Merge branch 'pre/v2.0' of https://github.com/datajoint/datajoint-python into impr/modernize-pre-commit

Author: d-v-b

.devcontainer/devcontainer.json

@@ -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"
+}

.gitattributes

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

.github/workflows/test.yaml

@@ -34,9 +34,7 @@ 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

.gitignore

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

activate.sh

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

docker-compose.yaml

@@ -1,4 +1,5 @@
-# HOST_UID=$(id -u) PY_VER=3.11 DJ_VERSION=$(grep -oP '\d+\.\d+\.\d+' datajoint/version.py) docker compose --profile test up --build --exit-code-from djtest djtest
+# Development environment with MySQL and MinIO services
+# To run tests: pytest --cov-report term-missing --cov=datajoint tests
 services:
   db:
     image: datajoint/mysql:${MYSQL_VER:-8.0}

pixi.lock

@@ -22,7 +22,7 @@ dependencies = [
   "urllib3",
   "setuptools",
 ]
-requires-python = ">=3.9,<4.0"
+requires-python = ">=3.9,<3.14"
 authors = [
   {name = "Dimitri Yatsenko", email = "[email protected]"},
   {name = "Thinh Nguyen", email = "[email protected]"},
@@ -78,11 +78,17 @@ Repository = "https://github.com/datajoint/datajoint-python"
 dj = "datajoint.cli:cli"
 datajoint = "datajoint.cli:cli"
 
-[project.optional-dependencies]
+[dependency-groups]
 test = [
   "pytest",
   "pytest-cov",
+  "pytest-env",
+  "docker",
+  "requests",
+  "graphviz"
 ]
+
+[project.optional-dependencies]
 dev = [
   "pre-commit",
   "ruff",

pyproject.toml

@@ -28,7 +28,7 @@
 logger = logging.getLogger(__name__.split(".")[0])
 
 
-if not diagram_active:
+if not diagram_active:  # noqa: C901
 
     class Diagram:
         """

src/datajoint/diagram.py

@@ -260,6 +260,7 @@ def __setitem__(self, key, value):
             "database.host",
             "database.user",
             "database.password",
+            "database.port",
             "external.aws_access_key_id",
             "external.aws_secret_access_key",
             "loglevel",
@@ -270,6 +271,7 @@ def __setitem__(self, key, value):
                 "DJ_HOST",
                 "DJ_USER",
                 "DJ_PASS",
+                "DJ_PORT",
                 "DJ_AWS_ACCESS_KEY_ID",
                 "DJ_AWS_SECRET_ACCESS_KEY",
                 "DJ_LOG_LEVEL",
@@ -278,6 +280,14 @@ def __setitem__(self, key, value):
     )
     if v is not None
 }
+
+# Convert DJ_PORT from string to int if present
+if "database.port" in mapping and mapping["database.port"] is not None:
+    try:
+        mapping["database.port"] = int(mapping["database.port"])
+    except ValueError:
+        logger.warning(f"Invalid DJ_PORT value: {mapping['database.port']}, using default port 3306")
+        del mapping["database.port"]
 if mapping:
     logger.info(f"Overloaded settings {tuple(mapping)} from environment variables.")
     config.update(mapping)