShortEpochCallback</h3>
 <blockquote class="blockquote">
 <pre><code> ShortEpochCallback (pct=0.01, short_valid=True)</code></pre>
 </blockquote>
-<p>Fit just <code>pct</code> of an epoch, then stop</p>
+<p><em>Fit just <code>pct</code> of an epoch, then stop</em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/training.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -310,7 +310,7 @@ <h3 class="anchored" data-anchor-id="gradientaccumulation">GradientAccumulation<
 <blockquote class="blockquote">
 <pre><code> GradientAccumulation (n_acc=32)</code></pre>
 </blockquote>
-<p>Accumulate gradients before updating weights</p>
+<p><em>Accumulate gradients before updating weights</em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/tracker.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -320,7 +320,7 @@ <h3 class="anchored" data-anchor-id="earlystoppingcallback">EarlyStoppingCallbac
 <pre><code> EarlyStoppingCallback (monitor='valid_loss', comp=None, min_delta=0.0,
                         patience=1, reset_on_fit=True)</code></pre>
 </blockquote>
-<p>A <code>TrackerCallback</code> that terminates training when monitored quantity stops improving.</p>
+<p><em>A <code>TrackerCallback</code> that terminates training when monitored quantity stops improving.</em></p>
 <table class="table">
 <colgroup>
 <col style="width: 6%">
@@ -379,7 +379,7 @@ <h3 class="anchored" data-anchor-id="savemodelcallback">SaveModelCallback</h3>
                     fname='model', every_epoch=False, at_end=False,
                     with_opt=False, reset_on_fit=True)</code></pre>
 </blockquote>
-<p>A <code>TrackerCallback</code> that saves the model’s best during training and loads it at the end.</p>
+<p><em>A <code>TrackerCallback</code> that saves the model’s best during training and loads it at the end.</em></p>
 <table class="table">
 <colgroup>
 <col style="width: 6%">
@@ -455,7 +455,7 @@ <h3 class="anchored" data-anchor-id="reducelronplateau">ReduceLROnPlateau</h3>
 <pre><code> ReduceLROnPlateau (monitor='valid_loss', comp=None, min_delta=0.0,
                     patience=1, factor=10.0, min_lr=0, reset_on_fit=True)</code></pre>
 </blockquote>
-<p>A <code>TrackerCallback</code> that reduces learning rate when a metric has stopped improving.</p>
+<p><em>A <code>TrackerCallback</code> that reduces learning rate when a metric has stopped improving.</em></p>
 <table class="table">
 <colgroup>
 <col style="width: 6%">
@@ -528,7 +528,7 @@ <h3 class="anchored" data-anchor-id="paramscheduler">ParamScheduler</h3>
 <blockquote class="blockquote">
 <pre><code> ParamScheduler (scheds)</code></pre>
 </blockquote>
-<p>Schedule hyper-parameters according to <code>scheds</code></p>
+<p><em>Schedule hyper-parameters according to <code>scheds</code></em></p>
 <p><code>scheds</code> is a dictionary with one key for each hyper-parameter you want to schedule, with either a scheduler or a list of schedulers as values (in the second case, the list must have the same length as the the number of parameters groups of the optimizer).</p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/schedule.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
@@ -538,7 +538,7 @@ <h3 class="anchored" data-anchor-id="schedcos">SchedCos</h3>
 <blockquote class="blockquote">
 <pre><code> SchedCos (start, end)</code></pre>
 </blockquote>
-<p>Cosine schedule function from <code>start</code> to <code>end</code></p>
+<p><em>Cosine schedule function from <code>start</code> to <code>end</code></em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/schedule.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -547,7 +547,7 @@ <h3 class="anchored" data-anchor-id="schedexp">SchedExp</h3>
 <blockquote class="blockquote">
 <pre><code> SchedExp (start, end)</code></pre>
 </blockquote>
-<p>Exponential schedule function from <code>start</code> to <code>end</code></p>
+<p><em>Exponential schedule function from <code>start</code> to <code>end</code></em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/schedule.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -556,7 +556,7 @@ <h3 class="anchored" data-anchor-id="schedlin">SchedLin</h3>
 <blockquote class="blockquote">
 <pre><code> SchedLin (start, end)</code></pre>
 </blockquote>
-<p>Linear schedule function from <code>start</code> to <code>end</code></p>
+<p><em>Linear schedule function from <code>start</code> to <code>end</code></em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/schedule.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -565,7 +565,7 @@ <h3 class="anchored" data-anchor-id="schedno">SchedNo</h3>
 <blockquote class="blockquote">
 <pre><code> SchedNo (start, end)</code></pre>
 </blockquote>
-<p>Constant schedule function with <code>start</code> value</p>
+<p><em>Constant schedule function with <code>start</code> value</em></p>
 
 
 </section>

_docs/core.html

@@ -307,7 +307,7 @@ <h3 class="anchored" data-anchor-id="datablock">DataBlock</h3>
             n_inp:int=None, item_tfms:list=None, batch_tfms:list=None,
             get_items=None, splitter=None, get_y=None, get_x=None)</code></pre>
 </blockquote>
-<p>Generic container to quickly build <code>Datasets</code> and <code>DataLoaders</code>.</p>
+<p><em>Generic container to quickly build <code>Datasets</code> and <code>DataLoaders</code>.</em></p>
 <table class="table">
 <colgroup>
 <col style="width: 6%">
@@ -394,13 +394,13 @@ <h3 class="anchored" data-anchor-id="dataloaders">DataLoaders</h3>
 <blockquote class="blockquote">
 <pre><code> DataLoaders (*loaders, path:str|pathlib.Path='.', device=None)</code></pre>
 </blockquote>
-<p>Basic wrapper around several <code>DataLoader</code>s.</p>
+<p><em>Basic wrapper around several <code>DataLoader</code>s.</em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/learner.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
 <section id="learner" class="level3">
 <h3 class="anchored" data-anchor-id="learner">Learner</h3>
-<p>Group together a <code>model</code>, some <code>dls</code> and a <code>loss_func</code> to handle training</p>
+<p><em>Group together a <code>model</code>, some <code>dls</code> and a <code>loss_func</code> to handle training</em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/progress.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -419,7 +419,7 @@ <h3 class="anchored" data-anchor-id="showgraphcallback">ShowGraphCallback</h3>
                     after_cancel_epoch=None, after_epoch=None,
                     after_cancel_fit=None, after_fit=None)</code></pre>
 </blockquote>
-<p>Update a graph of training and validation loss</p>
+<p><em>Update a graph of training and validation loss</em></p>
 <hr>
 <p><a href="https://github.com/fastai/fastai/blob/master/fastai/callback/progress.py#LNone" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
@@ -428,7 +428,7 @@ <h3 class="anchored" data-anchor-id="csvlogger">CSVLogger</h3>
 <blockquote class="blockquote">
 <pre><code> CSVLogger (fname='history.csv', append=False)</code></pre>
 </blockquote>
-<p>Log the results displayed in <code>learn.path/fname</code></p>
+<p><em>Log the results displayed in <code>learn.path/fname</code></em></p>
 <pre><code>Unknown section Notes</code></pre>
 <hr>
 </section>
@@ -437,15 +437,15 @@ <h3 class="anchored" data-anchor-id="cells3d">cells3d</h3>
 <blockquote class="blockquote">
 <pre><code> cells3d ()</code></pre>
 </blockquote>
-<p>3D fluorescence microscopy image of cells.</p>
-<p>The returned data is a 3D multichannel array with dimensions provided in <code>(z, c, y, x)</code> order. Each voxel has a size of <code>(0.29 0.26 0.26)</code> micrometer. Channel 0 contains cell membranes, channel 1 contains nuclei.</p>
+<p>*3D fluorescence microscopy image of cells.</p>
+<p>The returned data is a 3D multichannel array with dimensions provided in <code>(z, c, y, x)</code> order. Each voxel has a size of <code>(0.29 0.26 0.26)</code> micrometer. Channel 0 contains cell membranes, channel 1 contains nuclei.*</p>
 </section>
 </section>
 <section id="engine" class="level2">
 <h2 class="anchored" data-anchor-id="engine">Engine</h2>
 <p>Core engine for model training. See tutorials for usage examples.</p>
 <hr>
-<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L34" target="_blank" style="float:right; font-size:smaller">source</a></p>
+<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L36" target="_blank" style="float:right; font-size:smaller">source</a></p>
 <section id="fasttrainer" class="level3">
 <h3 class="anchored" data-anchor-id="fasttrainer">fastTrainer</h3>
 <blockquote class="blockquote">
@@ -464,7 +464,7 @@ <h3 class="anchored" data-anchor-id="fasttrainer">fastTrainer</h3>
               wd_bn_bias:bool=False, train_bn:bool=True,
               moms:tuple=Ellipsis, default_cbs:bool=True)</code></pre>
 </blockquote>
-<p>A custom implementation of the FastAI Learner class for training models in bioinformatics applications.</p>
+<p><em>A custom implementation of the FastAI Learner class for training models in bioinformatics applications.</em></p>
 <table class="table">
 <colgroup>
 <col style="width: 6%">
@@ -609,30 +609,30 @@ <h3 class="anchored" data-anchor-id="fasttrainer">fastTrainer</h3>
 <h2 class="anchored" data-anchor-id="utils">Utils</h2>
 <p>Utility functions.</p>
 <hr>
-<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L81" target="_blank" style="float:right; font-size:smaller">source</a></p>
+<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L83" target="_blank" style="float:right; font-size:smaller">source</a></p>
 <section id="attributesfromdict" class="level3">
 <h3 class="anchored" data-anchor-id="attributesfromdict">attributesFromDict</h3>
 <blockquote class="blockquote">
 <pre><code> attributesFromDict (d)</code></pre>
 </blockquote>
 <hr>
-<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L87" target="_blank" style="float:right; font-size:smaller">source</a></p>
+<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L89" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
 <section id="get_device" class="level3">
 <h3 class="anchored" data-anchor-id="get_device">get_device</h3>
 <blockquote class="blockquote">
 <pre><code> get_device ()</code></pre>
 </blockquote>
 <hr>
-<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L91" target="_blank" style="float:right; font-size:smaller">source</a></p>
+<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L93" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
 <section id="img2float" class="level3">
 <h3 class="anchored" data-anchor-id="img2float">img2float</h3>
 <blockquote class="blockquote">
 <pre><code> img2float (image, force_copy=False)</code></pre>
 </blockquote>
 <hr>
-<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L95" target="_blank" style="float:right; font-size:smaller">source</a></p>
+<p><a href="https://github.com/bmandracchia/bioMONAI/blob/main/bioMONAI/core.py#L97" target="_blank" style="float:right; font-size:smaller">source</a></p>
 </section>
 <section id="img2tensor" class="level3">
 <h3 class="anchored" data-anchor-id="img2tensor">img2Tensor</h3>