Merge branch 'main' into bc/bump-pydantic

Author: ml-evs

.docker/server_dockerfile

@@ -1,4 +1,6 @@
-# syntax=docker/dockerfile:1
+ARG UV_VERSION="0.8.4"
+FROM ghcr.io/astral-sh/uv:${UV_VERSION} AS uv_image
+
 FROM python:3.10 AS api
 SHELL ["/bin/bash", "--login", "-c"]
 
@@ -12,7 +14,7 @@ RUN apt update && apt install -y gnupg curl tree mdbtools && apt clean
 WORKDIR /opt
 RUN wget https://fastdl.mongodb.org/tools/db/mongodb-database-tools-ubuntu2204-x86_64-100.9.0.deb && apt install ./mongodb-database-tools-*-100.9.0.deb
 
-COPY --from=ghcr.io/astral-sh/uv:0.6.4 /uv /usr/local/bin/uv
+COPY --from=uv_image /uv /usr/local/bin/uv
 ENV UV_LINK_MODE=copy \
     UV_COMPILE_BYTECODE=1 \
     UV_PYTHON_DOWNLOADS=never \

.github/workflows/ci.yml

@@ -1,14 +1,14 @@
 name: CI tests
 on:
   pull_request:
-    types: [ready_for_review, opened, synchronize, reopened]
 
   push:
     branches:
       - main
 
 env:
   FORCE_COLOR: true
+  UV_VERSION: "0.8.4"
 
 concurrency:
   group: ${{ github.head_ref || github.run_id }}
@@ -30,7 +30,7 @@ jobs:
       - name: Set up uv
         uses: astral-sh/setup-uv@v6
         with:
-          version: "0.6.4"
+          version: ${{ env.UV_VERSION }}
           enable-cache: true
 
       - name: Install dependencies
@@ -78,7 +78,7 @@ jobs:
       - name: Set up uv
         uses: astral-sh/setup-uv@v6
         with:
-          version: "0.6.4"
+          version: ${{ env.UV_VERSION }}
           working-directory: "./pydatalab"
           enable-cache: true
 
@@ -129,7 +129,7 @@ jobs:
       fail-fast: false
       max-parallel: 3
       matrix:
-        browser-backend: ["electron", "chrome", "firefox"]
+        browser-backend: ["electron", "chrome"] # , "firefox"]  # Temporarily disable Firefox until migration to Cypress v14 (https://github.com/datalab-org/datalab/issues/1289)
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/dependable-bot.yml

@@ -8,6 +8,9 @@ permissions:
   contents: write
   pull-requests: write
 
+env:
+  UV_VERSION: "0.8.4"
+
 jobs:
   uv-update-pins:
     name: Update `uv.lock` pins
@@ -28,7 +31,7 @@ jobs:
       - name: Set up uv
         uses: astral-sh/setup-uv@v6
         with:
-          version: "0.6.4"
+          version: ${{ env.UV_VERSION }}
           working-directory: "./pydatalab"
           enable-cache: true
 

.github/workflows/license-check.yml

@@ -3,6 +3,9 @@ on:
   workflow_dispatch:
   workflow_call:
 
+env:
+  UV_VERSION: "0.8.4"
+
 jobs:
   licensing-checks:
     name: "Check dependency licensing"
@@ -21,12 +24,12 @@ jobs:
         with:
           python-version: "3.11"
 
-      - name: Set up uv
-        uses: astral-sh/setup-uv@v6
-        with:
-          version: "0.6.4"
-          working-directory: "./pydatalab"
-          enable-cache: true
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        version: ${{ env.UV_VERSION }}
+        working-directory: "./pydatalab"
+        enable-cache: true
 
       - name: Run liccheck
         working-directory: ./pydatalab

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
       - id: mixed-line-ending
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.2
+    rev: v0.12.7
     hooks:
       - id: ruff
         args: [--fix]
@@ -56,13 +56,13 @@ repos:
         args: [--fix]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.0
+    rev: v3.20.0
     hooks:
       - id: pyupgrade
         args: [--py310-plus]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.17.1
     hooks:
       - id: mypy
         additional_dependencies:

.readthedocs.yaml

@@ -12,4 +12,4 @@ build:
     - asdf global uv latest
     - cd pydatalab && uv sync --all-extras --dev
     - cd pydatalab && uv pip install .
-    - cd pydatalab && .venv/bin/mkdocs build --site-dir $READTHEDOCS_OUTPUT/html
+    - cd pydatalab && .venv/bin/mkdocs build --site-dir $READTHEDOCS_OUTPUT/html --strict

CHANGELOG.md

@@ -1,10 +1,10 @@
 # Changelog
 
-## v0.6.0 (June 2025)
+## v0.6.0 (August 2025)
 
-This release includes significant new functionality and UI redesign, as well as
-several bug and quality-of-life fixes, performance improvements and
-backwards-compatible API enhancements.
+This release includes significant new functionality and UI redesign, a  
+fledgling plugin ecosystem, as well as several bug and quality-of-life
+fixes, performance improvements and backwards-compatible API enhancements.
 
 > [!WARNING]
 > This release also bumps the supported MongoDB version all the way from v3 to v8. Whilst older MongoDB versions should still continue to work, version 8 will now be tested and used in the docker builds, so we recommend you upgrade. For existing databases this requires you to first dump the database using `mongodump` with the old MongoDB version, then upgrade to the new version and restore the database with `mongorestore`. If you unsure about this process then please ask us for help!
@@ -23,26 +23,30 @@ backwards-compatible API enhancements.
   [`datalab-app-plugin-insitu`](https://github.com/datalab-org/datalab-app-plugin-insitu)),
   as well as new file formats supported in the XRD (Rigaku's .rasx, variants of .xy), NMR (JCAMP-DX) blocks
   and media block (PDF documents).
+- A fledgling plugin ecosystem with ways to easily add new blocks to a specific
+  *datalab* instance ([docs](https://docs.datalab-org.io/en/v0.6.0/plugins/)), with [`datalab-server`](https://pypi.org/project/datalab-server) PyPI package for easier dependency management.
 - Improved item search throughout the API, removing the need to search on
-  whitespace or puncutation delimited words (e.g., ID matches will now begin after
+  whitespace or punctuation delimited words (e.g., ID matches will now begin after
   just 3 characters, rather than needing to type a full ID).
+- More powerful UI block interactions via "events" that can be written purely Python ([docs](https://docs.datalab-org.io/en/v0.6.0/blocks/)).
 
+**Full Changelog**: https://github.com/datalab-org/datalab/compare/v0.5.2...v0.6.0
 
 ## v0.5.2 (March 2025)
 
 This patch release makes several visual/interactivity improvements around
 loading states in the UI, and adds two new blocks: FTIR and a tabular data
 block for plotting data from within generic CSV/Excel files.
 
-## What's Changed
+### What's Changed
 * Fix docs link in mkdocs by @ml-evs in https://github.com/datalab-org/datalab/pull/1044
 * Improve loading state for data-intensive blocks by @BenjaminCharmes in https://github.com/datalab-org/datalab/pull/1049
 * Add support for reading excel-like spreadsheets in tabular data block by @ml-evs in https://github.com/datalab-org/datalab/pull/1052
 * Add Login Splash Screen by @BenjaminCharmes in https://github.com/datalab-org/datalab/pull/907
 * Added FTIR block and associated tests by @be-smith in https://github.com/datalab-org/datalab/pull/1061
 * Update CITATION.cff by @ml-evs in https://github.com/datalab-org/datalab/pull/1069
 
-## New Contributors
+### New Contributors
 * @be-smith made their first contribution in https://github.com/datalab-org/datalab/pull/1061
 
 **Full Changelog**: https://github.com/datalab-org/datalab/compare/v0.5.1...v0.5.2
@@ -51,7 +55,7 @@ block for plotting data from within generic CSV/Excel files.
 
 This patch release simply pins the `uv` version used in builds to avoid future breakages.
 
-## What's Changed
+### What's Changed
 
 * Bump the github-actions group across 1 directory with 2 updates by @dependabot in https://github.com/datalab-org/datalab/pull/1031
 * Update uv to 0.5.x now that dynamic versioning is supported by @ml-evs in https://github.com/datalab-org/datalab/pull/1032
@@ -68,11 +72,11 @@ The Ansible playbooks at [datalab-ansible-terraform](https://github.com/datalab-
 
 Many thanks to all contributors: developers, user feedback and deployment managers!
 
-## Breaking changes
+### Breaking changes
 
-* The Python server has been entirely repackaged with `uv` for much more streamlined dependency management (especially for external plugins). If you are using the docker deployments, then nothing should change for you, but developers may need to adjust their development setups following the instructions at [INSTALL.md](./INSTALL.md)
+* The Python server has been entirely repackaged with `uv` for much more streamlined dependency management (especially for external plugins). If you are using the docker deployments, then nothing should change for you, but developers may need to adjust their development setups following the [installation instructions](./INSTALL.md).
 
-## Highlights
+### Highlights
 
 * The table component used to display all items has been entirely rewritten, and is now more visually responsive and can accommodate custom schemas/components.
 * QR code generation and scanning for all items, optionally using the new [datalab pURL service](https://purl.datalab-org.io/) when configured with `VUE_APP_QR_CODE_RESOLVER_URL`.
@@ -91,6 +95,7 @@ Many thanks to all contributors: developers, user feedback and deployment manage
 This release primarily contains some bugfixes for the echem block, as well as tidying in preparation of the next release.
 
 ### What's Changed
+
 * Removed unused css by @BenjaminCharmes in https://github.com/datalab-org/datalab/pull/826
 * Remove final mentions of odbx.science by @ml-evs in https://github.com/datalab-org/datalab/pull/827
 * Add routes for resolving items by refcode by @ml-evs in https://github.com/datalab-org/datalab/pull/807