Changelog 2026 .md

Note

Get notified by watching releases for git repositories: lamindb · laminhub · laminr · nf-lamin · bionty

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See updates in other years: 2025 · 2024 · 2023 · 2022

2026-05-10 hub 1.34.0

  • ✨ Improve API key management with named keys, expiration date, and revocation PR @Ebad371

  • ⚡️ Speed up queries for large databases PR @Koncopd

2026-05-07 hub 1.33.0

2026-05-06 hub 1.32.0

2026-05-05 docs

2026-05-04 hub 1.31.0

2026-04-27 db 2.4.2

2026-04-27 hub 1.30.1

2026-04-25 hub 1.30.0

2026-04-24 nf 0.6.2

2026-04-23 blog

  • 📝 How I managed thousands of datasets to build the scPRINT family of scRNA-seq foundation models PR @falexwolf

2026-04-23 bionty 2.4.0

⚠️ Run bionty.core.sync_public_sources()

This will update the Source registry with the new organisms of Protein.

2026-04-23 db 2.4.1

  • 🔒️ Obfuscate user secrets in params and source code PR @falexwolf

  • 🚸 Detect project, space & branch args in @ln.flow() and detect LAMIN_INITIATED_BY_RUN_UID in ln.track() PR @falexwolf

  • 🚸 Validated transfer of artifacts to other storage locations PR @Koncopd

  • 🐛 Fix cleanup of internal files on instance init failures PR @Koncopd

2026-04-21 hub 1.29.2

  • 🚸 Sheets: bulk row addition and CSV template download PR @chaichontat

  • 🐛 Fix projects page highlighting and pagination PR @chaichontat

2026-04-20 db 2.4.0

⚠️ Run lamin migrate deploy

  • 🗃️ Add branch and created_on fields to BaseBlock and the _aux field to Branch PR @falexwolf

  • 🗃️ Make feature nullable on RunRecord PR @falexwolf

All instances connected to LaminHub have been migrated and there is no need to act.

If you are an admin of a self-managed instance, please migrate your database with lamin migrate deploy.

For details see the Compatibility Matrix and the source code.

Highlights:

  • ✨ Allow users to transfer artifacts between storage locations PR @Koncopd

  • ✨ Add Record.from_dataframe() and bulk saving of records PR @falexwolf

  • ✨ Saving markdown notes as records PR @falexwolf

UX:

  • 🚸 Enable lamin connect --here to scope instance to a development directory parallel to git PR @falexwolf

  • 🚸 Scope a lamindb connection to a development directory PR @falexwolf

  • 🚸 Skip hash lookup on empty files when creating an artifact PR @Koncopd

  • 🚸 Remove duplicated logging in ln.connect() if already connected PR @falexwolf

  • 🚸 Allow users to pass kwargs to write_h5ad and write_zarr in Artifact.from_anndata(...) PR @Koncopd

  • 🚸 Warn if working with a non-latest version of an artifact PR @Koncopd

  • 🚸 Do not error, only warn if running outside dev-dir PR @falexwolf

Integrations:

Bugs:

  • 🐛 Invoke original signal handlers in LogStreamTracker.cleanup() PR @Koncopd

  • 🐛 Except only specific import error in with_package_obj and with_package PR @Koncopd

  • 🐛 Fix single file directory upload when saving an artifact PR @Koncopd

  • 🐛 Fix record.to_artifact() export in case maximal_set is True and record names are not populated PR @falexwolf

Dependencies:

Refactors:

  • ♻️ In the lamidb.core.storage module, lazily import heavy dependencies like anndata PR @jorenretel

  • ♻️ Avoid unnecessary pandas and anndata imports on Artifact initialization PR @Koncopd

  • ♻️ Also save README as block, prepare transitioning away from README artifacts PR @falexwolf

  • ♻️ Do not show instance settings content on validation error PR @Koncopd

  • ♻️ Enable to_dataframe(include='features') also for Run PR @falexwolf

Docs:

  • 📝 Recommend FeatureManager.set_values() and warn that FeatureManager.add_values() can invalidate the dtype of categorical feature annotations under certain circumstances PR @ishitajain9717

  • 📝 Document dtype bool and improve documentation of DtypeStr PR @falexwolf

  • 📝 Prettify and simplify spatialdata schema creation script PR @falexwolf

  • 📝 Improve documentation for Artifact.from_anndata(...) PR @Koncopd

  • 📝 README v5.6: Added new features of lamindb 2.4 + clean ups PR @falexwolf

2026-04-20 hub 1.29.0

2026-04-19 hub 1.28.0

2026-04-16 hub 1.27.0

2026-04-15 blog

  • 📝 Managing spatial omics datasets with SpatialData & LaminDB PR @Zethson

2026-04-12 hub 1.26.0

  • 🚸 Rename Merge Requests to Change Requests and polish design PR @keller-mark

  • 🐛 Fix space information in new sheet workflow PR @chaichontat

  • 🐛 Fix overflow behavior in main navigation tabs PR @chaichontat

2026-04-10 hub 1.25.0

2026-04-08 hub 1.24.0

  • 🚸 Redesign the run cards and add a tabular view indexed by params and features PR @chaichontat

  • 💄 Move records number and schema info to the right and do not display ‘Root’ in breadcrumbs PR @falexwolf

  • 🐛 Fix data fetch error on collection page PR @falexwolf

2026-04-06 hub 1.23.1

  • 🐛 Fix request for space on User in sheet edit mode PR @falexwolf

2026-04-06 hub 1.23.0

  • ✨ General support for managing access with spaces in the UI PR @chaichontat

  • ✨ Make runs searchable PR @chaichontat

  • ✨ Add support for R source code highlighting PR @falexwolf

  • 🛂 Enable linking objects in a protected space for users who have read access to them PR @Koncopd

  • 🚸 Mention lamin save in notebook preview PR @falexwolf

  • 💄 Harmonize markdown font size PR @chaichontat

2026-04-02 blog

2026-03-31 hub 1.22.0

Experimental beta:

2026-03-27 nf 0.6.0

✨ This release adds support for spaces and branches, configurable artifact keys, and manual path tracking. @rcannood

  • Space & Branch support: New space_uid and branch_uid top-level config options to scope transforms, runs, and artifacts into a specific space and branch (PR).

    lamin {
  space_uid  = "abcdef1234"
  branch_uid = "abcdef1234"
}

  • Configurable artifact keys: New key option on output_artifacts, input_artifacts, and individual rules to control how artifact keys are derived. Accepts a string template, a closure, or a [relativize: ...] map shorthand (PR, PR).

    lamin {
  output_artifacts {
    key = [relativize: params.outdir]
  }
}

  • Manual path tracking: New include_paths setting on input_artifacts, output_artifacts, and individual rules to explicitly specify files that should be tracked — useful for files consumed in Groovy that are invisible to the task listener (PR).

    lamin {
  input_artifacts {
    include_paths = { params.input }
  }
}

  • Name-based references: UID fields (project_uids, ulabel_uids, space_uid, branch_uid) now accept prefixed names (?name, !name, +name) for convenience and cross-environment testing (PR). Note that this is experimental and may be subject to change in future releases.

Bug fixes.

  • Fixed key relativization to work uniformly across file://, s3://, gs://, and az:// paths using URI.relativize() PR @rcannood

  • Fixed assets directory detection for users with custom NXF_HOME or NXF_ASSETS by using nextflow.Const.DEFAULT_ROOT instead of a hardcoded path PR @rcannood

Breaking changes.

  • project_uids inside run {}, transform {}, and artifact rules is removed. Use the top-level field only PR @rcannood

Others.

  • ♻️ Restructured instance API functions and added tests PR @rcannood

  • 📝 Refactored documentation PR @rcannood

2026-03-20 bionty 2.3.1

  • 🐛 Fix duplicates in Ensembl prefixes for organisms PR @falexwolf

2026-03-20 db 2.3.1

  • 🐛 Fix incorrect read-only warning for ln.DB(...) PR @Koncopd

  • 📝 Coin the term “sync” instead of “transfer” for syncing data between databases PR @falexwolf

2026-03-18 bionty 2.3.0

Bionty now depends on lamindb-core instead of lamindb.

2026-03-18 db 2.3.0

Architecture:

  • 🏗️ Create lamindb-core to distribute lamindb without optional dependencies PR @ap– @falexwolf

UX improvements:

  • 🚸 Improve ln.connect() performance and robustness PR @falexwolf

  • 🚸 Enable feature-based query expressions PR @falexwolf

  • 🚸 Allow semantic queries by run & branch status PR @falexwolf

  • 🚸 FeatureManager.add_values(), set_values(), and remove_values() accept feature objects, not just feature name strings PR @falexwolf

  • 🚸 Enable configuring env modules PR @falexwolf

  • 🚸 Refresh federated AWS credentials on the botocore level PR @Koncopd

  • 🚸 Add informative record.describe() PR @falexwolf

  • 🚸 Print warning if truncating a query result PR @falexwolf

  • 🚸 Refactor agent plan saving to strip TODOs from description PR @falexwolf

  • 🚸 Treat composite suffixes with .zarr at the end differently from other unspecified composite suffixes PR @Koncopd

  • 🚸 Allow users to enforce ignoring local aws credentials via system.env PR @Koncopd

  • 🚸 Optimize DB interactions in lightning integration PR @falexwolf

  • 🚸 Warn when connecting the default database to a non-writable connection PR @Koncopd

  • 🚸 Adapt logging to refreshable credentials PR @Koncopd

  • 🚸 Do not issue track warning on clones PR @Koncopd

Database:

  • 🗃️ Make feature_id on TransformRecord link model nullable PR @falexwolf

Bug fixes:

  • 🐛 Fix model field tracking via _populate_tracked_fields for deferred fields PR @Koncopd

  • 🐛 Fix root inference for huggingface paths PR @Koncopd

  • 🐛 Fix synchronization of directory artifacts when the destination directory exists but is empty PR @Koncopd

  • 🐛 Fix feature collisions in lightning integration PR @falexwolf

  • 🐛 Account for host database in FeatureManager.__getitem__ PR @sunnyosun

MappedCollection:

  • 🚸 Improve data retrieval in MappedCollection PR @mojtababahrami

  • 🚸 Allow users to specify partially available keys in MappedCollection and retrieve raw.X PR @Koncopd

Ontologies:

Docs:

  • 📝 Improve the lamindb.record document PR @falexwolf

  • 📝 Document refresh behavior of federated s3 credentials for tiledbsoma PR @Koncopd

2026-03-16 hub 1.21.0

  • ✨ Enable linking transforms to a record PR @chaichontat

  • 🚸 Enhance artifact and transform cards on record page with pagination and filtering PR @chaichontat

  • 🚸 Enable searching for str-dtype features in sheets PR @falexwolf

  • 🚸 Set default sorting to updated_at descending for artifacts PR @chaichontat

  • 🐛 Resolve ULabel types in sheets’ dtype display and enforce these types during edit mode PR @chaichontat

  • 🐛 Disambiguate categorical values in CSV parser PR @chaichontat

  • 💄 Remove root element from typed sidebars for records, ulabels, features & schemas PR @falexwolf

  • 💄 Do not display schema names on records sidebar PR @falexwolf

2026-03-13 R 1.3.0

🚸 Simplify connecting to an instance PR @lazappi

Connecting via the main module object now works with lamindb>=2.3:

ln <- laminr::import_module("lamindb")
ln$connect("<owner>/<instance>")

Other changes:

  • ⬆️ Bump expected lamindb version to 2.3.0 PR @lazappi

  • ✨ Add silent arguments to get_current_lamin_*() utils PR @lazappi

  • ✨ Add ignore_none argument to get_current_lamin_instance() PR @lazappi

  • 🚸 Add as.list() coercion method for BasicQuerySet PR @lazappi

  • 🚸 Use absolute files paths for tracking PR @ap–

  • 🚸 Warn that Python messages will be lost on Jupyter PR @lazappi

2026-03-12 hub 1.20.0

2026-03-05 hub 1.19.0

2026-03-02 blog

  • 📝 A data lakehouse for biology’s sparse measurements PR @jejomath

2026-03-04 hub 1.18.0

2026-03-03 hub 1.17.0

Features & major design improvements:

GUI polish:

Frontend routes:

  • 🚚 Rename the write-logs/ route to dbwrites/ PR @falexwolf

Bug fixes:

  • 🐛 Fix instance deletion in on-prem infra due to missing permissions PR @Koncopd

  • 🐛 Improve pagination in artifact tables PR @chaichontat

  • 🐛 Invalidate instance README display cache on artifact upload PR @chaichontat

  • 🐛 Fix instance deletion in on-prem infra due to missing permissions PR @falexwolf

2026-03-02 blog

  • 📝 Interactive visualization of multimodal and spatial data with Vitessce PR @keller-mark

2026-02-27 blog

2026-02-26 hub 1.16.5

  • 🐛 Fix allowed suffixes in launch input selection PR @sunnyosun

2026-02-25 hub 1.16.4

  • 🚸 Respect Nextflow MIME suffix behavior in Launch page inputs form PR @sunnyosun

  • 💄 Account for recreated artifacts and recreated collections in lineage explorer PR @falexwolf

  • 💄 Display run entrypoints in transform, run, and lineage views PR @falexwolf

  • 💄 Pricing page v2 PR @falexwolf

2026-02-24 db 2.2.1

  • 🚸 Add backward compat for lamin switch --branch PR @falexwolf

  • 🚸 Improve logging during @ln.flow() and @ln.step() PR @falexwolf

  • 🚸 Enable defining a feature that restricts to a subset of artifacts PR @falexwolf

  • 🚸 Better handling of problematic access token refreshes PR @Koncopd

  • ⚡️ Call database RPC functions as read-only PR @Koncopd

2026-02-19 bionty 2.2.0

2026-02-19 db 2.2.0

⚠️ Run lamin migrate deploy

  • 🗃️ Add a _status_code: int field to Branch and BaseBlock PR @falexwolf

All instances connected to LaminHub have been migrated and there is no need to act.

If you are an admin of a self-managed instance, please migrate your database with lamin migrate deploy.

For details see the Compatibility Matrix and the source code.

Examples: Change management with branching, merging, and Merge Requests

To create a contribution branch and switch to it, run:

lamin switch -c my_branch

To merge a contribution branch into main, run:

lamin switch main  # switch to the main branch
lamin merge my_branch  # merge contribution branch into main

To see the current branch along with other information, run:

lamin info

To annotate the current branch with a README.md, run:

lamin annotate branch --readme README.md

To comment on the current branch, run:

lamin annotate branch --comment "I think we should revisit this, tomorrow, WDYT?"

To describe the current branch (optionally include comments), run:

lamin describe branch --include comments

To trace on which branch a SQLRecord object was created, run:

sqlrecord.created_on.describe()

To open a Merge Request for a branch:

lamin update branch --status draft  # for current branch
lamin update branch --name my_branch --status review  # for any branch

Just like Pull Requests on GitHub, branches are never deleted so that the provenance of a change stays traceable.

For more info, see: docs.lamin.ai/lamindb.branch

Examples: Agent plan traceability

Saving an agent plan automatically tags with artifact.kind = "plan" and infers a key starting with .plans/:

lamin save /path/to/.cursor/plans/my_task.plan.md
lamin save /path/to/.claude/plans/my_task.md

Link an agent plan against a run:

ln.track(plan=".plans/my-agent-plan.md")

This will link the plan artifact to a run in the same way in which transform, an initiating run (initiated_by_run) and report/environment artifacts are linked to the run.

While the transform acts as the deterministic source code for the run and initiated_by_run enables higher-level runs in workflow orchestration, the agent plan complements these two by allowing the linkage of plan that steers a non-deterministic agent.

Highlights:

  • ✨ Add lamin merge command, add lamin switch -c option & simplify lamin switch syntax PR @falexwolf

  • ✨ Add agent plan traceability PR @falexwolf

  • ✨ Enable linking a README.md to and commenting for any entity PR @falexwolf

  • ✨ Introduce Merge Request states on branches PR @falexwolf

  • ✨ Add lamin update and homogenize lamin get with other commands PR @falexwolf

  • ✨ Add UPath.from_auth(...) PR @Koncopd

UX:

  • 🚸 Quality of life improvements for saving via the CLI: saving plans, sync with git, annotating with version tags PR @falexwolf

  • 🚸 Extend lamin describe to more entities PR @falexwolf

  • 🚸 Prettier display for dtype for Record and ULabel sub types in schema.describe() PR @falexwolf

  • 🚸 Track record_type.to_dataframe() as an input for the current run PR @falexwolf

  • 🚸 Make it easier to query for all output artifacts including recreated ones PR @falexwolf

  • 🚸 Include comments in SQLRecord.describe() when passing include = "comments" PR @falexwolf

  • 🚸 Include comments in lamin describe upon --include comments PR @falexwolf

  • 🚸 Re-raise InvalidArgument in lamin annotate as ClickException PR @falexwolf

  • 🚸 Nicer error for lamin switch to non-existing branch PR @falexwolf

Performance:

Architecture:

  • 🏗️ Reconcile is_latest state across branches PR @falexwolf

Bux fixes:

  • 🐛 Fix bracket handling of describe PR @Zethson

  • 🐛 Scope feature query by schema member types in Curator PR @Zethson

  • 🐛 Fix DB snapshot sync PR @Zethson

Docs:

  • 📝 Add videos to docs, polish typos and wording PR @falexwolf

Security:

  • 🔒️ Scope AWS credential caches to users PR @Koncopd

Dependencies:

  • ⬆️ Relax AnnData version constraint PR @Zethson

2026-02-19 hub 1.16.3

  • 🐛 Fix between-page sidebar type navigation PR @chaichontat

  • 🐛 Fix pagination bar position in sheets PR @sunnyosun

  • 🐛 Run metadata settings includes the dtype sheet when a feature has the same dtype PR @chaichontat

2026-02-18 hub 1.16.2

2026-02-17 hub 1.16.1

  • 🚸 Fix clunky UX in left sidebar of typed entities PR @chaichontat

  • 💄 Simplify features header in artifact detail page, should be “Values” not “Categories / Values” PR @falexwolf

2026-02-15 hub 1.16.0

  • ⬆️ Enable compatibility with lamindb 2.2

  • 💄 Do not show pertdb link tables PR @sunnyosun

  • 💄 Fix text truncation in list cells of sheets PR @sunnyosun

  • 💄 Fix badge for recreated output artifacts PR @sunnyosun

2026-02-12 hub 1.15.2

2026-02-11 hub 1.15.1

2026-02-11 nf 0.5.1

  • 🐛 Exclude work dir and assets from input artifacts PR @rcannood

2026-02-10 hub 1.15.0

High-level organization of the top navbar:

2026-02-09 db 2.1.2

UX:

  • 🚸 Broaden curation to dtypes that are unions PR @Zethson

  • 🚸 More debug logging in case instance creation on hub fails due to quota exceeded PR @Koncopd

Performance:

  • ⚡️ Download large single files from s3 with boto3 by default in artifact.cache() PR @Koncopd

Bug fixes:

  • 🐛 Fix initializing an instance with a cloud storage and the db parameter passed PR @Koncopd

2026-02-09 hub 1.14.0

2026-02-02 db 2.1.1

UX:

  • 🚸 Better detection of read-only connections for write errors and tracking PR @Koncopd

  • 🚸 A lamin settings cache-dir reset CLI command for resetting the cache directory to the default path PR @Koncopd

  • 🚸 A S3QueryPath.is_bucket_versioned() method to check if the bucket in an s3 path is versioned PR @Koncopd

Bug fixes:

  • 🐛 Fix edge case in Django reset during ln.setup.init(...) PR @Koncopd

2026-02-03 nf 0.5.0

This release revamps the configuration (nextflow.config) for more control over which artifacts are registered and which metadata is attached (kind, projects, ulabels). Here is an example Nextflow config:

lamin {
  instance = "laminlabs/lamindata"
  api_key = secrets.LAMIN_API_KEY
  output_artifacts {
    rules {
      output {
        pattern = ".*"
        order = 1
        type = "include"
        project_uids = ["AbCdEfGhIjKl"]
        ulabel_uids = ["AbCd0123"]
      }
      // don't publish state.yaml files
      yaml {
        pattern = ".*\\.state\\.yaml"
        type = "exclude"
        order = 10
      }
    }
  }
}

New functionality:

  • ✨ Control which files are registered as artifacts using pattern-based rules PR @rcannood

  • ✨ Link projects and ulabels to transforms, runs, and artifacts with new run and transform config sections for granular control PR @rcannood

  • ✨ New api section for connection settings replaces root-level fields PR @rcannood

UX:

  • 🚸 Better mapping of HTTP error codes from the LaminDB API PR @rcannood

Bug fixes:

  • 🐛 Fixed edge case in tracking input files and improved S3 path rendering PR @rcannood

Deprecations: The following API components are now deprecated and are scheduled for removal in v0.6

Type

Deprecated

Replacement

Config

project

project_uids

Config

supabase_api_url, supabase_anon_key, max_retries, retry_delay

api { ... } section

Function

getArtifactFromUid()

file('lamin://owner/instance/artifact/uid')

2026-02-02 db 2.1.0 | bionty 2.1.0

MLOps:

Notebooks, scripts, workflows:

  • 🚸 Recognize packaged python source code across track(), @flow(), and @step() PR @falexwolf

  • 🚸 Default to creating a global run context in ln.flow() PR @falexwolf

  • 🚸 Serialize Path, UPath, and handle None in transform params PR @falexwolf

  • 🚸 Reflect user CLI calls in transform description PR @falexwolf

  • 🚸 Improve error message for running a script or notebook outside the development directory PR @falexwolf

Validation:

  • 🚸 Unify validating features with and without the presence of a schema, fix parsing ISO-format strings as datetime if mapped on a feature with dtype=str PR @falexwolf

CLI:

  • 🚸 Delete records via CLI PR @falexwolf

  • 🚸 Better error behavior in lamin save when transform is on a different branch PR @sunnyosun

General UX:

  • 🚸 Enable convenient re-upload of local file after upload failure PR @falexwolf

  • 🚸 Return information about deleted objects rather than None upon hard delete PR @falexwolf

  • 🚸 Introduce safe-guards in updating the space of artifacts PR @Koncopd

  • 🚸 Switch on SQL logging if ln.settings.verbosity is "debug" PR @sunnyosun

  • 🚸 Raise canonical InstanceNotFoundError in Registry.connect() PR @falexwolf

  • 🚸 Allow users to pass ids of foreign keys in Artifact() constructor PR @Koncopd

  • 🚸 Check local path existence on artifact.save() PR @Koncopd

Performance:

  • ⚡️ Much faster permanent run & transform deletion PR @falexwolf

  • ⚡️ 1 sec speed-up for basic CLI calls through optimized lamindb_setup import time PR @falexwolf

Ontology updates in bionty:

Better conventions in CLI (backward compatible):

  • 🚚 Support key-based deletion in lamin delete PR @falexwolf

  • 🚚 lamin cache is now lamin settings cache-dir, refactor settings managemennt PR @falexwolf

  • 🚚 More consistent lamin switch and lamin create commands PR @falexwolf

The wetlab plugin was renamed to pertdb (backward compatible):

Bugs:

  • 🐛 Refactor & fix feature-based queries for records PR @falexwolf

  • 🐛 Fix PyYAML serialization of NotebookNode PR @Zethson

  • 🐛 Fix Artifact.from_dataframe() to support path input PR @Zethson

  • 🐛 Fix standardize() ignoring passed source PR @Zethson

Docs:

  • 📝 Convert guides to markdown format PR @falexwolf

  • 📝 Legible API reference for lamindb.models PR @falexwolf

  • 📝 Consistent reference to Python/R alternative for all CLI commands, expand lamin annotate PR @falexwolf

  • 📝 Document backward relationships and add RelatedManager[T] to ManyToMany type annotations PR PR @falexwolf

  • 📝 README improvements PR @falexwolf

Refactoring:

  • ♻️ Rather flag _storage_ongoing than _storage_completed PR @falexwolf

  • ♻️ Efficiently encode uploading information PR @falexwolf

  • ♻️ Fully leverage Context to manage the run context of function executions PR @falexwolf

  • ♻️ Use publishable LaminHub key PR @Koncopd

  • ♻️ Remove internal use_proxy_db option PR @Koncopd

2026-01-31 hub 1.13.0

  • ⚡ Update JWT signing from HS256 to ES256 for better performance PR @fredericenard

  • 💄 Display output and input records on run detail page PR @falexwolf

2026-01-27 hub 1.12.1

2026-01-26 hub 1.12.0

  • ✨ Configurable default Seqera workspace and compute environment PR @chaichontat

  • ✨ Two new endpoints to help users authenticate and interact with instances through the API PR @fredericenard

  • 🐛 Fix attaching a space to an instance in case an org admin isn’t a collaborator of that space PR @fredericenard

  • 🐛 Prevent empty results when searching Artifacts PR @chaichontat

  • 💄 Landing page: re-format taglines and update schematic PR @chaichontat

2026-01-21 nf 0.4.0

✨ This release allows for the automatic tracking of input artifacts by discovering their remote URIs, using functionality implemented in Nextflow 25.10. Hence, it requires Nextflow >=25.10.0 PR @rcannood

export NXF_VER=25.10.2
nextflow run <pipeline> \
    --input "https://raw.githubusercontent.com/..." \
    -with-report report.html

2026-01-20 hub 1.11.0

2026-01-14 hub 1.10.0

  • ✨ Add /artifacts/by-path endpoint PR @fredericenard

  • 🐛 Write run annotations on the Launch page into the RunRecord registry PR @falexwolf

  • 📝 Improve landing page - metadata and lakehouse sections PR @falexwolf

2026-01-13 hub 1.9.1

  • 🐛 More strictly enforce schema during UI-based record creation PR @chaichontat

  • 🐛 Broaden database server access permissions to include shared database servers PR @fredericenard

  • 📝 Improve landing page - introduce tags and improve language PR @falexwolf

2026-01-13 R 1.2.2

2026-01-12 nf 0.3.0

  • ✨ Implement FileSystem for lamin:// URIs PR @rcannood

  • ⬆️ Bump lamindb to v2 PR @falexwolf

  • 🚸 Update formatting of source_code when a new transform is created PR @rcannood

  • 📝 Add version compatibility table PR @rcannood

2026-01-12 hub 1.9.0

  • ✨ Transform search bar also understands run names and UIDs PR @chaichontat

  • 🚸 Default to not listing inferred schemas without names PR @chaichontat

  • 🐛 Fix the broken “New schema” button on the records page due to lamindb v2 PR @chaichontat

  • 🐛 Fix the broken pipeline Launch button due to lamindb v2 PR @sunnyosun

2026-01-11 db 2.0.1

  • 🚸 Backward compatibility for querying features by dtype PR @falexwolf

2026-01-11 db 2.0.0

This release makes the database schema fully consistent and thereby improves UX, integrity, and enables long-term stability.

⚠️ With the exception of previous deprecations, your code continues to run as is, but you will receive new warnings about renamed API components.

Main changes:

What

Before

After

Backward compatible

Function tracking

@ln.tracked()

@ln.flow(), @ln.step()

✓

Feature field

dtype

_dtype_str

✓

Schema field

n

n_members

✓

IsVersioned field

version

version_tag

✓

Transform field

type

kind

✓

Artifact field

feature_sets

schemas

✓

Feature field

coerce_dtype

coerce

✓

Schema field

coerce_dtype

coerce

✓

FeatureValue registry

FeatureValue

JsonValue

✓

Private fields that are now public:

What

Before

After

Backward compatible

Artifact field

_subsequent_runs

recreating_runs

✗

Artifact field

_feature_values

json_values

✗

Run field

_recreated_artifacts

recreated_artifacts

✗

SQLRecord field

_branch_code (only on DB-level)

branch_id

✗

Changes to auxiliary (JSON) fields:

What

Before

After

Backward compatible

Run field

cli_args (in _aux)

cli_args (CharField(max_length=1024))

✓

Feature field

default_value (in _aux)

default_value (JSONField)

✓

Feature field

nullable (in _aux)

nullable (BooleanField)

✓

Schema field

flexible (in _aux)

flexible (BooleanField)

✓

Artifact field

_is_saved_to_storage_location (in _aux)

_save_completed (in _aux)

✗

On link models with labels:

What

Before

After

Backward compatible

IsLink model

feature_ref_is_name

removed

✗

IsLink model

label_ref_is_name

removed

✗

For completeness, changes in recently introduced unused API components:

What

Before

After

Backward compatible

RootBlock registry

RootBlock

Block

✗

Block field

context

key

✗

BaseBlock field

type

kind

✗

Run field

_logfile

removed

✗

Transform field

config

removed

✗

Transform field

flow

removed

✗

Transform field

is_flow

removed

✗

Transform field

_template

removed

✗

Changes in the bionty and wetlab modules:

What

Before

After

Backward compatible

BioRecord registry

uid (X chars)

uid (14 chars)

* .get() of the X chars uid continues to work

* uids are re-encoded to 14 chars with the first X chars conserved.

Changes in the wetlab module:

What

Before

After

Backward compatible

Experiment registry

Experiment

removed

✗

BioSample registry

BioSample

removed

✗

TechSample registry

TechSample

removed

✗

Donor registry

Donor

removed

✗

Well registry

Well

removed

✗

GeneticPerturbation field

system

type

✗

CompoundPerturbation field

targets

removed

✗

Compound field

targets

✓

If you have data in removed registries you’ll see a warning that your data gets exported to parquet files. You can import these parquet files into the Record registry under an Experiment type without losing of functionality.

⚠️ After migrating databases to v2 via lamin migrate deploy lamindb package installations with v1 will raise errors. This is the last planned database migration that breaks older clients.

All instances connected to LaminHub have been migrated and there is no need to act.

If you are an admin of a self-managed instance, please migrate your database with lamin migrate deploy.

For details see the Compatibility Matrix and the source code.

⚠️ For laminr and nf-lamin users

For laminr users with an auto-managed reticulate environment, please run this:

reticulate::py_require("lamindb>=2.0.1") # DO THIS FIRST
ln <- laminr::import_module("lamindb")

For nf-lamin users, please upgrade to 0.3.0.

Removals:

Features:

  • ✨ Track shell scripts PR @falexwolf

  • ✨ Enable managing workflows by decorating functions with @ln.flow() and @ln.step() and deprecate @ln.tracked() PR @falexwolf

Architecture:

  • 🏗️ For more robustness and to convey the field’s special nature in the API and the database schema, replace Feature.dtype with Feature._dtype_str to now hold a serialization that links object types (Record + ULabel) based on their uid instead of their name and type hierarchy PR @falexwolf

UX:

  • 🚸 Add feature.dtype_as_object PR @sunnyosun

  • 🚸 Add description argument to Transform.from_git() PR @falexwolf

  • 🚸 Allow passing _key_is_virtual on Artifact creation PR @Koncopd

  • 🚸 Raise SystemExit upon InstanceNotFound only from CLI PR @falexwolf

  • 🚸 Raise error for init or import issues in lamin io snapshot PR @Zethson

  • 🚸 Do not track inputs when calling collection.artifacts.all() PR @Koncopd

  • 🚸 Raise a clear error if calling CanCurate and similar registry class methods on objects PR @falexwolf

  • 🚸 Sort features in describe() PR @falexwolf

Database-level changes:

  • 🗃️ Rename RootBlock to Block with a column key akin to Artifact and Transform PR @falexwolf

  • 🗃️ Refactor _storage_completed mechanism and remove unique constraints on type names PR @falexwolf

  • 🗃️ Migrate most auxiliary fields to SQL columns PR @falexwolf

  • 🗃️ Simplify Transform PR @falexwolf

  • 🗃️ Rename IsVersioned.version to IsVersioned.version_tag, Transform.type to Transform.kind, FeatureValue to JsonValue, BaseBlock.type to BaseBlock.kind, delete Transform._template and Run._logfile PR @falexwolf

  • 🗃️ Rename Artifact._subsequent_runs to Artifact.recreating_runs and Run._recreated_artifacts to Run.recreated_artifacts PR @falexwolf

  • 🗃️ Rename SQLRecord._branch_code to SQLRecord.branch_id and remove feature_ref_is_name and label_ref_is_name fields from link models PR @falexwolf

  • 🗃️ Rename Artifact.feature_sets to Artifact.schemas PR @falexwolf

  • 🗃️ Migrate the Feature and Schema database tables to LaminDB v2 PR @falexwolf

  • 🗃️ Swap accessor names for SchemaComponent links, consistent ManyToMany field names for RecordRecord links PR @falexwolf

  • 🗃️ Better names for the ManyToMany fields for the annotating runs and artifacts of an Artifact PR @falexwolf

Bug fixes:

Bionty:

Wetlab:

  • 🗃️ Migrations for wetlab v2 PR @sunnyosun

  • 🗃️ Migrations for LaminDB v2 PR @falexwolf

  • 🗃️ Create a composite index for artifact, perturbationtarget fields in ArtifactPerturbationTarget PR @Koncopd

  • 🗃️ Create a composite index for artifact, geneticperturbation fields in ArtifactGeneticPerturbation PR @Koncopd

Docs:

  • 📝 Improve the Space document PR @falexwolf

  • 📝 Improve the Artifact.replace() docs PR @falexwolf

  • 📝 Improve FAQ doc on trashing and archiving PR @falexwolf

  • 📝 Render return type annotations of Artifact.open() in docs PR @falexwolf

Config:

Refactoring:

  • ♻️ Refactor require_organism PR @sunnyosun

  • ♻️ Better re-use Django’s ObjectDoesNotExist and MultipleObjectsReturned PR @falexwolf

  • ♻️ Return file size in hash_file() PR @falexwolf

  • ♻️ Squash migrations and re-build SQLite init database PR @falexwolf

  • ♻️ More verbose migration integrity check PR @falexwolf

  • ♻️ Call lamin migrate deploy even if initializing from pre-built sqlite file PR @falexwolf

Dependencies:

  • ⬆️ Bump fsspec packages upper bound PR @Koncopd

  • ⬆️ Bump anndata upper bound PR @Koncopd

  • ⬆️ Set the correct lower bound for websockets PR @Koncopd

2026-01-11 hub 1.8.0

2026-01-03 hub 1.7.0