Merge pull request #338 from murthylab/develop

First v0.2.x (0.2.1) on master
talmolab · Apr 13, 2020 · 2fcd195 · 2fcd195
2 parents f7da384 + ea6e541
commit 2fcd195
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Showing 222 changed files with 20,897 additions and 11,797 deletions.
diff --git a/.conda/bld.bat b/.conda/bld.bat
@@ -13,7 +13,8 @@ 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-headless==3.4.1.15 PySide2>=5.12 imgaug==0.3.0 qimage2ndarray==1.8 imgstore jsmin
+pip install cattrs==1.0.0rc0 opencv-python-headless==3.4.1.15 "PySide2>=5.12.0,<=5.14.1" imgaug==0.3.0 qimage2ndarray==1.8 imgstore jsmin seaborn
+pip install
 
 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

diff --git a/.conda/build.sh b/.conda/build.sh
@@ -11,7 +11,8 @@ export PIP_NO_INDEX=False
 export PIP_NO_DEPENDENCIES=False
 export PIP_IGNORE_INSTALLED=False
 
-pip install cattrs==1.0.0rc opencv-python-headless==3.4.1.15 PySide2>=5.12 imgaug==0.3.0 qimage2ndarray==1.8 imgstore jsmin
+pip install cattrs==1.0.0rc0 opencv-python-headless==3.4.1.15 "PySide2>=5.12.0,<=5.14.1" imgaug==0.3.0 qimage2ndarray==1.8 imgstore jsmin seaborn
+#pip install tensorflow==2.1
 
 pip install setuptools-scm
 

diff --git a/.conda/meta.yaml b/.conda/meta.yaml
@@ -4,7 +4,7 @@ package:
   # Repeating name because of the following issue:
   # https://github.com/conda/conda-build/issues/2475
   name: sleap
-  version: {{ data.get('version') }}
+  version: {{ GIT_DESCRIBE_TAG[1:] }}
 
 about:
   home: {{ data.get('url') }}
@@ -20,28 +20,15 @@ source:
 requirements:
   host:
     - python=3.6
-    - attrs
-    - jsonpickle=1.2
-    - networkx
-    - tensorflow-gpu=2.0
-    - scikit-learn
-    - h5py
-    - pandas
-    - Pillow
-    - Shapely
-    - psutil
-    - pyzmq
-    - pyyaml
-    - python-rapidjson
     - pip
 
-
   run:
     - python=3.6
     - attrs
     - jsonpickle=1.2
     - networkx
-    - tensorflow-gpu=2.0
+    - tensorflow-gpu=2.1
+    - tensorboard=2.1
     - scikit-learn
     - h5py
     - pandas

diff --git a/.gitignore b/.gitignore
@@ -65,6 +65,8 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/_autosummary/
+docs/api.rst  # this is created when making docs
 
 # PyBuilder
 target/
@@ -104,4 +106,10 @@ venv.bak/
 .mypy_cache/
 
 # Pycharm Files
-.idea/
+.idea/
+
+# Sublime files
+*.sublime-*
+
+# VSCode files
+.vscode/
diff --git a/README.rst b/README.rst
@@ -13,8 +13,7 @@
 Social LEAP Estimates Animal Pose (SLEAP)
 =========================================
 
-.. image:: https://sleap.ai/docs/_static/sleap_movie.gif
-    :alt: SLEAP demo movie
+.. image:: docs/_static/sleap_movie.gif
     :width: 600px
 
 |
@@ -33,4 +32,3 @@ If you use **SLEAP** in your research, cite `Pereira et al. Nature Methods 2019`
 .. _Pereira et al. Nature Methods 2019: https://www.nature.com/articles/s41592-018-0234-5
 .. _sleap.ai: https://sleap.ai
 
-
diff --git a/appveyor.yml b/appveyor.yml
@@ -127,4 +127,17 @@ for:
     - cmd: IF "%APPVEYOR_REPO_TAG%" == "true" (anaconda upload --force %BUILD_DIR%\win-64\*.tar.bz2)
     - cmd: IF "%APPVEYOR_REPO_TAG%" == "true" (anaconda logout)
 #    - ps: $blockRdp = $true; iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/appveyor/ci/master/scripts/enable-rdp.ps1'))
-
+
+# Deploy "dev" builds if develop branch is tagged
+-
+  branches:
+    only:
+      - develop
+  deploy_script:
+    # Deploy wheel to PyPi
+    - cmd: IF "%APPVEYOR_REPO_TAG%" == "true" (python setup.py bdist_wheel)
+    - cmd: IF "%APPVEYOR_REPO_TAG%" == "true" (python -m twine upload dist/* --non-interactive --skip-existing --disable-progress-bar)
+    # Deploy (Windows) Conda package to anaconda sleap channel
+    - cmd: IF "%APPVEYOR_REPO_TAG%" == "true" (conda build .conda --output-folder %BUILD_DIR%)
+    - cmd: IF "%APPVEYOR_REPO_TAG%" == "true" (anaconda upload --force %BUILD_DIR%\win-64\*.tar.bz2 --label dev)
+    - cmd: IF "%APPVEYOR_REPO_TAG%" == "true" (anaconda logout)
diff --git a/dev_requirements.txt b/dev_requirements.txt
@@ -7,4 +7,6 @@ sphinx_rtd_theme
 coveralls
 black
 pre-commit
+jupyterlab
 twine
+PyGithub
diff --git a/docs/Makefile b/docs/Makefile
@@ -19,7 +19,10 @@ help:
 
 .PHONY: help Makefile
 
+api.rst:
+	python make_api_doctree.py
+
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
+%: Makefile api.rst
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_static/inference-dialog.jpg b/docs/_static/inference-dialog.jpg
diff --git a/docs/_static/model-selection.jpg b/docs/_static/model-selection.jpg
diff --git a/docs/_static/receptive-field.jpg b/docs/_static/receptive-field.jpg
diff --git a/docs/_static/tracker.jpg b/docs/_static/tracker.jpg
diff --git a/docs/_static/training-dialog.jpg b/docs/_static/training-dialog.jpg
diff --git a/docs/_static/training-model-dialog.jpg b/docs/_static/training-model-dialog.jpg
diff --git a/docs/_templates/api_head.rst b/docs/_templates/api_head.rst
@@ -0,0 +1,11 @@
+.. _api:
+
+Developer API
+=============
+
+.. toctree::
+   :caption: API
+
+.. autosummary::
+   :toctree: _autosummary
+
diff --git a/docs/_templates/autosummary/module.rst b/docs/_templates/autosummary/module.rst
@@ -0,0 +1,5 @@
+{{ fullname }}
+{{ underline }}
+
+.. automodule:: {{ fullname }}
+   :members:
diff --git a/docs/api.rst b/docs/api.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -13,6 +13,7 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
 import os
+import re
 import sys
 
 sys.path.insert(0, os.path.abspath(".."))
@@ -21,15 +22,21 @@
 # -- Project information -----------------------------------------------------
 
 project = "SLEAP"
-copyright = "2019, Murthy Lab @ Princeton"
+copyright = "2019–2020, Murthy Lab @ Princeton"
 author = "Talmo D. Pereira, Nat Tabris, David M. Turner"
 
 # The short X.Y version
-version = ""
+version = "0.2.0"
 # The full version, including alpha/beta/rc tags
 release = ""
 
 
+# Get the sleap version
+# with open("../sleap/version.py") as f:
+#     version_file = f.read()
+#     version = re.search("\d.+(?=['\"])", version_file).group(0)
+
+
 # -- General configuration ---------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -41,11 +48,14 @@
 # ones.
 extensions = [
     "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
     "sphinx.ext.coverage",
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
 ]
 
+autosummary_generate = True
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -68,7 +78,7 @@
 # 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 = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = ["_build", "_templates", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = None
@@ -79,13 +89,15 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "alabaster"
+html_theme = 'alabaster'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-# html_theme_options = {}
+html_theme_options = {
+    'font_size': '15px'
+}
 
 # 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,

diff --git a/docs/dataset.rst b/docs/dataset.rst
diff --git a/docs/faq.rst b/docs/faq.rst