datajoint 2.0.2__tar.gz → 2.1.1__tar.gz

datajoint-2.1.1/.coveragerc

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

datajoint-2.1.1/.devcontainer/Dockerfile

@@ -0,0 +1,14 @@
+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
+ENV S3_ENDPOINT=minio:9000

datajoint-2.1.1/.devcontainer/devcontainer.json

@@ -0,0 +1,6 @@
+{
+  "dockerComposeFile": ["../docker-compose.yaml", "docker-compose.yml"],
+  "service": "app",
+  "workspaceFolder": "/src",
+  "postCreateCommand": "curl -fsSL https://pixi.sh/install.sh | bash && echo 'export PATH=\"$HOME/.pixi/bin:$PATH\"' >> ~/.bashrc"
+}

datajoint-2.1.1/.devcontainer/docker-compose.yml

@@ -0,0 +1,14 @@
+# Devcontainer overrides for the app service from ../docker-compose.yaml
+# Inherits db and minio services automatically
+services:
+  app:
+    container_name: datajoint-python-devcontainer
+    build:
+      context: ..
+      dockerfile: .devcontainer/Dockerfile
+      args:
+        - PY_VER=${PY_VER:-3.11}
+        - DISTRO=${DISTRO:-bookworm}
+    user: root
+    # Keep container running for devcontainer
+    command: /bin/sh -c "while sleep 1000; do :; done"

datajoint-2.1.1/.dockerignore

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

datajoint-2.1.1/.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

datajoint-2.1.1/.github/DISCUSSION_TEMPLATE/rfc.yml

@@ -0,0 +1,107 @@
+title: "[RFC] "
+labels:
+  - rfc
+  - "status: proposed"
+body:
+  - type: markdown
+    attributes:
+      value: |
+        ## DataJoint Enhancement Proposal
+
+        Use this template to propose changes to DataJoint specifications, APIs, or documentation structure.
+
+        **Before submitting:**
+        - Search existing discussions to avoid duplicates
+        - Consider starting with an informal discussion in the Ideas category first
+
+  - type: textarea
+    id: summary
+    attributes:
+      label: Summary
+      description: A brief, one-paragraph explanation of the proposal.
+      placeholder: This proposal adds/changes/removes...
+    validations:
+      required: true
+
+  - type: textarea
+    id: motivation
+    attributes:
+      label: Motivation
+      description: |
+        Why is this change needed? What problem does it solve?
+        Include concrete use cases and examples where possible.
+      placeholder: |
+        Currently, users need to...
+        This causes problems when...
+        With this change, users could...
+    validations:
+      required: true
+
+  - type: textarea
+    id: design
+    attributes:
+      label: Proposed Design
+      description: |
+        Detailed explanation of the proposed solution.
+        Include code examples, API signatures, or schema definitions as appropriate.
+      placeholder: |
+        ## API Changes
+        ```python
+        # Example usage
+        ```
+
+        ## Behavior
+        - When X happens, Y should occur
+        - Error handling: ...
+    validations:
+      required: true
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives Considered
+      description: What other approaches were considered and why were they not chosen?
+      placeholder: |
+        1. Alternative A: ...
+           Rejected because: ...
+
+        2. Alternative B: ...
+           Rejected because: ...
+
+  - type: textarea
+    id: compatibility
+    attributes:
+      label: Backwards Compatibility
+      description: |
+        How does this affect existing users?
+        - Breaking changes?
+        - Migration path?
+        - Deprecation timeline?
+      placeholder: |
+        This change is/is not backwards compatible.
+
+        Migration path:
+        1. ...
+
+  - type: textarea
+    id: implementation
+    attributes:
+      label: Implementation Notes
+      description: |
+        Optional: Technical details, affected files, estimated scope.
+        Prototyping in parallel with RFC discussion is encouraged.
+      placeholder: |
+        Affected components:
+        - datajoint-python/src/datajoint/...
+
+        Estimated scope: small/medium/large
+
+  - type: checkboxes
+    id: checklist
+    attributes:
+      label: Checklist
+      options:
+        - label: I have searched existing discussions and issues for duplicates
+          required: true
+        - label: I have considered backwards compatibility
+          required: true

datajoint-2.1.1/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,37 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "Bug: "
+labels: ["bug", "triage"]
+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-2.1.1/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,46 @@
+---
+name: Feature request
+about: Suggest an idea for a new feature
+title: "FEAT: "
+labels: ["enhancement", "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. 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-2.1.1/.github/ISSUE_TEMPLATE/improvement_request.md

@@ -0,0 +1,46 @@
+---
+name: Improvement request
+about: Suggest an idea for improvement
+title: "IMPR: "
+labels: ["enhancement", "triage"]
+assignees: ''
+
+---
+
+## Improvement Request
+
+### Problem
+A clear and concise description how this idea has manifested and the context. Elaborate on the need for what could be improved. Ex. I'm always frustrated when [...]
+
+### Requirements
+A clear and concise description of the requirements to satisfy the new improvement. Detail what you expect from a successful implementation of the improvement. Ex. When using this improvement, it should [...]
+
+### Justification
+Provide the key benefits in making this a supported improvement. Ex. Adding support for this improvement would ensure [...]
+
+### Alternative Considerations
+Do you currently have a work-around for this? Provide any alternative solutions or improvements you've considered.
+
+### Related Errors
+Add any errors as a direct result of not exposing this improvement.
+
+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 improvement.
+
+### Additional Research and Context
+Add any additional research or context that was conducted in creating this improvement 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 improvement request.

datajoint-2.1.1/.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+      day: "wednesday"
+      time: "9:00"
+      timezone: "America/Chicago"
+    groups:
+      all-actions:
+        patterns: [ "*" ]

datajoint-2.1.1/.github/release_drafter.yaml

@@ -0,0 +1,35 @@
+version-resolver:
+  major:
+    labels:
+      - 'breaking'
+  minor:
+    labels:
+      - 'feature'
+  patch:
+    labels:
+      - 'documentation'
+      - 'enhancement'
+      - 'bug'
+name-template: '$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+categories:
+  - title: '💥 Breaking Changes'
+    labels:
+      - 'breaking'
+  - title: '🚀 Features'
+    labels:
+      - 'feature'
+  - title: '⚡️ Enhancements'
+    labels:
+      - 'enhancement'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'bug'
+  - title: '📝 Documentation'
+    label: 'documentation'
+change-template: '- $TITLE(#$NUMBER)@$AUTHOR'
+change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
+template: |
+  $CHANGES
+
+  **Full Changelog**: https://github.com/$OWNER/$REPOSITORY/compare/$PREVIOUS_TAG...v$RESOLVED_VERSION

datajoint-2.1.1/.github/workflows/close_inactive_issues_prs.yaml

@@ -0,0 +1,33 @@
+name: Close inactive issues and PRs
+on:
+  schedule:
+    - cron: "30 1 * * *"
+  workflow_dispatch:
+
+jobs:
+  close-issues:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v9
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          operations-per-run: 500 # API rate limit
+          ## issues
+          # stale
+          days-before-issue-stale: 45 # for initial period, suggest 15
+          stale-issue-label: "stale"
+          stale-issue-message: "This issue is stale because it has been open for 45 days with no activity."
+          # close
+          days-before-issue-close: 365 # for initial period, suggest 30
+          close-issue-message: "This issue was closed because it has been inactive for 365 days since being marked as stale, please reopen if it's still applicable."
+          ## PRs
+          # stale
+          days-before-pr-stale: 45 # for initial period, suggest 15
+          stale-pr-label: "stale"
+          stale-pr-message: "This PR is stale because it has been open for 45 days with no activity."
+          # close
+          days-before-pr-close: 365 # for initial period, suggest 30
+          close-pr-message: "This PR was closed because it has been inactive for 365 days since being marked as stale, please reopen if it's still applicable."

datajoint-2.1.1/.github/workflows/draft_release.yaml

@@ -0,0 +1,31 @@
+name: Manual Draft Release
+on:
+  workflow_dispatch:
+    inputs:
+      testpypi:
+        description: 'Release to TestPyPI then skip following'
+        default: 'false'
+        type: choice
+        options:
+          - 'true'
+          - 'false'
+jobs:
+  build-release:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+      # write permission is required for autolabeler
+      # otherwise, read permission is required at least
+      pull-requests: read
+    runs-on: ubuntu-latest
+    steps:
+      # Drafts your next Release notes as Pull Requests are merged into "master"
+      - name: Draft release notes
+        id: create_gh_release
+        uses: release-drafter/release-drafter@v6
+        with:
+          config-name: release_drafter.yaml
+          disable-autolabeler: true
+          name: ${{ github.event.inputs.testpypi == 'true' && 'Test $RESOLVED_VERSION' || 'Release $RESOLVED_VERSION' }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

datajoint-2.1.1/.github/workflows/lint.yaml

@@ -0,0 +1,29 @@
+name: Lint
+on:
+  push:
+    branches:
+      - "**" # every branch
+      - "!gh-pages" # exclude gh-pages branch
+      - "!stage*" # exclude branches beginning with stage
+  pull_request:
+    branches:
+      - "**" # every branch
+      - "!gh-pages" # exclude gh-pages branch
+      - "!stage*" # exclude branches beginning with stage
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+    # enforce the same check as pre-commit
+    # but only run important checks
+    - uses: pre-commit/action@v3.0.1
+      with:
+        extra_args: codespell --all-files
+    - uses: pre-commit/action@v3.0.1
+      with:
+        extra_args: ruff --all-files
+    - uses: pre-commit/action@v3.0.1
+      with:
+        extra_args: ruff-format --all-files

datajoint-2.1.1/.github/workflows/post_draft_release_published.yaml

@@ -0,0 +1,152 @@
+name: Post Draft Release Published
+
+on:
+  release:
+    types:
+      ## pre-release and stable release
+      #- published
+      ## stable release only
+      - released
+run-name: Post ${{ github.event.release.name }}
+
+jobs:
+  pypi-release:
+    permissions:
+      # write permission is required to update version.py
+      contents: write
+      pull-requests: write
+    # Use the oldest supported version to build, just in case there are issues
+    # for our case, this doesn't matter that much, since the build is for 3.x
+    strategy:
+      matrix:
+        include:
+          - py_ver: "3.10"
+    runs-on: ubuntu-latest
+    env:
+      PY_VER: ${{matrix.py_ver}}
+      TWINE_USERNAME: ${{secrets.twine_username}}
+      TWINE_PASSWORD: ${{secrets.twine_password}}
+      TWINE_TEST_USERNAME: ${{secrets.twine_test_username}}
+      TWINE_TEST_PASSWORD: ${{secrets.twine_test_password}}
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+      # new release needs the updated version.py
+      - name: Update version.py
+        run: |
+          VERSION=$(echo "${{ github.event.release.name }}" | grep -oP '\d+\.\d+\.\d+')
+          sed -i "s/^__version__ = .*/__version__ = \"$VERSION\"/" src/datajoint/version.py
+          cat src/datajoint/version.py
+          # Commit the changes
+          BRANCH_NAME="update-version-$VERSION"
+          git switch -c $BRANCH_NAME
+          git config --global user.name "github-actions"
+          git config --global user.email "github-actions@github.com"
+          git add src/datajoint/version.py
+          git commit -m "Update version.py to $VERSION"
+          echo "BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
+      - name: Update README.md badge
+        run: |
+          # commits since the last release
+          NEW_HREF="https://github.com/datajoint/datajoint-python/compare/${{ github.event.release.tag_name }}...master"
+          NEW_SRC="https://img.shields.io/github/commits-since/datajoint/datajoint-python/${{ github.event.release.tag_name }}?color=red"
+          # Update href in the <a> tag
+          sed -i 's|\(<a id="commit-since-release-link"[^>]*href="\)[^"]*\(".*\)|\1'"$NEW_HREF"'\2|' README.md
+          # Update src in the <img> tag
+          sed -i 's|\(<img id="commit-since-release-img"[^>]*src="\)[^"]*\(".*\)|\1'"$NEW_SRC"'\2|' README.md
+          git add README.md
+          # Only commit if there are changes (handles re-runs gracefully)
+          git diff --cached --quiet README.md || git commit -m "Update README.md badge to ${{ github.event.release.tag_name }}"
+      - name: Set up Python ${{matrix.py_ver}}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{matrix.py_ver}}
+      # Merging build and release steps just for the simplicity,
+      # since datajoint-python doesn't have platform specific dependencies or binaries,
+      # and the build process is fairly fast, so removed upload/download artifacts
+      - name: Build package
+        id: build
+        run: |
+          python -m pip install build
+          python -m build .
+          echo "DJ_WHEEL_PATH=$(ls dist/datajoint-*.whl)" >> $GITHUB_ENV
+          echo "DJ_SDIST_PATH=$(ls dist/datajoint-*.tar.gz)" >> $GITHUB_ENV
+          echo "NEW_VERSION=${{github.event.release.resolved_version}}" >> $GITHUB_ENV
+      - name: Publish package
+        id: publish
+        env:
+          RELEASE_NAME: ${{ github.event.release.name }}
+        run: |
+          export HOST_UID=$(id -u)
+          if [[ "$RELEASE_NAME" =~ ^Test ]]; then
+            LATEST_PYPI=$(curl -s https://test.pypi.org/pypi/datajoint/json | jq -r '.info.version')
+            echo "TEST_PYPI=true" >> $GITHUB_ENV
+            export TWINE_REPOSITORY="testpypi"
+            export TWINE_USERNAME=${TWINE_TEST_USERNAME}
+            export TWINE_PASSWORD=${TWINE_TEST_PASSWORD}
+          else
+            LATEST_PYPI=$(curl -s https://pypi.org/pypi/datajoint/json | jq -r '.info.version')
+            echo "TEST_PYPI=false" >> $GITHUB_ENV
+            export TWINE_REPOSITORY="pypi"
+          fi
+          # Check if the new version is different from the latest on PyPI, avoid re-uploading error
+          if [ "$NEW_VERSION" != "$LATEST_PYPI" ]; then
+            docker compose run --build --quiet-pull \
+            -e TWINE_USERNAME=${TWINE_USERNAME} \
+            -e TWINE_PASSWORD=${TWINE_PASSWORD} \
+            -e TWINE_REPOSITORY=${TWINE_REPOSITORY} \
+            app sh -c "pip install twine && python -m twine upload dist/*"
+          else
+            echo "::warning::Latest version $LATEST_PYPI on $TWINE_REPOSITORY is the new version $NEW_VERSION"
+          fi
+      # Upload package as release assets
+      - name: Upload pip wheel asset to release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        with:
+          upload_url: ${{github.event.release.upload_url}}
+          asset_path: ${{env.DJ_WHEEL_PATH}}
+          asset_name: pip-datajoint-${{ github.event.release.tag_name }}.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: ${{github.event.release.upload_url}}
+          asset_path: ${{env.DJ_SDIST_PATH}}
+          asset_name: pip-datajoint-${{ github.event.release.tag_name }}.tar.gz
+          asset_content_type: application/gzip
+      - name: Create Pull Request
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          git push origin ${{ env.BRANCH_NAME }}
+          gh pr create \
+            --title "[github-actions]Update version.py to ${{ github.event.release.name }}" \
+            --body "This PR updates \`version.py\` to match the latest release: ${{ github.event.release.name }}" \
+            --base master \
+            --head ${{ env.BRANCH_NAME }} \
+            --reviewer dimitri-yatsenko,drewyangdev,ttngu207
+      - name: Post release notification to Slack
+        if: ${{ env.TEST_PYPI == 'false' }}
+        uses: slackapi/slack-github-action@v2.0.0
+        with:
+          webhook: ${{ secrets.SLACK_WEBHOOK_URL }}
+          webhook-type: incoming-webhook
+          payload: |
+            {
+              "text": "*New Release Published!* :tada: \n*Repository:* ${{ github.repository }}\n*Version:* ${{ github.event.release.tag_name }}\n*URL:* ${{ github.event.release.html_url }}",
+              "blocks": [
+                {
+                  "type": "section",
+                  "text": {
+                    "type": "mrkdwn",
+                    "text": "*New Release Published!* :tada:\n*Repository:* ${{ github.repository }}\n*Version:* ${{ github.event.release.tag_name }}\n*URL:* <${{ github.event.release.html_url }}|View Release>"
+                  }
+                }
+              ]
+            }

datajoint-2.1.1/.github/workflows/test.yaml

@@ -0,0 +1,55 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - "**"
+      - "!gh-pages"
+      - "!stage*"
+    paths:
+      - "src/datajoint/**"
+      - "tests/**"
+      - "pyproject.toml"
+      - "pixi.lock"
+      - ".github/workflows/test.yaml"
+  pull_request:
+    branches:
+      - "**"
+      - "!gh-pages"
+      - "!stage*"
+    paths:
+      - "src/datajoint/**"
+      - "tests/**"
+      - "pyproject.toml"
+      - "pixi.lock"
+      - ".github/workflows/test.yaml"
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.9.3
+        with:
+          cache: true
+          locked: false
+
+      - name: Run tests
+        run: pixi run -e test test-cov
+
+  # Unit tests run without containers (faster feedback)
+  unit-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.9.3
+        with:
+          cache: true
+          locked: false
+
+      - name: Run unit tests
+        run: pixi run -e test pytest tests/unit -v