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Merge pull request #196 from NeLy-EPFL/dev-v1.0.0
Merge release v1.0.0
2 parents f32302b + 1fb303a commit c75c722

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‎.dockerignore‎

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‎.github/workflows/black.yaml‎

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lint:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- uses: psf/black@stable
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with:
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version: "23.3.0"

‎.github/workflows/documentation.yaml‎

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docs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v3
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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- name: Install dependencies
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run: |
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pip install sphinxcontrib-googleanalytics
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pip install "flyvision @ https://github.com/Nely-EPFL/flyvis/archive/refs/heads/main.zip"
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pip install -e ."[dev,examples]"
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pip install toolz
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- name: Sphinx build

‎.github/workflows/tests_docker.yaml‎

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name: Build and test Docker image
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on: [push]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Cache Docker layers
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uses: actions/cache@v4
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with:
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path: /tmp/.buildx-cache
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key: ${{ runner.os }}-buildx-${{ github.sha }}
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restore-keys: |
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${{ runner.os }}-buildx-
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- name: Build Docker image
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run: docker build --tag flygym:temp .
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- name: Run tests inside Docker container
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run: docker run --rm flygym:temp -c "pytest"

.github/workflows/tests.yaml renamed to .github/workflows/tests_full.yaml

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name: MuJoCo Tests
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name: Unit tests (full)
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on: [push]
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# env:
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# LD_PRELOAD: /usr/lib/x86_64-linux-gnu/libGLEW.so
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jobs:
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build:
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runs-on: ubuntu-latest
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runs-on: ubuntu-24.04
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strategy:
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Set up renderer
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run: |
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sudo apt-get update
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sudo apt-get install -y libgl1-mesa-dev libgl1-mesa-glx libosmesa6-dev
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sudo apt-get install -y libegl1-mesa-dev
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echo "MUJOCO_GL=egl" >> $GITHUB_ENV
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echo "PYOPENGL_PLATFORM=egl" >> $GITHUB_ENV
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- name: Install dependencies
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run: |
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sudo apt-get install ffmpeg
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pip install --upgrade pip
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pip cache purge
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pip install -e ."[dev,examples]"
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pip install toolz
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pip install "flyvision @ https://github.com/Nely-EPFL/flyvis/archive/refs/heads/main.zip"
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pip install -e ".[dev,examples]"
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- name: Lint with ruff
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run: |
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# stop the build if there are Python syntax errors or undefined names

‎.github/workflows/tests_macos.yaml‎

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name: Unit tests (macOS)
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on: [push]
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env:
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SKIP_RENDERING: "true"
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jobs:
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build:
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strategy:
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matrix:
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os: ["macos-13", "macos-latest"]
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python-version: ["3.12"]
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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pip install --upgrade pip
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pip cache purge
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pip install "flyvision @ https://github.com/Nely-EPFL/flyvis/archive/refs/heads/main.zip"
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pip install -e ".[dev,examples]"
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- name: Lint with ruff
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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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ruff --output-format=github --select=E9,F63,F7,F82 --target-version=py38 .
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- name: Test with pytest
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run: |
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python -m pytest

‎.github/workflows/tests_ubuntu22.yaml‎

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name: Unit tests (Ubuntu 22.04)
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on: [push]
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jobs:
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build:
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runs-on: ubuntu-22.04
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strategy:
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matrix:
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python-version: ["3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Set up renderer
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run: |
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sudo apt-get update
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sudo apt-get install -y libegl1-mesa-dev
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echo "MUJOCO_GL=egl" >> $GITHUB_ENV
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echo "PYOPENGL_PLATFORM=egl" >> $GITHUB_ENV
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- name: Install dependencies
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run: |
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sudo apt-get install ffmpeg
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pip install --upgrade pip
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pip cache purge
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pip install "flyvision @ https://github.com/Nely-EPFL/flyvis/archive/refs/heads/main.zip"
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pip install -e ".[dev,examples]"
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- name: Lint with ruff
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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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ruff --output-format=github --select=E9,F63,F7,F82 --target-version=py38 .
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- name: Test with pytest
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run: |
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python -m pytest

‎.github/workflows/tests_windows.yaml‎

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name: Unit tests (Windows)
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on: [push]
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env:
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SKIP_RENDERING: "true"
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jobs:
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build:
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runs-on: windows-latest
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strategy:
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matrix:
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python-version: ["3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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pip install --upgrade pip
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pip cache purge
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pip install "flyvision @ https://github.com/nely-epfl/flyvis/archive/refs/heads/main.zip"
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pip install -e .[dev,examples]
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- name: Lint with ruff
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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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ruff --output-format=github --select=E9,F63,F7,F82 --target-version=py38 .
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- name: Test with pytest
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run: |
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python -m pytest

‎Dockerfile‎

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FROM python:3.12-bookworm
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# Set shell to bash (instead of sh)
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SHELL ["/bin/bash", "-c"]
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# Change working directory
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ENV HOME /root
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WORKDIR $HOME/flygym
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# Install system dependencies
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RUN apt update && \
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apt-get install -y libegl1-mesa-dev ffmpeg
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# Set renderer
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ENV MUJOCO_GL=egl
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ENV PYOPENGL_PLATFORM=egl
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# Copy flygym package to the container and install the package
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ADD . $HOME/flygym/
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# Set up virtual environment and install dependencies
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RUN pip install "flyvision @ https://github.com/Nely-EPFL/flyvis/archive/refs/heads/main.zip" && \
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pip install -e ".[examples,dev]"
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# Set entrypoint
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ENTRYPOINT ["/bin/bash"]

‎README.md‎

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[![PyPI version](https://badge.fury.io/py/flygym.svg)](https://badge.fury.io/py/flygym)
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![Repo Size](https://img.shields.io/github/repo-size/NeLy-EPFL/flygym)
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[![Docker](https://img.shields.io/badge/docker-%230db7ed.svg?style=for-the-badge&logo=docker&logoColor=white)](https://hub.docker.com/r/nelyepfl/flygym)
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![Docker image size](https://img.shields.io/docker/image-size/nelyepfl/flygym/latest)
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![overview_video](https://github.com/NeLy-EPFL/_media/blob/main/flygym/overview_video.gif?raw=true)
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This repository contains the source code for FlyGym, the Python library for NeuroMechFly v2, a digital twin of the adult fruit fly *Drosophila* melanogaster that can see, smell, walk over challenging terrain, and interact with the environment (see our [NeuroMechFly v2 paper](https://www.biorxiv.org/content/10.1101/2023.09.18.556649)).
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In brief:
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```bash
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pip install "flygym"
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# or pip install "flygym[examples]" to install additional dependencies needed for examples
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```
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See [our website](https://neuromechfly.org/installation.html) for details, especially if you plan to install FlyGym in the developer mode (i.e. if you plan to make changes to the code). Dependencies are specified in [`setup.py`](https://github.com/NeLy-EPFL/flygym/blob/main/setup.py) and will be installed automatically upon installation using pip. Installation should take no more than a few minutes. NeuroMechFly has been tested on Linux (Ubuntu 22.04.3) and macOS (13.5.2). All commits are tested automatically using the latest Ubuntu version on Python versions 3.9 through 3.12 (see [CI workflow](https://github.com/NeLy-EPFL/flygym/blob/main/.github/workflows/tests.yaml) for exact test specification). The PyPI version of the current release of FlyGym is indicated on the shield at the top of this page. No special or paid software is required to use FlyGym.
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Alternatively, we provide a [Docker image](https://hub.docker.com/r/nelyepfl/flygym). See [our website](https://neuromechfly.org/installation.html) for details, especially if you plan to install FlyGym in the developer mode (i.e. if you plan to make changes to the code). Dependencies are specified in [`setup.py`](https://github.com/NeLy-EPFL/flygym/blob/main/setup.py) and will be installed automatically upon installation using pip. Installation should take no more than a few minutes. The PyPI version of the current release of FlyGym is indicated on the shield at the top of this page. No special, paid software is required to use FlyGym.
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## Demos
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See [our website](https://neuromechfly.org/tutorials/index.html) for tutorials, including expected outputs. For code blocks that take more than a few seconds to run, the running time (on a 2020 MacBook Pro with M1 processor running macOS 13.5.2) is indicated, typically in the form of a progress bar.

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