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‎.github/workflows/test_and_deploy.yml‎

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name: tests
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on:
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push:
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branches:
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- '*'
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tags:
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- '*'
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pull_request:
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jobs:
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linting:
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runs-on: ubuntu-latest
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steps:
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- uses: neuroinformatics-unit/actions/lint@v2
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manifest:
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name: Check Manifest
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runs-on: ubuntu-latest
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steps:
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- uses: neuroinformatics-unit/actions/check_manifest@v2
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test:
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needs: [linting, manifest]
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name: ${{ matrix.os }} py${{ matrix.python-version }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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# Run all supported Python versions on linux
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python-version: ["3.9", "3.10", "3.11"]
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os: [ubuntu-latest]
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# Include one windows and macos run
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include:
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- os: macos-latest
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python-version: "3.10"
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- os: windows-latest
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python-version: "3.10"
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steps:
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# Run tests
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- uses: neuroinformatics-unit/actions/test@v2
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with:
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python-version: ${{ matrix.python-version }}
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build_sdist_wheels:
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name: Build source distribution
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needs: [test]
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if: github.event_name == 'push' && github.ref_type == 'tag'
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runs-on: ubuntu-latest
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steps:
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- uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
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upload_all:
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name: Publish build distributions
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needs: [build_sdist_wheels]
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runs-on: ubuntu-latest
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steps:
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- uses: neuroinformatics-unit/actions/upload_pypi@v2
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with:
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secret-pypi-key: ${{ secrets.TWINE_API_KEY }}

‎.gitignore‎

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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*.egg-info/
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.installed.cfg
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*.egg
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*,cover
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.hypothesis/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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# Flask instance folder
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instance/
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# Sphinx documentation
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docs/_build/
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# MkDocs documentation
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/site/
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# PyBuilder
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target/
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# Pycharm and VSCode
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.idea/
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venv/
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.vscode/
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# IPython Notebook
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.ipynb_checkpoints
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# pyenv
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.python-version
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# OS
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.DS_Store
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# written by setuptools_scm
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**/_version.py

‎.pre-commit-config.yaml‎

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# Configuring https://pre-commit.ci/
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ci:
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autoupdate_schedule: monthly
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: check-docstring-first
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- id: check-executables-have-shebangs
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- id: check-merge-conflict
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- id: check-toml
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- id: end-of-file-fixer
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- id: mixed-line-ending
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args: [--fix=lf]
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- id: requirements-txt-fixer
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- id: trailing-whitespace
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- repo: https://github.com/charliermarsh/ruff-pre-commit
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rev: v0.0.272
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hooks:
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- id: ruff
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- repo: https://github.com/psf/black
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rev: 23.3.0
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hooks:
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- id: black
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.3.0
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hooks:
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- id: mypy
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additional_dependencies:
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- types-setuptools
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- repo: https://github.com/mgedmin/check-manifest
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rev: "0.49"
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hooks:
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- id: check-manifest
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args: [--no-build-isolation]
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additional_dependencies: [setuptools-scm]

‎LICENSE‎

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Copyright (c) 2024, Adam Tyson
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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* Neither the name of ethology nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎MANIFEST.in‎

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include LICENSE
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include README.md
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exclude .pre-commit-config.yaml
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recursive-exclude * __pycache__
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recursive-exclude * *.py[co]
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recursive-exclude docs *
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recursive-exclude tests *

‎README.md‎

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# ethology

‎ethology/__init__.py‎

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from importlib.metadata import PackageNotFoundError, version
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try:
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__version__ = version("ethology")
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except PackageNotFoundError:
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# package is not installed
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pass

‎pyproject.toml‎

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[project]
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name = "ethology"
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authors = [{name = "Adam Tyson", email= "code@adamltyson.com"}]
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description = "Data processing tools for animal behavioural analysis"
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readme = "README.md"
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requires-python = ">=3.9.0"
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dynamic = ["version"]
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license = {text = "BSD-3-Clause"}
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classifiers = [
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"Development Status :: 2 - Pre-Alpha",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Operating System :: OS Independent",
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"License :: OSI Approved :: BSD License",
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]
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[project.urls]
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"Homepage" = "https://github.com/neuroinformatics-unit/ethology"
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"Bug Tracker" = "https://github.com/neuroinformatics-unit/ethology/issues"
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"Documentation" = "https://github.com/neuroinformatics-unit/ethology"
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"Source Code" = "https://github.com/neuroinformatics-unit/ethology"
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"User Support" = "https://github.com/neuroinformatics-unit/ethology/issues"
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[project.optional-dependencies]
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dev = [
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"pytest",
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"pytest-cov",
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"coverage",
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"tox",
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"black",
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"mypy",
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"pre-commit",
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"ruff",
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"setuptools_scm",
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]
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[build-system]
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requires = [
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"setuptools>=45",
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"wheel",
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"setuptools_scm[toml]>=6.2",
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]
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build-backend = "setuptools.build_meta"
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[tool.setuptools]
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include-package-data = true
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[tool.setuptools.packages.find]
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include = ["ethology*"]
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exclude = ["tests*"]
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[tool.pytest.ini_options]
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addopts = "--cov=ethology"
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[tool.black]
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target-version = ['py39', 'py310', 'py311']
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skip-string-normalization = false
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line-length = 79
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[tool.setuptools_scm]
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[tool.check-manifest]
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ignore = [
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".yaml",
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"tox.ini",
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"tests/",
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"tests/test_unit/",
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"tests/test_integration/",
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]
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[tool.ruff]
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line-length = 79
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exclude = ["__init__.py","build",".eggs"]
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select = ["I", "E", "F"]
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fix = true
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[tool.tox]
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legacy_tox_ini = """
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[tox]
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envlist = py{39,310,311}
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isolated_build = True
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[gh-actions]
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python =
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3.9: py39
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3.10: py310
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3.11: py311
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[testenv]
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extras =
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dev
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commands =
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pytest -v --color=yes --cov=ethology --cov-report=xml
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"""

‎tests/__init__.py‎

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‎tests/test_integration/__init__.py‎

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