Merge branch 'develop' into shrivaths/changelog-announcement-1

talmolab · Sep 29, 2023 · 83d34ad · 83d34ad
2 parents c0ea01d + ed77b49
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diff --git a/.conda/build.sh b/.conda/build.sh
@@ -16,8 +16,8 @@ python setup.py install --single-version-externally-managed --record=record.txt
 
 # Copy the activate scripts to $PREFIX/etc/conda/activate.d.
 # This will allow them to be run on environment activation.
-export CHANGE=activate
-
-mkdir -p "${PREFIX}/etc/conda/${CHANGE}.d"
-ls "${RECIPE_DIR}"
-cp "${RECIPE_DIR}/${PKG_NAME}_${CHANGE}.sh" "${PREFIX}/etc/conda/${CHANGE}.d/${PKG_NAME}_${CHANGE}.sh"
+for CHANGE in "activate" "deactivate"
+do
+    mkdir -p "${PREFIX}/etc/conda/${CHANGE}.d"
+    cp "${RECIPE_DIR}/${PKG_NAME}_${CHANGE}.sh" "${PREFIX}/etc/conda/${CHANGE}.d/${PKG_NAME}_${CHANGE}.sh"
+done
diff --git a/.conda/sleap_activate.sh b/.conda/sleap_activate.sh
@@ -1,4 +1,6 @@
 #!/bin/sh
 
+# Remember the old library path for when we deactivate
+export SLEAP_OLD_LD_LIBRARY_PATH=$LD_LIBRARY_PATH
 # Help CUDA find GPUs!
 export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
diff --git a/.conda/sleap_deactivate.sh b/.conda/sleap_deactivate.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+# Reset to the old library path for when deactivating the environment
+export LD_LIBRARY_PATH=$SLEAP_OLD_LD_LIBRARY_PATH
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -28,7 +28,7 @@ Please include information about how you installed.
 - OS:
 <!-- [e.g. ubuntu 20.04, macOS 11.0] -->
 - Version(s):
-<!-- e.g. [SLEAP v1.3.2, python 3.8] --->
+<!-- e.g. [SLEAP v1.3.3, python 3.8] --->
 - SLEAP installation method (listed [here](https://sleap.ai/installation.html#)):
   - [ ] [Conda from package](https://sleap.ai/installation.html#conda-package)
   - [ ] [Conda from source](https://sleap.ai/installation.html#conda-from-source)

diff --git a/docs/conf.py b/docs/conf.py
@@ -28,15 +28,15 @@
 copyright = f"2019–{date.today().year}, Talmo Lab"
 
 # The short X.Y version
-version = "1.3.2"
+version = "1.3.3"
 
 # Get the sleap version
 # with open("../sleap/version.py") as f:
 #     version_file = f.read()
 #     version = re.search("\d.+(?=['\"])", version_file).group(0)
 
 # Release should be the full branch name
-release = "v1.3.2"
+release = "v1.3.3"
 
 html_title = f"SLEAP ({release})"
 html_short_title = "SLEAP"

diff --git a/docs/guides/cli.md b/docs/guides/cli.md
@@ -389,6 +389,9 @@ optional arguments:
   --distinctly_color DISTINCTLY_COLOR
                         Specify how to color instances. Options include: "instances",
                         "edges", and "nodes" (default: "instances")
+  --background BACKGROUND
+                        Specify the type of background to be used to save the videos.
+                        Options: original, black, white and grey. (default: "original")
 ```
 
 ## Debugging

diff --git a/docs/installation.md b/docs/installation.md
@@ -137,13 +137,13 @@ SLEAP can be installed three different ways: via {ref}`conda package<condapackag
 **Windows** and **Linux**
 
 ```bash
-mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.2
+mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.3
 ```
 
 **Mac OS X** and **Apple Silicon**
 
 ```bash
-mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.3.2
+mamba create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.3.3
 ```
 
 **This is the recommended installation method**.
@@ -232,7 +232,7 @@ Although you do not need Mambaforge installed to perform a `pip install`, we rec
 3. Finally, we can perform the `pip install`:
 
    ```bash
-   pip install sleap[pypi]==1.3.2
+   pip install sleap[pypi]==1.3.3
    ```
 
    This works on **any OS except Apple silicon** and on **Google Colab**.
@@ -343,18 +343,19 @@ python -c "import tensorflow as tf; print(tf.config.list_physical_devices('GPU')
 ````{warning}
 TensorFlow 2.7+ is currently failing to detect CUDA Toolkit and CuDNN on some systems (see [Issue thread](https://github.com/tensorflow/tensorflow/issues/52988)).
 
-If you run into issues, try downgrading the TensorFlow 2.6:
+If you run into issues, either try downgrading the TensorFlow 2.6:
 ```bash
 pip install tensorflow==2.6.3
 ```
+or follow the note below.
 ````
 
 ````{note}
-If you are on Linux, have a NVIDIA GPU, and are having trouble utilizing your GPU:
+If you are on Linux, have a NVIDIA GPU, but cannot detect your GPU:
 
 ```bash
-W tensorflow/stream_executor/platform/default/dso_loader.cc:64 Could not load dynamic 
-library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object 
+W tensorflow/stream_executor/platform/default/dso_loader.cc:64 Could not load dynamic
+library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object
 file: No such file or directory
 ```
 
@@ -368,10 +369,19 @@ and run the commands:
 ```bash
 mkdir -p $CONDA_PREFIX/etc/conda/activate.d
 echo '#!/bin/sh' >> $CONDA_PREFIX/etc/conda/activate.d/sleap_activate.sh
+echo 'export SLEAP_OLD_LD_LIBRARY_PATH=$LD_LIBRARY_PATH' >> $CONDA_PREFIX/etc/conda/activate.d/sleap_activate.sh
 echo 'export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH' >> $CONDA_PREFIX/etc/conda/activate.d/sleap_activate.sh
 source $CONDA_PREFIX/etc/conda/activate.d/sleap_activate.sh
 ```
-These commands only need to be run once and will subsequently run automatically upon activating your `sleap` environment.
+
+This will set the environment variable `LD_LIBRARY_PATH` each time the environment is activated. The environment variable will remain set in the current terminal even if we deactivate the environment. Although not strictly necessary, if you would also like the environment variable to be reset to the original value when deactivating the environment, we can run the following commands:
+```bash
+mkdir -p $CONDA_PREFIX/etc/conda/deactivate.d
+echo '#!/bin/sh' >> $CONDA_PREFIX/etc/conda/deactivate.d/sleap_deactivate.sh
+echo 'export LD_LIBRARY_PATH=$SLEAP_OLD_LD_LIBRARY_PATH' >> $CONDA_PREFIX/etc/conda/deactivate.d/sleap_deactivate.sh
+```
+
+These commands only need to be run once and will subsequently run automatically upon [de]activating your `sleap` environment.
 ````
 
 ## Upgrading and uninstalling

diff --git a/docs/notebooks/Data_structures.ipynb b/docs/notebooks/Data_structures.ipynb
@@ -56,7 +56,7 @@
       "source": [
         "# This should take care of all the dependencies on colab:\n",
         "!pip uninstall -qqq -y opencv-python opencv-contrib-python\n",
-        "!pip install -qqq sleap==1.3.1111\n",
+        "!pip install -qqq \"sleap[pypi]>=1.3.3\"\n",
         "\n",
         "# But to do it locally, we'd recommend the conda package (available on Windows + Linux):\n",
         "# conda create -n sleap -c sleap -c conda-forge -c nvidia sleap"

diff --git a/docs/notebooks/Interactive_and_realtime_inference.ipynb b/docs/notebooks/Interactive_and_realtime_inference.ipynb
@@ -60,7 +60,7 @@
       "source": [
         "# This should take care of all the dependencies on colab:\n",
         "!pip uninstall -qqq -y opencv-python opencv-contrib-python\n",
-        "!pip install -qqq sleap==1.3.1\n",
+        "!pip install -qqq \"sleap[pypi]>=1.3.3\"\n",
         "\n",
         "\n",
         "# But to do it locally, we'd recommend the conda package (available on Windows + Linux):\n",

diff --git a/docs/notebooks/Interactive_and_resumable_training.ipynb b/docs/notebooks/Interactive_and_resumable_training.ipynb
@@ -62,7 +62,7 @@
       "source": [
         "# This should take care of all the dependencies on colab:\n",
         "!pip uninstall -qqq -y opencv-python opencv-contrib-python\n",
-        "!pip install -qqq sleap==1.3.1\n",
+        "!pip install -qqq \"sleap[pypi]>=1.3.3\"\n",
         "\n",
         "\n",
         "# But to do it locally, we'd recommend the conda package (available on Windows + Linux):\n",

diff --git a/docs/notebooks/Model_evaluation.ipynb b/docs/notebooks/Model_evaluation.ipynb
@@ -40,7 +40,7 @@
       ],
       "source": [
         "!pip uninstall -qqq -y opencv-python opencv-contrib-python\n",
-        "!pip install -qqq sleap==1.3.1\n",
+        "!pip install -qqq \"sleap[pypi]>=1.3.3\"\n",
         "!apt -qq install tree\n",
         "!wget -q https://storage.googleapis.com/sleap-data/reference/flies13/td_fast.210505_012601.centered_instance.n%3D1800.zip\n",
         "!unzip -qq -o -d \"td_fast.210505_012601.centered_instance.n=1800\" \"td_fast.210505_012601.centered_instance.n=1800.zip\""

diff --git a/docs/notebooks/Post_inference_tracking.ipynb b/docs/notebooks/Post_inference_tracking.ipynb
@@ -61,7 +61,7 @@
       "source": [
         "# This should take care of all the dependencies on colab:\n",
         "!pip uninstall -qqq -y opencv-python opencv-contrib-python\n",
-        "!pip install -qqq sleap==1.3.1\n",
+        "!pip install -qqq \"sleap[pypi]>=1.3.3\"\n",
         "\n",
         "# But to do it locally, we'd recommend the conda package (available on Windows + Linux):\n",
         "# conda create -n sleap -c sleap -c conda-forge -c nvidia sleap"

diff --git a/docs/notebooks/Training_and_inference_on_an_example_dataset.ipynb b/docs/notebooks/Training_and_inference_on_an_example_dataset.ipynb
@@ -62,7 +62,7 @@
    ],
    "source": [
     "!pip uninstall -qqq -y opencv-python opencv-contrib-python\n",
-    "!pip install -qqq sleap==1.3.1"
+    "!pip install -qqq \"sleap[pypi]>=1.3.3\""
    ]
   },
   {

diff --git a/docs/notebooks/Training_and_inference_using_Google_Drive.ipynb b/docs/notebooks/Training_and_inference_using_Google_Drive.ipynb
@@ -59,7 +59,7 @@
    ],
    "source": [
     "!pip uninstall -qqq -y opencv-python opencv-contrib-python\n",
-    "!pip install -qqq sleap==1.3.1"
+    "!pip install -qqq \"sleap[pypi]>=1.3.3\""
    ]
   },
   {

diff --git a/pypi_requirements.txt b/pypi_requirements.txt
@@ -12,24 +12,34 @@ jsonpickle==1.2
 networkx
 numpy>=1.19.5,<1.23.0
 opencv-python>=4.2.0,<=4.6.0
-# opencv-python-headless>=4.2.0.34,<=4.5.5.62
 pandas
 pillow>=8.3.1,<=8.4.0
 psutil
 pykalman==0.9.5
 PySide2>=5.13.2,<=5.14.1; platform_machine != 'arm64'
 PySide6; sys_platform == 'darwin' and platform_machine == 'arm64'
-python-rapidjson
+# Otherwise error: Microsoft Visual C++ 14.0 is required. 
+python-rapidjson <=1.10; sys_platform == 'win32'
+python-rapidjson; sys_platform != 'win32'
 pyyaml
 pyzmq
 qtpy>=2.0.1
 rich==10.16.1
-imageio<=2.15.0
 imgaug==0.4.0
 scipy>=1.4.1,<=1.9.0
 scikit-image
 scikit-learn ==1.0.*
 scikit-video
 seaborn
-tensorflow
-tensorflow-hub
+tensorflow>=2.6.3,<2.9; platform_machine != 'arm64'
+tensorflow-hub<=0.14.0
+# These dependencies are untested since we do not offer a wheel for apple silicon atm.
+tensorflow-macos==2.9.2; sys_platform == 'darwin' and platform_machine == 'arm64'
+tensorflow-metal==0.5.0; sys_platform == 'darwin' and platform_machine == 'arm64'
+
+# Dependencies of dependencies
+# google-auth 2.23.0 has requirement urllib3<2.0
+urllib3<2.0  # Not a 'noticed' runtime-dependency
+# tensorboard 2.11.2 has requirement protobuf<4,>=3.9.2
+# tensorflow 2.11.0 has requirement protobuf<3.20,>=3.9.2
+protobuf<3.20  # Makes GUI work in windows
diff --git a/sleap/config/labeled_clip_form.yaml b/sleap/config/labeled_clip_form.yaml
@@ -18,6 +18,10 @@ main:
     label: Use GUI Visual Settings (colors, line widths)
     type: bool
     default: true
+  - name: background
+    label: Video Background
+    type: list
+    options: original,black,white,grey
   - name: open_when_done
     label: Open When Done Saving
     type: bool

diff --git a/sleap/config/training_editor_form.yaml b/sleap/config/training_editor_form.yaml
@@ -661,6 +661,7 @@ optimization:
   label: Batch Size
   name: optimization.batch_size
   type: int
+  range: 1,512
 - default: 100
   help: Maximum number of epochs to train for. Training can be stopped manually or automatically if early stopping is enabled and a plateau is detected.
   label: Epochs

diff --git a/sleap/gui/commands.py b/sleap/gui/commands.py
@@ -1295,6 +1295,7 @@ def do_action(context: CommandContext, params: dict):
             frames=list(params["frames"]),
             fps=params["fps"],
             color_manager=params["color_manager"],
+            background=params["background"],
             show_edges=params["show edges"],
             edge_is_wedge=params["edge_is_wedge"],
             marker_size=params["marker size"],
@@ -1354,6 +1355,7 @@ def ask(context: CommandContext, params: dict) -> bool:
         params["fps"] = export_options["fps"]
         params["scale"] = export_options["scale"]
         params["open_when_done"] = export_options["open_when_done"]
+        params["background"] = export_options["background"]
 
         params["crop"] = None
 

diff --git a/sleap/gui/overlays/base.py b/sleap/gui/overlays/base.py
@@ -71,7 +71,6 @@ def remove_from_scene(self):
 
             except RuntimeError as e:  # Internal C++ object (PySide2.QtWidgets.QGraphicsPathItem) already deleted.
                 logger.debug(e)
-                pass
 
         # Stop tracking the items after they been removed from the scene
         self.items = []