Merge pull request #140 from AllenNeuralDynamics/release-0.9

Release v0.9

.github/workflows/ci.yml

@@ -1,6 +1,7 @@
-name: CI
+name: ci/cd
 
 on:
+  workflow_dispatch:
   pull_request:
     branches:
       - main
@@ -9,100 +10,15 @@ on:
       - main
 
 jobs:
-  linters:
-    runs-on: windows-latest
-    name: Lint ${{ matrix.python-version }}
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ['3.11', '3.12', '3.13']
-    steps:
-      - uses: actions/checkout@v4
 
-      - uses: astral-sh/setup-uv@v3
-        with:
-          enable-cache: true
-
-      - name: Set up Python ${{ matrix.python-version }}
-        run: uv python install ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: uv sync --extra dev
-      - name: Run ruff format
-        run: uv run ruff format . --config .\pyproject.toml
-      - name: Run ruff check
-        run: uv run ruff check . --config .\pyproject.toml
-      - name: Run codespell
-        run : uv run codespell .
-
-  setup-bonsai:
-    runs-on: windows-latest
-    name: Setup Bonsai
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Setup .NET Core SDK
-        uses: actions/[email protected]
-        with:
-          dotnet-version: 8.x
-
-      - name: Restore dotnet tools
-        run: dotnet tool restore
-
-      - name: Setup Bonsai
-        working-directory: bonsai
-        run: .\Setup.ps1
-
-      - name: Upload Bonsai Files
-        uses: actions/upload-artifact@v3
-        with:
-          name: bonsai-environment
-          path: bonsai
-
-
-  tests:
-    runs-on: windows-latest
-    name: Testing ${{ matrix.python-version }}
-    needs: setup-bonsai
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ['3.11', '3.12', '3.13']
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Setup .NET Core SDK
-        uses: actions/[email protected]
-        with:
-          dotnet-version: 8.x
-
-      - name: Restore dotnet tools
-        run: dotnet tool restore
-
-      - name: Download Bonsai artifact
-        uses: actions/download-artifact@v3
-        with:
-          name: bonsai-environment
-          path: bonsai-environment
-
-      - name: Remove and Move Bonsai Files
-        run: |
-          Remove-Item -Recurse -Force bonsai\*
-          move bonsai-environment\* bonsai
-
-      - uses: astral-sh/setup-uv@v3
-        with:
-          enable-cache: true
-
-      - name: Set up Python ${{ matrix.python-version }}
-        run: uv python install ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: uv sync --extra dev
-      - name: Run tests
-        run: uv run -m unittest
-      - name: Regenerate schemas
-        run: uv run regenerate
-      - name: Check for uncommitted changes
-        run: |
-          git config --global core.safecrlf false
-          git diff --exit-code || (echo "Untracked changes found" && exit 1)
+  python-linting:
+    uses: AllenNeuralDynamics/Aind.Behavior.GitHubActions/.github/workflows/python-linting.yml@main
+    with:
+        runs-on: ubuntu-latest
+
+  aind-behavior-framework-testing:
+    uses: AllenNeuralDynamics/Aind.Behavior.GitHubActions/.github/workflows/test-aind-behavior-framework.yml@main
+    with:
+        python-version-path: .python-version
+        run-coverage: false
+        run-schema: true

.github/workflows/tag_and_publish.yml

@@ -4,64 +4,7 @@ on:
     workflow_dispatch: {}
 
 jobs:
-  tag:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - name: Pull latest changes
-      run: git pull origin ${{ env.DEFAULT_BRANCH }}
-    - uses: astral-sh/setup-uv@v3
-      with:
-        enable-cache: true
-    - name: Set up Python
-      run: uv python install
-
-    - name: Extract version from __init__.py and package name from pyproject.toml
-      id: get_version_and_name
-      run: |
-        package_name=$(uv run python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['name'])")
-        package_name=${package_name//-/_}
-        version=$(uv run python -c "import re; 
-        with open(f'./src/${package_name}/__init__.py', 'r') as f: 
-          content = f.read(); 
-          match = re.search(r'__version__\s*=\s*[\'\"]([^\'\"]+)[\'\"]', content); 
-          print(match.group(1)) if match else exit(1)")
-        echo "PACKAGE_NAME=$package_name" >> $GITHUB_ENV
-        echo "PACKAGE_VERSION=$version" >> $GITHUB_ENV
-      shell: bash
-
-    - name: Create Git tag
-      run: |
-        git config --global user.name "github-actions[bot]"
-        git config --global user.email "github-actions[bot]@users.noreply.github.com"
-        git tag -a v${{ env.PACKAGE_VERSION }} -m "v${{ env.PACKAGE_VERSION }}"
-        git push origin v${{ env.PACKAGE_VERSION }}
-
-    - name: Create GitHub Release
-      uses: softprops/action-gh-release@v2
-      with:
-        token: ${{ secrets.SERVICE_TOKEN }}
-        tag_name: v${{ env.PACKAGE_VERSION }}
-        name: Release v${{ env.PACKAGE_VERSION }}
-        generate_release_notes: true
-
-  publish:
-    needs: tag
-    if: ${{ always() && contains(join(needs.*.result, ','), 'success') }}
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Pull latest changes
-        run: git pull origin ${{ env.DEFAULT_BRANCH }}
-      - uses: astral-sh/setup-uv@v3
-        with:
-          enable-cache: true
-
-      - name: Set up Python
-        run: uv python install
-
-      - name: Build
-        run: uv build
-
-      - name: Publish
-        run: uv publish --token ${{ secrets.AIND_PYPI_TOKEN }}
+  tag-and-publish:
+    uses : AllenNeuralDynamics/Aind.Behavior.GitHubActions/.github/workflows/python-package-tag-and-publish.yml@main
+    with:
+        publish: true

.gitignore

@@ -12,7 +12,6 @@ Bonsai.exe.WebView2
 *.exe.settings
 *.bonsai.layout
 local
-.venv
 *.snl
 
 # Byte-compiled / optimized / DLL files
@@ -82,3 +81,6 @@ ipython_config.py
 #   For a library or package, you might want to ignore these files since the code is
 #   intended to run in multiple environments; otherwise, check them in:
 # .python-version
+
+# venv
+.venv

docs/api.base.rst

@@ -1,14 +1,6 @@
 base
 -------------
 
-.. toctree::
-   :maxdepth: 2
-
-   api.base/session
-   api.base/rig
-   api.base/task_logic
-
-
 .. automodule:: aind_behavior_services.base
    :members:
    :undoc-members:

docs/api.calibration.rst

@@ -4,22 +4,11 @@ calibration
 Calibration Module
 ####################
 
-The calibration module of this library is used to generate the metadata necessary configure and run calibration workflows for different assets/devices.
+The calibration module of this library keep a collection of models used to keep track of calibration metadata.
 
-The metadata follows the general logic of the library by implementing the three core classes:
-   - :py:class:`~aind_behavior_services.session.AindBehaviorSessionModel`
-   - :py:class:`~aind_behavior_services.rig.AindBehaviorRigModel`
-   - :py:class:`~aind_behavior_services.task_logic.AindBehaviorTaskLogicModel`
-
-A fourth class :py:class:`~aind_behavior_services.calibration.Calibration`,
-specific to the Calibration module, is also implemented to keep track of the calibration metrics.
+Every submodule has a single :py:class:`~aind_behavior_services.calibration.Calibration` class that is used to store the calibration metadata.
 This class was written to be aligned to the Calibration class in `aind-data-schemas
-<https://github.com/AllenNeuralDynamics/aind-data-schema/blob/2fd0e403bf46f0f1a47e5922c4228517e68376a3/src/aind_data_schema/components/devices.py#L274>`_.
-An application example will be provided below.
-
-While we use the base :py:class:`~aind_behavior_services.session.AindBehaviorSessionModel` class to keep track of the session metadata,
-both :py:class:`~aind_behavior_services.rig.AindBehaviorRigModel` and :py:class:`~aind_behavior_services.task_logic.AindBehaviorTaskLogicModel` are
-expected to be sub-classed to specify the necessary dependencies of the calibration workflow.
+<https://github.com/AllenNeuralDynamics/aind-data-schema/blob/2fd0e403bf46f0f1a47e5922c4228517e68376a3/src/aind_data_schema/components/devices.py#L274>`_ as to provide an easy way to map calibration data.
 
 Sub-classing :py:class:`~aind_behavior_services.calibration.Calibration`
 ##########################################################################
@@ -59,58 +48,6 @@ An example of a sub-class of `Calibration` is provided below:
       input: DeviceCalibrationInput = Field(..., title="Input of the calibration")
       output: DeviceCalibrationOutput = Field(..., title="Output of the calibration")
 
-Sub-classing :py:class:`~aind_behavior_services.rig.AindBehaviorRigModel`
-##########################################################################
-
-We adopt the following pattern to sub-class the :py:class:`~aind_behavior_services.rig.AindBehaviorRigModel` class:
-
-.. code-block:: python
-
-   from aind_behavior_services.rig import AindBehaviorRigModel, Device
-
-   RIG_VERSION = "1.0.0" # Use SemVer
-
-   class FooDevice(Device):
-      calibration: DeviceCalibration = Field(..., title="Calibration of the device foo")
-
-
-   class CalibrationRig(AindBehaviorRigModel):
-      version: Literal[RIG_VERSION] = RIG_VERSION
-      device_foo: FooDevice = Field(..., title="Device Foo")
-      device_bar: Device = Field(..., title="Device Bar")
-
-
-For an example see :py:class:`aind_behavior_services.calibration.olfactometer.CalibrationRig`.
-
-
-
-Sub-classing :py:class:`~aind_behavior_services.task_logic.AindBehaviorTaskLogicModel`
-########################################################################################
-
-The same way a :py:class:`~aind_behavior_services.task_logic.AindBehaviorTaskLogicModel` is used to define
-the settings to run a behavior task, it is also used to define the settings to run a calibration workflow.
-It will thus follow an identical sub-classing pattern:
-
-
-.. code-block:: python
-
-   from aind_behavior_services.task_logic import AindBehaviorTaskLogicModel, TaskParameters
-
-   TASK_LOGIC_VERSION = "0.1.0"
-
-   class CalibrationParameters(TaskParameters):
-      n_iterations: int = Field(default=10, description="Number of iterations to run the calibration")
-      channels_to_calibrate: List[Literal[1,2,3]] = Field(default=[1], description="List of channels to calibrate")
-
-   class CalibrationLogic(AindBehaviorTaskLogicModel):
-      name: Literal["CalibrationLogic"] = "CalibrationLogic
-      version: Literal[TASK_LOGIC_VERSION] = TASK_LOGIC_VERSION
-      task_parameters: CalibrationParameters = Field(default=CalibrationParameters(), title="Task parameters", validate_default=True)
-
-
-For an example see :py:class:`aind_behavior_services.calibration.olfactometer.CalibrationLogic`.
-
-
 
 .. toctree::
    :maxdepth: 4

docs/api.calibration/water_valve.rst

@@ -10,4 +10,4 @@ Example
 ########
 
 .. literalinclude:: ../../examples/water_valve.py
-      :language: python
+      :language: python

docs/api.rig.rst

@@ -0,0 +1,7 @@
+rig
+-------------------------
+
+.. automodule:: aind_behavior_services.rig
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/api.rst

@@ -5,6 +5,9 @@ API
    :maxdepth: 2
 
    api.base
-   api.calibration
+   api.rig
+   api.task_logic
+   api.session
    api.data_types
+   api.calibration
    api.utils

docs/api.session.rst

@@ -0,0 +1,10 @@
+session
+--------------------------
+
+.. image:: _static/AindBehaviorSessionModel.svg
+   :target: _static/AindBehaviorSessionModel.svg
+
+.. automodule:: aind_behavior_services.session
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/api.task_logic.rst

@@ -0,0 +1,7 @@
+task_logic
+--------------------------------
+
+.. automodule:: aind_behavior_services.task_logic
+   :members:
+   :undoc-members:
+   :show-inheritance: