Fixes to docs.

Changed "sLEAP" to "SLEAP".
Added modules to tree.
Misc fixes to docstrings.

docs/Makefile

@@ -5,7 +5,7 @@
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 SOURCEDIR     = .
-BUILDDIR      = ..\..\sleap-docs
+BUILDDIR      = ../../sleap-docs
 
 # Export the BUILDDIR so we can pick it up in conf.py. We need this to
 # be able to copy some the files in _static to an alternative location

docs/conf.py

@@ -19,7 +19,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'LEAP'
+project = 'SLEAP'
 copyright = '2019, Murthy Lab @ Princeton'
 author = 'Talmo D. Pereira, Nat Tabris, David M. Turner'
 
@@ -105,7 +105,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'sLEAPdoc'
+htmlhelp_basename = 'SLEAPdoc'
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -132,7 +132,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'sLEAP.tex', 'sLEAP Documentation',
+    (master_doc, 'SLEAP.tex', 'SLEAP Documentation',
      'Talmo D. Pereira, Nat Tabris, David M. Turner', 'manual'),
 ]
 
@@ -142,7 +142,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'sleap', 'sLEAP Documentation',
+    (master_doc, 'Sleap', 'SLEAP Documentation',
      [author], 1)
 ]
 
@@ -153,8 +153,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'sLEAP', 'sLEAP Documentation',
-     author, 'sLEAP', 'One line description of project.',
+    (master_doc, 'SLEAP', 'SLEAP Documentation',
+     author, 'SLEAP', 'One line description of project.',
      'Miscellaneous'),
 ]
 

docs/gui.rst

@@ -3,18 +3,100 @@ GUI
 
 .. automodule:: sleap.gui.app
    :members:
+
+Video Player
+-------------
 .. automodule:: sleap.gui.video
    :members:
+
+Dialogs
+-------------
+
+Active Learning
+^^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.active
+   :members:
+
+Video Importer
+^^^^^^^^^^^^^^
 .. automodule:: sleap.gui.importvideos
    :members:
-.. automodule:: sleap.gui.confmapsplot
+
+Merging
+^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.merge
    :members:
-.. automodule:: sleap.gui.quiverplot
+
+Shortcuts
+^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.shortcuts
    :members:
-.. automodule:: sleap.gui.dataviews
+
+Suggestions
+^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.suggestions
    :members:
-.. automodule:: sleap.gui.multicheck
+
+Training Profiles
+^^^^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.training_editor
+   :members:
+
+Other Widgets
+-------------
+
+Form builder
+^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.formbuilder
    :members:
+
+Slider
+^^^^^^^^^^^^^^
 .. automodule:: sleap.gui.slider
    :members:
 
+Multicheck
+^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.multicheck
+   :members:
+
+Overlays
+-------------
+
+Instances
+^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.overlays.instance
+   :members:
+
+Tracks
+^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.overlays.tracks
+   :members:
+
+Anchors
+^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.overlays.anchors
+   :members:
+
+Datasource classes
+^^^^^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.overlays.base
+   :members:
+
+Confidence maps
+^^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.overlays.confmaps
+   :members:
+
+
+Part affinity fields
+^^^^^^^^^^^^^^^^^^^^
+.. automodule:: sleap.gui.overlays.pafs
+   :members:
+
+
+
+Dataviews
+-------------
+.. automodule:: sleap.gui.dataviews
+   :members:

docs/index.rst

@@ -3,7 +3,7 @@
 
 .. _sleap:
 .. toctree::
-    :caption: sLEAP Package
+    :caption: SLEAP Package
     :maxdepth: 3
 
     tutorial
@@ -14,6 +14,7 @@
     training
     inference
     gui
+    misc
 
 .. _Indices_and_Tables:
 

docs/misc.rst

@@ -0,0 +1,35 @@
+Misc
+========
+
+Utils
+-------------
+.. automodule:: sleap.util
+   :members:
+
+Range list
+-------------
+.. automodule:: sleap.rangelist
+   :members:
+
+Legacy formats
+--------------
+.. automodule:: sleap.io.legacy
+   :members:
+
+Info tools
+----------
+
+Metrics
+^^^^^^^^^^^^^^
+.. automodule:: sleap.info.metrics
+   :members:
+
+Summary
+^^^^^^^^^^^^^^
+.. automodule:: sleap.info.summary
+   :members:
+
+Track Analysis
+^^^^^^^^^^^^^^
+.. automodule:: sleap.info.write_tracking_h5
+   :members:

docs/tutorial.rst

@@ -1,11 +1,11 @@
 Tutorial
 ========
 
-Before you can use sLEAP, you’ll need to install it. Follow the
-instructions at :ref:`Installation` to install sLEAP and
+Before you can use SLEAP, you’ll need to install it. Follow the
+instructions at :ref:`Installation` to install SLEAP and
 start the GUI app.
 
-There are three main stages of using sLEAP:
+There are three main stages of using SLEAP:
 
 1. Creating a project, opening a movie and defining the skeleton;
 
@@ -18,7 +18,7 @@ There are three main stages of using sLEAP:
 Stage 1: Creating a project
 ---------------------------
 
-When you first start sLEAP you’ll see an open dialog. Since you don’t
+When you first start SLEAP you’ll see an open dialog. Since you don’t
 yet have a project to open, click “Cancel” and you’ll be left with a
 new, empty project.
 
@@ -32,7 +32,7 @@ on the right side of the main window, the “Add Video” command in the
 |image0|
 
 You’ll then be able to select one or more video files and click “Open”.
-sLEAP currently supports mp4, avi, and h5 files. For mp4 and avi files,
+SLEAP currently supports mp4, avi, and h5 files. For mp4 and avi files,
 you’ll be asked whether to import the video as grayscale. For h5 files,
 you’ll be asked the dataset and whether the video is stored with
 channels first or last.
@@ -65,7 +65,7 @@ Stage 2: Labeling and learning
 
 We start by assembling a candidate group of images to label. You can
 either pick your own frames or let the system suggest a set of frames
-using the “Generate Suggestions” panel. sLEAP can choose these frames
+using the “Generate Suggestions” panel. SLEAP can choose these frames
 (i) randomly, or using (ii) Strides (evenly spaced samples), (iii) PCA
 (runs Principle Component Analysis on the images, clusters the images
 into groups, and uses sample frames from each cluster), or (iv) BRISK
@@ -102,9 +102,9 @@ Saving
 ~~~~~~
 
 Since this is a new project, you’ll need to select a location and name
-the first time you save. sLEAP will ask you to save before closing any
+the first time you save. SLEAP will ask you to save before closing any
 project that has been changed to avoid losing any work. Note: There is
-not yet an “undo” feature built into sLEAP. If you want to make
+not yet an “undo” feature built into SLEAP. If you want to make
 temporary changes to a project, use the “Save As…” command first to save
 a copy of your project.
 
@@ -197,7 +197,7 @@ model doesn’t improve for a certain number of epochs (15 by default)
 First we train a model for confidence maps, part affinity fields, and
 centroids, and then we run inference. The GUI doesn’t yet give you a way
 to monitor the progress during inference, although you can get more
-information in the console window from which you started sLEAP.
+information in the console window from which you started SLEAP.
 
 When active learning finishes, you’ll be told how many instances were
 predicted. Suggested frames with predicted instances will be marked in
@@ -265,7 +265,7 @@ Running inference remotely (optional)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 It’s also possible to run inference using the command line interface, which is
-useful if you’re going to run on a cluster). The command to run inference on
+useful if you’re going to run on a cluster. The command to run inference on
 an entire video is:
 
 ::
@@ -276,7 +276,7 @@ an entire video is:
       -m path/to/models/your_paf_model.json \
       -m path/to/models/your_centroid_model.json
 
-The predictions will be saved in path/to/video.mp4.predictions.json.zip,
+The predictions will be saved in path/to/video.mp4.predictions.h5,
 which you can open from the GUI app. You can also import these predictions into
 your project by opening your project and then using the "Import Predictions..."
 command in the "Predict" menu.

sleap/gui/app.py

@@ -57,11 +57,11 @@ class MainWindow(QMainWindow):
     """The SLEAP GUI application.
 
     Each project (`Labels` dataset) that you have loaded in the GUI will
-    have it's own `MainWindow` object.
+    have its own `MainWindow` object.
 
     Attributes:
         labels: The :class:`Labels` dataset. If None, a new, empty project
-            (i.e., :class:`Labels' object) will be created.
+            (i.e., :class:`Labels` object) will be created.
         skeleton: The active :class:`Skeleton` for the project in the gui
         video: The active :class:`Video` in view in the gui
     """

sleap/gui/formbuilder.py

@@ -2,6 +2,7 @@
 Module for creating a form from a yaml file.
 
 Example:
+
 >>> widget = YamlFormWidget(yaml_file="example.yaml")
 >>> widget.mainAction.connect(my_function)
 
@@ -81,7 +82,7 @@ class FormBuilderLayout(QtWidgets.QFormLayout):
     Custom QFormLayout which populates itself from list of form fields.
 
     Args:
-        items_to_create: list which gets passed to :method:`get_form_data`
+        items_to_create: list which gets passed to :meth:`get_form_data`
                          (see there for details about format)
     """
 
@@ -183,7 +184,8 @@ def build_form(self, items_to_create: List[Dict[str, Any]]):
         """Adds widgets to form layout for each item in items_to_create.
 
         Args:
-            items_to_create: list of dictionaries with fields:
+            items_to_create: list of dictionaries with keys
+
               * name: used as key when we return form data as dict
               * label: string to show in form
               * type: supports double, int, bool, list, button, stack
@@ -311,7 +313,7 @@ class StackBuilderWidget(QtWidgets.QWidget):
             The "options" key will give the list of options to show in
             menu. Each of the "options" will also be the key of a dictionary
             within stack_data that has the same structure as the dictionary
-            passed to :method:`FormBuilderLayout.build_form()`.
+            passed to :meth:`FormBuilderLayout.build_form()`.
     """
 
     def __init__(self, stack_data, *args, **kwargs):

sleap/gui/importvideos.py

@@ -17,6 +17,7 @@
 method while passing the user-selected params as the named parameters:
 
 >>> vid = item["video_class"](**item["params"])
+
 """
 
 from PySide2.QtCore import Qt, QRectF, Signal

sleap/gui/merge.py

@@ -217,7 +217,7 @@ class MergeTable(QtWidgets.QTableView):
 
     Args:
         merged: The frames that were cleanly merged.
-            See :method:`Labels.complex_merge_between` for details.
+            See :meth:`Labels.complex_merge_between` for details.
     """
 
     def __init__(self, merged, *args, **kwargs):

sleap/gui/overlays/tracks.py

@@ -167,7 +167,7 @@ class TrackTrailOverlay:
         trail_length: The maximum number of frames to include in trail.
 
     Usage:
-        After class is instantiated, call :method:`add_to_scene(frame_idx)`
+        After class is instantiated, call :meth:`add_to_scene(frame_idx)`
         to plot the trails in scene.
     """
 

sleap/gui/suggestions.py

@@ -28,7 +28,7 @@ class VideoFrameSuggestions:
     * proofreading
 
     Each of algorithm method should accept `video`; other parameters will be
-    passed from the `params` dict given to :method:`suggest()`.
+    passed from the `params` dict given to :meth:`suggest`.
 
     """
 
@@ -343,9 +343,10 @@ def clusters_to_list(
 
     @classmethod
     def get_scale_factor(cls, video: "Video") -> int:
-        """Determines how much we need to scale to get video within size.
+        """
+        Determines how much we need to scale to get video within size.
 
-        Size is specified by :attribute:`rescale_below`.
+        Size is specified by :attr:`rescale_below`.
         """
         factor = 1
         if cls.rescale: