Reformat docs

.gitignore

@@ -4,3 +4,4 @@ build_doc.sh
 build/
 build_wheel.sh
 /dist/
+docs/source/generated/

docs/source/_templates/autosummary/class.rst

@@ -0,0 +1,35 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. add toctree option to make autodoc generate the pages
+
+.. autoclass:: {{ objname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: .
+   {% for item in attributes %}
+      {% if has_attr(fullname, item) %}
+      ~{{ fullname }}.{{ item }}
+      {% endif %}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: .
+   {% for item in methods %}
+      {%- if item != '__init__' %}
+      ~{{ fullname }}.{{ item }}
+      {%- endif -%}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/source/api_train.rst

@@ -0,0 +1,10 @@
+Model training and prediction
+==================================
+
+.. currentmodule:: sctour
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+   train.Trainer

docs/source/api_vf.rst

@@ -0,0 +1,4 @@
+Vector field visualization
+==================================
+
+.. autofunction:: sctour.vf.plot_vector_field

docs/source/conf.py

@@ -1,15 +1,3 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
 import os
 import sys
 sys.path.insert(0, os.path.abspath('../../'))
@@ -22,47 +10,32 @@
 project = 'sctour'
 author = 'Qian Li'
 copyright = f'{datetime.now():%Y}, {author}'
-
-# The full version, including alpha/beta/rc tags
 release = sctour.__version__
 
 
 # -- General configuration ---------------------------------------------------
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
 extensions = [
     'sphinx.ext.autodoc',
+    'sphinx.ext.mathjax',
     'sphinx.ext.napoleon',
     'sphinx.ext.intersphinx',
     'sphinx.ext.viewcode',
     'myst_parser',
-    'nbsphinx'
+    'nbsphinx',
+    'sphinx.ext.autosummary',
 ]
+autosummary_generate = True
+autodoc_member_order = 'bysource'
+napoleon_include_init_with_doc = False
+napoleon_numpy_docstring = True
+napoleon_use_rtype = True
+napoleon_use_param = True
 
-# Add any paths that contain templates here, relative to this directory.
-source_suffix = ['.rst', '.md']
+# settings
 master_doc = 'index'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
-
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 pygments_style = 'sphinx'
-# -- Options for HTML output -------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'sphinx_rtd_theme'
-napoleon_numpy_docstring = True
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
 
 intersphinx_mapping = dict(
         python=('https://docs.python.org/3/', None),
@@ -71,5 +44,11 @@
         anndata=('https://anndata.readthedocs.io/en/stable/', None),
         scanpy=('https://scanpy.readthedocs.io/en/stable/', None),
         scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
-        torch=('https://pytorch.org/docs/master/', None)
+        torch=('https://pytorch.org/docs/master/', None),
+        matplotlib=('https://matplotlib.org/stable/', None),
 )
+
+
+# -- Options for HTML output -------------------------------------------------
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']

docs/source/index.rst

@@ -1,9 +1,4 @@
-.. sctour documentation master file, created by
-   sphinx-quickstart on Fri Apr  8 21:15:33 2022.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to sctour's documentation!
+Welcome to scTour's documentation!
 ==================================
 
 .. include:: ../../README.md
@@ -26,7 +21,8 @@ Welcome to sctour's documentation!
 
 .. toctree::
    :maxdepth: 2
-   :caption: Main API:
+   :caption: API:
    :hidden:
 
-   sctour
+   api_train
+   api_vf

sctour/train.py

@@ -197,7 +197,7 @@ def __init__(
         self.log = defaultdict(list)
 
 
-    def get_data_loaders(self) -> None:
+    def _get_data_loaders(self) -> None:
         """
         Generate Data Loaders for training and validation datasets.
         """
@@ -213,23 +213,23 @@ def get_data_loaders(self) -> None:
 
 
     def train(self):
-        self.get_data_loaders()
+        self._get_data_loaders()
 
         params = filter(lambda p: p.requires_grad, self.model.parameters())
         self.optimizer = torch.optim.Adam(params, lr = self.lr, weight_decay = self.wt_decay, eps = self.eps)
 
         with tqdm(total=self.nepoch, unit='epoch') as t:
             for tepoch in range(t.total):
-                train_loss = self.on_epoch_train(self.train_dl)
-                val_loss = self.on_epoch_val(self.val_dl)
+                train_loss = self._on_epoch_train(self.train_dl)
+                val_loss = self._on_epoch_val(self.val_dl)
                 self.log['train_loss'].append(train_loss)
                 self.log['validation_loss'].append(val_loss)
                 t.set_description(f"Epoch {tepoch + 1}")
                 t.set_postfix({'train_loss': train_loss, 'val_loss': val_loss}, refresh=False)
                 t.update()
 
 
-    def on_epoch_train(self, DL) -> float:
+    def _on_epoch_train(self, DL) -> float:
         """
         Go through the model and update the model parameters.
 
@@ -263,7 +263,7 @@ def on_epoch_train(self, DL) -> float:
 
 
     @torch.no_grad()
-    def on_epoch_val(self, DL) -> float:
+    def _on_epoch_val(self, DL) -> float:
         """
         Validate using validation dataset.
 
@@ -354,7 +354,7 @@ def get_vector_field(
             The estimated vector field.
         """
 
-        model = self.get_model(model)
+        model = self._get_model(model)
         model.eval()
         if not (isinstance(T, np.ndarray) and isinstance(Z, np.ndarray)):
             raise TypeError('The inputs must be numpy arrays.')
@@ -440,7 +440,7 @@ def get_latentsp(
             3-tuple of mixed latent space, encoder-derived latent space, and ODE-solver-derived latent space.
         """
 
-        model = self.get_model(model)
+        model = self._get_model(model)
         model.eval()
 
         if (alpha_z < 0) or (alpha_z > 1):
@@ -563,7 +563,7 @@ def predict_time(
         The predicted pseudotime and (if `get_ltsp = True`) the latent space.
         """
 
-        model = self.get_model(model)
+        model = self._get_model(model)
         model.eval()
 
         if self.time_reverse is None:
@@ -680,7 +680,7 @@ def predict_ltsp_from_time(
             Predicted latent space for the unobserved time interval.
         """
 
-        model = self.get_model(model)
+        model = self._get_model(model)
         model.eval()
 
         if not isinstance(T, np.ndarray):
@@ -735,7 +735,7 @@ def predict_ltsp_from_time(
         return pred_T_zs.numpy()
 
 
-    def get_model(self, model):
+    def _get_model(self, model):
         """
         Get the model for inference/prediction (for internal use).
         """