Full API documentation

kboone · May 28, 2019 · 56a7d91 · 56a7d91
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diff --git a/avocado/augment.py b/avocado/augment.py
@@ -12,8 +12,10 @@
 class Augmentor():
     """Class used to augment a dataset.
 
-    This class takes :class:`AstronomicalObject`s as input and generates new
-    :class:`AstronomicalObject`s with the following transformations applied:
+    This class takes :class:`AstronomicalObject` instances as input and
+    generates new :class:`AstronomicalObject` instances with the following
+    transformations applied:
+
     - Drop random observations.
     - Drop large blocks of observations.
     - For galactic observations, adjust the brightness (= distance).
@@ -31,10 +33,12 @@ class Augmentor():
 
     This class needs to be subclassed to implement survey specific methods.
     These methods are:
-    - `_augment_metadata`
-    - Either `_choose_sampling_times` or `_choose_target_observation_count`
-    - `_simulate_light_curve_uncertainties`
-    - `_simulate_detection`
+
+    - :func:`Augmentor._augment_metadata`
+    - Either :func:`Augmentor._choose_sampling_times` or
+      :func:`Augmentor._choose_target_observation_count`
+    - :func:`Augmentor._simulate_light_curve_uncertainties`
+    - :func:`Augmentor._simulate_detection`
 
     Parameters
     ----------
@@ -136,6 +140,7 @@ def _choose_sampling_times(self, reference_object, augmented_metadata,
         =======
         sampling_times : pandas Dataframe
             A pandas Dataframe that has the following columns:
+
             - time : the times of the simulated observations.
             - band : the bands of the simulated observations.
             - reference_time : the times in the reference light curve that

diff --git a/docs/reference.rst b/docs/reference.rst
@@ -4,40 +4,162 @@ Reference / API
 
 .. currentmodule:: avocado
 
-Dataset
-=======
+
+Datasets
+========
+
+*Loading/saving a dataset*
 
 .. autosummary::
    :toctree: api
 
    Dataset
    Dataset.load
    Dataset.from_objects
-   Dataset.get_object
-
    Dataset.path
    Dataset.write
 
+*Retrieving objects from the dataset*
+
+.. autosummary::
+   :toctree: api
+
+   Dataset.get_object
+
+*Plotting lightcurves of objects in the dataset*
+
+.. autosummary::
+   :toctree: api
+
    Dataset.plot_light_curve
    Dataset.plot_interactive
 
+*Extracting features from objects in the dataset*
+
+.. autosummary::
+   :toctree: api
+
    Dataset.extract_raw_features
    Dataset.get_raw_features_path
    Dataset.write_raw_features
    Dataset.load_raw_features
    Dataset.select_features
 
-   Dataset.label_folds
+*Classifying objects in the dataset*
+
+.. autosummary::
+   :toctree: api
 
    Dataset.predict
    Dataset.get_predictions_path
    Dataset.write_predictions
    Dataset.load_predictions
+   Dataset.label_folds
 
-AstronomicalObject
-==================
+
+Astronomical objects
+====================
 
 .. autosummary::
    :toctree: api
 
    AstronomicalObject
+   AstronomicalObject.bands
+   AstronomicalObject.subtract_background
+   AstronomicalObject.preprocess_observations
+   AstronomicalObject.fit_gaussian_process
+   AstronomicalObject.get_default_gaussian_process
+   AstronomicalObject.predict_gaussian_process
+   AstronomicalObject.plot_light_curve
+   AstronomicalObject.print_metadata
+
+
+Dataset augmentation
+====================
+
+*Augmentor API*
+
+.. autosummary::
+   :toctree: api
+
+   Augmentor
+   Augmentor.augment_object
+   Augmentor.augment_dataset
+
+*Augmentor Implementations*
+
+.. autosummary::
+   :toctree: api
+
+   plasticc.PlasticcAugmentor
+
+*Augmentor methods to implement in subclasses*
+
+.. autosummary::
+   :toctree: api
+
+   Augmentor._augment_metadata
+   Augmentor._choose_sampling_times
+   Augmentor._choose_target_observation_count
+   Augmentor._simulate_light_curve_uncertainties
+   Augmentor._simulate_detection
+
+
+Classification
+==============
+
+*Classifier API*
+
+.. autosummary::
+   :toctree: api
+
+   Classifier
+   Classifier.train
+   Classifier.predict
+   Classifier.path
+   Classifier.write
+   Classifier.load
+
+*Classifier Implementations*
+
+.. autosummary::
+   :toctree: api
+
+   LightGBMClassifier
+
+*Weights and metrics*
+
+.. autosummary::
+
+   evaluate_weights_flat
+   evaluate_weights_redshift
+   weighted_multi_logloss
+
+
+Feature extraction
+==================
+
+*Featurizer API*
+
+.. autosummary::
+   :toctree: api
+
+   Featurizer
+   Featurizer.extract_raw_features
+   Featurizer.select_features
+   Featurizer.extract_features
+
+*Featurizer Implementations*
+
+.. autosummary::
+   :toctree: api
+
+   plasticc.PlasticcFeaturizer
+
+Exceptions
+==========
+
+.. autosummary::
+   :toctree: api
+
+   AvocadoException