Update python versions and dependencies

.conda/condarc.yaml

@@ -1,4 +1,5 @@
 channels:
+  - sleap-deps/label/dev
   - conda-forge
   - nvidia
   - https://conda.anaconda.org/sleap/label/dev

.conda/meta.yaml

@@ -20,8 +20,10 @@ build:
 
 requirements:
   host:
-    - conda-forge::python ==3.7.12  # Run into _MAX_WINDOWS_WORKERS not found if <
-    - numpy >=1.19.5,<1.23.0  # Linux likes anaconda, windows likes conda-forge
+    # - conda-forge::python ==3.7.12  # Run into _MAX_WINDOWS_WORKERS not found if <
+    - conda-forge::python >=3.10.0,<3.11.0
+    # - numpy >=1.19.5,<1.23.0  # Linux likes anaconda, windows likes conda-forge
+    - numpy >=1.16.5,<2.0 # SciPy 1.7 requires numpy >=1.16.5
     - conda-forge::cudatoolkit ==11.3.1
     - conda-forge::cudnn=8.2.1
     - nvidia::cuda-nvcc=11.3
@@ -30,69 +32,101 @@ requirements:
 
     # Only the packages above are required to build, but listing them all ensures no 
     # unnecessary pypi packages are installed via the build script (bld.bat, build.sh)
-    - conda-forge::attrs ==21.4.0
-    - conda-forge::cattrs ==1.1.1
-    - conda-forge::h5py ==3.7.0
+    # - conda-forge::attrs ==21.4.0
+    - conda-forge::attrs 
+    # - conda-forge::cattrs ==1.1.1
+    - conda-forge::cattrs
+    # - conda-forge::h5py ==3.7.0
+    - conda-forge::h5py
+    - conda-forge::imageio
+    - conda-forge::imageio-ffmpeg
     - conda-forge::jsmin
-    - conda-forge::jsonpickle ==1.2
+    # - conda-forge::jsonpickle ==1.2
+    - conda-forge::jsonpickle
     - conda-forge::networkx
-    - conda-forge::opencv <4.9.0
+    # - conda-forge::opencv <4.9.0
+    - conda-forge::opencv
     - conda-forge::pandas
     - conda-forge::pillow >=8.3.2
     - conda-forge::psutil
     - conda-forge::pykalman
-    - conda-forge::pyside2 >=5.12,<5.14
+    # - conda-forge::pyside2 >=5.12,<5.14  # To ensure works correctly with QtPy.
+    - conda-forge::pyside6 >=6.5.0 # >=6.2 is compatible with Python 3.10, conda package exists for >=6.4, 6.4 conda package uses problematic QtCharts https://github.com/roomrys/envexp/pull/3
     - conda-forge::python-rapidjson
     - conda-forge::pyyaml
     - conda-forge::pyzmq
     - conda-forge::qtpy >=2.0.1
     - conda-forge::rich
-    - conda-forge::scipy >=1.4.1,<=1.9.0
+    # - conda-forge::scipy >=1.4.1,<=1.9.0
+    - conda-forge::scipy >=1.7.0 # Python 3.10 requires scipy >=1.7
     - conda-forge::scikit-image
-    - conda-forge::scikit-learn ==1.0
-    - conda-forge::scikit-video
+    # - conda-forge::scikit-learn ==1.0
+    - conda-forge::scikit-learn >=1.0.0 # Python 3.10 requires scikit-learn >=1.0
+    # - conda-forge::scikit-video
     - conda-forge::seaborn
+    # - sleap/label/dev::tensorflow ==2.7.0  # TODO: Switch to main label when updated
+    - sleap-deps/label/dev::tensorflow ==2.9.2a0 # TODO: Switch to main label when updated
     - conda-forge::qudida
     - conda-forge::albumentations
     - conda-forge::ndx-pose
-    - conda-forge::importlib-metadata ==4.11.4
+    # - conda-forge::importlib-metadata ==4.11.4
+    - conda-forge::importlib-metadata
   run:
-    - conda-forge::python ==3.7.12  # Run into _MAX_WINDOWS_WORKERS not found if <
-    - conda-forge::attrs ==21.4.0
-    - conda-forge::cattrs ==1.1.1
+    # - conda-forge::python ==3.7.12  # Run into _MAX_WINDOWS_WORKERS not found if <
+    - conda-forge::python >=3.10.0,<3.11.0
+    # - numpy >=1.19.5,<1.23.0  # Linux likes anaconda, windows likes conda-forge
+    - numpy >=1.16.5,<2.0 # SciPy 1.7 requires numpy >=1.16.5
+    # - conda-forge::attrs ==21.4.0
+    - conda-forge::attrs
+    # - conda-forge::cattrs ==1.1.1
+    - conda-forge::cattrs
     - conda-forge::cudatoolkit ==11.3.1
     - conda-forge::cudnn=8.2.1
     - nvidia::cuda-nvcc=11.3
-    - conda-forge::h5py ==3.7.0
+    # - conda-forge::h5py ==3.7.0
+    - conda-forge::h5py
+    - conda-forge::imageio
+    - conda-forge::imageio-ffmpeg
     - conda-forge::jsmin
-    - conda-forge::jsonpickle ==1.2
+    # - conda-forge::jsonpickle ==1.2
+    - conda-forge::jsonpickle
     - conda-forge::networkx
-    - numpy >=1.19.5,<1.23.0  # Linux likes anaconda, windows likes conda-forge
-    - conda-forge::opencv <4.9.0
+    # - conda-forge::opencv <4.9.0
+    - conda-forge::opencv
     - conda-forge::pandas
     - conda-forge::pillow >=8.3.2
     - conda-forge::psutil
     - conda-forge::pykalman
-    - conda-forge::pyside2 >=5.12,<5.14  # To ensure works correctly with QtPy.
+    # - conda-forge::pyside2 >=5.12,<5.14  # To ensure works correctly with QtPy.
+    - conda-forge::pyside6 >=6.5.0 # >=6.2 is compatible with Python 3.10, conda package exists for >=6.4, 6.4 conda package uses problematic QtCharts https://github.com/roomrys/envexp/pull/3
     - conda-forge::python-rapidjson
     - conda-forge::pyyaml
     - conda-forge::pyzmq
     - conda-forge::qtpy >=2.0.1
     - conda-forge::rich
-    - conda-forge::scipy >=1.4.1,<=1.9.0
+    # - conda-forge::scipy >=1.4.1,<=1.9.0
+    - conda-forge::scipy >=1.7.0 # Python 3.10 requires scipy >=1.7
     - conda-forge::scikit-image
-    - conda-forge::scikit-learn ==1.0
-    - conda-forge::scikit-video
+    # - conda-forge::scikit-learn ==1.0
+    - conda-forge::scikit-learn >=1.0.0 # Python 3.10 requires scikit-learn >=1.0
+    # - conda-forge::scikit-video
     - conda-forge::seaborn
-    - sleap/label/dev::tensorflow ==2.7.0  # TODO: Switch to main label when updated
-    - conda-forge::tensorflow-hub <0.14.0  # Causes pynwb conflicts on linux GH-1446
+    # - sleap/label/dev::tensorflow ==2.7.0  # TODO: Switch to main label when updated
+    - sleap-deps/label/dev::tensorflow ==2.9.2a0 # TODO: Switch to main label when updated
+    # - conda-forge::tensorflow-hub <0.14.0  # Causes pynwb conflicts on linux GH-1446
+    - conda-forge::tensorflow-hub
     - conda-forge::qudida
     - conda-forge::albumentations
     - conda-forge::ndx-pose
-    - conda-forge::importlib-metadata ==4.11.4
+    # - conda-forge::importlib-metadata ==4.11.4
+    - conda-forge::importlib-metadata
 
 # This no longer works so we have moved it to the build workflow
 # https://github.com/talmolab/sleap/pull/1744
 # test:
 #   imports:
-#     - sleap
+#     - sleap
+test:
+  requires:
+    - pip
+    - libopencv *=headless*  # [linux] https://github.com/conda-forge/opencv-feedstock/issues/401#issuecomment-2028099423

.conda_mac/condarc.yaml

@@ -1,5 +1,6 @@
 # https://github.com/github/roadmap/issues/528
 
 channels:
+  - sleap-deps/label/dev
   - conda-forge
   - anaconda

.conda_mac/meta.yaml

@@ -23,68 +23,88 @@ source:
 
 requirements:
   host:  
-    - conda-forge::python >=3.9.0, <3.10.0
-    - anaconda::numpy >=1.19.5,<1.23.0
+    - conda-forge::python >=3.10.0,<3.11.0
+    # - anaconda::numpy >=1.19.5,<1.23.0
+    - conda-forge::numpy >=1.16.5 # Scipy 1.7.0 requires numpy >=1.16.5
     - conda-forge::setuptools
     - conda-forge::packaging
     - conda-forge::pip
 
     # Only the packages above are required to build, but listing them all ensures no 
     # unnecessary pypi packages are installed via the build script (bld.bat, build.sh)
     - conda-forge::attrs >=21.2.0
-    - conda-forge::cattrs ==1.1.1
+    # - conda-forge::cattrs ==1.1.1
+    - conda-forge::cattrs
     - conda-forge::h5py
+    - conda-forge::imageio
+    - conda-forge::imageio-ffmpeg
     - conda-forge::jsmin
-    - conda-forge::jsonpickle ==1.2
-    - conda-forge::keras <2.10.0,>=2.9.0rc0  # Required by tensorflow-macos
-    - conda-forge::networkx <3.3
+    # - conda-forge::jsonpickle ==1.2
+    - conda-forge::jsonpickle
+    # - conda-forge::keras <2.10.0,>=2.9.0rc0  # Required by tensorflow-macos in sleap-deps now
+    # - conda-forge::networkx <3.3
+    - conda-forge::networkx
     - conda-forge::opencv
     - conda-forge::pandas
     - conda-forge::pillow
     - conda-forge::psutil
     - conda-forge::pykalman
-    - conda-forge::pyside2 >=5.12
+    # - conda-forge::pyside2 >=5.12 # To ensure application works correctly with QtPy.
+    - conda-forge::pyside6 >=6.5.0 # >=6.2 is compatible with Python 3.10, conda package exists for >=6.4, 6.4 conda package uses problematic QtCharts https://github.com/roomrys/envexp/pull/3
     - conda-forge::python-rapidjson
     - conda-forge::pyyaml
     - conda-forge::pyzmq
     - conda-forge::qtpy >=2.0.1
     - conda-forge::rich
-    - conda-forge::scipy >=1.4.1,<=1.9.0
+    # - conda-forge::scipy >=1.4.1,<=1.9.0
+    - conda-forge::scipy >=1.7.0 # Python 3.10 needs scipy >= 1.7
     - conda-forge::scikit-image
-    - conda-forge::scikit-learn ==1.0
-    - conda-forge::scikit-video
+    # - conda-forge::scikit-learn ==1.0
+    - conda-forge::scikit-learn >=1.0.0 # Python 3.10 needs scikit-learn >= 1.0
+    # - conda-forge::scikit-video
     - conda-forge::seaborn
+    - sleap-deps/label/dev::tensorflow ==2.9.2a0 # TODO: Switch to main label when updated
     - conda-forge::qudida
     - conda-forge::albumentations
     - conda-forge::ndx-pose
 
   run:
-    - conda-forge::python >=3.9.0, <3.10.0
+    - conda-forge::python >=3.10.0,<3.11.0
     - conda-forge::attrs >=21.2.0
-    - conda-forge::cattrs ==1.1.1
+    # - conda-forge::cattrs ==1.1.1
+    - conda-forge::cattrs
     - conda-forge::h5py
+    - conda-forge::imageio
+    - conda-forge::imageio-ffmpeg
     - conda-forge::jsmin
-    - conda-forge::jsonpickle ==1.2
-    - conda-forge::keras <2.10.0,>=2.9.0rc0  # Required by tensorflow-macos
-    - conda-forge::networkx <3.3
-    - anaconda::numpy >=1.19.5,<1.23.0
+    # - conda-forge::jsonpickle ==1.2
+    - conda-forge::jsonpickle
+    # - conda-forge::keras <2.10.0,>=2.9.0rc0  # Required by tensorflow-macos in sleap-deps now
+    # - conda-forge::networkx <3.3
+    - conda-forge::networkx
+    # - anaconda::numpy >=1.19.5,<1.23.0
+    - conda-forge::numpy >=1.16.5 # Scipy 1.7.0 requires numpy >=1.16.5
     - conda-forge::opencv
     - conda-forge::pandas
     - conda-forge::pillow
     - conda-forge::psutil
     - conda-forge::pykalman
-    - conda-forge::pyside2 >=5.12
+    # - conda-forge::pyside2 >=5.12
+    - conda-forge::pyside6 >=6.5.0 # >=6.2 is compatible with Python 3.10, conda package exists for >=6.4, 6.4 conda package uses problematic QtCharts https://github.com/roomrys/envexp/pull/3
     - conda-forge::python-rapidjson
     - conda-forge::pyyaml
     - conda-forge::pyzmq
     - conda-forge::qtpy >=2.0.1
     - conda-forge::rich
-    - conda-forge::scipy >=1.4.1,<=1.9.0
+    # - conda-forge::scipy >=1.4.1,<=1.9.0
+    - conda-forge::scipy >=1.7.0 # Python 3.10 is compatible with scipy >=1.7.0
     - conda-forge::scikit-image
-    - conda-forge::scikit-learn ==1.0
-    - conda-forge::scikit-video
+    # - conda-forge::scikit-learn ==1.0
+    - conda-forge::scikit-learn >=1.0.0 # Python 3.10 is compatible with scikit-learn >=1.0.0
+    # - conda-forge::scikit-video
     - conda-forge::seaborn
     # - conda-forge::tensorflow-hub  # pulls in tensorflow cpu from conda-forge
+    - sleap-deps/label/dev::tensorflow ==2.9.2a0 # TODO: Switch to main label when updated
     - conda-forge::qudida
     - conda-forge::albumentations
     - conda-forge::ndx-pose

.github/workflows/build.yml

@@ -18,11 +18,11 @@ jobs:
         include:
           # Use this condarc as default
           - condarc: .conda/condarc.yaml
-          - pyver: "3.7"
+          - pyver: "3.10"
           # Use special condarc if macos
           - os: "macos-14"
             condarc: .conda_mac/condarc.yaml
-            pyver: "3.9"
+            pyver: "3.10"
     steps:
       # Setup
       - name: Checkout

.github/workflows/build_ci.yml

@@ -26,7 +26,7 @@ jobs:
           # Use this condarc as default
           - condarc: .conda/condarc.yaml
           - wheel_name: sleap-wheel-linux
-          - pyver: "3.7"
+          - pyver: "3.10"
     steps:
       # Setup
       - name: Checkout
@@ -83,7 +83,7 @@ jobs:
               pip install '$wheel_path'[dev]
           - test_args: pytest --durations=-1 tests/
           - condarc: .conda/condarc.yaml
-          - pyver: "3.7"
+          - pyver: "3.10"
           # Use special condarc if macos
           - os: "macos-14"
             condarc: .conda_mac/condarc.yaml
@@ -93,6 +93,7 @@ jobs:
             # Otherwise core dumped in github actions
             test_args: |
               sudo apt install xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0
+              sudo apt-get install libglapi-mesa libegl-mesa0 libegl1 libopengl0 libgl1-mesa-glx
               sudo Xvfb :1 -screen 0 1024x768x24 </dev/null &
               export DISPLAY=":1"
               pytest tests -k 'not exclude_from_linux_pip_test'

.github/workflows/build_manual.yml

@@ -7,11 +7,14 @@ on:
   push:
     paths:
       - '.conda/meta.yaml'
+      - '.conda/condarc.yaml'
       - '.conda_mac/meta.yaml'
+      - '.conda_mac/condarc.yaml'
       - '.github/workflows/build_manual.yml'
     branches:
       # - develop
-      - fakebranch
+      # - fakebranch
+      - elizabeth/update-python-and-dependencies
 
 jobs:
   build:
@@ -25,11 +28,11 @@ jobs:
         include:
           # Use this condarc as default
           - condarc: .conda/condarc.yaml
-          - pyver: "3.7"
+          - pyver: "3.10"
           # Use special condarc if macos
           - os: "macos-14"
             condarc: .conda_mac/condarc.yaml
-            pyver: "3.9"
+            pyver: "3.10"
     steps:
       # Setup
       - name: Checkout
@@ -92,9 +95,45 @@ jobs:
           conda build .conda_mac --output-folder build
           echo "BUILD_PATH=$(pwd)/build" >> "$GITHUB_ENV"
 
-      # Test built conda package (Ubuntu and Windows)
-      - name: Test built conda package (Ubuntu and Windows)
-        if: matrix.os != 'macos-14'
+      # Test built conda package (Ubuntu)
+      - name: Test built conda package (Ubuntu)
+        if: matrix.os == 'ubuntu-22.04'
+        shell: bash -l {0}
+        run: |
+          echo "Current build path: $BUILD_PATH"
+          conda deactivate
+
+          echo "Python executable before activating environment:"
+          which python
+          echo "Python version before activating environment:"
+          python --version
+          echo "Conda info before activating environment:"
+          conda info
+
+          echo "Creating and testing conda environment with sleap package..."
+          sudo apt-get update
+          sudo apt-get install libglapi-mesa libegl-mesa0 libegl1 libopengl0 libgl1-mesa-glx
+          conda create -y -n sleap_test -c file://$BUILD_PATH -c sleap/label/dev -c conda-forge -c nvidia -c anaconda sleap
+          conda activate sleap_test
+
+          echo "Python executable after activating sleap_test environment:"
+          which python
+          echo "Python version after activating sleap_test environment:"
+          python --version
+          echo "Conda info after activating sleap_test environment:"
+          conda info
+          echo "List of installed conda packages in the sleap_test environment:"
+          conda list
+          echo "List of installed pip packages in the sleap_test environment:"
+          pip list
+
+          echo "Testing sleap package installation..."
+          sleap_version=$(python -c "import sleap; print(sleap.__version__)")
+          echo "Test completed using sleap version: $sleap_version"
+
+      # Test built conda package (Windows)
+      - name: Test built conda package (Windows)
+        if: matrix.os == 'windows-2022'
         shell: bash -l {0}
         run: |
           echo "Current build path: $BUILD_PATH"