datajoint 0.14.2__tar.gz → 0.14.3__tar.gz

datajoint-0.14.3/.codespellrc

@@ -0,0 +1,5 @@
+[codespell]
+skip = .git,*.pdf,*.svg,*.csv,*.ipynb,*.drawio
+# Rever -- nobody knows
+# numer -- numerator variable
+ignore-words-list = rever,numer

datajoint-0.14.3/.coveragerc

@@ -0,0 +1,6 @@
+[run]
+branch = False
+source = datajoint
+
+[report]
+show_missing = True

datajoint-0.14.3/.devcontainer/Dockerfile

@@ -0,0 +1,13 @@
+ARG PY_VER
+ARG DISTRO
+FROM mcr.microsoft.com/devcontainers/python:${PY_VER}-${DISTRO}
+RUN \
+    apt update && \
+    apt-get install bash-completion graphviz default-mysql-client -y && \
+    pip install flake8 black faker ipykernel pytest pytest-cov nose nose-cov datajoint jupyterlab && \
+    pip uninstall datajoint -y
+
+USER root
+ENV DJ_HOST db
+ENV DJ_USER root
+ENV DJ_PASS password

datajoint-0.14.3/.devcontainer/devcontainer.json

@@ -0,0 +1,50 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-docker-compose
+{
+	"name": "Existing Docker Compose (Extend)",
+	// Update the 'dockerComposeFile' list if you have more compose files or use different names.
+	// The .devcontainer/docker-compose.yml file contains any overrides you need/want to make.
+	"dockerComposeFile": [
+		"../docker-compose.yaml",
+		"docker-compose.yml"
+	],
+	// The 'service' property is the name of the service for the container that VS Code should
+	// use. Update this value and .devcontainer/docker-compose.yml to the real service name.
+	"service": "app",
+	// The optional 'workspaceFolder' property is the path VS Code should open by default when
+	// connected. This is typically a file mount in .devcontainer/docker-compose.yml
+	"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	"forwardPorts": [
+		80,
+		443,
+		3306,
+		8080,
+		9000
+	],
+	// Uncomment the next line if you want start specific services in your Docker Compose config.
+	// "runServices": [],
+	// Uncomment the next line if you want to keep your containers running after VS Code shuts down.
+	"shutdownAction": "stopCompose",
+	"onCreateCommand": "python3 -m pip install -q -e .[test]",
+	"features": {
+		"ghcr.io/devcontainers/features/git:1": {},
+		"ghcr.io/devcontainers/features/docker-in-docker:2": {},
+		"ghcr.io/devcontainers/features/github-cli:1": {},
+	},
+	// Configure tool-specific properties.
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"ms-python.python"
+			]
+		}
+	},
+	"remoteEnv": {
+		"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
+	}
+	// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "devcontainer"
+}

datajoint-0.14.3/.devcontainer/docker-compose.yml

@@ -0,0 +1,32 @@
+version: '2.4'
+services:
+  # Update this to the name of the service you want to work with in your docker-compose.yml file
+  app:
+    # Uncomment if you want to override the service's Dockerfile to one in the .devcontainer
+    # folder. Note that the path of the Dockerfile and context is relative to the *primary*
+    # docker-compose.yml file (the first in the devcontainer.json "dockerComposeFile"
+    # array). The sample below assumes your primary file is in the root of your project.
+    container_name: datajoint-python-devcontainer
+    image: datajoint/datajoint-python-devcontainer:${PY_VER:-3.11}-${DISTRO:-buster}
+    build:
+      context: .
+      dockerfile: .devcontainer/Dockerfile
+      args:
+        - PY_VER=${PY_VER:-3.11}
+        - DISTRO=${DISTRO:-buster}
+
+    volumes:
+      # Update this to wherever you want VS Code to mount the folder of your project
+      - ..:/workspaces:cached
+
+    # Uncomment the next four lines if you will use a ptrace-based debugger like C++, Go, and Rust.
+    # cap_add:
+    #   - SYS_PTRACE
+    # security_opt:
+    #   - seccomp:unconfined
+
+    user: root
+
+    # Overrides default command so things don't shut down after the process ends.
+    command: /bin/sh -c "while sleep 1000; do :; done"
+

datajoint-0.14.3/.dockerignore

@@ -0,0 +1,6 @@
+notebook
+build
+*.egg-info
+dist
+.vscode
+__pycache__

datajoint-0.14.3/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,37 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+
+## Bug Report
+
+### Description
+A clear and concise description of what is the overall operation that is intended to be performed that resulted in an error.
+
+### Reproducibility
+Include:
+- OS (WIN | MACOS | Linux)
+- Python Version OR MATLAB Version
+- MySQL Version
+- MySQL Deployment Strategy (local-native | local-docker | remote)
+- DataJoint Version
+- Minimum number of steps to reliably reproduce the issue
+- Complete error stack as a result of evaluating the above steps
+
+### Expected Behavior
+A clear and concise description of what you expected to happen.
+
+### Screenshots
+If applicable, add screenshots to help explain your problem.
+
+### Additional Research and Context
+Add any additional research or context that was conducted in creating this report.
+
+For example:
+- Related GitHub issues and PR's either within this repository or in other relevant repositories.
+- Specific links to specific lines or a focus within source code.
+- Relevant summary of Maintainers development meetings, milestones, projects, etc.

datajoint-0.14.3/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,46 @@
+---
+name: Feature request
+about: Suggest an idea for a new feature
+title: ''
+labels: 'enhancement, awaiting-triage'
+assignees: ''
+
+---
+
+## Feature Request
+
+### Problem
+A clear and concise description how this idea has manifested and the context. Elaborate on the need for this feature and/or what could be improved. Ex. I'm always frustrated when [...]
+
+### Requirements
+A clear and concise description of the requirements to satisfy the new feature. Detail what you expect from a successful implementation of the feature. Ex. When using this feature, it should [...]
+
+### Justification
+Provide the key benefits in making this a supported feature. Ex. Adding support for this feature would ensure [...]
+
+### Alternative Considerations
+Do you currently have a work-around for this? Provide any alternative solutions or features you've considered.
+
+### Related Errors
+Add any errors as a direct result of not exposing this feature.
+
+Please include steps to reproduce provided errors as follows:
+- OS (WIN | MACOS | Linux)
+- Python Version OR MATLAB Version
+- MySQL Version
+- MySQL Deployment Strategy (local-native | local-docker | remote)
+- DataJoint Version
+- Minimum number of steps to reliably reproduce the issue
+- Complete error stack as a result of evaluating the above steps
+
+### Screenshots
+If applicable, add screenshots to help explain your feature.
+
+### Additional Research and Context
+Add any additional research or context that was conducted in creating this feature request.
+
+For example:
+- Related GitHub issues and PR's either within this repository or in other relevant repositories.
+- Specific links to specific line or focus within source code.
+- Relevant summary of Maintainers development meetings, milestones, projects, etc.
+- Any additional supplemental web references or links that would further justify this feature request.

datajoint-0.14.3/.github/workflows/development.yaml

@@ -0,0 +1,239 @@
+name: Development
+on:
+  push:
+    branches:
+      - "**" # every branch
+      - "!gh-pages" # exclude gh-pages branch
+      - "!stage*" # exclude branches beginning with stage
+    tags:
+      - '\d+\.\d+\.\d+' # only semver tags
+  pull_request:
+    branches:
+      - "**" # every branch
+      - "!gh-pages" # exclude gh-pages branch
+      - "!stage*" # exclude branches beginning with stage
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - py_ver: "3.9"
+            distro: debian
+            image: djbase
+    env:
+      PY_VER: ${{matrix.py_ver}}
+      DISTRO: ${{matrix.distro}}
+      IMAGE: ${{matrix.image}}
+      DOCKER_CLIENT_TIMEOUT: "120"
+      COMPOSE_HTTP_TIMEOUT: "120"
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{matrix.py_ver}}
+      - name: Validate version and release notes
+        run: |
+          DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' datajoint/version.py)
+          RELEASE_BODY=$(python3 -c \
+            'print(open("./CHANGELOG.md").read().split("\n\n")[1].split("\n", 1)[1])' \
+          )
+          echo "DJ_VERSION=${DJ_VERSION}" >> $GITHUB_ENV
+          echo "RELEASE_BODY<<EOF" >> $GITHUB_ENV
+          echo "$RELEASE_BODY" >> $GITHUB_ENV
+          echo "EOF" >> $GITHUB_ENV
+      - name: Build pip artifacts
+        run: |
+          python3 -m pip install build
+          python3 -m build .
+          echo "DJ_VERSION=${DJ_VERSION}" >> $GITHUB_ENV
+      - if: matrix.py_ver == '3.9' && matrix.distro == 'debian'
+        name: Add pip artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: pip-datajoint-${{env.DJ_VERSION}}
+          path: dist
+          retention-days: 1
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        py_ver: ["3.9"]
+        mysql_ver: ["8.0", "5.7"]
+        include:
+          - py_ver: "3.12"
+            mysql_ver: "8.0"
+          - py_ver: "3.11"
+            mysql_ver: "8.0"
+          - py_ver: "3.10"
+            mysql_ver: "8.0"
+          - py_ver: "3.8"
+            mysql_ver: "5.7"
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{matrix.py_ver}}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{matrix.py_ver}}
+      - name: Run primary tests
+        env:
+          PY_VER: ${{matrix.py_ver}}
+          DJ_PASS: password
+          MYSQL_VER: ${{matrix.mysql_ver}}
+          DISTRO: alpine
+          MINIO_VER: RELEASE.2021-09-03T03-56-13Z
+          DOCKER_CLIENT_TIMEOUT: "120"
+          COMPOSE_HTTP_TIMEOUT: "120"
+        run: |
+          export HOST_UID=$(id -u)
+          docker compose --profile test up --quiet-pull --build --exit-code-from djtest djtest
+  lint:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        py_ver: ["3.11"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{matrix.py_ver}}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{matrix.py_ver}}
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install ".[test]"
+      - name: Run syntax tests
+        run: flake8 datajoint --count --select=E9,F63,F7,F82 --show-source --statistics
+      - name: Run style tests
+        run: |
+          flake8 --ignore=E203,E722,W503 datajoint \
+                 --count --max-complexity=62 --max-line-length=127 --statistics \
+                 --per-file-ignores='datajoint/diagram.py:C901'
+          black --required-version '24.2.0' --check -v datajoint tests
+  codespell:
+    name: Check for spelling errors
+    permissions:
+      contents: read
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
+  publish-docs:
+    if: |
+      github.event_name == 'push' &&
+      startsWith(github.ref, 'refs/tags')
+    needs: test
+    runs-on: ubuntu-latest
+    env:
+      DOCKER_CLIENT_TIMEOUT: "120"
+      COMPOSE_HTTP_TIMEOUT: "120"
+    steps:
+      - uses: actions/checkout@v4
+      - name: Deploy docs
+        run: |
+          export MODE=BUILD
+          export PACKAGE=datajoint
+          export UPSTREAM_REPO=https://github.com/${GITHUB_REPOSITORY}.git
+          export HOST_UID=$(id -u)
+          docker compose -f docs/docker-compose.yaml up --quiet-pull --exit-code-from docs --build
+          git push origin gh-pages
+  publish-release:
+    if: |
+      github.event_name == 'push' &&
+      startsWith(github.ref, 'refs/tags')
+    needs: test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - py_ver: "3.9"
+            distro: debian
+            image: djbase
+    env:
+      PY_VER: ${{matrix.py_ver}}
+      DISTRO: ${{matrix.distro}}
+      IMAGE: ${{matrix.image}}
+      TWINE_USERNAME: ${{secrets.twine_username}}
+      TWINE_PASSWORD: ${{secrets.twine_password}}
+      DOCKER_CLIENT_TIMEOUT: "120"
+      COMPOSE_HTTP_TIMEOUT: "120"
+    outputs:
+      release_upload_url: ${{steps.create_gh_release.outputs.upload_url}}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{matrix.py_ver}}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{matrix.py_ver}}
+      - name: Determine package version
+        run: |
+          DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' datajoint/version.py)
+          RELEASE_BODY=$(python -c \
+            'print(open("./CHANGELOG.md").read().split("\n\n")[1].split("\n", 1)[1])' \
+          )
+          echo "DJ_VERSION=${DJ_VERSION}" >> $GITHUB_ENV
+          echo "RELEASE_BODY<<EOF" >> $GITHUB_ENV
+          echo "$RELEASE_BODY" >> $GITHUB_ENV
+          echo "EOF" >> $GITHUB_ENV
+      - name: Create GH release
+        id: create_gh_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          tag_name: ${{env.DJ_VERSION}}
+          release_name: Release ${{env.DJ_VERSION}}
+          body: ${{env.RELEASE_BODY}}
+          prerelease: false
+          draft: false
+      - name: Fetch pip artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: pip-datajoint-${{env.DJ_VERSION}}
+          path: dist
+      - name: Determine pip artifact paths
+        run: |
+          echo "DJ_WHEEL_PATH=$(ls dist/datajoint-*.whl)" >> $GITHUB_ENV
+          echo "DJ_SDIST_PATH=$(ls dist/datajoint-*.tar.gz)" >> $GITHUB_ENV
+      - name: Upload pip wheel asset to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          upload_url: ${{steps.create_gh_release.outputs.upload_url}}
+          asset_path: ${{env.DJ_WHEEL_PATH}}
+          asset_name: pip-datajoint-${{env.DJ_VERSION}}.whl
+          asset_content_type: application/zip
+      - name: Upload pip sdist asset to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          upload_url: ${{steps.create_gh_release.outputs.upload_url}}
+          asset_path: ${{env.DJ_SDIST_PATH}}
+          asset_name: pip-datajoint-${{env.DJ_VERSION}}.tar.gz
+          asset_content_type: application/gzip
+      - name: Publish pip release
+        run: |
+          export HOST_UID=$(id -u)
+          docker compose run --build --quiet-pull \
+            -e TWINE_USERNAME=${TWINE_USERNAME} -e TWINE_PASSWORD=${TWINE_PASSWORD} app \
+            sh -c "pip install twine && python -m twine upload dist/*"
+      - name: Login to DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{secrets.docker_username}}
+          password: ${{secrets.docker_password}}
+      - name: Publish image
+        run: |
+          IMAGE=$(docker images --filter "reference=datajoint/datajoint*" --format "{{.Repository}}")
+          TAG=$(docker images --filter "reference=datajoint/datajoint*" --format "{{.Tag}}")
+          docker push "${IMAGE}:${TAG}"
+          docker tag "${IMAGE}:${TAG}" "${IMAGE}:${TAG}-${GITHUB_SHA:0:7}"
+          docker push "${IMAGE}:${TAG}-${GITHUB_SHA:0:7}"
+          [ "$PY_VER" == "3.9" ] && [ "$DISTRO" == "debian" ] \
+                  && docker tag "${IMAGE}:${TAG}" "${IMAGE}:latest" \
+                  && docker push "${IMAGE}:latest" \
+              || echo "skipping 'latest' tag..."

datajoint-0.14.3/.github/workflows/docs.yaml

@@ -0,0 +1,19 @@
+name: Manual docs release
+on:
+  workflow_dispatch:
+jobs:
+  publish-docs:
+    runs-on: ubuntu-latest
+    env:
+      DOCKER_CLIENT_TIMEOUT: "120"
+      COMPOSE_HTTP_TIMEOUT: "120"
+    steps:
+      - uses: actions/checkout@v4
+      - name: Deploy docs
+        run: |
+          export MODE=BUILD
+          export PACKAGE=datajoint
+          export UPSTREAM_REPO=https://github.com/${GITHUB_REPOSITORY}.git
+          export HOST_UID=$(id -u)
+          docker compose -f docs/docker-compose.yaml up --exit-code-from docs --build
+          git push origin gh-pages

datajoint-0.14.3/.gitignore

@@ -0,0 +1,35 @@
+.ipynb_checkpoints/
+*.json
+*/.*.swp
+*/.*.swo
+*/*.pyc
+.DS_Store
+__*__
+.idea/
+*.pyc
+.python-version
+*.egg-info/
+dist/
+MANIFEST
+.vagrant/
+dj_local_conf.json
+build/
+.coverage
+./tests/.coverage
+./tests/dj-store/*
+*.log
+*.env
+docker-compose.yml
+notebook
+__main__.py
+jupyter_custom.js
+.eggs
+*.code-workspace
+docs/site
+
+
+!.vscode/settings.json
+!.vscode/launch.json
+!.devcontainer/devcontainer.json
+!.devcontainer/docker-compose.yml
+

datajoint-0.14.3/.vscode/launch.json

@@ -0,0 +1,16 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "justMyCode": false
+        }
+    ]
+}

datajoint-0.14.3/.vscode/settings.json

@@ -0,0 +1,21 @@
+{
+    "editor.formatOnPaste": false,
+    "editor.formatOnSave": false,
+    "editor.rulers": [
+        94
+    ],
+    "python.formatting.provider": "black",
+    "[python]": {
+        "editor.defaultFormatter": null
+    },
+    "[markdown]": {
+        "editor.defaultFormatter": "disable"
+    },
+    "[yaml]": {
+        "editor.defaultFormatter": "disable"
+    },
+    "[dockercompose]": {
+        "editor.defaultFormatter": "disable"
+    },
+    "files.autoSave": "off"
+}