Swap Packaging to Poetry

.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       # You can use PyPy versions in python-version. For example, pypy2 and pypy3
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.7, 3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -29,4 +29,4 @@ jobs:
       run: python -c "import sys; print(sys.version)"
     #test installation of DLC-core dependencies:
     - name: Install dependencies
-      run: pip install -r requirements.txt
+      run: pip install .

.github/workflows/testing.yml

@@ -31,11 +31,6 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip setuptools wheel
-          pip install -r requirements.txt
       - name: Install ffmpeg
         run: |
           if [ "$RUNNER_OS" == "Linux" ]; then
@@ -47,12 +42,8 @@ jobs:
             choco install ffmpeg
           fi
         shell: bash
-
-      - name: Run pytest tests
-        run: |
-          pip install pytest
-          python -m pytest
-      - name: Run functional tests
+      - name: Install and test
         run: |
-          pip install git+git://github.com/${{ github.repository }}.git@${{ github.sha }}
-          dlc-live-test
+          python -m pip install --upgrade pip wheel poetry
+          python -m poetry install
+          python -m poetry run dlc-live-test --nodisplay

CITATION.cff

@@ -0,0 +1,55 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: >-
+  Real-time, low-latency closed-loop feedback using
+  markerless posture tracking
+message: >-
+  If you utilize our tool, please [cite Kane et al,
+  eLife
+  2020](https://elifesciences.org/articles/61909).
+  The preprint is available here:
+  https://www.biorxiv.org/content/10.1101/2020.08.04.236422v2
+type: software
+authors:
+  - given-names: Gary
+    name-particle: A
+    family-names: Kane
+    affiliation: >-
+      The Rowland Institute at Harvard, Harvard
+      University, Cambridge, United States
+  - given-names: Gonçalo
+    family-names: Lopes
+    affiliation: 'NeuroGEARS Ltd, London, United Kingdom'
+  - given-names: Jonny
+    name-particle: L
+    family-names: Saunders
+    affiliation: >-
+      Institute of Neuroscience, Department of
+      Psychology, University of Oregon, Eugene,
+      United States
+  - given-names: Alexander
+    family-names: Mathis
+    affiliation: >-
+      The Rowland Institute at Harvard, Harvard
+      University, Cambridge, United States; Center
+      for Neuroprosthetics, Center for Intelligent
+      Systems, & Brain Mind Institute, School of Life
+      Sciences, Swiss Federal Institute of Technology
+      (EPFL), Lausanne, Switzerland
+  - given-names: Mackenzie
+    name-particle: W
+    family-names: Mathis
+    affiliation: >-
+      The Rowland Institute at Harvard, Harvard
+      University, Cambridge, United States; Center
+      for Neuroprosthetics, Center for Intelligent
+      Systems, & Brain Mind Institute, School of Life
+      Sciences, Swiss Federal Institute of Technology
+      (EPFL), Lausanne, Switzerland
+    email: [email protected]
+date-released: 2020-08-05
+doi: "10.7554/eLife.61909"
+license: "AGPL-3.0-or-later"
+version:  "1.0.2"

dlclive/check_install/check_install.py

@@ -7,42 +7,88 @@
 
 
 import os
+import sys
 import shutil
+import warnings
+
 from dlclive import benchmark_videos
 import urllib.request
+import argparse
+from pathlib import Path
+import tarfile
+
+
+def urllib_pbar(count, blockSize, totalSize):
+    percent = int(count * blockSize * 100 / totalSize)
+    outstr = f"{round(percent)}%"
+    sys.stdout.write(outstr)
+    sys.stdout.write("\b"*len(outstr))
+    sys.stdout.flush()
 
+def main(display:bool=None):
+    parser = argparse.ArgumentParser(
+        description="Test DLC-Live installation by downloading and evaluating a demo DLC project!")
+    parser.add_argument('--nodisplay', action='store_false', help="Run the test without displaying tracking")
+    args = parser.parse_args()
 
-def main():
+    if display is None:
+        display = args.nodisplay
+
+    if not display:
+        print('Running without displaying video')
 
     # make temporary directory in $HOME
     print("\nCreating temporary directory...\n")
-    home = os.path.expanduser("~")
-    tmp_dir = os.path.normpath(f"{home}/dlc-live-tmp")
-    os.makedirs(tmp_dir, exist_ok=True)
-    os.chdir(tmp_dir)
+    tmp_dir = Path().home() / 'dlc-live-tmp'
+    tmp_dir.mkdir(mode=0o775,exist_ok=True)
+
+    video_file = str(tmp_dir / 'dog_clip.avi')
+    model_tarball = tmp_dir / 'DLC_Dog_resnet_50_iteration-0_shuffle-0.tar.gz'
+    model_dir = model_tarball.with_suffix('').with_suffix('') # remove two suffixes (tar.gz)
+
 
     # download dog test video from github:
+    print(f"Downloading Video to {video_file}")
     url_link = "https://github.com/DeepLabCut/DeepLabCut-live/blob/master/check_install/dog_clip.avi?raw=True"
-    urllib.request.urlretrieve(url_link, "dog_clip.avi")
-    video_file = os.path.join(url_link, "dog_clip.avi")
+    urllib.request.urlretrieve(url_link, video_file, reporthook=urllib_pbar)
 
     # download exported dog model from DeepLabCut Model Zoo
-    print("Downloading full_dog model from the DeepLabCut Model Zoo...")
-    model_url = "http://deeplabcut.rowland.harvard.edu/models/DLC_Dog_resnet_50_iteration-0_shuffle-0.tar.gz"
-    os.system(f"curl {model_url} | tar xvz")
+    if Path(model_tarball).exists():
+        print('Tarball already downloaded, using cached version')
+    else:
+        print("Downloading full_dog model from the DeepLabCut Model Zoo...")
+        model_url = "http://deeplabcut.rowland.harvard.edu/models/DLC_Dog_resnet_50_iteration-0_shuffle-0.tar.gz"
+        urllib.request.urlretrieve(model_url, str(model_tarball), reporthook=urllib_pbar)
+
+    print('Untarring compressed model')
+    model_file = tarfile.open(str(model_tarball))
+    model_file.extractall(str(model_dir.parent))
+    model_file.close()
+
+    # assert these things exist so we can give informative error messages
+    assert Path(video_file).exists()
+    assert Path(model_dir).exists() and Path(model_dir).is_dir()
 
     # run benchmark videos
     print("\n Running inference...\n")
-    model_dir = "DLC_Dog_resnet_50_iteration-0_shuffle-0"
-    print(video_file)
-    benchmark_videos(model_dir, video_file, display=True, resize=0.5, pcutoff=0.25)
+    # model_dir = "DLC_Dog_resnet_50_iteration-0_shuffle-0"
+    # print(video_file)
+    benchmark_videos(str(model_dir), video_file, display=display, resize=0.5, pcutoff=0.25)
 
     # deleting temporary files
     print("\n Deleting temporary files...\n")
-    shutil.rmtree(tmp_dir)
+    try:
+        shutil.rmtree(tmp_dir)
+    except PermissionError:
+        warnings.warn(f'Could not delete temporary directory {str(tmp_dir)} due to a permissions error, but otherwise dlc-live seems to be working fine!')
 
     print("\nDone!\n")
 
 
 if __name__ == "__main__":
-    main()
+
+
+    display = args.nodisplay
+
+
+    main(display=args.nodisplay)

dlclive/dlclive.py

@@ -11,6 +11,9 @@
 import warnings
 import numpy as np
 import tensorflow as tf
+import typing
+from pathlib import Path
+from typing import Optional, Tuple, List
 
 try:
     TFVER = [int(v) for v in tf.__version__.split(".")]
@@ -32,7 +35,8 @@
 from dlclive.display import Display
 from dlclive import utils
 from dlclive.exceptions import DLCLiveError, DLCLiveWarning
-
+if typing.TYPE_CHECKING:
+    from dlclive.processor import Processor
 
 class DLCLive(object):
     """
@@ -99,23 +103,23 @@ class DLCLive(object):
 
     def __init__(
         self,
-        model_path,
-        model_type="base",
-        precision="FP32",
+        model_path:str,
+        model_type:str="base",
+        precision:str="FP32",
         tf_config=None,
-        cropping=None,
-        dynamic=(False, 0.5, 10),
-        resize=None,
-        convert2rgb=True,
-        processor=None,
-        display=False,
-        pcutoff=0.5,
-        display_radius=3,
-        display_cmap="bmy",
+        cropping:Optional[List[int]]=None,
+        dynamic:Tuple[bool, float, float]=(False, 0.5, 10),
+        resize:Optional[float]=None,
+        convert2rgb:bool=True,
+        processor:Optional['Processor']=None,
+        display:typing.Union[bool, Display]=False,
+        pcutoff:float=0.5,
+        display_radius:int=3,
+        display_cmap:str="bmy",
     ):
 
         self.path = model_path
-        self.cfg = None
+        self.cfg = None # type: typing.Optional[dict]
         self.model_type = model_type
         self.tf_config = tf_config
         self.precision = precision
@@ -125,11 +129,12 @@ def __init__(
         self.resize = resize
         self.processor = processor
         self.convert2rgb = convert2rgb
-        self.display = (
-            Display(pcutoff=pcutoff, radius=display_radius, cmap=display_cmap)
-            if display
-            else None
-        )
+        if isinstance(display, Display):
+            self.display = display
+        elif display:
+            self.display = Display(pcutoff=pcutoff, radius=display_radius, cmap=display_cmap)
+        else:
+            self.display = None
 
         self.sess = None
         self.inputs = None
@@ -141,7 +146,7 @@ def __init__(
         # checks
 
         if self.model_type == "tflite" and self.dynamic[0]:
-            self.dynamic[0] = False
+            self.dynamic = (False, *self.dynamic[1:])
             warnings.warn(
                 "Dynamic cropping is not supported for tensorflow lite inference. Dynamic cropping will not be used...",
                 DLCLiveWarning,
@@ -158,14 +163,14 @@ def read_config(self):
             error thrown if pose configuration file does nott exist
         """
 
-        cfg_path = os.path.normpath(self.path + "/pose_cfg.yaml")
-        if not os.path.isfile(cfg_path):
+        cfg_path = Path(self.path).resolve() / "pose_cfg.yaml"
+        if not cfg_path.exists():
             raise FileNotFoundError(
-                f"The pose configuration file for the exported model at {cfg_path} was not found. Please check the path to the exported model directory"
+                f"The pose configuration file for the exported model at {str(cfg_path)} was not found. Please check the path to the exported model directory"
             )
 
         ruamel_file = ruamel.yaml.YAML()
-        self.cfg = ruamel_file.load(open(cfg_path, "r"))
+        self.cfg = ruamel_file.load(open(str(cfg_path), "r"))
 
     @property
     def parameterization(self) -> dict: