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Changelog

v0.4.0 (June 2024)

This release of datalab contains significant new functionality whilst broadly maintaining compatibility with the 0.3.x series.

It is also accompanied by the first release of the datalab Python API package (https://github.com/datalab-org/datalab-api), as well as the first release of the Ansible playbooks and Terraform rules (Azure only, for now) to automated datalab deployments (https://github.com/datalab-org/datalab-ansible-terraform).

Special thanks go to @vrajpatel9988 and especially @BenjaminCharmes who both made their first contributions to datalab in this release!

Highlights

  • User accounts: users can now update their name and contact info, as well as connect external accounts and regenerate API keys directly from the web UI. The ability to login via ORCID is now enabled by default (but must be configured at the instance level).
  • Admin dashboard: adds the ability for admins to do user management from the UI directly.
  • Electrochemistry block: support for Neware file formats, MPR files written by ECLab > 11.50 and cyclic voltammetry data.
  • Equipment: A new entry type has been added to record the equipment in the lab used for certain operations
  • Better default permissions on inventories: users can now create and edit inventory entries without requiring an admin.
  • Automatic random IDs: The ability to generate random IDs for new samples was added, allowing datalab to be used as the source of IDs.
  • Enhanced block-level documentation in the UI, and dynamic syncing of block-type metadata for improved extensibility.
  • Added the admin ability to verify all user accounts before they can use datalab.
  • General improvements to block error reporting and reactivity, as well as several bug fixes.

Notes for upgrading to v0.4.0

  • Users now have an "unverified" status by default. For some deployments, this may require an admin to first self-verify their account directly with a database update ("account_status" -> "active"), after which they can verify all other users in the UI.
  • The data mount point of the database container in the default ./docker-compose.yml has changed to use /data/db on the host system. Deployments using this configuration should be careful to backup and restore from their existing database, or continue to use the docker volume approach (feel free to raise an issue with any questions).
  • Similarly, the development set up has changed slightly and may need to be remade after upgrading.

What's Changed

  • Dynamically set production app container config in entrypoint by @ml-evs in datalab-org#605
  • Visual style improvements, test updates and improved block UI by @jdbocarsly in datalab-org#608
  • Refactor mail config settings by @ml-evs in datalab-org#614
  • Add Neware support and fix MPR issue by @ml-evs in datalab-org#617
  • Hotfix for block errors and warnings UI that arise over multiple renderings by @ml-evs in datalab-org#615
  • Use newly released galvani and NewareNDA packages by @ml-evs in datalab-org#625
  • Update xrdml parser so it works with v2.0 by @jdbocarsly in datalab-org#631
  • Restrict relationship types in UI synthesis and constituents tables by @ml-evs in datalab-org#630
  • Update copyright year in LICENSE by @ml-evs in datalab-org#622
  • Allow browser context menu in tinymce fields by @jdbocarsly in datalab-org#635
  • Allow any authenticated user to generate an API key by @ml-evs in datalab-org#641
  • Serve the identifier prefix in the /info response by @ml-evs in datalab-org#638
  • Return user role from /get-current-user endpoint by @ml-evs in datalab-org#644
  • Created component for editing account settings by @BenjaminCharmes in datalab-org#627
  • User registration: default display name to GitHub username when no profile name is set by @ml-evs in datalab-org#655
  • Fix typo where CI tests were never run in chrome by @ml-evs in datalab-org#656
  • Temporarily disable Firefox tests by @ml-evs in datalab-org#659
  • Bump webpack-dev-middleware from 5.3.3 to 5.3.4 in /webapp by @dependabot in datalab-org#660
  • Bump follow-redirects from 1.15.4 to 1.15.6 in /webapp by @dependabot in datalab-org#647
  • Allow echem block to plot non-cyclic data by @ml-evs in datalab-org#665
  • Add optional functionality to add starting materials from within the webapp by @jdbocarsly in datalab-org#642
  • Added validation for the user update route/UI by @BenjaminCharmes in datalab-org#646
  • Improve block warning/error reactivity in the UI by @ml-evs in datalab-org#666
  • Add ability to generate .csv files within block callbacks by @ml-evs in datalab-org#621
  • Debug flaky e2e tests by @jdbocarsly in datalab-org#670
  • Add option to generate ID automatically when creating items by @jdbocarsly in datalab-org#668
  • Add default config for VUE_APP_EDITABLE_INVENTORY by @ml-evs in datalab-org#673
  • Add codecov upload to CI by @ml-evs in datalab-org#677
  • Disable codecov PR annotations by @ml-evs in datalab-org#681
  • Add "equipment" item type by @jdbocarsly in datalab-org#531
  • Convert Whinchat to use langchain by @vrajpatel9988 in datalab-org#661
  • Bump langchain-core from 0.1.33 to 0.1.35 in /pydatalab by @dependabot in datalab-org#686
  • Bump prettier, pre-commit hooks and some other deps by @ml-evs in datalab-org#685
  • Allow starting materials and equipment to be edited by normal users by @ml-evs in datalab-org#672
  • Bump pymongo from 4.6.2 to 4.6.3 in /pydatalab by @dependabot in datalab-org#689
  • Use mocked API keys in API tests to fake different authentication scenarios by @ml-evs in datalab-org#676
  • Significant refactor of deployment docs by @ml-evs in datalab-org#690
  • Enable ORCID connection by default by @ml-evs in datalab-org#693
  • Only fix PRs with pre-commit CI when asked by @ml-evs in datalab-org#697
  • Upgrade cypress and other testing deps to allow Firefox testing by @ml-evs in datalab-org#699
  • Update README with links to Python API by @ml-evs in datalab-org#701
  • Add public deployment badge in README by @ml-evs in datalab-org#702
  • Separate each browser test into separate run and temporarily disable Firefox by @ml-evs in datalab-org#703
  • Add admin dashboard with user management controls by @BenjaminCharmes in datalab-org#674
  • Added a way to refresh API Key from Account Settings UI by @BenjaminCharmes in datalab-org#700
  • Recreate user index with new settings if already existing by @ml-evs in datalab-org#707
  • Fix for saving collection blocks and error handling for excessively large blocks by @ml-evs in datalab-org#709
  • Add account_status field (active, unverified or deactivated) to People model by @BenjaminCharmes in datalab-org#687
  • Update deployment instructions wrt. new datalab-ansible-terraform repo by @ml-evs in datalab-org#712
  • Add UI for email registration/login by @ml-evs in datalab-org#528
  • Serve data about available block types in API by @ml-evs in datalab-org#667
  • Add upper pin to rosettasciio by @ml-evs in datalab-org#720
  • Update tests for current user by @ml-evs in datalab-org#723
  • Add ability to select between different chat models in the whinchat by @vrajpatel9988 in datalab-org#680
  • Bump Flask and Werkzeug to the latest releases on the v3 series by @ml-evs in datalab-org#722
  • Added HelpBubble component to display inline documentation in the UI by @BenjaminCharmes in datalab-org#706
  • Fix API key help message by @ml-evs in datalab-org#725
  • Fix README badges by @ml-evs in datalab-org#730
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in datalab-org#728
  • Revert pre-commit autoupdate for prettier by @ml-evs in datalab-org#734
  • Populating dynamic block-level documentation as UI tooltips by @BenjaminCharmes in datalab-org#719
  • Make account status on registration be configurable by provider by @ml-evs in datalab-org#733
  • Add notification-dot for user with unverified account_status by @BenjaminCharmes in datalab-org#724
  • Consider account status during auth and refactor API around blueprints by @ml-evs in datalab-org#727
  • Add gravatar instructions and tweak account settings modal by @ml-evs in datalab-org#744
  • Add block help to block title by @ml-evs in datalab-org#737
  • Fix NMR block layout issue by @ml-evs in datalab-org#745
  • Fix issue with landing page and tweak default docker-compose deployment by @ml-evs in datalab-org#746
  • Improve admin dashboard styling and functionality by @BenjaminCharmes in datalab-org#748
  • Add API_URL as a meta tag in HTML header of all UI responses by @ml-evs in datalab-org#750
  • Add CONFIG.APP_URL to allow for customisable redirects on login/registration by @ml-evs in datalab-org#749
  • Fix StyledInput component (v2) by @jdbocarsly in datalab-org#751
  • Bump version numbers by @ml-evs in datalab-org#753
  • Add a Tabular data block that can handle simple CSVs and text files by @ml-evs in datalab-org#592
  • Remove GET-out of route permissions by @ml-evs in datalab-org#754
  • Tweak mount points, production Docker entrypoint and development environment by @ml-evs in datalab-org#763
  • Default to ORCID ID as display name when ORCID user's name is private by @ml-evs in datalab-org#769
  • Add process lock for remote filesystem scraper by @ml-evs in datalab-org#562
  • Bump version number to v0.4.0 by @ml-evs in datalab-org#770

New Contributors

Full Changelog: https://github.com/the-grey-group/datalab/compare/v0.3.2...v0.4.0

v0.3.2 (February 2024)

This is a build hotfix for 0.3.x, where the incorrect versions of navani and galvani were being installed in docker builds (leading to missing support for ECLab >= 11.50).

What's Changed

  • Force galvani and navani update in lockfile by @ml-evs in datalab-org#602

Full Changelog: https://github.com/the-grey-group/datalab/compare/v0.3.1...v0.3.2

v0.3.1 (February 2024)

This release makes a few fixes relative to 0.3.0, primarily around file uploads and internal database storage.

It also adds the ability for data blocks to pass errors and warnings to the front-end, which can be useful for helping describe incompatibilities in data, analysis or plotting dynamically.

What's Changed

  • Pin prettier version in Webapp to same version that is specified in pre-commit by @jdbocarsly in datalab-org#589
  • Downgrade pre-commit prettier by @ml-evs in datalab-org#593
  • CSS cleanup by @jdbocarsly in datalab-org#588
  • Fix issue where plot data was always stored in db by @ml-evs in datalab-org#599
  • Add ability for block errors and warnings to be passed through API to UI by @ml-evs in datalab-org#590
  • Fix issue where previously uploaded file cannot be replaced by @ml-evs in datalab-org#594

Full Changelog: https://github.com/the-grey-group/datalab/compare/v0.3.0...v0.3.1

v0.3.0 (Feburary 2024)

This is the long overdue v0.3.0 release of datalab, which coincides with many new deployments popping up. It is strongly recommended to upgrade and continue to keep up-to-date with releases as they come out. There are no intentional breaking changes between this release and the previous release candidates, so please report any issues you come across on the GitHub issue tracker.

Thanks to new contributor @elbee99 who has added support for Raman spectroscopy, plus new contributors with as-of-yet unreleased changes!

Highlights

  • Support for Biologic data files created with the most recent versions of ECLab 11.50+, plus enhanced support for Arbin data files
  • A new 1D Raman block that can parse both Renishaw WDF and Oxford Instrument's spectra
  • Ability to group samples and other entries into collections
  • Support for new authentication methods, such as magic links via email
  • Significant refactoring and modularization to ease the process of new contributions
  • Simplified deployment procedure via Docker
  • Automated snapshot backups

What's changed?

New Contributors

Full Changelog: https://github.com/the-grey-group/datalab/compare/v0.2.5...v0.3.0