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Merge branch 'master' into dj-top-1084-continued
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‎.codespellrc‎

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[codespell]
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skip = .git,*.pdf,*.svg,*.csv,*.ipynb,*.drawio
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# Rever -- nobody knows
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# numer -- numerator variable
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ignore-words-list = rever,numer

‎.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
3-
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ARG PY_VER
2+
ARG DISTRO
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FROM mcr.microsoft.com/devcontainers/python:${PY_VER}-${DISTRO}
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RUN \
55
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 pytest pytest-cov nose nose-cov datajoint && \
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pip uninstall datajoint -y
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USER root
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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
13+
ENV DJ_PASS password

‎.devcontainer/devcontainer.json‎

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@@ -1,34 +1,49 @@
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// For format details, see https://aka.ms/devcontainer.json. For config options, see the
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// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-docker-compose
23
{
3-
"name": "Development",
4-
"dockerComposeFile": "docker-compose.yaml",
4+
"name": "Existing Docker Compose (Extend)",
5+
// Update the 'dockerComposeFile' list if you have more compose files or use different names.
6+
// The .devcontainer/docker-compose.yml file contains any overrides you need/want to make.
7+
"dockerComposeFile": [
8+
"../LNX-docker-compose.yml",
9+
"docker-compose.yml"
10+
],
11+
// The 'service' property is the name of the service for the container that VS Code should
12+
// use. Update this value and .devcontainer/docker-compose.yml to the real service name.
513
"service": "app",
14+
// The optional 'workspaceFolder' property is the path VS Code should open by default when
15+
// connected. This is typically a file mount in .devcontainer/docker-compose.yml
616
"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
7-
// Use this environment variable if you need to bind mount your local source code into a new container.
8-
"remoteEnv": {
9-
"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
10-
},
11-
// https://containers.dev/features
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"features": {
13-
"ghcr.io/devcontainers/features/docker-in-docker:2": {},
14-
"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": {}
17-
},
18-
"onCreateCommand": "pip install -e .",
19-
"postStartCommand": "MYSQL_VER=8.0 MINIO_VER=RELEASE.2022-08-11T04-37-28Z docker compose -f local-docker-compose.yml down && docker volume prune -f && MYSQL_VER=8.0 MINIO_VER=RELEASE.2022-08-11T04-37-28Z docker compose -f local-docker-compose.yml up --build --wait",
17+
// Features to add to the dev container. More info: https://containers.dev/features.
18+
// "features": {},
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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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80,
2222
443,
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3306,
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8080,
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9000
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],
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// Uncomment the next line if you want start specific services in your Docker Compose config.
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// "runServices": [],
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// Uncomment the next line if you want to keep your containers running after VS Code shuts down.
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"shutdownAction": "stopCompose",
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"onCreateCommand": "python3 -m pip install -e .",
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"features": {
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"ghcr.io/devcontainers/features/git:1": {},
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"ghcr.io/devcontainers/features/docker-in-docker:2": {},
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},
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// Configure tool-specific properties.
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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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"remoteEnv": {
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"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
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}
47+
// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
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// "remoteUser": "devcontainer"
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}

‎.devcontainer/docker-compose.yaml‎

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This file was deleted.

‎.devcontainer/docker-compose.yml‎

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version: '2.4'
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services:
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# Update this to the name of the service you want to work with in your docker-compose.yml file
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app:
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# Uncomment if you want to override the service's Dockerfile to one in the .devcontainer
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# folder. Note that the path of the Dockerfile and context is relative to the *primary*
7+
# docker-compose.yml file (the first in the devcontainer.json "dockerComposeFile"
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# array). The sample below assumes your primary file is in the root of your project.
9+
container_name: datajoint-python-devcontainer
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image: datajoint/datajoint-python-devcontainer:${PY_VER:-3.11}-${DISTRO:-buster}
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build:
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context: .
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dockerfile: .devcontainer/Dockerfile
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args:
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- PY_VER=${PY_VER:-3.11}
16+
- DISTRO=${DISTRO:-buster}
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volumes:
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# Update this to wherever you want VS Code to mount the folder of your project
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- ..:/workspaces:cached
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# Uncomment the next four lines if you will use a ptrace-based debugger like C++, Go, and Rust.
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# cap_add:
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# - SYS_PTRACE
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# security_opt:
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# - seccomp:unconfined
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28+
user: root
29+
30+
# Overrides default command so things don't shut down after the process ends.
31+
command: /bin/sh -c "while sleep 1000; do :; done"
32+

‎.github/workflows/development.yaml‎

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@@ -28,7 +28,7 @@ jobs:
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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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- uses: actions/checkout@v4
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- name: Validate version and release notes
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run: |
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DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' datajoint/version.py)
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- name: Build pip artifacts
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run: |
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export HOST_UID=$(id -u)
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docker-compose -f docker-compose-build.yaml up --exit-code-from app --build
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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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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: "3.11"
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mysql_ver: "8.0"
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- py_ver: "3.10"
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mysql_ver: "8.0"
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- py_ver: "3.8"
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mysql_ver: "5.7"
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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@v3
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- uses: actions/checkout@v4
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- name: Set up Python ${{matrix.py_ver}}
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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.py_ver}}
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- name: Install dependencies
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- name: Run primary tests
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env:
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PY_VER: ${{matrix.py_ver}}
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DJ_PASS: simple
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DJ_PASS: password
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MYSQL_VER: ${{matrix.mysql_ver}}
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DISTRO: alpine
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MINIO_VER: RELEASE.2021-09-03T03-56-13Z
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DOCKER_CLIENT_TIMEOUT: "120"
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COMPOSE_HTTP_TIMEOUT: "120"
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run: |
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export HOST_UID=$(id -u)
88-
docker-compose -f LNX-docker-compose.yml up --build --exit-code-from app
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docker compose -f LNX-docker-compose.yml up --build --exit-code-from app
91+
lint:
92+
runs-on: ubuntu-latest
93+
strategy:
94+
matrix:
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py_ver: ["3.11"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{matrix.py_ver}}
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uses: actions/setup-python@v5
100+
with:
101+
python-version: ${{matrix.py_ver}}
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- name: Install dependencies
103+
run: |
104+
python -m pip install --upgrade pip
105+
pip install flake8 black==24.2.0
106+
- 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 style tests
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run: |
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flake8 --ignore=E203,E722,W503 datajoint \
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--count --max-complexity=62 --max-line-length=127 --statistics
93-
black datajoint --check -v
94-
black tests --check -v
95-
black tests_old --check -v
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black --required-version '24.2.0' --check -v datajoint tests tests_old
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codespell:
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name: Check for spelling errors
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permissions:
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contents: read
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Codespell
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uses: codespell-project/actions-codespell@v2
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publish-docs:
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if: |
98125
github.event_name == 'push' &&
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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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- uses: actions/checkout@v4
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- name: Deploy docs
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run: |
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export MODE=BUILD
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outputs:
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release_upload_url: ${{steps.create_gh_release.outputs.upload_url}}
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steps:
138-
- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Set up Python ${{matrix.py_ver}}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
141168
with:
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python-version: ${{matrix.py_ver}}
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- name: Determine package version
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- name: Publish pip release
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run: |
193220
export HOST_UID=$(id -u)
194-
docker-compose -f docker-compose-build.yaml run \
221+
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

‎.github/workflows/docs.yaml‎

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name: Manual docs release
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on:
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workflow_dispatch:
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jobs:
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publish-docs:
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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@v4
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- name: Deploy docs
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run: |
14+
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

‎.gitignore‎

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!.vscode/settings.json
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!.vscode/launch.json
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!.devcontainer/devcontainer.json
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!.devcontainer/devcontainer.json
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!.devcontainer/docker-compose.yml
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‎CHANGELOG.md‎

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## Release notes
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3-
### Upcoming
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### 0.14.3 -- TBD
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- Added - `dj.Top` restriction ([#1024](https://github.com/datajoint/datajoint-python/issues/1024)) PR [#1084](https://github.com/datajoint/datajoint-python/pull/1084)
55

6+
### 0.14.2 -- Aug 19, 2024
7+
- Added - Migrate nosetests to pytest - PR [#1142](https://github.com/datajoint/datajoint-python/pull/1142)
8+
- Added - Codespell GitHub Actions workflow
9+
- Added - GitHub Actions workflow to manually release docs
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- Changed - Update `datajoint/nginx` to `v0.2.6`
11+
- Changed - Migrate docs from `https://docs.datajoint.org/python` to `https://datajoint.com/docs/core/datajoint-python`
12+
- Fixed - [DevContainer](https://containers.dev/) configuration - PR [#1115](https://github.com/datajoint/datajoint-python/pull/1115)
13+
- Fixed - Updated set_password to work on MySQL 8 - PR [#1106](https://github.com/datajoint/datajoint-python/pull/1106)
14+
- Added - Missing tests for set_password - PR [#1106](https://github.com/datajoint/datajoint-python/pull/1106)
15+
- Changed - Returning success count after the .populate() call - PR [#1050](https://github.com/datajoint/datajoint-python/pull/1050)
16+
- Fixed - `Autopopulate.populate` excludes `reserved` jobs in addition to `ignore` and `error` jobs
17+
- Fixed - Issue [#1159](https://github.com/datajoint/datajoint-python/pull/1159) (cascading delete) - PR [#1160](https://github.com/datajoint/datajoint-python/pull/1160)
18+
- Changed - Minimum Python version for Datajoint-Python is now 3.8 PR #1163
19+
- Fixed - `docker compose` commands in CI [#1164](https://github.com/datajoint/datajoint-python/pull/1164)
20+
- Changed - Default delete behavior now includes masters of part tables - PR [#1158](https://github.com/datajoint/datajoint-python/pull/1158)
21+
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### 0.14.1 -- Jun 02, 2023
723
- Fixed - Fix altering a part table that uses the "master" keyword - PR [#991](https://github.com/datajoint/datajoint-python/pull/991)
824
- Fixed - `.ipynb` output in tutorials is not visible in dark mode ([#1078](https://github.com/datajoint/datajoint-python/issues/1078)) PR [#1080](https://github.com/datajoint/datajoint-python/pull/1080)
@@ -34,7 +50,7 @@
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- Fixed - Fix queries with backslashes ([#999](https://github.com/datajoint/datajoint-python/issues/999)) PR [#1052](https://github.com/datajoint/datajoint-python/pull/1052)
3551

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### 0.13.7 -- Jul 13, 2022
37-
- Fixed - Fix networkx incompatable change by version pinning to 2.6.3 (#1035) PR #1036
53+
- Fixed - Fix networkx incompatible change by version pinning to 2.6.3 (#1035) PR #1036
3854
- Added - Support for serializing numpy datetime64 types (#1022) PR #1036
3955
- Changed - Add traceback to default logging PR #1036
4056

@@ -86,7 +102,7 @@
86102
- Fixed - `schema.list_tables()` is not topologically sorted (#838) PR #893
87103
- Fixed - Diagram part tables do not show proper class name (#882) PR #893
88104
- Fixed - Error in complex restrictions (#892) PR #893
89-
- Fixed - WHERE and GROUP BY clases are dropped on joins with aggregation (#898, #899) PR #893
105+
- Fixed - WHERE and GROUP BY classes are dropped on joins with aggregation (#898, #899) PR #893
90106

91107
### 0.13.0 -- Mar 24, 2021
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- Re-implement query transpilation into SQL, fixing issues (#386, #449, #450, #484, #558). PR #754

‎LNX-docker-compose.yml‎

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services:
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db:
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<<: *net
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image: datajoint/mysql:${MYSQL_VER}
10+
image: datajoint/mysql:${MYSQL_VER:-8.0}
1111
environment:
12-
- MYSQL_ROOT_PASSWORD=${DJ_PASS}
12+
- MYSQL_ROOT_PASSWORD=${DJ_PASS:-password}
13+
command: mysqld --default-authentication-plugin=mysql_native_password
1314
# ports:
1415
# - "3306:3306"
1516
# volumes:
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2122
interval: 15s
2223
minio:
2324
<<: *net
24-
image: minio/minio:${MINIO_VER}
25+
image: minio/minio:${MINIO_VER:-RELEASE.2022-08-11T04-37-28Z}
2526
environment:
2627
- MINIO_ACCESS_KEY=datajoint
2728
- MINIO_SECRET_KEY=datajoint
@@ -44,7 +45,7 @@ services:
4445
interval: 15s
4546
fakeservices.datajoint.io:
4647
<<: *net
47-
image: datajoint/nginx:v0.2.6
48+
image: datajoint/nginx:latest
4849
environment:
4950
- ADD_db_TYPE=DATABASE
5051
- ADD_db_ENDPOINT=db:3306
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# - "3306:3306"
5960
app:
6061
<<: *net
61-
image: datajoint/djtest:py${PY_VER}-${DISTRO}
62+
image: datajoint/djtest:py${PY_VER:-3.8}-${DISTRO:-alpine}
6263
depends_on:
6364
db:
6465
condition: service_healthy
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environment:
7071
- DJ_HOST=fakeservices.datajoint.io
7172
- DJ_USER=root
72-
- DJ_PASS
73+
- DJ_PASS=password
7374
- DJ_TEST_HOST=fakeservices.datajoint.io
7475
- DJ_TEST_USER=datajoint
7576
- DJ_TEST_PASSWORD=datajoint
@@ -86,14 +87,12 @@ services:
8687
- -c
8788
- |
8889
set -e
89-
pip install --user nose nose-cov
9090
pip install -e .
9191
pip list --format=freeze | grep datajoint
9292
pytest -sv --cov-report term-missing --cov=datajoint tests
93-
nosetests -vsw tests_old --with-coverage --cover-package=datajoint
9493
# ports:
9594
# - "8888:8888"
96-
user: ${HOST_UID}:anaconda
95+
user: ${HOST_UID:-1000}:anaconda
9796
volumes:
9897
- .:/src
9998
- /tmp/.X11-unix:/tmp/.X11-unix:rw

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