Merge branch 'liezl/add-camera-group' of https://github.com/talmolab/…

…sleap into liezl/acg-add-recording-session

.conda/README.md

@@ -3,7 +3,7 @@ This folder defines the conda package build for Linux and Windows. There are run
 To build, first go to the base repo directory and install the build environment:
 
 ```
-conda env create -f environment_build.yml -n sleap_build && conda activate sleap_build
+mamba env create -f environment_build.yml -n sleap_build && conda activate sleap_build
 ```
 
 And finally, run the build command pointing to this directory:
@@ -15,7 +15,7 @@ conda build .conda --output-folder build -c conda-forge -c nvidia -c https://con
 To install the local package:
 
 ```
-conda create -n sleap_0 -c conda-forge -c nvidia -c ./build -c https://conda.anaconda.org/sleap/ -c anaconda sleap=x.x.x
+mamba create -n sleap_0 -c conda-forge -c nvidia -c ./build -c https://conda.anaconda.org/sleap/ -c anaconda sleap=x.x.x
 ```
 
 replacing x.x.x with the version of SLEAP that you just built.

.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 HACK(LM): (untested) Uninstall all opencv packages and install opencv-contrib-python
 for /f "tokens=1" %%a in ('conda list ^| findstr opencv') do pip uninstall %%a -y

.conda/build.sh

@@ -7,12 +7,20 @@ 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
 
 # HACK(LM): (untested) Uninstall all opencv packages and install opencv-contrib-python
 conda list | grep opencv | awk '{system("pip uninstall " $1 " -y")}'
 pip install "opencv-contrib-python<4.7.0"
 
 # Install sleap itself. This does not install the requirements, but will list which 
 # requirements are missing (see "install_requires") when user attempts to install.
-python setup.py install --single-version-externally-managed --record=record.txt
+python setup.py install --single-version-externally-managed --record=record.txt
+
+# Copy the activate scripts to $PREFIX/etc/conda/activate.d.
+# This will allow them to be run on environment activation.
+for CHANGE in "activate" "deactivate"
+do
+    mkdir -p "${PREFIX}/etc/conda/${CHANGE}.d"
+    cp "${RECIPE_DIR}/${PKG_NAME}_${CHANGE}.sh" "${PREFIX}/etc/conda/${CHANGE}.d/${PKG_NAME}_${CHANGE}.sh"
+done

.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:

.conda/sleap_activate.sh

@@ -0,0 +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

.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

.conda_mac/build.sh

@@ -7,7 +7,7 @@ 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
 
 # HACK(LM): (untested) Uninstall all opencv packages and install opencv-contrib-python
 conda list | grep opencv | awk '{system("pip uninstall " $1 " -y")}'

.conda_mac/meta.yaml

@@ -16,7 +16,7 @@ about:
   summary: {{ data.get('description') }}
 
 build:
-  number: 5
+  number: 1
 
 source:
   path: ../

.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 v1.3.3, 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)

.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}}

.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"

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>`_.

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

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 = "1.3.3"
 
 # 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 = "v1.3.1"
+release = "v1.3.3"
 
 html_title = f"SLEAP ({release})"
 html_short_title = "SLEAP"