v0.5.0-rc.4

Close database port by default to not assume firewall works (#876)

v0.5.0-rc.3

What's Changed

• CI build time and fork compatibility improvements by @ml-evs in #833
• Tweak cache usage on docker builds by @ml-evs in #841
• Repackage server as proper Python package, removing pipenv by @ml-evs in #604
• Re-enable dependabot for Python dependencies by @ml-evs in #845
• Remove release workflow now that versions are dynamic by @ml-evs in #847
• Bump the github-actions group with 3 updates by @dependabot in #846
• Fix docs formatting and update versioning scheme by @ml-evs in #850
• Use uv and deps lockfiles in CI & pre-commit by @ml-evs in #851
• Attempt to configure lockfile-only dependabot strategy by @ml-evs in #853
• Re-attempt to use lockfile-only strategy with dependabot by @ml-evs in #854
• Do not show option to connect accounts in account settings if not configured in server by @ml-evs in #856
• Use node v20 in build, CI and dev environments by @ml-evs in #858
• Let linting settings reflect development usage by @ml-evs in #859
• Add QR code generation and scanning to UI by @ml-evs in #808
• Refactor login components by @ml-evs in #857
• Bump webpack from 5.88.2 to 5.94.0 in /webapp by @dependabot in #863
• Bump elliptic from 6.5.4 to 6.5.7 in /webapp by @dependabot in #837
• Deprecate gpt-3.5-turbo series and handle missing models in chatblock by @ml-evs in #855
• Bump flask-cors from 4.0.1 to 5.0.0 in /pydatalab by @dependabot in #867
• Bump cryptography from 43.0.0 to 43.0.1 in /pydatalab by @dependabot in #871
• Filter out b64-encoded data before sending to LLM by @ml-evs in #870
• Fix deployment config options for new VUE_APP settings by @ml-evs in #874
• Lockfile compatibility by @ml-evs in #873
• Fix QR code warning showing when not required by @ml-evs in #875

Full Changelog: v0.4.4...v0.5.0-rc.3

v0.5.0-rc.2

What's Changed

• CI build time and fork compatibility improvements by @ml-evs in #833
• Tweak cache usage on docker builds by @ml-evs in #841
• Repackage server as proper Python package, removing pipenv by @ml-evs in #604
• Re-enable dependabot for Python dependencies by @ml-evs in #845
• Remove release workflow now that versions are dynamic by @ml-evs in #847
• Bump the github-actions group with 3 updates by @dependabot in #846
• Fix docs formatting and update versioning scheme by @ml-evs in #850
• Use uv and deps lockfiles in CI & pre-commit by @ml-evs in #851
• Attempt to configure lockfile-only dependabot strategy by @ml-evs in #853
• Re-attempt to use lockfile-only strategy with dependabot by @ml-evs in #854
• Do not show option to connect accounts in account settings if not configured in server by @ml-evs in #856
• Use node v20 in build, CI and dev environments by @ml-evs in #858
• Let linting settings reflect development usage by @ml-evs in #859
• Add QR code generation and scanning to UI by @ml-evs in #808
• Refactor login components by @ml-evs in #857
• Bump webpack from 5.88.2 to 5.94.0 in /webapp by @dependabot in #863
• Bump elliptic from 6.5.4 to 6.5.7 in /webapp by @dependabot in #837
• Deprecate gpt-3.5-turbo series and handle missing models in chatblock by @ml-evs in #855

Full Changelog: v0.4.4...v0.5.0-rc.2

v0.4.4

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 #826
• Remove final mentions of odbx.science by @ml-evs in #827
• Add routes for resolving items by refcode by @ml-evs in #807
• Fix block errors caused by seemingly defunct theme options in bokeh by @ml-evs in #829
• Update to latest navani version, fixing Neware normalisation issues by @ml-evs in #836
• Reload echem data by default, unless disabled by @ml-evs in #840

Full Changelog: v0.4.3...v0.4.4

v0.4.3

This release simply tweaks some testing and release procedures.

What's Changed

• Re-enable Firefox e2e tests by @ml-evs in #711
• Try to group cypress tests in same run by @ml-evs in #825

Full Changelog: v0.4.2...v0.4.3

v0.4.2

This release adds an update to the batch item creation UI to include other item types, and includes a new preview of the tabular UI which can be accessed at the path /next, as well as several UI tweaks and fixes.

What's Changed

• Rebrand repo to the group-agnostic gh organisation by @ml-evs in #809
• Change docker compose restart policy to "unless-stopped" by @ml-evs in #810
• Update INSTALL.md by @jdbocarsly in #816
• Fix logo link taking full screen width by @ml-evs in #821
• Improve sample table component by @BenjaminCharmes in #784
• Add simple component test for ChemFormInput by @ml-evs in #743
• Add ability to add batch of cells by @jdbocarsly in #797
• Add config options to automatically activate accounts from GitHub, email or any auth source by @ml-evs in #822
• Bump version number to 0.4.2 by @ml-evs in #824

Full Changelog: v0.4.1...v0.4.2

v0.4.1

This minor release adds some quality-of-life fixes to the UI, a new cell format type "in situ (optical)" and tweaks to our development workflow.

What's Changed

• Run vue3-recommended linting by @jdbocarsly in #756
• Corrected blockInfo computed property value by @BenjaminCharmes in #775
• Changes to pre-commit by @jdbocarsly in #785
• Add 'optical' cellFormat by @BenjaminCharmes in #788
• Remove cheminventory import task (which is now in datalab-api) by @ml-evs in #793
• Add gpt4o and other updated models by @jdbocarsly in #736
• Report runtime server config at /info and use this in UI by @ml-evs in #801
• Development docker, pre-commit and eslint updates & refactoring by @ml-evs in #805
• Disable ChemicalFormula component by @ml-evs in #806

Full Changelog: v0.4.0...v0.4.1

v0.4.0

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

v0.4.0-rc.4

🚧 PRE-RELEASE 🚧
This is the FINAL pre-release for the upcoming 0.4.0 release. The CHANGELOG below may be missing some information. It is not recommended that you update to this pre-release unless you have a good reason, or want to test new features before they are finished.

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 @BenjaminCharmes and @vrajpatel9988 who 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

These notes will be populated for the final release, but not yet.

Full changelog

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

v0.4.0-rc.3

🚧 PRE-RELEASE 🚧
This is the pre-release for the upcoming 0.4.0 release. The CHANGELOG below may be missing some information. It is not recommended that you update to this pre-release unless you have a good reason, or want to test new features before they are finished.

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 @BenjaminCharmes and @vrajpatel9988 who 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

These notes will be populated for the final release, but not yet.

Full changelog

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