aind-behavior-services 0.8.0__tar.gz

aind_behavior_services-0.8.0/.config/dotnet-tools.json

@@ -0,0 +1,12 @@
+{
+  "version": 1,
+  "isRoot": true,
+  "tools": {
+    "bonsai.sgen": {
+      "version": "0.3.0",
+      "commands": [
+        "bonsai.sgen"
+      ]
+    }
+  }
+}

aind_behavior_services-0.8.0/.editorconfig

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+# To learn more about .editorconfig see https://aka.ms/editorconfigdocs
+###############################
+# Core EditorConfig Options   #
+###############################
+# All files
+[*]
+indent_style = space
+
+# XML project files
+[*.{csproj,vcxproj,vcxproj.filters,proj,projitems,shproj,bonsai}]
+indent_size = 2
+
+# XML config files
+[*.{props,targets,ruleset,config,nuspec,resx,vsixmanifest,vsct}]
+indent_size = 2
+
+# Code files
+[*.{cs,csx}]
+indent_size = 4
+insert_final_newline = true
+charset = utf-8-bom
+###############################
+# .NET Coding Conventions     #
+###############################
+[*.{cs}]
+# Organize usings
+dotnet_sort_system_directives_first = true

aind_behavior_services-0.8.0/.flake8

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+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    .venv,
+    build
+max-complexity = 10
+max-line-length = 120

aind_behavior_services-0.8.0/.gitattributes

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+* text=auto
+*.cmd text eol=crlf
+*.bat text eol=crlf
+*.bonsai text

aind_behavior_services-0.8.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  linters:
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          python -m pip install -e .[linters] --no-cache-dir
+      - name: Run ruff format
+        run: ruff format . --config .\pyproject.toml
+      - name: Run ruff check
+        run: ruff check . --config .\pyproject.toml
+      - name: Run codespell
+        run : codespell .
+
+  tests:
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup .NET Core SDK
+        uses: actions/setup-dotnet@v4.0.0
+        with:
+          dotnet-version: 7.x
+      - name: Restore dotnet tools
+        run: dotnet tool restore
+      - name: Setup Bonsai
+        working-directory: bonsai
+        run: .\Setup.ps1
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install -e . --no-cache-dir
+      - name: Run tests
+        run: python -m unittest
+      - name: Regenerate schemas
+        run: python .\scripts\regenerate.py
+      - name: Check for uncommitted changes
+        run: |
+          git config --global core.safecrlf false
+          git diff --exit-code || (echo "Untracked changes found" && exit 1)

aind_behavior_services-0.8.0/.github/workflows/docs.yml

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+name: Deploy Sphinx documentation to Pages
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [main]
+
+jobs:
+  pages:
+    runs-on: ubuntu-20.04
+    steps:
+    - name: Setup Graphviz
+      uses: ts-graphviz/setup-graphviz@v2.0.2
+    - id: deployment
+      uses: sphinx-notes/pages@v3
+      with:
+        publish: false
+        python_version: 3.11
+        checkout: true
+    - uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ${{ steps.deployment.outputs.artifact }}
+        force_orphan: true

aind_behavior_services-0.8.0/.github/workflows/tag_and_publish.yml

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+name: Tag and Publish
+
+on:
+    workflow_dispatch: {}
+
+jobs:
+  tag:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.11
+    - uses: actions/checkout@v3
+    - name: Extract version from __init__.py and package name from pyproject.toml
+      id: get_version_and_name
+      run: |
+        package_name=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['name'])")
+        package_name=${package_name//-/_}
+        version=$(python -c "import re; 
+        with open(f'./src/${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()  # Enable publishing
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Pull latest changes
+        run: git pull origin ${{ env.DEFAULT_BRANCH }}
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+      - name: Install dependencies
+        run: |
+          pip install --upgrade setuptools wheel twine build
+          python -m build
+          twine check dist/*
+      - name: Publish on PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.AIND_PYPI_TOKEN }}

aind_behavior_services-0.8.0/.gitignore

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+# Bonsai scripting files
+.vs
+.vscode
+bin
+obj
+Packages
+Bonsai.exe.WebView2
+*.bin
+*.avi
+*.dll
+*.exe
+*.exe.settings
+*.bonsai.layout
+local
+.venv
+*.snl
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Sphinx documentation
+docs/_build/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   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

aind_behavior_services-0.8.0/LICENSE

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+MIT License
+
+Copyright (c) 2022 Allen Institute for Neural Dynamics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

aind_behavior_services-0.8.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: aind-behavior-services
+Version: 0.8.0
+Summary: A library that defines AIND data schema and validates JSON files for behavior rig models.
+Author-email: Bruno Cruz <bruno.cruz@alleninstitute.org>
+License: MIT
+Project-URL: Documentation, https://allenneuraldynamics.github.io/Aind.Behavior.Services/
+Project-URL: Repository, https://github.com/AllenNeuralDynamics/Aind.Behavior.Services/
+Project-URL: Issues, https://github.com/AllenNeuralDynamics/Aind.Behavior.Services/issues
+Project-URL: Changelog, https://github.com/AllenNeuralDynamics/Aind.Behavior.Services/releases
+Classifier: Programming Language :: Python :: 3.11
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: Microsoft :: Windows
+Requires-Python: >=3.11
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: pydantic<3.0,>=2.7
+Requires-Dist: harp-python>=0.2
+Requires-Dist: aind-behavior-curriculum==0.0.27
+Requires-Dist: gitpython<4.0,>=3.1
+Requires-Dist: scikit-learn
+Requires-Dist: semver
+Provides-Extra: linters
+Requires-Dist: ruff; extra == "linters"
+Requires-Dist: codespell; extra == "linters"
+Provides-Extra: docs
+Requires-Dist: Sphinx<7.3; extra == "docs"
+Requires-Dist: furo; extra == "docs"
+Requires-Dist: sphinx-jinja; extra == "docs"
+Requires-Dist: autodoc_pydantic[erdantic]; extra == "docs"
+Requires-Dist: sphinx-jsonschema; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Requires-Dist: sphinx_mdinclude; extra == "docs"
+
+# aind-behavior-services
+
+A repository containing code for data acquisition and processing for AIND behavior rigs.
+
+---
+
+## Deployment
+
+Install the [prerequisites](#prerequisites) mentioned below.
+From the root of the repository, run `./scripts/deploy.ps1` to bootstrap both python and bonsai environments.
+
+---
+
+## Prerequisites
+
+These should only need to be installed once on a fresh new system, and are not required if simply refreshing the install or deploying to a new folder.
+
+- Windows 10 or 11
+- Run `./scripts/install_dependencies.ps1` to automatically install dependencies
+- The following dependencies should be manually installed:
+  - [Spinnaker SDK 1.29.0.5](https://www.flir.co.uk/support/products/spinnaker-sdk/#Downloads) (device drivers for FLIR cameras)
+
+    - On FLIR website: `Download > archive > 1.29.0.5 > SpinnakerSDK_FULL_1.29.0.5_x64.exe`
+
+---
+
+## Generating valid JSON input files
+
+One of the core principles of this repository is the strict adherence to [json-schemas](https://json-schema.org/). We use [Pydantic](https://pydantic.dev/) as a way to write and compile our schemas, but also to generate valid JSON input files. These files can be used by Bonsai (powered by [Bonsai.SGen](https://github.com/bonsai-rx/sgen) code generation tool) or to simply record metadata. Examples of how to interact with the library can be found in the `./examples` folder.
+
+---
+
+## Regenerating schemas
+
+Once a Pydantic model is updated, updates to all downstream dependencies must be made to ensure that the ground-truth data schemas (and all dependent interoperability tools) are also updated. This can be achieved by running the `./scripts/renegerate.ps1` script from the root of the repository.
+This script will regenerate all `json-schemas` along with `C#` code (`./scr/Extensions`) used by the Bonsai environment.
+
+---
+
+## Contributors
+
+Contributions to this repository are welcome! However, please ensure that your code adheres to the recommended DevOps practices below:
+
+### Linting
+
+We use [ruff](https://docs.astral.sh/ruff/) as our primary linting tool.
+
+### Testing
+
+Attempt to add tests when new features are added.
+To run the currently available tests, run `python -m unittest` from the root of the repository.
+
+### Versioning
+
+Where possible, adhere to [Semantic Versioning](https://semver.org/).
+
+---
+
+## Project dependency tree
+
+![Dependency tree](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services/raw/main/assets/dependency_tree.drawio.svg)

aind_behavior_services-0.8.0/README.md

@@ -0,0 +1,61 @@
+# aind-behavior-services
+
+A repository containing code for data acquisition and processing for AIND behavior rigs.
+
+---
+
+## Deployment
+
+Install the [prerequisites](#prerequisites) mentioned below.
+From the root of the repository, run `./scripts/deploy.ps1` to bootstrap both python and bonsai environments.
+
+---
+
+## Prerequisites
+
+These should only need to be installed once on a fresh new system, and are not required if simply refreshing the install or deploying to a new folder.
+
+- Windows 10 or 11
+- Run `./scripts/install_dependencies.ps1` to automatically install dependencies
+- The following dependencies should be manually installed:
+  - [Spinnaker SDK 1.29.0.5](https://www.flir.co.uk/support/products/spinnaker-sdk/#Downloads) (device drivers for FLIR cameras)
+
+    - On FLIR website: `Download > archive > 1.29.0.5 > SpinnakerSDK_FULL_1.29.0.5_x64.exe`
+
+---
+
+## Generating valid JSON input files
+
+One of the core principles of this repository is the strict adherence to [json-schemas](https://json-schema.org/). We use [Pydantic](https://pydantic.dev/) as a way to write and compile our schemas, but also to generate valid JSON input files. These files can be used by Bonsai (powered by [Bonsai.SGen](https://github.com/bonsai-rx/sgen) code generation tool) or to simply record metadata. Examples of how to interact with the library can be found in the `./examples` folder.
+
+---
+
+## Regenerating schemas
+
+Once a Pydantic model is updated, updates to all downstream dependencies must be made to ensure that the ground-truth data schemas (and all dependent interoperability tools) are also updated. This can be achieved by running the `./scripts/renegerate.ps1` script from the root of the repository.
+This script will regenerate all `json-schemas` along with `C#` code (`./scr/Extensions`) used by the Bonsai environment.
+
+---
+
+## Contributors
+
+Contributions to this repository are welcome! However, please ensure that your code adheres to the recommended DevOps practices below:
+
+### Linting
+
+We use [ruff](https://docs.astral.sh/ruff/) as our primary linting tool.
+
+### Testing
+
+Attempt to add tests when new features are added.
+To run the currently available tests, run `python -m unittest` from the root of the repository.
+
+### Versioning
+
+Where possible, adhere to [Semantic Versioning](https://semver.org/).
+
+---
+
+## Project dependency tree
+
+![Dependency tree](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services/raw/main/assets/dependency_tree.drawio.svg)