Draft Pull Request to Visualize all the changes

.devcontainer/Dockerfile

@@ -1,10 +1,13 @@
-FROM python:3.9-slim@sha256:5f0192a4f58a6ce99f732fe05e3b3d00f12ae62e183886bca3ebe3d202686c7f
+ARG PY_VER=3.11
+ARG DISTRO=bullseye
+FROM mcr.microsoft.com/devcontainers/python:${PY_VER}-${DISTRO}
 
-ENV PATH /usr/local/bin:$PATH
-ENV PYTHON_VERSION 3.9.17
+# Avoid warnings by switching to noninteractive
+ENV DEBIAN_FRONTEND=noninteractive
+
+USER root
 
 RUN \
-    adduser --system --disabled-password --shell /bin/bash vscode && \
     # install docker
     apt-get update && \
     apt-get install ca-certificates curl gnupg lsb-release -y && \
@@ -45,4 +48,5 @@ ENV EPHYS_ROOT_DATA_DIR /workspaces/element-array-ephys/example_data
 ENV DATABASE_PREFIX neuro_
 
 USER vscode
-CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd"
+
+CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd"

.devcontainer/devcontainer.json

@@ -22,8 +22,8 @@
 		},
 		"vscode": {
 			"extensions": [
-				"ms-python.python@2023.8.0",
-				"ms-toolsai.jupyter@2023.3.1201040234"
+				"ms-python.python@2025.6.1",
+				"ms-toolsai.jupyter@2025.4.1"
 			]
 		}
 	}

.github/ISSUE_TEMPLATE/config.yml

@@ -1,5 +1,5 @@
 blank_issues_enabled: false
 contact_links:
   - name: DataJoint Contribution Guideline
-    url: https://docs.datajoint.org/python/community/02-Contribute.html
+    url: https://docs.datajoint.com/about/contribute/
     about: Please make sure to review the DataJoint Contribution Guidelines

.github/workflows/devcontainer-build-publish-caller.yml

@@ -0,0 +1,10 @@
+name: devcontainer_build_publish
+on:
+  workflow_dispatch:
+
+jobs:
+  call_devcontainer_build_publish:
+    uses: datajoint/.github/.github/workflows/devcontainer-build-publish.yaml@main
+    secrets:
+      DOCKERHUB_USERNAME: ${{secrets.DOCKERHUB_USERNAME}}
+      DOCKERHUB_TOKEN: ${{secrets.DOCKERHUB_TOKEN_FOR_ELEMENTS}}

.github/workflows/mkdocs-release-caller.yml

@@ -0,0 +1,9 @@
+name: mkdocs-release
+on:
+  workflow_dispatch:
+
+jobs:
+  mkdocs_release:
+    uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main
+    permissions: 
+      contents: write

.github/workflows/semantic-release-caller.yml

@@ -0,0 +1,10 @@
+name: semantic-release
+on:
+  workflow_dispatch:
+
+jobs:
+  call_semantic_release:
+    uses: datajoint/.github/.github/workflows/semantic-release.yaml@main
+    secrets:
+      APP_ID: ${{ secrets.ELEMENT_APP_ID }}
+      GET_TOKEN_KEY: ${{ secrets.ELEMENT_GET_TOKEN_KEY }}

.github/workflows/test.yaml

@@ -1,22 +1,19 @@
 name: Test
 on:
   push:
+    branches:
+      - main
   pull_request:
+    branches:
+      - main
   workflow_dispatch:
 jobs:
-  devcontainer-build:
-    uses: datajoint/.github/.github/workflows/devcontainer-build.yaml@main
   tests:
     runs-on: ubuntu-latest
     strategy:
       matrix:
         py_ver: ["3.9", "3.10"]
-        mysql_ver: ["8.0", "5.7"]
-        include:
-          - py_ver: "3.8"
-            mysql_ver: "5.7"
-          - py_ver: "3.7"
-            mysql_ver: "5.7"
+        mysql_ver: ["8.0"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{matrix.py_ver}}
@@ -31,4 +28,4 @@ jobs:
         run: |
           python_version=${{matrix.py_ver}}
           black element_array_ephys --check --verbose --target-version py${python_version//.}
-
+          black notebooks --check --verbose --target-version py${python_version//.}

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ exclude: (^.github/|^docs/|^images/)
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -16,7 +16,7 @@ repos:
 
   # black
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 24.2.0
     hooks:
       - id: black
       - id: black-jupyter
@@ -25,15 +25,15 @@ repos:
 
   # isort
   - repo: https://github.com/pycqa/isort
-    rev: 5.11.2
+    rev: 5.13.2
     hooks:
       - id: isort
         args: ["--profile", "black"]
         description: Sorts imports in an alphabetical order
 
   # flake8
   - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+    rev: 7.0.0
     hooks:
       - id: flake8
         args: # arguments to configure flake8