Merge pull request #207 from murthylab/develop

Develop

.conda/bld.bat

@@ -13,7 +13,7 @@ rem # this out myself, ughhh.
 set PIP_NO_INDEX=False
 set PIP_NO_DEPENDENCIES=False
 set PIP_IGNORE_INSTALLED=False
-pip install cattrs==1.0.0rc opencv-python==3.4.2.17 PySide2==5.12.0 imgaug qimage2ndarray==1.8 imgstore
+pip install cattrs==1.0.0rc opencv-python-headless==3.4.1.15 PySide2==5.12.0 imgaug qimage2ndarray==1.8 imgstore
 
 rem # Use and update environment.yml call to install pip dependencies. This is slick.
 rem # While environment.yml contains the non pip dependencies, the only thing left

.coveralls.yml

@@ -0,0 +1 @@
+service_name: appveyor

README.rst

@@ -10,16 +10,16 @@
 .. |GitHub release| image:: https://img.shields.io/github/release/murthylab/sleap.js.svg
    :target: https://GitHub.com/murthylab/sleap/releases/
 
-Social LEAP Estimates Animal Pose (sLEAP)
+Social LEAP Estimates Animal Pose (SLEAP)
 =========================================
 
 .. image:: docs/_static/supp_mov1-long_clip.gif
     :width: 500px
 
 |
 
-**S**\ ocial **L**\ EAP **E**\ stimates **A**\ nimal **P**\ ose (**sLEAP**) is a framework for multi-animal
-body part position estimation via deep learning. It is the successor to LEAP_. **sLEAP** is written entirely in
+**S**\ ocial **L**\ EAP **E**\ stimates **A**\ nimal **P**\ ose (**SLEAP**) is a framework for multi-animal
+body part position estimation via deep learning. It is the successor to LEAP_. **SLEAP** is written entirely in
 Python, supports multi-animal pose estimation, animal instance tracking, and a labeling/training GUI that
 supports active learning.
 
@@ -30,19 +30,19 @@ supports active learning.
 Installation
 ------------
 
-**sLEAP** is compatible with Python versions 3.6 and above, with support for Windows and Linux. Mac OS X works but without GPU support.
+**SLEAP** is compatible with Python versions 3.6 and above, with support for Windows and Linux. Mac OS X works but without GPU support.
 
 Windows
 -------
 
-Since **sLEAP** has a number of complex binary dependencies (TensorFlow, Keras, OpenCV), it is recommended to use the
+Since **SLEAP** has a number of complex binary dependencies (TensorFlow, Keras, OpenCV), it is recommended to use the
 Anaconda_ Python distribution to simplify installation.
 
 Once Anaconda_ has been installed, go to start menu and type in *Anaconda*, which should bring up a menu entry
 **Anaconda Prompt** which opens a command line with the base anaconda environment activated. One of the key
 advantages to using `Anaconda Environments`_ is the ability to create separate Python installations (environments) for
 different projects, mitigating issues of managing complex dependencies. To create a new conda environment for
-**sLEAP** related development and use:
+**SLEAP** related development and use:
 
 ::
 
@@ -59,7 +59,7 @@ Any Python installation commands (:code:`conda install` or :code:`pip install`)
 environment will only effect the environment. Thus it is important to make sure the environment is active when issuing
 any commands that deal with Python on the command line.
 
-**sLEAP** is now installed in the :code:`sleap_env` conda environment. With the environment active,
+**SLEAP** is now installed in the :code:`sleap_env` conda environment. With the environment active,
 you can run the labeling GUI by entering the following command:
 
 ::
@@ -72,18 +72,18 @@ you can run the labeling GUI by entering the following command:
 Linux
 -----
 
-No Linux conda packages are currently provided by the **sLEAP** channel. However, installing via :code:`pip` should not
+No Linux conda packages are currently provided by the **SLEAP** channel. However, installing via :code:`pip` should not
 be difficult on most Linux systems. The first step is to get a working version of TensorFlow installed in your Python
 environment. Follow official directions for installing TensorFlow_ with GPU support. Once TensorFlow is installed, simple
-issue the following command to install **sLEAP**
+issue the following command to install **SLEAP**
 
 .. _TensorFlow: https://www.tensorflow.org/install/gpu
 
 ::
 
     pip install git+https://github.com/murthylab/sleap.git
 
-**sLEAP** is now installed you can run the labeling GUI by entering the following command:
+**SLEAP** is now installed you can run the labeling GUI by entering the following command:
 
 ::
 
@@ -93,7 +93,7 @@ Mac OS
 ------
 
 The installation for Mac OS X is the same as for Linux, although there's no TensorFlow GPU support for Mac OS.
-You can install TensorFlow and **sLEAP** together by running
+You can install TensorFlow and **SLEAP** together by running
 
 ::
 
@@ -102,6 +102,6 @@ You can install TensorFlow and **sLEAP** together by running
 
 Research
 --------
-If you use **sLEAP** in your research please acknowledge ... 
+If you use **SLEAP** in your research please acknowledge ... 
 
 

appveyor.yml

@@ -3,11 +3,13 @@ version: '{build}'
 clone_depth: 5
 
 environment:
+  COVERALLS_REPO_TOKEN:
+    secure: VsCyKmdi8x0OFK+Jbzk7ZRAW3EtojWP85TWqWKi+vuGmdiQFX7rLPnuaw3kt++a8
   access_token:
     secure: T7XuBtHDu85Tk/d1AeyfhW3CVyzaoddTWmR4xsPIdQ3di0R6x8ncWqw3KrYXkWJm
 
   BUILD_DIR: "build"
-  
+
   conda_access_token:
     secure: d+v++uejbVEhIuaJSuFIOA==
   matrix:
@@ -56,14 +58,20 @@ install:
   # We need to install this separately, what a mess.
   # - pip install PySide2 opencv-python imgaug cattrs
 
-# Install dev requirements too.
+  # Install dev requirements too.
   - pip install -r dev_requirements.txt
 
+  # Install sleap package
+  - pip install .
+
 build: off
 test_script:
   - cmd: activate sleap_appveyor
   - cmd: where python
-  - cmd: python -m pytest tests/
+  - cmd: pytest --cov=sleap tests/
+
+on_success:
+  - cmd: coveralls
 
 # here we are going to override common configuration
 for:

dev_requirements.txt

@@ -3,4 +3,5 @@ pytest-qt
 pytest-cov
 ipython
 sphinx
-sphinx_rtd_theme
+sphinx_rtd_theme
+coveralls

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: