Merge pull request #324 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-headless==3.4.1.15 PySide2==5.12.0 imgaug==0.3.0 qimage2ndarray==1.8 imgstore jsmin
+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
 
 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

.conda/build.sh

@@ -11,7 +11,7 @@ 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==5.12.0 imgaug==0.3.0 qimage2ndarray==1.8 imgstore jsmin
+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 setuptools-scm
 

README.rst

@@ -13,7 +13,8 @@
 Social LEAP Estimates Animal Pose (SLEAP)
 =========================================
 
-.. image:: docs/_static/sleap_movie.gif
+.. image:: https://sleap.ai/docs/_static/sleap_movie.gif
+    :alt: SLEAP demo movie
     :width: 600px
 
 |

appveyor.yml

@@ -8,6 +8,12 @@ environment:
   access_token:
     secure: T7XuBtHDu85Tk/d1AeyfhW3CVyzaoddTWmR4xsPIdQ3di0R6x8ncWqw3KrYXkWJm
 
+  TWINE_USERNAME: ntabris
+  TWINE_PASSWORD:
+    secure: wZhRRgqJ8AdK4LpRBLPg8kA/udXvNrOpeMaaEGnUdUQ=
+  # use the test PyPi server until we're ready for public release
+  TWINE_REPOSITORY_URL: https://test.pypi.org/legacy/
+
   BUILD_DIR: "build"
 
   conda_access_token:
@@ -72,6 +78,12 @@ test_script:
 
 on_success:
   - cmd: coveralls
+  # Remove package tarballs so there's less to cache
+  - conda clean -a
+
+cache:
+  - C:\Miniconda36-x64\pkgs -> environment.yml
+  - '%LOCALAPPDATA%\pip\Cache'
 
 # here we are going to override common configuration
 for:
@@ -104,10 +116,13 @@ for:
     - cd ..\..\sleap\docs
     - make html push
 
-  # Deploy the windows conda package to the sleap channel, only on tagged
-  # builds though.
+  # Deploy packages on tagged builds
   after_deploy:
     - cmd: cd ..\
+    # 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)
     - cmd: IF "%APPVEYOR_REPO_TAG%" == "true" (anaconda logout)

dev_requirements.txt

@@ -7,3 +7,4 @@ sphinx_rtd_theme
 coveralls
 black
 pre-commit
+twine

environment.yml

@@ -18,7 +18,7 @@ dependencies:
 - pip
 - pip:
     - opencv-python-headless==3.4.1.15
-    - PySide2==5.12.0
+    - PySide2>=5.12.0
     - imgaug==0.3.0
     - cattrs==1.0.0rc0
     - qimage2ndarray==1.8

requirements.txt

@@ -8,7 +8,7 @@ python-rapidjson
 opencv-python-headless==3.4.1.15
 pandas
 psutil
-PySide2
+PySide2>=5.12
 pyzmq
 pyyaml
 imgaug==0.3.0

setup.py

@@ -6,43 +6,54 @@
 from codecs import open
 from os import path
 
+import re
+
 here = path.abspath(path.dirname(__file__))
 
 # Get the long description from the README file
-with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
+with open(path.join(here, "README.rst"), encoding="utf-8") as f:
     long_description = f.read()
 
+# Get the sleap version
+with open(path.join(here, "sleap/version.py")) as f:
+    version_file = f.read()
+    sleap_version = re.search("\d.+(?=['\"])", version_file).group(0)
+
+
 def get_requirements(require_name=None):
-    prefix = require_name + '_' if require_name is not None else ''
-    with open(path.join(here, prefix + 'requirements.txt'), encoding='utf-8') as f:
-        return f.read().strip().replace('-gpu','').split('\n')
+    prefix = require_name + "_" if require_name is not None else ""
+    with open(path.join(here, prefix + "requirements.txt"), encoding="utf-8") as f:
+        return f.read().strip().replace("-gpu", "").split("\n")
 
 
 setup(
-    name='sleap',
-    use_scm_version=True,
-    setup_requires=['setuptools_scm'],
+    name="sleap",
+    version=sleap_version,
+    setup_requires=["setuptools_scm"],
     install_requires=get_requirements(),
-    extras_require={
-        'dev': get_requirements('dev'),
-    },
-    description='SLEAP (Social LEAP Estimates Animal Pose) is a deep learning framework for estimating animal pose.',
+    extras_require={"dev": get_requirements("dev"),},
+    description="SLEAP (Social LEAP Estimates Animal Pose) is a deep learning framework for estimating animal pose.",
     long_description=long_description,
-    author='Talmo Pereira, David Turner, Nat Tabris',
-    author_email='talmo@princeton.edu',
-    url='https://github.com/murthylab/sleap',
-    keywords='deep learning, pose estimation, tracking, neuroscience',
-    license='BSD 3-Clause License',
-    packages=find_packages(exclude=['tensorflow']),
+    long_description_content_type="text/x-rst",
+    author="Talmo Pereira, David Turner, Nat Tabris",
+    author_email="talmo@princeton.edu",
+    project_urls={
+        "Documentation": "https://sleap.ai/#sleap",
+        "Bug Tracker": "https://github.com/murthylab/sleap/issues",
+        "Source Code": "https://github.com/murthylab/sleap",
+    },
+    url="https://sleap.ai",
+    keywords="deep learning, pose estimation, tracking, neuroscience",
+    license="BSD 3-Clause License",
+    packages=find_packages(exclude=["tensorflow"]),
     include_package_data=True,
-    entry_points = {
-        'console_scripts': [
-            'sleap-label=sleap.gui.app:main',
-            'sleap-train=sleap.nn.training:main',
-            'sleap-track=sleap.nn.inference:main'
+    entry_points={
+        "console_scripts": [
+            "sleap-label=sleap.gui.app:main",
+            "sleap-train=sleap.nn.training:main",
+            "sleap-track=sleap.nn.inference:main",
+            "sleap-diagnostic=sleap.diagnostic:main",
         ],
     },
-    python_requires='>=3.6'
-
+    python_requires=">=3.6",
 )
-

sleap/__init__.py

@@ -9,3 +9,5 @@
 from sleap.io.video import Video
 from sleap.instance import LabeledFrame, Instance, PredictedInstance
 from sleap.skeleton import Skeleton
+
+from sleap.version import __version__

sleap/config/colors.yaml

@@ -1,6 +1,8 @@
 alphabet:
+# 26 visually distinct colors
 # Source: "A Colour Alphabet and the Limits of Colour Coding", Paul Green-Armytage
 # https://graphicdesign.stackexchange.com/questions/3682/where-can-i-find-a-large-palette-set-of-contrasting-colors-for-coloring-many-d
+# https://github.com/Netflix/atlas/wiki/Color-Palettes#armytage (Apache 2.0 license)
 - 240,163,255
 - 0,117,220
 - 153,63,0
@@ -38,6 +40,8 @@ five+:
 - 255,127,0
 
 solarized:
+# Solarized copyright (c) 2011 Ethan Schoonover (MIT license)
+# source: https://github.com/altercation/solarized
 - 181,137,0
 - 203,75,22
 - 220,50,47
@@ -55,18 +59,3 @@ standard:
 - 119,172,48
 - 77,190,238
 - 162,20,47
-
-twelve:
-# Source: http://colorbrewer2.org/#type=qualitative&scheme=Paired&n=12
-- 31,120,180
-- 51,160,44
-- 227,26,28
-- 255,127,0
-- 106,61,154
-- 177,89,40
-- 166,206,227
-- 178,223,138
-- 251,154,153
-- 253,191,111
-- 202,178,214
-- 255,255,153

sleap/config/shortcuts.yaml

@@ -31,3 +31,9 @@ show edges: Ctrl+Shift+Tab
 show labels: Ctrl+Tab
 show trails: 
 transpose: Ctrl+T
+frame next: Right
+frame prev: Left
+frame next medium step: Down
+frame prev medium step: Up
+frame next large step: Space
+frame prev large step: /