diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 2d0e9261..f461f088 100644 --- a/.devcontainer/Dockerfile +++ b/.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" \ No newline at end of file + +CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd" diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index bf939e88..1c062f18 100644 --- a/.devcontainer/devcontainer.json +++ b/.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" ] } } diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index d31fbace..74368549 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.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 \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index 0e3593d2..fff5cd7a 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 2bd0f498..61a342d6 100644 --- a/CONTRIBUTING.md +++ b/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. diff --git a/README.md b/README.md index 85277136..aad51cad 100644 --- a/README.md +++ b/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 diff --git a/env.yml b/conda_env.yml similarity index 100% rename from env.yml rename to conda_env.yml diff --git a/docs/mkdocs.yaml b/docs/mkdocs.yaml index e211069a..2fec112c 100644 --- a/docs/mkdocs.yaml +++ b/docs/mkdocs.yaml @@ -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: diff --git a/docs/src/.overrides/partials/nav.html b/docs/src/.overrides/partials/nav.html index cd6326b6..faac796a 100644 --- a/docs/src/.overrides/partials/nav.html +++ b/docs/src/.overrides/partials/nav.html @@ -7,15 +7,14 @@ {% endif %}