Changelog
Follow up on the latest improvements and updates.
RSS
Fixed
- Fixed a bug that prevented public and shared notebooks from being accessible without logging in.
Fixed
- Fixed a bug that prevented access of public ghcr.io images in user-developed Workflows
Fixed
- Fixed a bug where searching for samples that do not yet have a metadata name set was not searching by filename. Now we will return samples that do not have a metadata name but do have the searched text in their filename.
Changed
- We've changed how functional data is exported from the samples page. Rather than exporting a long table, we now export a folder, containing a functional file for each sample. This allows us to now export more than 200 samples worth of functional data at once.
improved
fixed
Various bug fixes
Improved
- Expanded search options on sequencing order dashboard. Users can now search by tube barcode, order number, external order ID, address, batch number, and inbound or outbound tracking numbers.
Fixed
- We fixed an issue whereby users received a 500 error when trying to delete an asset that is in use. Instead, users will be informed that the asset is in use, and will receive a more-appropriate 400 error.
- We fixed a bug that prevented some organization owners/admins from inviting certain existing users to their organization.
- We've fixed an issue with exporting functional data with taxonomic stratification from the samples page.
New
- Added support for GitLab repositories to be used in workflow creation
Fixed
- Fixes TypeError in ocx.Api() constructor
Changed
- Lowers minimum pydantic version to 2.10.6
New
- We've added a new API route for organization owners or admins within One Codex, to be able to view samples within their organization. The API route is /api/v1/samples/organization, and can be used with the onecodex client library, i.e.ocx.Samples.where(organization=True), to get all samples uploaded by users within the organization. Note, this functionality was available on the web application at https://app.onecodex.com/organization/samples, and remains unchanged.
improved
fixed
Client Library
Client library v0.19.0 released
The
onecodex
client library has a new release - v0.19.0. Details here.Added
- Adds Python 3.13 support
- Adds numpy v2 support
Changed
- Upgrades Altair to 5.5.0
- Upgrades scikit-bio to 0.7.0. IMPORTANT: This changes the log base used in Shannon alpha diversity calculations from base 2 to e(natural log)
- Upgrades urllib3 to >=2.5.0
- Modernizes packaging and tooling by migrating to pyproject.toml,uv, andruff
- Updates pytestto fail on warnings
- Replaces Potion-Client resources with Pydantic v2 models
- Changes metric=autobehavior based on the number of classification results with abundance estimates
Fixed
- Fixes SampleCollectionmetadata fetching to only match canonical ranks
- Fixes issue when plotting fields that look like JavaScript paths (e.g. field.nameorfield[name])
- Fixes various documentation issues
Removed
- Removes Samples.init_multipart_upload()in favor ofSamples.upload()
New
- The latest version of the One Codex Database has been released. This includes increased viral genomes, for improved viral detection. The unique ID for the new database is 7f6b028b9d964d87.
Improved
- Metadata fields with leading or trailing whitespaces will now be stripped of those whitespaces upon metadata sheet uploads. This will prevent mismatches of metadata due to excess whitespaces
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