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nipreps-botoesteban
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oesteban
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maint: first codebase add
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‎.dockerignore

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# python cache
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__pycache__/**/*
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__pycache__
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*.pyc
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# python distribution
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build/**/*
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build
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dist/**/*
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dist
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src/eddymotion.egg-info/**/*
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src/eddymotion.egg-info
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.eggs/**/*
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.eggs
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# housekeeping tools
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.maint/**/*
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.maint
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# pip installs
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src/**/*
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src/
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# git
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.git_archival.txt
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.gitattributes
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.gitignore
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.git/**/*
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.git
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.mailmap
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# other
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work/**/*
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work
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out/**/*
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out/
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.idea/**/*
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.idea
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# CI, etc.
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tox.ini
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.circleci
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.circleci/**/*
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.github
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.github/**/*
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.pytest_cache
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.pytest_cache/**/*
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.codecov.yml
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.coveragerc
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.pep8speaks.yml
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.pre-commit-config.yaml
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.readthedocs.yml
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.travis.yml
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.zenodo.json
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.afq

‎.git_archival.txt

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ref-names: $Format:%D$

‎.gitattributes

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.git_archival.txt export-subst

‎.github/workflows/contrib.yml

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name: Contribution checks
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on: [push, pull_request]
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defaults:
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run:
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shell: bash
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jobs:
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stable:
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name: Run ruff
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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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with:
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submodules: recursive
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fetch-depth: 0
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- name: Set up Python 3
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uses: actions/setup-python@v5
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with:
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python-version: 3
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- name: Lint EddyMotion
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run: pipx run ruff check --diff
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- name: Format EddyMotion
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run: pipx run ruff format --diff

‎.github/workflows/docs-build-pr.yml

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name: Build docs
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on:
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pull_request:
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branches: [ main, 'maint/*' ]
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jobs:
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build:
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if: "!contains(github.event.head_commit.message, '[skip ci]')"
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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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with:
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fetch-depth: 0
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- name: Determine current branch/tag name
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run: |
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if [[ "$GITHUB_REF" == refs/pull/* ]]; then
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CURBRANCH=${GITHUB_REF%/*}
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CURBRANCH=${CURBRANCH##*/}
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elif [[ "$GITHUB_REF" == refs/heads/* ]]; then
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CURBRANCH=${GITHUB_REF##*/}
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elif [[ "$GITHUB_REF" == refs/tags/* ]]; then
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echo "This build should not be picking up a tag, cancelling."
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exit 1
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fi
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# Remove forward slashes
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CURBRANCH=$( echo $CURBRANCH | sed 's+/+_+g' )
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echo "Building branch/tag ${CURBRANCH:-<unkwown>}, from git ref <$GITHUB_REF>"
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echo "CURBRANCH=${CURBRANCH}" >> ${GITHUB_ENV}
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- name: Install GraphViz
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run: |
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sudo apt-get update -y
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sudo apt-get install -y --no-install-recommends graphviz
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- name: Install dependencies
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run: |
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pip install -U build hatch pip
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pip install .[doc]
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python -m hatch version | tail -n1
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- name: Build docs
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run: |
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python -m hatch build --hooks-only
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make -C docs/ SPHINXOPTS="-W -v" BUILDDIR="$HOME/docs" OUTDIR="${CURBRANCH:-html}" html

‎.github/workflows/docs-build-update.yml

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name: Build & update docs
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on:
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push:
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branches: [ 'doc/*', 'docs/*', main, "maint/*" ]
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tags: [ '*' ]
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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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with:
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ssh-key: "${{ secrets.NIPREPS_DEPLOY }}"
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fetch-depth: 0
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- name: Determine current branch/tag name & set-up git author
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run: |
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if [[ "$GITHUB_REF" == refs/tags/* ]]; then
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CURBRANCH=${GITHUB_REF##*/}
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elif [[ "$GITHUB_REF" == refs/pull/* ]]; then
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CURBRANCH=${GITHUB_REF%/*}
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CURBRANCH=${CURBRANCH##*/}
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elif [[ "$GITHUB_REF" == refs/heads/* ]]; then
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CURBRANCH=${GITHUB_REF##*/}
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fi
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# Remove forward slashes
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CURBRANCH=$( echo $CURBRANCH | sed 's+/+_+g' )
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echo "Building branch/tag ${CURBRANCH:-<unkwown>}, from git ref <$GITHUB_REF>"
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echo "CURBRANCH=${CURBRANCH}" >> ${GITHUB_ENV}
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# Pacify git if we were to commit something
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git config user.email "[email protected]"
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git config user.name "NiPreps Bot"
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- name: Install GraphViz
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run: |
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sudo apt-get update -y
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sudo apt-get install -y --no-install-recommends graphviz
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- name: Install dependencies
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run: |
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pip install -U build hatch pip
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pip install .[doc]
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python -m hatch version | tail -n1
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- name: Build docs
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run: |
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python -m hatch build --hooks-only
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make -C docs/ SPHINXOPTS="-W -v" BUILDDIR="$HOME/docs" OUTDIR="${CURBRANCH:-html}" html
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- name: Push created tag to gh-pages
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if: startsWith(github.ref, 'refs/tags/')
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run: |
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MAJOR_MINOR=${CURBRANCH%.*}
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if [[ "${MAJOR_MINOR}" == "" ]]; then
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echo "Could not identify release series"
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exit 1
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fi
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git checkout -b gh-pages origin/gh-pages
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git rm -r ${MAJOR_MINOR}/ || true
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# It is fundamental that the directory does not exist at all.
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rm -rf ${MAJOR_MINOR}
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cp -r $HOME/docs/$CURBRANCH $PWD/${MAJOR_MINOR}
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git add ${MAJOR_MINOR}
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python -c "from pathlib import Path; import json; f=Path('versions.json'); d=json.loads(f.read_text()); d['tags'].append(\"${MAJOR_MINOR}\"); d['tags'] = list(sorted(set(d['tags']))); f.write_text(json.dumps(d, indent=4)); print('Updated versions.json')"
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git add versions.json
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git commit -m "rel(${CURBRANCH}): Update docs of ${MAJOR_MINOR} series" || true
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git push
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- name: Push "main" docs to gh-pages after a push to main (typically, a PR merge).
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if: github.ref == 'refs/heads/main'
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run: |
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if [[ "${CURBRANCH}" != "main" ]]; then
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echo "$CURBRANCH is not the default development branch"
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exit 1
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fi
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git checkout -b gh-pages origin/gh-pages
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git rm -r main/ || true
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# It is fundamental that the directory does not exist at all.
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rm -rf main
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cp -r $HOME/docs/$CURBRANCH $PWD/main
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git add main
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git commit -am "docs(main): Update docs of development line" || true
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git push

‎.github/workflows/pypi-package.yml

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---
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name: Build and upload package
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on:
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push:
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branches: [main]
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tags: ["*"]
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release:
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types:
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- published
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workflow_dispatch:
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permissions:
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contents: read
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jobs:
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build-package:
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name: Build & verify package
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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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with:
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fetch-depth: 0
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- uses: hynek/build-and-inspect-python-package@v2
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auto-release-test-pypi:
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runs-on: ubuntu-latest
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needs: [build-package]
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if: github.event_name == 'push' && github.ref == 'refs/heads/main'
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permissions:
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id-token: write
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steps:
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- name: Download packages built by build-and-inspect-python-package
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uses: actions/download-artifact@v4
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with:
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name: Packages
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path: dist
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- uses: pypa/gh-action-pypi-publish@release/v1
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with:
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repository-url: https://test.pypi.org/legacy/
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skip-existing: true
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auto-release-pypi:
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runs-on: ubuntu-latest
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environment: "Release"
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needs: [build-package]
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
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permissions:
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id-token: write
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steps:
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- name: Download packages built by build-and-inspect-python-package
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uses: actions/download-artifact@v4
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with:
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name: Packages
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path: dist
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- uses: pypa/gh-action-pypi-publish@release/v1

‎.github/workflows/pythonpackage.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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push:
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branches: [ main ]
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tags: [ '*' ]
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pull_request:
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branches: [ main ]
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jobs:
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build:
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if: "!startsWith(github.ref, 'refs/tags/') && !contains(github.event.head_commit.message, '[skip ci]')"
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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fetch-depth: 0
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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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- uses: actions/cache@v4
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with:
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path: $HOME/.cache/pip
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key: pip-cache-v1
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restore-keys: |
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pip-cache-
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- name: Build in confined environment and interpolate version
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run: |
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python -m venv /tmp/buildenv
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source /tmp/buildenv/bin/activate
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pip install -U build hatch pip twine
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python -m build -s -w
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python -m twine check dist/eddymotion-*
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mv dist /tmp/package
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# Interpolate version
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if [[ "$GITHUB_REF" == refs/tags/* ]]; then
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TAG=${GITHUB_REF##*/}
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fi
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THISVERSION=$( python -m hatch version | tail -n1 | xargs )
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THISVERSION=${TAG:-$THISVERSION}
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echo "Expected VERSION: \"${THISVERSION}\""
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echo "THISVERSION=${THISVERSION}" >> $GITHUB_ENV
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- name: Install in confined environment [pip]
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run: |
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python -m venv /tmp/pip
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source /tmp/pip/bin/activate
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pip install -U pip
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python -m pip install .
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INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
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echo "VERSION: \"${THISVERSION}\""
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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- name: Install in confined environment [sdist]
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run: |
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python -m venv /tmp/install_sdist
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source /tmp/install_sdist/bin/activate
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pip install -U pip
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python -m pip install /tmp/package/eddymotion*.tar.gz
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INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
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echo "VERSION: \"${THISVERSION}\""
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"
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- name: Install in confined environment [wheel]
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run: |
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python -m venv /tmp/install_wheel
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source /tmp/install_wheel/bin/activate
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pip install -U pip
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python -m pip install /tmp/package/eddymotion*.whl
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INSTALLED_VERSION=$(python -c 'import eddymotion as em; print(em.__version__, end="")')
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${THISVERSION}"

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