Merge branch 'claude/refine-primary-key-rules-lVgTt' into claude/review-code-organization-9135z

Merges restructured project with src/datajoint/ layout and code organization
improvements including docstrings, type hints, and modern Python 3.10+ features.

Co-authored-by: dimitri-yatsenko <[email protected]>

Author: claude

.codespellrc

@@ -1,56 +1,7 @@
-// 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/${localWorkspaceFolderBasename}",
-	// Features to add to the dev container. More info: https://containers.dev/features.
-	// "features": {},
-	// Use 'forwardPorts' to make a list of ports inside the container available locally.
-	"forwardPorts": [
-		80,
-		443,
-		3306,
-		8080,
-		9000
-	],
-	"mounts": [
-	  "type=bind,source=${env:SSH_AUTH_SOCK},target=/ssh-agent"
-	],
-	"containerEnv": {
-	  "SSH_AUTH_SOCK": "/ssh-agent"
-	},
-	// 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 .[dev]",
-	"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": "${localWorkspaceFolder}"
-	}
-	// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
-	// "remoteUser": "devcontainer"
-}
+  "image": "mcr.microsoft.com/devcontainers/typescript-node:0-18",
+  "features": {
+    "ghcr.io/devcontainers/features/docker-in-docker:2": {}
+  },
+  "postCreateCommand": "curl -fsSL https://pixi.sh/install.sh | bash && echo 'export PATH=\"$HOME/.pixi/bin:$PATH\"' >> ~/.bashrc"
+}

.devcontainer/devcontainer.json

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

.gitattributes

@@ -23,7 +23,7 @@ jobs:
         extra_args: codespell --all-files
     - uses: pre-commit/[email protected]
       with:
-        extra_args: black --all-files
+        extra_args: ruff --all-files
     - uses: pre-commit/[email protected]
       with:
-        extra_args: flake8 --all-files
+        extra_args: ruff-format --all-files

.github/workflows/lint.yaml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         include:
-          - py_ver: "3.9"
+          - py_ver: "3.10"
     runs-on: ubuntu-latest
     env:
       PY_VER: ${{matrix.py_ver}}
@@ -40,14 +40,14 @@ jobs:
       - name: Update version.py
         run: |
           VERSION=$(echo "${{ github.event.release.name }}" | grep -oP '\d+\.\d+\.\d+')
-          sed -i "s/^__version__ = .*/__version__ = \"$VERSION\"/" datajoint/version.py
-          cat datajoint/version.py
+          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 "[email protected]"
-          git add datajoint/version.py
+          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

.github/workflows/post_draft_release_published.yaml

@@ -6,26 +6,23 @@ on:
       - "!gh-pages" # exclude gh-pages branch
       - "!stage*" # exclude branches beginning with stage
     paths:
-      - "datajoint"
+      - "src/datajoint"
       - "tests"
   pull_request:
     branches:
       - "**" # every branch
       - "!gh-pages" # exclude gh-pages branch
       - "!stage*" # exclude branches beginning with stage
     paths:
-      - "datajoint"
+      - "src/datajoint"
       - "tests"
 jobs:
   test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        py_ver: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        py_ver: ["3.10", "3.11", "3.12", "3.13"]
         mysql_ver: ["8.0"]
-        include:
-          - py_ver: "3.9"
-            mysql_ver: "5.7"
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{matrix.py_ver}}
@@ -34,9 +31,7 @@ jobs:
           python-version: ${{matrix.py_ver}}
       - name: Integration test
         env:
-          PY_VER: ${{matrix.py_ver}}
           MYSQL_VER: ${{matrix.mysql_ver}}
-          # taking default variables set in docker-compose.yaml to sync with local test
         run: |
-          export HOST_UID=$(id -u)
-          docker compose --profile test up --quiet-pull --build --exit-code-from djtest djtest
+          pip install -e ".[test]"
+          pytest --cov-report term-missing --cov=datajoint tests

.github/workflows/test.yaml

@@ -185,3 +185,5 @@ cython_debug/
 dj_local_conf.json
 *.env
 !.vscode/launch.json
+# pixi environments
+.pixi

.gitignore

@@ -20,38 +20,17 @@ repos:
   rev: v2.4.1
   hooks:
     - id: codespell
-- repo: https://github.com/pycqa/isort
-  rev: 6.0.1  # Use the latest stable version
+      args: [--toml, pyproject.toml]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.8.4
   hooks:
-    - id: isort
-      args:
-        - --profile=black  # Optional, makes isort compatible with Black
-- repo: https://github.com/psf/black
-  rev: 25.1.0 # matching versions in pyproject.toml and github actions
-  hooks:
-  - id: black
-    args: ["--check", "-v", "datajoint", "tests", "--diff"] # --required-version is conflicting with pre-commit
-- repo: https://github.com/PyCQA/flake8
-  rev: 7.3.0
-  hooks:
-  # syntax tests
-  - id: flake8
-    args:
-      - --select=E9,F63,F7,F82
-      - --count
-      - --show-source
-      - --statistics
-    files: datajoint # a lot of files in tests are not compliant
-  # style tests
-  - id: flake8
-    args:
-      - --ignore=E203,E722,W503
-      - --count
-      - --max-complexity=62
-      - --max-line-length=127
-      - --statistics
-      - --per-file-ignores=datajoint/diagram.py:C901
-    files: datajoint # a lot of files in tests are not compliant
+    # Run the linter
+    - id: ruff
+      args: [--fix]
+      files: ^(src/|tests/)
+    # Run the formatter
+    - id: ruff-format
+      files: ^(src/|tests/)
 - repo: https://github.com/rhysd/actionlint
   rev: v1.7.7
   hooks:

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ RUN ${CONDA_BIN} install --no-pin -qq -y -n base -c conda-forge \
 ENV PATH="$PATH:/home/mambauser/.local/bin"
 
 COPY --chown=${HOST_UID:-1000}:mambauser ./pyproject.toml ./README.md ./LICENSE.txt /main/
-COPY --chown=${HOST_UID:-1000}:mambauser ./datajoint /main/datajoint
+COPY --chown=${HOST_UID:-1000}:mambauser ./src/datajoint /main/src/datajoint
 
 VOLUME /src
 WORKDIR /src

Dockerfile

@@ -0,0 +1,4 @@
+#! /usr/bin/bash
+# This script registers dot plugins so that we can use graphviz 
+# to write png images
+dot -c