Merge branch 'develop' into elise/multiple-inputs-for-sleap-track

.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 v1.3.3, python 3.8] --->
+<!-- e.g. [SLEAP v1.4.1a2, 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)

.github/workflows/build.yml

@@ -18,34 +18,32 @@ jobs:
         include:
           # Use this condarc as default
           - condarc: .conda/condarc.yaml
+          - pyver: "3.7"
           # Use special condarc if macos
           - os: "macos-14"
             condarc: .conda_mac/condarc.yaml
+            pyver: "3.9"
     steps:
       # Setup
-      - uses: actions/checkout@v2
-      - name: Cache conda
-        uses: actions/cache@v1
-        env:
-          # Increase this value to reset cache if environment_build.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment_build.yml', 'requirements.txt') }}
+      - name: Checkout
+        uses: actions/checkout@v4
+
       - name: Setup Miniconda
-        # https://github.com/conda-incubator/setup-miniconda
-        uses: conda-incubator/setup-miniconda@v2.0.1
+        uses: conda-incubator/setup-miniconda@v3.0.3
         with:
-          python-version: 3.7
-          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-          environment-file: environment_build.yml
+          miniforge-version: latest
           condarc-file: ${{ matrix.condarc }}
+          python-version: ${{ matrix.pyver }}
+          environment-file: environment_build.yml
           activate-environment: sleap_ci
+          conda-solver: "libmamba"
+
       - name: Print environment info
         shell: bash -l {0}
         run: |
           which python
           conda info
+          conda list
 
       # Build pip wheel (Ubuntu)
       - name: Build pip wheel (Ubuntu)
@@ -69,20 +67,23 @@ jobs:
         shell: bash -l {0}
         run: |
           conda build .conda --output-folder build
+          echo "BUILD_PATH=$(pwd)/build" >> "$GITHUB_ENV"
 
-      # Build conda package (Windows)
+      # Build conda package (Windows) 
       - name: Build conda package (Windows)
         if: matrix.os == 'windows-2022'
         shell: powershell
         run: |
           conda build .conda --output-folder build
+          echo "BUILD_PATH=\$(pwd)\build" >> "$env:GITHUB_ENV"
 
       # Build conda package (Mac)
       - name: Build conda package (Mac)
         if: matrix.os == 'macos-14'
         shell: bash -l {0}
         run: |
           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)
@@ -91,7 +92,7 @@ jobs:
         run: |
           echo "Current build path: $BUILD_PATH"
           conda deactivate
-
+    
           echo "Python executable before activating environment:"
           which python
           echo "Python version before activating environment:"
@@ -113,7 +114,7 @@ jobs:
           conda list
           echo "List of installed pip packages in the sleap_test environment:"
           pip list
-
+    
           echo "Testing sleap package installation..."
           sleap_version=$(python -c "import sleap; print(sleap.__version__)")
           echo "Test completed using sleap version: $sleap_version"
@@ -125,18 +126,18 @@ jobs:
         run: |
           echo "Current build path: $BUILD_PATH"
           conda deactivate
-
+    
           echo "Python executable before activating environment:"
           which python
           echo "Python version before activating environment:"
           python --version
           echo "Conda info before activating environment:"
           conda info
-
+    
           echo "Creating and testing conda environment with sleap package..."
           conda create -y -n sleap_test -c file://$BUILD_PATH -c conda-forge -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:"
@@ -147,7 +148,7 @@ jobs:
           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"
@@ -163,7 +164,7 @@ jobs:
 
       # Login to conda (Windows)
       - name: Login to Anaconda (Windows)
-        if: matrix.os == 'windows-2019'
+        if: matrix.os == 'windows-2022'
         env:
           ANACONDA_LOGIN: ${{ secrets.ANACONDA_LOGIN }}
         shell: powershell
@@ -181,12 +182,12 @@ jobs:
       
       # Upload conda package (Windows)
       - name: Upload conda package (Windows/main)
-        if: matrix.os == 'windows-2019' && !github.event.release.prerelease
+        if: matrix.os == 'windows-2022' && !github.event.release.prerelease
         shell: powershell
         run: |
           anaconda -v upload "build\win-64\*.tar.bz2"
       - name: Upload conda package (Windows/dev)
-        if: matrix.os == 'windows-2019' && github.event.release.prerelease
+        if: matrix.os == 'windows-2022' && github.event.release.prerelease
         shell: powershell
         run: |
           anaconda -v upload "build\win-64\*.tar.bz2" --label dev

.github/workflows/build_ci.yml

@@ -29,16 +29,8 @@ jobs:
           - pyver: "3.7"
     steps:
       # Setup
-      - uses: actions/checkout@v2
-
-      - name: Cache conda
-        uses: actions/cache@v1
-        env:
-          # Increase this value to reset cache if environment_build.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment_build.yml', 'pyproject.toml') }}
+      - name: Checkout
+        uses: actions/checkout@v4
 
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v3.0.3
@@ -49,7 +41,6 @@ jobs:
           environment-file: environment_build.yml
           activate-environment: sleap_ci
           conda-solver: "libmamba"
-          # use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
 
       - name: Print build environment info
         shell: bash -l {0}
@@ -66,7 +57,7 @@ jobs:
       
       # Upload artifact "tests" can use it
       - name: Upload wheel artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.wheel_name }}
           path: dist/*.whl
@@ -111,16 +102,16 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.pyver }}
 
       # Download wheel
       - name: Download wheel artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         id: download
         with:
           name: ${{ matrix.wheel_name }}

.github/workflows/build_manual.yml

@@ -32,15 +32,8 @@ jobs:
             pyver: "3.9"
     steps:
       # Setup
-      - uses: actions/checkout@v2
-      - name: Cache conda
-        uses: actions/cache@v1
-        env:
-          # Increase this value to reset cache if environment_build.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment_build.yml', 'requirements.txt') }}
+      - name: Checkout
+        uses: actions/checkout@v4
 
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v3.0.3
@@ -51,7 +44,6 @@ jobs:
           environment-file: environment_build.yml
           activate-environment: sleap_ci
           conda-solver: "libmamba"
-          # use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
 
       - name: Print environment info
         shell: bash -l {0}
@@ -67,14 +59,14 @@ jobs:
         run: |
           python setup.py bdist_wheel
 
-      # Upload pip wheel (Ubuntu)
-      - name: Upload pip wheel (Ubuntu)
-        if: matrix.os == 'ubuntu-22.04'
-        env:
-          PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
-        shell: bash -l {0}
-        run: |
-          twine upload -u __token__ -p "$PYPI_TOKEN" dist/* --non-interactive --skip-existing --disable-progress-bar
+      # # Upload pip wheel (Ubuntu)
+      # - name: Upload pip wheel (Ubuntu)
+      #   if: matrix.os == 'ubuntu-22.04'
+      #   env:
+      #     PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+      #   shell: bash -l {0}
+      #   run: |
+      #     twine upload -u __token__ -p "$PYPI_TOKEN" dist/* --non-interactive --skip-existing --disable-progress-bar
 
       # Build conda package (Ubuntu)
       - name: Build conda package (Ubuntu)

.github/workflows/ci.yml

@@ -30,9 +30,9 @@ jobs:
     runs-on: "ubuntu-22.04"
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python 3.7
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.7
       - name: Install Dependencies
@@ -60,7 +60,7 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Conda
         uses: conda-incubator/setup-miniconda@v3.0.3

.github/workflows/website.yml

@@ -8,7 +8,7 @@ on:
       # 'main' triggers updates to 'sleap.ai', all others to 'sleap.ai/develop'
       - main
       - develop
-      - liezl/add-abl-2023-workshop-link
+      - fakebranch
     paths:
       - "docs/**"
       - "README.rst"
@@ -20,21 +20,13 @@ jobs:
     steps:
       # Setup
       - name: Checkout
-        uses: actions/checkout@v2
-      - name: Cache conda
-        uses: actions/cache@v1
-        env:
-          # Increase this value to reset cache if environment_build.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment_build.yml', 'requirements.txt') }}
+        uses: actions/checkout@v4
+
       - name: Setup Miniconda
         # https://github.com/conda-incubator/setup-miniconda
-        uses: conda-incubator/setup-miniconda@v2.0.1
+        uses: conda-incubator/setup-miniconda@v3.0.3
         with:
           python-version: 3.7
-          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
           environment-file: environment_no_cuda.yml
           activate-environment: sleap_ci
       - name: Print environment info
@@ -44,14 +36,18 @@ jobs:
           conda info
 
       - name: Build
+        # """Could not import extension myst_nb (exception: lxml.html.clean module is now 
+        # a separate project lxml_html_clean. Install lxml[html_clean] or 
+        # lxml_html_clean directly.)"""
         shell: bash -l {0}
         run: |
+          pip install lxml[html_clean]
           cd docs
           python make_api_doctree.py
           make html
 
       - name: Deploy (sleap.ai)
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         if: github.ref == 'refs/heads/main'
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
@@ -60,7 +56,7 @@ jobs:
           keep_files: true
 
       - name: Deploy (test)
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         if: github.ref != 'refs/heads/main'
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}

docs/conf.py

@@ -28,15 +28,15 @@
 copyright = f"2019–{date.today().year}, Talmo Lab"
 
 # The short X.Y version
-version = "1.3.3"
+version = "1.4.1a2"
 
 # 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 = "v1.3.3"
+release = "v1.4.1a2"
 
 html_title = f"SLEAP ({release})"
 html_short_title = "SLEAP"
@@ -85,6 +85,7 @@
 pygments_style = "sphinx"
 pygments_dark_style = "monokai"
 
+
 # Autosummary linkcode resolution
 # https://www.sphinx-doc.org/en/master/usage/extensions/linkcode.html
 def linkcode_resolve(domain, info):

docs/guides/cli.md

@@ -36,8 +36,8 @@ optional arguments:
 
 ```none
 usage: sleap-train [-h] [--video-paths VIDEO_PATHS] [--val_labels VAL_LABELS]
-                   [--test_labels TEST_LABELS] [--tensorboard] [--save_viz]
-                   [--zmq] [--run_name RUN_NAME] [--prefix PREFIX]
+                   [--test_labels TEST_LABELS] [--tensorboard] [--save_viz] 
+                   [--keep_viz] [--zmq] [--run_name RUN_NAME] [--prefix PREFIX]
                    [--suffix SUFFIX]
                    training_job_path [labels_path]
 
@@ -68,6 +68,8 @@ optional arguments:
   --save_viz            Enable saving of prediction visualizations to the run
                         folder if not already specified in the training job
                         config.
+  --keep_viz            Keep prediction visualization images in the run
+                        folder after training if --save_viz is enabled.
   --zmq                 Enable ZMQ logging (for GUI) if not already specified
                         in the training job config.
   --run_name RUN_NAME   Run name to use when saving file, overrides other run

docs/guides/gui.md

@@ -60,7 +60,7 @@ Note that many of the menu command have keyboard shortcuts which can be configur
 
 "**Edge Style**" controls whether edges are drawn as thin lines or as wedges which indicate the {ref}`orientation` of the instance (as well as the direction of the part affinity field which would be used to predict the connection between nodes when using a "bottom-up" approach).
 
-"**Trail Length**" allows you to show a trail of where each instance was located in prior frames (the length of the trail is the number of prior frames). This can be useful when proofreading predictions since it can help you detect swaps in the identities of animals across frames.
+"**Trail Length**" allows you to show a trail of where each instance was located in prior frames (the length of the trail is the number of prior frames). This can be useful when proofreading predictions since it can help you detect swaps in the identities of animals across frames. By default, you can only select trail lengths of up to 250 frames. You can use a custom trail length by modifying the default length in the `preferences.yaml` file. However, using trail lengths longer than about 500 frames can result in significant lag.
 
 "**Fit Instances to View**" allows you to toggle whether the view is auto-zoomed to the instances in each frame. This can be useful when proofreading predictions.