Release 2.1.0

See https://docs.lamin.ai/changelog/2026#db-2-1-0-bionty-2-1-0

What's Changed

• 🐛 Fix Artifact.from_dataframe to support path input by @Zethson in #3455
• 🐛 Fix str behavior of Artifact.from_dataframe() by @Zethson in #3457
• ⬆️ Update standard ontology by @sunnyosun in #3461
• 👽️ Fix broken setup due to laminhub refactoring by @fredericenard in #3464
• 📝 Fix Artifact.from_anndata example by @Zethson in #3463
• 🔒️ Introduce safe-guards in updating the space of artifacts by @Koncopd in #3458
• ⬆️ New Gene Organism sources by @sunnyosun in #3467
• 🚸 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 by @falexwolf in #3456
• 🚸 Return information about deleted objects rather than None upon hard delete by @falexwolf in #3469
• 🍱 Update CellLine default source by @sunnyosun in #3471
• 🚸 Raise canonical InstanceNotFoundError in Registry.connect() by @falexwolf in #3470
• 🚚 Rename wetlab to pertdb by @falexwolf in #3472
• ♻️ Efficiently encode uploading information by @falexwolf in #3473
• 📝 Consistently mention backward relationships and type-annotate ManyToMany fields with QueryManager[T] by @falexwolf in #3474
• 🚸 Enable convenient re-upload of local file after upload failure by @falexwolf in #3079
• ♻️ Rather flag _storage_ongoing than _storage_completed by @falexwolf in #3475
• ⚡ Start monitoring performance profiling by @falexwolf in #3477
• 📝 README v5.1 by @falexwolf in #3478
• ⬆️ Update lamin-utils by @sunnyosun in #3479
• ⬆️ Released bionty 2.1.0 by @sunnyosun in #3482
• 📝 Better return typing of feature.__getitem__ by @sunnyosun in #3481
• 🚸 Improve error message for running a script or notebook outside the development directory by @falexwolf in #3484
• 📝 README v5.2 by @falexwolf in #3486
• 💚 Fix white-space formatting in tests for new Rich behavior by @Zethson in #3489
• 💚 Fix curator tests by @Zethson in #3490
• 🚸 Check local path existence on artifact.save() by @Koncopd in #3487
• 📝 Improve the Artifact.open() docs by @falexwolf in #3415
• 🚸 Default to creating a global run context in ln.flow() by @falexwolf in #3492
• ♻️ Enable memorizing the global run context of a flow by @falexwolf in #3493
• 🐛 Refactor & fix feature-based queries for records and expand tests by @falexwolf in #3494
• 🚚 Move lamin cache CLI command to be lamin settings cache-dir, refactor lamin settings, expand lamin annotate, and overhaul CLI docs by @falexwolf in #3495
• 📝 Document RelatedManager[T] and fix ManyToMany type annotations by @falexwolf in #3496
• 👷 Refactor performance profiling by @falexwolf in #3497
• 📝 Move lazy upload out of arrays guide and into from_lazy() docstring + unit tests by @falexwolf in #3499
• 🚸 Allow users to pass ids of foreign keys in Artifact() constructor by @Koncopd in #3498
• 🐛 Fix PyYAML serialization of NotebookNode by @Zethson in #3488
• 📝 Convert guides to markdown format by @falexwolf in #3501
• 🐛 Fix standardize ignoring passed source by @Zethson in #3500
• 👷 Simplify test/docs CI setup by @falexwolf in #3502
• 🚸 Overhaul the pytorch lightning integration by @Zethson in #3425
• 🚸 Better error behavior in lamin save by @sunnyosun in #3503
• 📝 README v5.3 by @falexwolf in #3504
• ♻️ Fully leverage Context to manage the run context of function executions by @falexwolf in #3506
• 🚸 Serialize Path, UPath, and handle None params by @falexwolf in #3507
• 🚸 Recognize packaged python source code across track(), @flow(), and @step() by @falexwolf in #3508
• ⚡️ Much faster permanent run & transform deletion by @falexwolf in #3509
• 📝 README v5.4: properly document workflows by @falexwolf in #3510
• 📝 Legible API reference for lamindb.models by @falexwolf in #3511
• 🚸 Save CLI tool in transform description by @falexwolf in #3512

Full Changelog: 2.0.1...2.1.0