Merge pull request #18 from dj-sciops/main

Pull from `main`

Author: ttngu207

.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

CHANGELOG.md

@@ -3,6 +3,20 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
  [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.4.5] - 2025-09-17
+
++ Fix - Rename `env.yml` to `conda_env.yml` for consistency with other projects
++ Update - Passing tests by blackifying previous updates
+
+## [0.4.4] - 2025-06-06
+
++ Update - Update params in test/tutorial
++ Fix - Moved KiloSort's template_features  to additional_files 
+
+## [0.4.3] - 2025-06-03
+
++ Update - Use `Spikeinterface` official released versions (instead of install directly from source)
+
 ## [0.4.2] - 2025-03-25
 
 + Fix - Add key_source to `ProbeLevelReport` to filter for 'good' quality units

CONTRIBUTING.md

@@ -1,5 +1,5 @@
 # Contribution Guidelines
 
 This project follows the
-[DataJoint Contribution Guidelines](https://datajoint.com/docs/about/contribute/).
+[DataJoint Contribution Guidelines](https://docs.datajoint.com/about/contribute/).
 Please reference the link for more full details.

README.md

@@ -44,7 +44,7 @@ environment and notebooks to learn the pipeline.
 + [Interactive tutorial on GitHub
   Codespaces](https://github.com/datajoint/element-array-ephys#interactive-tutorial)
 
-+ [Documentation](https://datajoint.com/docs/elements/element-array-ephys)
++ [Documentation](https://docs.datajoint.com/elements/element-array-ephys/)
 
 ## Support
 

env.yml conda_env.ymlenv.yml renamed to conda_env.yml

@@ -1,7 +1,7 @@
 --- # ---------------------- PROJECT SPECIFIC ---------------------------
 
 site_name: DataJoint Documentation
-site_url: http://localhost/docs/elements/element-array-ephys
+site_url: https://docs.datajoint.com/elements/element-array-ephys/
 repo_url: https://github.com/datajoint/element-array-ephys
 repo_name: datajoint/element-array-ephys
 nav:

docs/mkdocs.yaml

@@ -7,15 +7,14 @@
 {% endif %}
 <nav class="{{ class }}" aria-label="{{ lang.t('nav.title') }}" data-md-level="0">
     <label class="md-nav__title" for="__drawer">
-        <a href="{{ config.extra.homepage | d(nav.homepage.url, true) | url }}"
-            title="{{ config.site_name | e }}" class="md-nav__button md-logo"
-            aria-label="{{ config.site_name }}" data-md-component="logo">
+        <a href="{{ config.extra.homepage | d(nav.homepage.url, true) | url }}" title="{{ config.site_name | e }}"
+            class="md-nav__button md-logo" aria-label="{{ config.site_name }}" data-md-component="logo">
             {% include "partials/logo.html" %}
         </a>
         {#-
         Add DataJoint home link to navigation header, otherwise unchanged
         -#}
-        <a href="https://datajoint.com/docs/elements/" title="DataJoint Elements">
+        <a href="https://docs.datajoint.com/elements/" title="DataJoint Elements">
             ⬅ Home
         </a>
     </label>

docs/src/.overrides/partials/nav.html

@@ -103,15 +103,15 @@ is a table within the Element or a table connected to the Element.
 
 ![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg)
 
-### `subject` schema ([API docs](https://datajoint.com/docs/elements/element-animal/api/element_animal/subject))
+### `subject` schema ([API docs](https://docs.datajoint.com/elements/element-animal/0.1/api/element_animal/subject/))
 
 Although not required, most choose to connect the `Session` table to a `Subject` table.
 
 | Table | Description |
 | --- | --- |
 | Subject | A table containing basic information of the research subject. |
 
-### `session` schema ([API docs](https://datajoint.com/docs/elements/element-session/api/element_session/session_with_datetime))
+### `session` schema ([API docs](https://docs.datajoint.com/elements/element-session/))
 
 | Table | Description |
 | --- | --- |