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updating Dockerfile for test, and github actions
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‎.github/workflows/python-package.yml

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: Python package
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on:
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branches: [ master ]
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jobs:
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build-edm:
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strategy:
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matrix:
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os: [ubuntu-latest]
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runs-on: ${{ matrix.os }}
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Cache EDM packages
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uses: actions/cache@v4
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with:
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path: ~/.cache
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key: ${{ runner.os }}--${{ hashFiles('requirements.txt') }}
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- name: Setup EDM
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uses: enthought/setup-edm-action@v3
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- name: Set up Miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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edm-version: 3.7.0
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- name: Install Python packages
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python-version: "3.11"
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auto-activate-base: false
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activate-environment: pyptv
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- name: Install dependencies
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shell: bash -l {0}
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run: |
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edm install -y enable
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edm install -y numpy"==1.26.4"
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edm install -y matplotlib
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edm shell
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edm run -- python -m pip install optv==0.3.0 tqdm flake8 pytest pyptv \
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--index-url https://pypi.fury.io/pyptv \
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--extra-index-url https://pypi.org/simple
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conda install -y numpy==1.26.4 matplotlib pytest flake8 tqdm
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pip install optv==0.3.0 pyptv \
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--index-url https://pypi.fury.io/pyptv \
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--extra-index-url https://pypi.org/simple
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- name: Setup test data
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shell: bash -l {0}
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run: |
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git clone https://github.com/openptv/test_cavity
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mkdir -p tests/test_cavity/parameters
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cp -r test_cavity/parameters/* tests/test_cavity/parameters/
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- name: Verify environment
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shell: bash -l {0}
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run: python scripts/verify_environment.py
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# Uncomment if you want to run linting
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# - name: Lint with flake8
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# shell: bash -l {0}
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# run: |
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# # stop the build if there are Python syntax errors or undefined names
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# flake8 . --count --select=E9,F63,F7,F82 --ignore=F821 --show-source --statistics
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# # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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# # exit-zero treats all errors as warnings
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# flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Test with pytest
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run: |
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# First clone test data to a specific location
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git clone https://github.com/openptv/test_cavity
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# Copy necessary parameter files
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cp -r test_cavity/parameters/* tests/test_cavity/parameters/
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# Run tests with more verbose output and fail on first error
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edm run -- pytest -v -x --tb=short
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- name: Run tests
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shell: bash -l {0}
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run: pytest -v -x --tb=short

‎DEVELOP.md

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# PyPTV Development Guide
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## Testing with Docker
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The easiest way to test PyPTV without affecting your local environment is using Docker:
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```bash
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# Run all tests in Docker
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./run_docker_tests.sh
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```
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### Docker Test Environment Details
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The test environment is defined in `Dockerfile.test` and uses:
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- Ubuntu latest
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- Python 3.11
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- Miniconda
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- NumPy 1.26.4
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- OpenPTV (optv) 0.3.0
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### Debugging in Docker
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To debug issues interactively:
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```bash
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# Build the test image
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docker build -t pyptv-test -f Dockerfile.test .
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# Run container interactively
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docker run -it --rm pyptv-test bash
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# Inside container, run tests:
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./run_tests.sh
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# Or run specific components:
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python scripts/verify_environment.py
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pytest -v -x tests/test_environment.py
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```
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## Local Development Setup
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If you prefer local development:
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1. Install EDM (Enthought Deployment Manager)
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2. Create and activate environment:
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```bash
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edm install -y enable
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edm install -y numpy==1.26.4
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edm install -y matplotlib
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edm shell
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```
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3. Install dependencies:
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```bash
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python -m pip install optv==0.3.0 tqdm flake8 pytest pyptv \
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--index-url https://pypi.fury.io/pyptv \
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--extra-index-url https://pypi.org/simple
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```
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## Development Workflow
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1. Create feature branch:
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```bash
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git checkout -b feature/your-feature-name
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```
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2. Make changes and test:
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```bash
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# Run tests in Docker (recommended)
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./run_docker_tests.sh
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# Or run tests locally
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pytest -v -x --tb=short
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```
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3. Lint code:
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```bash
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flake8 . --count --select=E9,F63,F7,F82 --ignore=F821 --show-source --statistics
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```
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4. Submit PR:
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- Ensure all tests pass
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- Update documentation if needed
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- Follow code style guidelines
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## Version Management
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- Bump version: `python bump_version.py --patch`
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- Build package: `python -m build`
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- Install locally: `pip install dist/pyptv-{version}-py3-none-any.whl`
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## Code Style Guidelines
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- Use Black formatter (line length 88)
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- Follow PEP 8 naming conventions
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- Add docstrings for public functions
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- Keep functions focused and small
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- Write tests for new features
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## Dependencies
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Critical version requirements:
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- Python >= 3.10
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- NumPy == 1.26.4
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- OpenPTV (optv) == 0.3.0
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- See `pyproject.toml` for complete list
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## Common Issues
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1. EDM Installation Problems:
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- Verify EDM version (3.7.0 required)
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- Check system dependencies
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2. Test Data Issues:
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- Ensure test_cavity repository is cloned
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- Verify parameter files are copied correctly
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3. Version Conflicts:
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- Use `scripts/verify_environment.py` to check versions
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- Follow exact versions in `pyproject.toml`
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## Getting Help
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- Open an issue on GitHub
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- Contact the mailing list: openptv@googlegroups.com
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- Check existing documentation: http://openptv-python.readthedocs.io

‎Dockerfile.test

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# Use Ubuntu as base image to match GitHub Actions
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FROM ubuntu:latest
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# Set environment variables
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ENV DEBIAN_FRONTEND=noninteractive
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ENV PATH="/root/miniconda3/bin:${PATH}"
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# Install system dependencies
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RUN apt-get update && apt-get install -y \
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wget \
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git \
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&& rm -rf /var/lib/apt/lists/*
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# Install Miniconda
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RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
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&& bash miniconda.sh -b -p /root/miniconda3 \
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&& rm miniconda.sh
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# Initialize conda for bash
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RUN conda init bash
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# Create and activate conda environment
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RUN conda create -y -n pyptv python=3.11 \
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&& echo "conda activate pyptv" >> ~/.bashrc
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# Set working directory
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WORKDIR /app
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# Copy project files
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COPY . .
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# Setup test environment script
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RUN echo '#!/bin/bash \n\
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source ~/.bashrc && \
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conda install -y numpy==1.26.4 matplotlib pytest flake8 tqdm && \
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pip install optv==0.3.0 pyptv \
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--index-url https://pypi.fury.io/pyptv \
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--extra-index-url https://pypi.org/simple && \
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git clone https://github.com/openptv/test_cavity && \
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mkdir -p tests/test_cavity/parameters && \
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cp -r test_cavity/parameters/* tests/test_cavity/parameters/ && \
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python scripts/verify_environment.py && \
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pytest -v -x --tb=short \
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' > run_tests.sh && chmod +x run_tests.sh
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# Default command
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CMD ["./run_tests.sh"]

‎run_docker_tests.sh

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#!/bin/bash
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# Build the test container
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docker build -t pyptv-test -f Dockerfile.test .
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# Run tests
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docker run --rm pyptv-test

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