Merge pull request #1311 from datajoint/pre/v2.0

DataJoint 2.0

Author: dimitri-yatsenko

.codespellrc

@@ -8,6 +8,7 @@ RUN \
     pip uninstall datajoint -y
 
 USER root
-ENV DJ_HOST db
-ENV DJ_USER root
-ENV DJ_PASS password
+ENV DJ_HOST=db
+ENV DJ_USER=root
+ENV DJ_PASS=password
+ENV S3_ENDPOINT=minio:9000

.devcontainer/Dockerfile

@@ -1,56 +1,6 @@
-// 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": "${localWorkspaceFolder}"
-	}
-	// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
-	// "remoteUser": "devcontainer"
+  "dockerComposeFile": ["../docker-compose.yaml", "docker-compose.yml"],
+  "service": "app",
+  "workspaceFolder": "/src",
+  "postCreateCommand": "curl -fsSL https://pixi.sh/install.sh | bash && echo 'export PATH=\"$HOME/.pixi/bin:$PATH\"' >> ~/.bashrc"
 }

.devcontainer/devcontainer.json

@@ -1,30 +1,14 @@
+# Devcontainer overrides for the app service from ../docker-compose.yaml
+# Inherits db and minio services automatically
 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:-bookworm}
     build:
-      context: .
+      context: ..
       dockerfile: .devcontainer/Dockerfile
       args:
         - PY_VER=${PY_VER:-3.11}
         - DISTRO=${DISTRO:-bookworm}
-
-    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.
+    # Keep container running for devcontainer
     command: /bin/sh -c "while sleep 1000; do :; done"

.devcontainer/docker-compose.yml

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

.gitattributes

@@ -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

.github/DISCUSSION_TEMPLATE/rfc.yml

@@ -1,8 +1,8 @@
 # https://github.com/actions/labeler
 breaking:
-- head-branch: ['breaking', 'BREAKING']
+- head-branch: ['breaking', 'BREAKING', 'pre/v2.0']
 bug:
-- head-branch: ['fix', 'FIX', 'bug', 'BUG']
+- head-branch: ['fix', 'FIX', 'bug', 'BUG', 'pre/v2.0']
 feature:
 - head-branch: ['feat', 'FEAT']
 documentation:

.github/pr_labeler.yaml

@@ -14,5 +14,5 @@ jobs:
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         configuration-path: .github/pr_labeler.yaml
-        sync-labels: true
+        sync-labels: false  # Don't remove manually added labels
         dot: true

.github/workflows/label_prs.yaml

@@ -23,7 +23,7 @@ jobs:
         extra_args: codespell --all-files
     - uses: pre-commit/action@v3.0.1
       with:
-        extra_args: black --all-files
+        extra_args: ruff --all-files
     - uses: pre-commit/action@v3.0.1
       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 "github-actions@github.com"
-          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