Model annotations (#4)

* annotations to model.py

* Annotations of Bicycle.__init__()

* Annotation of lyapunov_direct function

* Further annotation and pylint optimization of model.py

* Further annotations for functions and classes in data.py, callbacks.py, plotting.py and dictlogger.py

* Apply suggestions from code review

Co-authored-by: Martin Rohbeck <35061428+martinrohbeck@users.noreply.github.com>

* Compliance with code review from pull request Model annotations #4

Co-authored-by: Martin Rohbeck <35061428+martinrohbeck@users.noreply.github.com>

* Update src/bicycle/model.py

Co-authored-by: Martin Rohbeck <35061428+martinrohbeck@users.noreply.github.com>

* Compliance with code review.

Co-authored-by: Martin Rohbeck <martin.rohbeck@quantco.com>

* Compliance with PR #4.

Co-authored-by: Martin Rohbeck <martin.rohbeck@quantco.com>

* Compliance with PR #4.

Co-authored-by: Martin Rohbeck <martin.rohbeck@quantco.com>

* minor docstring changes to callbacks.py

* minor docstring changes to data.py

* Minor docstring edits for plotting.py

* Minor docstring edits for training.py

* Update model.py

Minor docstring updates to model.py

* Compliance with PR #4

Co-authored-by: Martin Rohbeck <martin.rohbeck@quantco.com>

* Removed comments

---------

Co-authored-by: Martin Rohbeck <35061428+martinrohbeck@users.noreply.github.com>
Co-authored-by: Martin Rohbeck <martin.rohbeck@quantco.com>

Author: NTBiotech

src/bicycle/callbacks.py

@@ -65,7 +65,25 @@ def on_validation_end(self, trainer: "pl.Trainer", pl_module: "pl.LightningModul
 
 
 class GenerateCallback(pl.Callback):
+    """
+    Class for generating a callback at the end of each training epoch of the bicycle model.
+    Subclasses pytorch_lightnings Callback function.
+
+    Notes:
+    - Calls the plot_training_results function from bicycle.utils.plotting
+        after each epoch that's a multiple of `plot_epoch_callback`. 
+    """
     def __init__(self, file_name_plot, plot_epoch_callback=10, true_beta=None, labels=None):
+        """
+        Initializes the GenerateCallback function for plotting training results during training.
+
+        Args:
+            file_name_plot (str): containing the file_name for the saved plots.
+                Can be given with or without the suffix.
+            plot_epoch_callback (int): specifying the callback interval.
+            true_beta (Optional|torch.Tensor): containing the ground truth gene adjacency matrix.
+            labels (Iterable): contains the gene labels.
+        """
         super().__init__()
         self.plot_epoch_callback = plot_epoch_callback
         self.true_beta = true_beta

src/bicycle/dictlogger.py

@@ -14,6 +14,10 @@ def __missing__(self, key):
 
 
 class DictLogger(Logger):
+    """
+    Class for logging model hyperparameters and metrics. 
+    Subclasses the pytorch_lightning.loggers Logger class.
+    """
     def __init__(self, version=None):
         self._version = version
         self.experiment = None