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Merge branch 'master' into fix/alter_part
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‎.devcontainer/Dockerfile‎

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# Note: You can use any Debian/Ubuntu based image you want.
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FROM mcr.microsoft.com/devcontainers/python:3.7-bullseye
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RUN \
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apt update && \
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apt-get install bash-completion graphviz default-mysql-client -y && \
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pip install flake8 black faker ipykernel nose nose-cov datajoint && \
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pip uninstall datajoint -y
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ENV DJ_HOST fakeservices.datajoint.io
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ENV DJ_USER root
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ENV DJ_PASS simple

‎.devcontainer/devcontainer.json‎

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// For format details, see https://aka.ms/devcontainer.json. For config options, see the
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{
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"name": "Development",
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"dockerComposeFile": "docker-compose.yaml",
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"service": "app",
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"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
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// Use this environment variable if you need to bind mount your local source code into a new container.
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"remoteEnv": {
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"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
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},
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// https://containers.dev/features
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"features": {
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"ghcr.io/devcontainers/features/docker-in-docker:2": {},
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"ghcr.io/devcontainers/features/git:1": {},
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"ghcr.io/eitsupi/devcontainer-features/jq-likes:1": {},
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"ghcr.io/guiyomh/features/vim:0": {}
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},
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"onCreateCommand": "pip install -e .",
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"postStartCommand": "MYSQL_VER=8.0 MINIO_VER=RELEASE.2022-08-11T04-37-28Z docker compose -f local-docker-compose.yml down && MYSQL_VER=8.0 MINIO_VER=RELEASE.2022-08-11T04-37-28Z docker compose -f local-docker-compose.yml up --build --wait",
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"forwardPorts": [
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80,
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443,
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3306,
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8080,
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9000
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],
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"customizations": {
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"vscode": {
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"extensions": [
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"ms-python.python"
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]
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}
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}
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}

‎.devcontainer/docker-compose.yaml‎

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version: "3"
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services:
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app:
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build: .
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extra_hosts:
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- fakeservices.datajoint.io:127.0.0.1
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volumes:
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- ../..:/workspaces:cached
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entrypoint: /usr/local/share/docker-init.sh
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command: tail -f /dev/null

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: 'bug, awaiting-triage'
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labels: 'bug'
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assignees: ''
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---

‎.github/workflows/development.yaml‎

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on:
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push:
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branches:
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- '**' # every branch
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- '!stage*' # exclude branches beginning with stage
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- "**" # every branch
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- "!gh-pages" # exclude gh-pages branch
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- "!stage*" # exclude branches beginning with stage
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tags:
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- '\d+\.\d+\.\d+' # only semver tags
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pull_request:
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branches:
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- '**' # every branch
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- '!stage*' # exclude branches beginning with stage
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- "**" # every branch
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- "!gh-pages" # exclude gh-pages branch
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- "!stage*" # exclude branches beginning with stage
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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include:
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- py_ver: "3.9"
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distro: debian
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image: djbase
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env:
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PY_VER: ${{matrix.py_ver}}
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DISTRO: ${{matrix.distro}}
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IMAGE: ${{matrix.image}}
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DOCKER_CLIENT_TIMEOUT: "120"
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COMPOSE_HTTP_TIMEOUT: "120"
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steps:
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- uses: actions/checkout@v3
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- name: Validate version and release notes
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run: |
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DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' datajoint/version.py)
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RELEASE_BODY=$(python -c \
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'print(open("./CHANGELOG.md").read().split("\n\n")[1].split("\n", 1)[1])' \
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)
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echo "DJ_VERSION=${DJ_VERSION}" >> $GITHUB_ENV
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echo "RELEASE_BODY<<EOF" >> $GITHUB_ENV
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echo "$RELEASE_BODY" >> $GITHUB_ENV
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echo "EOF" >> $GITHUB_ENV
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- name: Build pip artifacts
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run: |
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export HOST_UID=$(id -u)
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docker-compose -f docker-compose-build.yaml up --exit-code-from app --build
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echo "DJ_VERSION=${DJ_VERSION}" >> $GITHUB_ENV
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- if: matrix.py_ver == '3.9' && matrix.distro == 'debian'
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name: Add pip artifacts
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uses: actions/upload-artifact@v3
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with:
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name: pip-datajoint-${{env.DJ_VERSION}}
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path: dist
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retention-days: 1
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test:
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if: github.event_name == 'push' || github.event_name == 'pull_request'
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runs-on: ubuntu-latest
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strategy:
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matrix:
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py_ver: ["3.8"]
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py_ver: ["3.9"]
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mysql_ver: ["8.0", "5.7"]
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include:
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- py_ver: "3.7"
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- py_ver: "3.8"
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mysql_ver: "5.7"
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- py_ver: "3.6"
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- py_ver: "3.7"
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mysql_ver: "5.7"
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- name: Set up Python ${{matrix.py_ver}}
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uses: actions/setup-python@v2
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uses: actions/setup-python@v4
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with:
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python-version: ${{matrix.py_ver}}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install flake8
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pip install flake8 black
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- name: Run syntax tests
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run: flake8 datajoint --count --select=E9,F63,F7,F82 --show-source --statistics
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- name: Run primary tests
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env:
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UID: "1001"
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GID: "121"
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PY_VER: ${{matrix.py_ver}}
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DJ_PASS: simple
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MYSQL_VER: ${{matrix.mysql_ver}}
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ALPINE_VER: "3.10"
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DISTRO: alpine
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MINIO_VER: RELEASE.2021-09-03T03-56-13Z
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DOCKER_CLIENT_TIMEOUT: "120"
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COMPOSE_HTTP_TIMEOUT: "120"
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COVERALLS_SERVICE_NAME: travis-ci
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COVERALLS_REPO_TOKEN: fd0BoXG46TPReEem0uMy7BJO5j0w1MQiY
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run: docker-compose -f LNX-docker-compose.yml up --build --exit-code-from app
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run: |
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export HOST_UID=$(id -u)
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docker-compose -f LNX-docker-compose.yml up --build --exit-code-from app
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- name: Run style tests
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run: |
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flake8 --ignore=E121,E123,E126,E226,E24,E704,W503,W504,E722,F401,W605 datajoint \
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flake8 --ignore=E203,E722,W503 datajoint \
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--count --max-complexity=62 --max-line-length=127 --statistics
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black datajoint --check -v
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black tests --check -v
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publish-docs:
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if: |
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github.event_name == 'push' &&
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startsWith(github.ref, 'refs/tags')
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needs: test
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runs-on: ubuntu-latest
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env:
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DOCKER_CLIENT_TIMEOUT: "120"
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COMPOSE_HTTP_TIMEOUT: "120"
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steps:
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- uses: actions/checkout@v3
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- name: Deploy docs
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run: |
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export MODE=BUILD
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export PACKAGE=datajoint
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export UPSTREAM_REPO=https://github.com/${GITHUB_REPOSITORY}.git
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export HOST_UID=$(id -u)
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docker compose -f docs/docker-compose.yaml up --exit-code-from docs --build
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git push origin gh-pages
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publish-release:
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if: |
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github.event_name == 'push' &&
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startsWith(github.ref, 'refs/tags')
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needs: test
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runs-on: ubuntu-latest
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strategy:
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matrix:
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include:
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- py_ver: "3.9"
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distro: debian
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image: djbase
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env:
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PY_VER: ${{matrix.py_ver}}
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DISTRO: ${{matrix.distro}}
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IMAGE: ${{matrix.image}}
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TWINE_USERNAME: ${{secrets.twine_username}}
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TWINE_PASSWORD: ${{secrets.twine_password}}
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DOCKER_CLIENT_TIMEOUT: "120"
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COMPOSE_HTTP_TIMEOUT: "120"
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outputs:
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release_upload_url: ${{steps.create_gh_release.outputs.upload_url}}
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{matrix.py_ver}}
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uses: actions/setup-python@v4
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with:
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python-version: ${{matrix.py_ver}}
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- name: Determine package version
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run: |
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DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' datajoint/version.py)
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RELEASE_BODY=$(python -c \
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'print(open("./CHANGELOG.md").read().split("\n\n")[1].split("\n", 1)[1])' \
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)
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echo "DJ_VERSION=${DJ_VERSION}" >> $GITHUB_ENV
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echo "RELEASE_BODY<<EOF" >> $GITHUB_ENV
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echo "$RELEASE_BODY" >> $GITHUB_ENV
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echo "EOF" >> $GITHUB_ENV
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- name: Create GH release
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id: create_gh_release
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uses: actions/create-release@v1
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env:
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GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
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with:
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tag_name: ${{env.DJ_VERSION}}
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release_name: Release ${{env.DJ_VERSION}}
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body: ${{env.RELEASE_BODY}}
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prerelease: false
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draft: false
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- name: Fetch pip artifacts
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uses: actions/download-artifact@v3
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with:
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name: pip-datajoint-${{env.DJ_VERSION}}
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path: dist
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- name: Determine pip artifact paths
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run: |
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echo "DJ_WHEEL_PATH=$(ls dist/datajoint-*.whl)" >> $GITHUB_ENV
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echo "DJ_SDIST_PATH=$(ls dist/datajoint-*.tar.gz)" >> $GITHUB_ENV
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- name: Upload pip wheel asset to release
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uses: actions/upload-release-asset@v1
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env:
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GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
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with:
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upload_url: ${{steps.create_gh_release.outputs.upload_url}}
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asset_path: ${{env.DJ_WHEEL_PATH}}
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asset_name: pip-datajoint-${{env.DJ_VERSION}}.whl
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asset_content_type: application/zip
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- name: Upload pip sdist asset to release
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uses: actions/upload-release-asset@v1
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env:
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GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
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with:
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upload_url: ${{steps.create_gh_release.outputs.upload_url}}
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asset_path: ${{env.DJ_SDIST_PATH}}
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asset_name: pip-datajoint-${{env.DJ_VERSION}}.tar.gz
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asset_content_type: application/gzip
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- name: Publish pip release
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run: |
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export HOST_UID=$(id -u)
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docker-compose -f docker-compose-build.yaml run \
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-e TWINE_USERNAME=${TWINE_USERNAME} -e TWINE_PASSWORD=${TWINE_PASSWORD} app \
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sh -c "pip install twine && python -m twine upload dist/*"
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- name: Login to DockerHub
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uses: docker/login-action@v1
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with:
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username: ${{secrets.docker_username}}
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password: ${{secrets.docker_password}}
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- name: Publish image
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run: |
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IMAGE=$(docker images --filter "reference=datajoint/datajoint*" --format "{{.Repository}}")
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TAG=$(docker images --filter "reference=datajoint/datajoint*" --format "{{.Tag}}")
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docker push "${IMAGE}:${TAG}"
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docker tag "${IMAGE}:${TAG}" "${IMAGE}:${TAG}-${GITHUB_SHA:0:7}"
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docker push "${IMAGE}:${TAG}-${GITHUB_SHA:0:7}"
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[ "$PY_VER" == "3.9" ] && [ "$DISTRO" == "debian" ] \
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&& docker tag "${IMAGE}:${TAG}" "${IMAGE}:latest" \
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&& docker push "${IMAGE}:latest" \
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|| echo "skipping 'latest' tag..."

‎.gitignore‎

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*.env
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docker-compose.yml
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notebook
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.vscode
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__main__.py
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jupyter_custom.js
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apk_requirements.txt
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.eggs
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.eggs
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*.code-workspace
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docs/site
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!.vscode/settings.json
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!.vscode/launch.json
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!.devcontainer/devcontainer.json

‎.vscode/launch.json‎

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{
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// Use IntelliSense to learn about possible attributes.
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// Hover to view descriptions of existing attributes.
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// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
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"version": "0.2.0",
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"configurations": [
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{
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"name": "Python: Current File",
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"type": "python",
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"request": "launch",
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"program": "${file}",
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"console": "integratedTerminal",
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"justMyCode": false
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}
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]
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}

‎.vscode/settings.json‎

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{
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"editor.formatOnPaste": false,
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"editor.formatOnSave": true,
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"editor.rulers": [
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94
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],
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"python.formatting.provider": "black",
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"[python]": {
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"editor.defaultFormatter": null
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},
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"[markdown]": {
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"editor.defaultFormatter": "disable"
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},
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"files.autoSave": "off"
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}

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