SLEAP 1.3.2

commit 734283a Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Sun Sep 10 08:19:36 2023 -0700 Bump to 1.3.2 (#1482) * Bump to 1.3.2 * Run manual build w/o pip upload * Use `importlib.resources` if available * Rebuild mac conda package * Lint * Build/upload pip wheel * Reset build_manual and up build number commit e424501 Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Sat Sep 9 10:32:29 2023 -0700 Add pip extras (#1481) * Rename pip to pypi, add tensorflow * Move out jupyter requirements from dev * Add extras for conda/pip jupyter and dev * Rename `pip` extra to `pypi` * Add build_ci workflow * Install pip package using extras * Rerun notebooks with new pip wheel * Internal import after adding relative path to sys * Build develop docs on this branch * Add comments to setup.py extras * Update installation docs * Add wget bypass for apple silicon mambaforge * Create func to combine req * Italicize jupyter instead of bold --------- Co-authored-by: modularizer <modularizer@gmail.com> Co-authored-by: roomrys <> commit 93ef288 Author: Shrivaths Shyam <52810689+shrivaths16@users.noreply.github.com> Date: Sat Sep 9 03:12:58 2023 +0530 Limit max tracks via track-local queues (#1447) * Initial commit * format files * [wip] adding local deque for tracks * format files * [wip] adding local deque for tracks * [wip] Add max tracking for simpletracker * [wip] Add max tracking for simple tracker * [wip] add missing argument * [wip] Add and modify test functions * [wip] Add and modify test functions * Bug fix and refactoring code * [wip] Add max tracking for flow tracker. * [wip] Including suggested changes * [wip] refactor code * Add test function to check max tracks * Added suggestions and feedback * Prevent the creation of more than max tracks when we have unmatched detections * Add tests * Use maximum tracking by default when loading model via high level API * Lint * Fix integration test * Refactor max tracker tests * Add integration test for CLI * typo * Add max tracks to the tracking GUI * Update CLI docs and add examples --------- Co-authored-by: Talmo Pereira <talmo@princeton.edu> Co-authored-by: Talmo Pereira <talmo@salk.edu> commit 64655d6 Author: DivyaSesh <64513125+gitttt-1234@users.noreply.github.com> Date: Wed Sep 6 09:50:35 2023 -0700 Fix Auto-select GPU (#1474) * Fix Auto-select GPU * Format file * Add variable in init * Format files * Add small test to ensure environment variable is set * Make linter happy --------- Co-authored-by: roomrys <lmaree@ucsd.edu> commit 0ef52cd Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Thu Aug 17 11:03:51 2023 -0700 Migrate to `importlib_resources` backport (#1458) * Switch to backport * Remove `pkg_resources` * Clean-up function (non-logical) * Make linter happy * Fix-up path for last few stragglers * Use `Path.as_posix` method instead of `str` commit e0eebb2 Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Tue Aug 15 13:10:06 2023 -0700 Handle error message edge case when finding yaml paths (#1456) commit 6858563 Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Fri Aug 11 11:33:14 2023 -0700 Add message if drag drop fails (#1451) * Fix drag and drop * Feedback when user drops invalid file type * Change wording on message commit 88fdb68 Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Fri Aug 11 11:27:57 2023 -0700 Pin `tensorflow-hub<0.14.0` (#1446) * Pin pynwb 2.3.3 * Remove pynwb pin, add comments commit 4730788 Author: Talmo Pereira <talmo@salk.edu> Date: Fri Aug 11 10:52:09 2023 -0700 Fix drag and drop (#1449) commit 47f8096 Author: DivyaSesh <64513125+gitttt-1234@users.noreply.github.com> Date: Thu Aug 10 16:29:39 2023 -0700 Add Option to Export CSV (#1438) * Add Option to Export CSV * Add Test Functions * Fomat Files * Change FormatID commit 5ba6bc1 Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Thu Aug 10 10:17:45 2023 -0700 Add model folder to the unzip path (#1445) * Add model folder to the unzip path * Handle cases where zipped model either has no extra directory * Add test * Fix-up test and implementation * Manually lint commit d61a184 Author: KevinZ0217 <96039456+KevinZ0217@users.noreply.github.com> Date: Wed Aug 9 14:47:21 2023 -0700 Change the hotkey for exporting h5 analysis (#1444) * Change the hotkey for export h5 files to Ctrl+Alt+E commit ad7529e Author: KevinZ0217 <96039456+KevinZ0217@users.noreply.github.com> Date: Wed Aug 9 14:46:09 2023 -0700 Add a button for copying model config to clipboard (#1433) * Add shortcur for export_analysis_current * Fix the linting issue * Add the button without copy method' * Add button for copying model config to clipboard * Fix linting by reformatting * Use Qtpy for clipboard rather than pyperclip * Pretty print model config json to clipboard and fix missing command * Fix the overwriting problem for dict object * Delete unnecessary print statement * Add a few comments & Remove unnecessary variables & remove unused function commit 2611e7d Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Wed Aug 9 11:52:57 2023 -0700 Improve error message for detecting video backend (#1441) * Improve error message for detecting video backend * Lint * Add small test commit 1151a95 Author: Shrivaths Shyam <52810689+shrivaths16@users.noreply.github.com> Date: Wed Aug 2 17:08:38 2023 -0700 Fix error thrown when last video is deleted (#1421) * Handle None Video case during callbacks * format files * remove unused comments * Disable remove video button when there are no videos * Display default background when all videos are removed * Format files * Remove overlay error after removing last video * Redraw overlays on plot change (#1435) * Redraw overlays after changedPlot, changedPlot on reset * Update instance state on player reset --------- Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> commit 6002332 Author: Shrivaths Shyam <52810689+shrivaths16@users.noreply.github.com> Date: Mon Jul 31 13:28:53 2023 -0700 Update status message on status bar (#1411) * Update status message on status bar * Update statusbar to show correct video count * remove additional conditional check commit 3a01ef3 Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Mon Jul 31 12:09:50 2023 -0700 Correct GUI state emulation (#1422) commit e94b516 Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Thu Jul 27 12:11:41 2023 -0700 Add video path and frame indices to metrics (#1396) * Add `Instance`s and `PredictedInstance`s to metrics * Add tests * Add frame/video info to metrics, wip: test writing * Fix metrics save test commit b2ad203 Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Thu Jul 27 12:08:19 2023 -0700 Fix labels export for json (#1410) * wip: fix labels export for json * Add test for json.zip labels pkg * Add test for .slp labels pkg * Make linter happy commit 90c012d Author: KevinZ0217 <96039456+KevinZ0217@users.noreply.github.com> Date: Wed Jul 26 13:30:22 2023 -0700 Add shortcut to export analysis for current video (#1414) * Add shortcur for export_analysis_current * Fix the linting issue commit f9d0a22 Author: Shrivaths Shyam <52810689+shrivaths16@users.noreply.github.com> Date: Tue Jul 25 09:37:52 2023 -0700 Modify compute OKS function (#1399) * Update compute OKS function * Update compute OKS function * Modify compute OKS function * Added suggested changes * Added further suggestions and comments * Added the permalink to the cocoeval function * Added permalink to cocoeval function --------- Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> Co-authored-by: Talmo Pereira <talmo@salk.edu> commit 904338c Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Tue Jul 25 06:34:25 2023 -0700 Add `Video` to cache when adding `Track` (#1407) * Add `Video` to cache when adding `Track` * Use methods instead of rewriting code * Simplify code commit 845214c Author: DivyaSesh <64513125+gitttt-1234@users.noreply.github.com> Date: Mon Jul 24 21:20:02 2023 -0700 Fix Remove Videos in Batch (#1406) * Fix Remove Videos in Batch * Remove Unused Testing Code commit 0afbb9b Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Mon Jul 24 17:37:42 2023 -0700 Add `Track` when add `Instance` (#1408) commit d173303 Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Mon Jul 24 08:25:09 2023 -0700 Fix skeleton templates (#1404) commit 0e7a372 Author: DivyaSesh <64513125+gitttt-1234@users.noreply.github.com> Date: Fri Jul 21 09:49:51 2023 -0700 Fix panning bounding box (#1398) commit fb61b6c Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Wed Jul 19 15:30:43 2023 -0700 Fix `Filedialog` to work across (mac)OS (#1393) * Always use dir instead of directory * Wrap `FileDialog` methods for OS-specific calls * Clean-up os-specific wrapper to check for linux only * Lint * Fix test for non native `FileDialog` commit 19cd2b5 Author: DivyaSesh <64513125+gitttt-1234@users.noreply.github.com> Date: Mon Jul 17 17:55:29 2023 -0700 Add option to remove videos in batch (#1382) * add option to remove videos in batch * Add option to remove videos in batch * Add option to remove videos in batches * Modify Lint format * Add Test cases * Modify Test Cases for Removing Videos in Batch * Add Comment to test_docks * Remove commented line * Format files commit 3b5c4ff Author: Shrivaths Shyam <52810689+shrivaths16@users.noreply.github.com> Date: Fri Jul 14 17:06:58 2023 -0700 Minor fix in computation of OKS (#1383) * fix compute oks * Update the oks fix commit 1c2be11 Author: Liezl Maree <38435167+roomrys@users.noreply.github.com> Date: Thu Jul 6 14:44:01 2023 -0700 Pin micromamba version (#1376) * Pin micromamba version * Add build number to pin
talmolab · Sep 10, 2023 · bbc43c1 · bbc43c1
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diff --git a/.conda/bld.bat b/.conda/bld.bat
@@ -7,7 +7,7 @@ set PIP_IGNORE_INSTALLED=False
 
 @REM Install the pip dependencies. Note: Using urls to wheels might be better: 
 @REM https://docs.conda.io/projects/conda-build/en/stable/user-guide/wheel-files.html)
-pip install -r .\requirements.txt
+pip install --no-cache-dir -r .\requirements.txt
 
 @REM Install sleap itself. This does not install the requirements, but will list which 
 @REM requirements are missing (see "install_requires") when user attempts to install.

diff --git a/.conda/build.sh b/.conda/build.sh
@@ -7,7 +7,7 @@ export PIP_IGNORE_INSTALLED=False
 
 # Install the pip dependencies. Note: Using urls to wheels might be better: 
 # https://docs.conda.io/projects/conda-build/en/stable/user-guide/wheel-files.html)
-pip install -r ./requirements.txt
+pip install --no-cache-dir -r ./requirements.txt
 
 
 # Install sleap itself. This does not install the requirements, but will list which 

diff --git a/.conda/meta.yaml b/.conda/meta.yaml
@@ -16,7 +16,7 @@ source:
   path: ../
 
 build:
-  number: 9
+  number: 1
 
 requirements:
   host:
@@ -83,7 +83,7 @@ requirements:
     - conda-forge::scikit-video
     - conda-forge::seaborn
     - sleap::tensorflow >=2.6.3,<2.11  # No windows GPU support for >2.10, sleap channel has 2.6.3
-    - conda-forge::tensorflow-hub
+    - conda-forge::tensorflow-hub <0.14.0  # Causes pynwb conflicts on linux GH-1446
 
 test:
   imports:

diff --git a/.conda_mac/build.sh b/.conda_mac/build.sh
@@ -7,6 +7,6 @@ export PIP_NO_INDEX=False
 export PIP_NO_DEPENDENCIES=False
 export PIP_IGNORE_INSTALLED=False
 
-pip install -r requirements.txt
+pip install --no-cache-dir -r requirements.txt
 
 python setup.py install --single-version-externally-managed --record=record.txt
diff --git a/.conda_mac/meta.yaml b/.conda_mac/meta.yaml
@@ -16,7 +16,7 @@ about:
   summary: {{ data.get('description') }}
 
 build:
-  number: 5
+  number: 1
 
 source:
   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 v1.3.1, python 3.8] --->
+<!-- e.g. [SLEAP v1.3.2, 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/.github/workflows/build_ci.yml b/.github/workflows/build_ci.yml
@@ -0,0 +1,155 @@
+# Run tests using built conda packages and wheels.
+name: Build CI (no upload)
+
+# Run when changes to pip wheel
+on:
+  push:
+    paths:
+      - 'setup.py'
+      - 'requirements.txt'
+      - 'dev_requirements.txt'
+      - 'jupyter_requirements.txt'
+      - 'pypi_requirements.txt'
+      - 'environment_build.yml'
+      - '.github/workflows/build_ci.yml'
+
+jobs:
+  build:
+    name: Build wheel (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-22.04"]
+        # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstrategymatrixinclude
+        include:
+          # Use this condarc as default
+          - condarc: .conda/condarc.yaml
+          - wheel_name: sleap-wheel-linux
+    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: Setup Miniconda for Build
+        # https://github.com/conda-incubator/setup-miniconda
+        uses: conda-incubator/setup-miniconda@v2.0.1
+        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
+          condarc-file: ${{ matrix.condarc }}
+          activate-environment: sleap_ci
+
+      - name: Print build environment info
+        shell: bash -l {0}
+        run: |
+          which python
+          conda list
+          pip freeze
+
+      # Build pip wheel
+      - name: Build pip wheel
+        shell: bash -l {0}
+        run: |
+          python setup.py bdist_wheel
+      
+      # Upload artifact "tests" can use it
+      - name: Upload wheel artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ matrix.wheel_name }}
+          path: dist/*.whl
+          retention-days: 1
+
+  tests:
+    name: Run tests using wheel (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    needs: build  # Ensure the build job has completed before starting this job.
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-22.04", "windows-2022", "macos-latest"]
+        # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstrategymatrixinclude
+        include:
+          # Default values
+          - wheel_name: sleap-wheel-linux
+          - venv_cmd: source venv/bin/activate
+          - pip_cmd: |
+              wheel_path=$(find dist -name "*.whl")
+              echo $wheel_path
+              pip install '$wheel_path'[dev]
+          - test_args: pytest --durations=-1 tests/
+          - condarc: .conda/condarc.yaml
+          # Use special condarc if macos
+          - os: "macos-latest"
+            condarc: .conda_mac/condarc.yaml
+          # Ubuntu specific values
+          - os: ubuntu-22.04
+            # 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 Xvfb :1 -screen 0 1024x768x24 </dev/null &
+              export DISPLAY=":1"
+              pytest tests -k 'not exclude_from_linux_pip_test'
+          # Windows specific values
+          - os: windows-2022
+            venv_cmd: .\venv\Scripts\activate
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.7
+
+      # Download wheel
+      - name: Download wheel artifact
+        uses: actions/download-artifact@v3
+        id: download
+        with:
+          name: ${{ matrix.wheel_name }}
+          path: dist
+
+      - name: Create virtual environment
+        run: python -m venv venv
+
+      - name: Activate virtual environment
+        run: ${{ matrix.venv_cmd }}
+
+      - name: Install the built wheel (not Mac)
+        if: runner.os != 'macOS'
+        shell: bash -l {0}
+        run: |
+          wheel_path=$(find dist -name "*.whl")
+          echo wheel_path
+          pip install "$wheel_path"[dev]
+
+      - name: Install the built wheel (Mac)
+        if: runner.os == 'macOS'
+        shell: bash -e {0}
+        run: |
+          wheel_path=$(find dist -name "*.whl")
+          echo wheel_path
+          pip install "$wheel_path"[dev]
+
+      - name: Print test environment info
+        shell: bash -l {0}
+        run: |
+          which python
+          pip freeze
+        
+      # Install and test the wheel
+      - name: Test the built wheel
+        run: |
+          ${{ matrix.test_args}}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -84,6 +84,7 @@ jobs:
         # https://github.com/mamba-org/setup-micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
+          micromamba-version: '1.4.6-0'
           environment-file: ${{ matrix.env_file }}
           environment-name: sleap_ci
           init-shell: >-

diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml
@@ -8,7 +8,7 @@ on:
       # 'main' triggers updates to 'sleap.ai', all others to 'sleap.ai/develop'
       - main
       - develop
-      - liezl/update_installation_docs
+      - liezl/add-pip-extras
     paths:
       - "docs/**"
       - "README.rst"

diff --git a/README.rst b/README.rst
@@ -75,7 +75,7 @@ Quick install
 
 .. code-block:: bash
 
-    pip install sleap
+    pip install sleap[pypi]
 
 
 See the docs for `full installation instructions <https://sleap.ai/installation.html>`_.

diff --git a/dev_requirements.txt b/dev_requirements.txt
@@ -18,7 +18,5 @@ black==21.6b0
 pre-commit
 twine==3.3.0
 PyGithub
-jupyterlab
 jedi==0.17.2
-ipykernel
 click==8.0.4
diff --git a/docs/conf.py b/docs/conf.py
@@ -15,10 +15,10 @@
 import os
 import sys
 import shutil
-import docs.utils
 from datetime import date
 
 sys.path.insert(0, os.path.abspath(".."))
+import docs.utils
 
 
 # -- Project information -----------------------------------------------------
@@ -28,15 +28,15 @@
 copyright = f"2019–{date.today().year}, Talmo Lab"
 
 # The short X.Y version
-version = "1.3.1"
+version = "1.3.2"
 
 # 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 = "v1.3.1"
+release = "v1.3.2"
 
 html_title = f"SLEAP ({release})"
 html_short_title = "SLEAP"