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‎.devcontainer/Dockerfile

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# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.245.2/containers/python-3/.devcontainer/base.Dockerfile
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# [Choice] Python version (use -bullseye variants on local arm64/Apple Silicon): 3, 3.10, 3.9, 3.8, 3.7, 3.6, 3-bullseye, 3.10-bullseye, 3.9-bullseye, 3.8-bullseye, 3.7-bullseye, 3.6-bullseye, 3-buster, 3.10-buster, 3.9-buster, 3.8-buster, 3.7-buster, 3.6-buster
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ARG VARIANT="3.10-bullseye"
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FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT}
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# [Choice] Node.js version: none, lts/*, 16, 14, 12, 10
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ARG NODE_VERSION="none"
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RUN if [ "${NODE_VERSION}" != "none" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
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RUN apt-get update && \
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export DEBIAN_FRONTEND=noninteractive && \
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sudo apt install -y gcc g++ pigz libhdf5-dev vim
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USER vscode
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ENV PATH="${PATH}:/home/vscode/.local/bin/:/home/vscode/micromamba/bin"
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ENV ENV_NAME="base"
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ENV MAMBA_ROOT_PREFIX="/home/vscode/conda"
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ENV MAMBA_EXE="/home/vscode/micromamba"
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RUN curl micro.mamba.pm/install.sh > /tmp/micromamba_install.sh && \
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yes | bash /tmp/micromamba_install.sh
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RUN micromamba shell init -p "$MAMBA_ROOT_PREFIX" -s bash > /dev/null && \
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echo "micromamba activate \$ENV_NAME" >> ~/.bashrc
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COPY .devcontainer/mamba_environment.yaml /tmp/mamba_environment.yaml
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RUN micromamba install -y -f /tmp/mamba_environment.yaml

‎.devcontainer/devcontainer.json

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// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
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// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.2/containers/python-3
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{
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"name": "Python 3",
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"build": {
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"dockerfile": "Dockerfile",
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"context": "..",
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"args": {
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// Update 'VARIANT' to pick a Python version: 3, 3.10, 3.9, 3.8, 3.7, 3.6
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// Append -bullseye or -buster to pin to an OS version.
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// Use -bullseye variants on local on arm64/Apple Silicon.
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"VARIANT": "3.8",
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// Options
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"NODE_VERSION": "none"
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}
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},
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// Configure tool-specific properties.
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"customizations": {
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// Configure properties specific to VS Code.
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"vscode": {
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// Set *default* container specific settings.json values on container create.
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"settings": {
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"python.defaultInterpreterPath": "/home/vscode/conda/bin/python",
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"python.linting.enabled": true,
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"python.linting.pylintEnabled": true,
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"python.formatting.provider": "black",
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"editor.formatOnSave": true
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},
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// Add the IDs of extensions you want installed when the container is created.
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"extensions": [
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"ms-python.python",
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"ms-python.vscode-pylance"
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]
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}
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},
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// Use 'forwardPorts' to make a list of ports inside the container available locally.
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// "forwardPorts": [],
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// Use 'postCreateCommand' to run commands after the container is created.
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"postCreateCommand": "conda init && poetry config virtualenvs.create false && poetry install",
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// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
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"remoteUser": "vscode",
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"features": {
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"git": "os-provided",
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}
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}

‎.devcontainer/mamba_environment.yaml

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name: base
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channels:
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- conda-forge
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- bioconda
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dependencies:
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# TODO lock versions?
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- python=3.10
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- mamba
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- fastp
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- python-annoy
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- tox
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- poetry

‎.dockerignore

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# Ignore everything
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.github
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cue.mod
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docker-bake.hcl
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docs
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CHANGELOG.md
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pytest-results
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conda-recipe
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# Dockerfiles
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*.Dockerfile
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# Editors
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.idea
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.vscode
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# Tools caches
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.mypy_cache
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.pytest_cache
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.ruff_cache
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.tox
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.coverage
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.coverage.*
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.cache
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# Misc
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**/*.pyc
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playground/
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__pycache__/
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*.py[cod]
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*$py.class
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*.so
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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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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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*.manifest
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*.spec
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pip-log.txt
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pip-delete-this-directory.txt
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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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.pytest_cache/
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*.mo
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*.pot
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*.log
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local_settings.py
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instance/
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.webassets-cache
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.scrapy
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docs/_build/
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target/
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.ipynb_checkpoints
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.python-version
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celerybeat-schedule
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*.sage.py
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.env
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.venv
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venv/
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ENV/
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.spyderproject
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.spyproject
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.ropeproject
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/site

‎.editorconfig

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# http://editorconfig.org
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root = true
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[*]
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indent_style = space
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indent_size = 4
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trim_trailing_whitespace = true
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insert_final_newline = true
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charset = utf-8
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end_of_line = lf
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[*.{yaml,yml}]
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indent_style = space
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indent_size = 2
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trim_trailing_whitespace = true
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insert_final_newline = true
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charset = utf-8
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end_of_line = lf
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[*.json]
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indent_size = 2
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[*.bat]
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indent_style = tab
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end_of_line = crlf
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[LICENSE]
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insert_final_newline = false
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[Makefile]
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indent_style = tab

‎.flake8

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[flake8]
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extend-ignore = E501,E402,W503,E203,D213,D203,DOC301
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exclude = .git,__pycache__,docs/source/conf.py,old,build,dist,cue.mod
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docstring-convention = all
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style = sphinx
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require-return-section-when-returning-none = False
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arg-type-hints-in-signature = True
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arg-type-hints-in-docstring = False

‎.gitattributes

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src/pixelator/report/webreport/template.html linguist-vendored

‎.github/PULL_REQUEST_TEMPLATE.md

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<!--
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# Pixelgen Technologies pull request template
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Many thanks for contributing to it if you think it could be improved. This is a self-improving process!
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Please fill in the appropriate checklist below (delete whatever is not relevant).
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These are the most common things requested on pull requests (PRs).
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Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
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Learn more about contributing: [CONTRIBUTING.md](https://github.com/PixelgenTechnologies/pixelator/blob/main/CONTRIBUTING.md)
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-->
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## Description
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Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.
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Fixes # (issue)
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## Type of change
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Please delete options that are not relevant.
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- [ ] Bug fix (non-breaking change which fixes an issue)
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- [ ] New feature (non-breaking change which adds functionality)
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- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
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- [ ] This change requires a documentation update
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## How Has This Been Tested?
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Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration
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- [ ] Test A
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- [ ] Test B
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**Test Configuration**:
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* Firmware version:
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* Hardware:
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* Toolchain:
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* SDK:
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## PR checklist:
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- [ ] This comment contains a description of changes (with reason).
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- [ ] My code follows the style guidelines of this project
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- [ ] Make sure your code lints, is well-formatted and type checks
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- [ ] I have performed a self-review of my own code
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- [ ] I have commented my code, particularly in hard-to-understand areas
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- [ ] I have made corresponding changes to the documentation
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- [ ] My changes generate no new warnings
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- [ ] I have added tests that prove my fix is effective or that my feature works
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- [ ] If you've added a new stage - have you followed the pipeline CLI conventions in the [USAGE guide](../USAGE.md)
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- [ ] [README.md](./README.md) is updated
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- [ ] If a new tool or package is included, update poetry.lock, [the conda recipe](../conda-recipe/pixelator/meta.yaml) and [cited it properly](../CITATIONS.md)
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- [ ] Include any new [authors/contributors](../AUTHORS.md)
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- [ ] New and existing unit tests pass locally with my changes
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- [ ] Any dependent changes have been merged and published in downstream modules
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- [ ] I have checked my code and documentation and corrected any misspellings
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- [ ] Usage Documentation in [USAGE.md](../USAGE.md) is updated
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- [ ] If you are doing a [release](../RELEASING.md#Releasing), or a significant change to the code, update [CHANGELOG.md](../CHANGELOG.md)

‎.github/actions/build-dev-image/action.yml

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name: "build-dev-image"
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description: "Build a dev image and push it to the Pixelgen container registries"
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inputs:
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tag:
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description: "The tag to use for the image"
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required: true
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cache-from:
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description: "The cache to use for the build"
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default: ""
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cache-to:
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description: "The cache to push to for the build"
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default: ""
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platforms:
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description: "The platforms to build for (seperated by comma) - defaults to linux/amd64/v3"
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default: linux/amd64/v3
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outputs:
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dev-tag:
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description: "The tags that were pushed"
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value: ${{ steps.meta.outputs.tags }}
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runs:
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using: "composite"
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steps:
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- name: Docker meta
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id: meta
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uses: docker/metadata-action@v4
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with:
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images: |
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ghcr.io/pixelgentechnologies/pixelator
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890888997283.dkr.ecr.eu-north-1.amazonaws.com/pixelator
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tags: |
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type=ref,event=branch
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type=ref,event=pr
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type=semver,pattern={{version}}
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type=semver,pattern={{major}}.{{minor}}
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type=sha
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- name: Build input options
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id: build_input_options
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uses: actions/github-script@v4
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with:
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script: |
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const shaShort = context.sha.substring(0, 7)
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const inputParams = ${{ toJSON(inputs) }}
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const meta = ${{ steps.meta.outputs.json }}
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const tags = meta["tags"]
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const cacheFromArray = inputParams["cache-from"].split('\n').map((line) => line.trim())
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.filter((line) => line !== "")
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.map((line) => "*.cache-from=" + line)
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const cacheToArray = inputParams["cache-to"].split('\n').map((line) => line.trim())
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.filter((line) => line !== "")
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.map((line) => "*.cache-to=" + line)
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const tagsArray = tags.map((tag) => "*.tags=" + tag)
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const platformArray = inputParams["platforms"].split(',').map((line) => line.trim())
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.filter((line) => line !== "")
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.map((line) => "*.platform=" + line)
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let bakeSetCommands = []
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bakeSetCommands.push(...tagsArray)
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bakeSetCommands.push(...cacheFromArray)
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bakeSetCommands.push(...cacheToArray)
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bakeSetCommands.push(...platformArray)
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const gitSHAtag = tagsArray.find((tag) => tag.includes('ghcr') && tag.includes('sha'))
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bakeSetCommandsText = bakeSetCommands.join('\n')
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core.setOutput('set', bakeSetCommandsText)
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core.setOutput('dev-tag', gitSHAtag)
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- name: Build and push to ghcr and ecr
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uses: docker/bake-action@v3
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with:
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push: true
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targets: pixelator-prod
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provenance: false
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set: ${{ steps.build_input_options.outputs.set }}

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