Lamindb

- 🎨 Allow passing `QuerySet` to `.features.add_labels()` [PR969](https://github.com/laminlabs/lamindb/pull/969) [sunnyosun](https://github.com/sunnyosun)
- ⚡️ Speed up & remove auto-generation of feature name [PR963](https://github.com/laminlabs/lamindb/pull/963) [falexwolf](https://github.com/falexwolf)

- ✨ Add a progress monitoring to file.load() and file.stage() [PR959](https://github.com/laminlabs/lamindb/pull/959) [Koncopd](https://github.com/Koncopd)
- 🚚 Rename `Registry.select()` to `Registry.filter()` [PR958](https://github.com/laminlabs/lamindb/pull/958) [falexwolf](https://github.com/falexwolf)
- 🚚 Rename `Feature.label_orms` to `Feature.registries` [PR957](https://github.com/laminlabs/lamindb/pull/957) [falexwolf](https://github.com/falexwolf)
- ♻️ Aggregate ref_field, ref_orm, ref_schema into ref_field [PR955](https://github.com/laminlabs/lamindb/pull/955) [falexwolf](https://github.com/falexwolf)
- 🎨 Move feature foreignkey from label to link between label and file [PR954](https://github.com/laminlabs/lamindb/pull/954) [falexwolf](https://github.com/falexwolf)
- 🎨 Enable file/dataset-external feature sets [PR953](https://github.com/laminlabs/lamindb/pull/953) [falexwolf](https://github.com/falexwolf)

- 📝 Add MuData example [PR945](https://github.com/laminlabs/lamindb/pull/945) [sunnyosun](https://github.com/sunnyosun)
- 🎨 Add `Modality` [PR940](https://github.com/laminlabs/lamindb/pull/940) [falexwolf](https://github.com/falexwolf)
- 🎨 Describe based on provenance and features [PR936](https://github.com/laminlabs/lamindb/pull/936) [sunnyosun](https://github.com/sunnyosun)
- 🚸 Add `File.features` accessor: `FeaturesManager` [PR933](https://github.com/laminlabs/lamindb/pull/933) [falexwolf](https://github.com/falexwolf)
- 📝 Add spatial data example [PR930](https://github.com/laminlabs/lamindb/pull/930) [falexwolf](https://github.com/falexwolf)
- ✨ Added `with_children` to `view_parents` [PR921](https://github.com/laminlabs/lamindb/pull/921) [sunnyosun](https://github.com/sunnyosun)
- 📝 Added comprehensive lineage graph example [PR919](https://github.com/laminlabs/lamindb/pull/919) [sunnyosun](https://github.com/sunnyosun)
- 🚸 `File` methods work prior to `save()` [PR918](https://github.com/laminlabs/lamindb/pull/918) [Koncopd](https://github.com/Koncopd)
- 🚚 Integrate `Project` and `Tag` into `Label` [PR914](https://github.com/laminlabs/lamindb/pull/914) [falexwolf](https://github.com/falexwolf)
- ♻️ Replace `lamin_logger` with `lamin_utils` [PR912](https://github.com/laminlabs/lamindb/pull/912) [falexwolf](https://github.com/falexwolf)
- ♻️ Replace `Run.name` with `Run.reference_type` and more [PR910](https://github.com/laminlabs/lamindb/pull/910) [falexwolf](https://github.com/falexwolf)
- ✨ Enable to create `File` outside default storage [PR891](https://github.com/laminlabs/lamindb/pull/891) [falexwolf](https://github.com/falexwolf)
- ✨ Multi-field search [PR898](https://github.com/laminlabs/lamindb/pull/898) [sunnyosun](https://github.com/sunnyosun)
- ✨ Better `Feature` management [PR897](https://github.com/laminlabs/lamindb/pull/897) [falexwolf](https://github.com/falexwolf)
- 🎨 Make `ensembl_gene_id`` unique for `Gene` [PR895](https://github.com/laminlabs/lamindb/pull/895) [sunnyosun](https://github.com/sunnyosun)
- ⚡ Speed up file creation [PR894](https://github.com/laminlabs/lamindb/pull/894) [falexwolf](https://github.com/falexwolf)
- 🚚 Rename `Readout` to `ExperimentalFactor` [PR893](https://github.com/laminlabs/lamindb/pull/893) [sunnyosun](https://github.com/sunnyosun)
- 🎨 `set_abbr` adds `abbr` to `synonyms` [PR892](https://github.com/laminlabs/lamindb/pull/892) [sunnyosun](https://github.com/sunnyosun)

- ✨ View parents [PR858](https://github.com/laminlabs/lamindb/pull/858) [sunnyosun](https://github.com/sunnyosun)
- ✨ Track parent notebooks [PR859](https://github.com/laminlabs/lamindb/pull/859) [falexwolf](https://github.com/falexwolf)
- 🚸 Improve data-lineage guide, auto-track run inputs [PR869](https://github.com/laminlabs/lamindb/pull/869) [falexwolf](https://github.com/falexwolf)
- 🚸 More reliably detect interactive environments `ln.track()` [PR878](https://github.com/laminlabs/lamindb/pull/878) [Koncopd](https://github.com/Koncopd)
- 🚸 Case insensitive search [PR877](https://github.com/laminlabs/lamindb/pull/877) [falexwolf](https://github.com/falexwolf)
- 🚸 Fix bug and add test for tracking multiple parent transforms [PR875](https://github.com/laminlabs/lamindb/pull/875) [falexwolf](https://github.com/falexwolf)
- ✨ Read remote h5ad in backed mode in `File.from_anndata` [PR871](https://github.com/laminlabs/lamindb/pull/871) [falexwolf](https://github.com/falexwolf)
- ⚡️ Speed up search [PR868](https://github.com/laminlabs/lamindb/pull/868) [falexwolf](https://github.com/falexwolf)
- ✨ Added `File.inherit_relationships` [PR867](https://github.com/laminlabs/lamindb/pull/867) [sunnyosun](https://github.com/sunnyosun)
- ⚡️ Better cache management [PR864](https://github.com/laminlabs/lamindb/pull/864) [Koncopd](https://github.com/Koncopd)
- ✨ Added `Manager.list()` and allow passing field name [PR863](https://github.com/laminlabs/lamindb/pull/863) [sunnyosun](https://github.com/sunnyosun)
- ✨ Added `.describe()` for rich repr of related objects [PR862](https://github.com/laminlabs/lamindb/pull/862) [sunnyosun](https://github.com/sunnyosun)
- ✨ Track `hash_type` [PR861](https://github.com/laminlabs/lamindb/pull/861) [falexwolf](https://github.com/falexwolf)
- 🚸 It should be possible to use a schema module prior to importing `lamindb` [PR852](https://github.com/laminlabs/lamindb/pull/852) [falexwolf](https://github.com/falexwolf)
- ✨ Enable `search`, `lookup`, `inspect`, `map_synonyms` from `QuerySet` [PR849](https://github.com/laminlabs/lamindb/pull/849) [sunnyosun](https://github.com/sunnyosun)

Features:

- ✨ Enable hierarchical metadata, e.g., cell types, tissues, etc. [PR810](https://github.com/laminlabs/lamindb/pull/810) [sunnyosun](https://github.com/sunnyosun)
- ✨ Add `Dataset` & `Feature` ORMs, e.g., easily track column names of dataframes [PR805](https://github.com/laminlabs/lamindb/pull/805) [falexwolf](https://github.com/falexwolf)

Breaking changes:

- 🚚 Rename `File.name` to `File.description` [PR824](https://github.com/laminlabs/lamindb/pull/824) [falexwolf](https://github.com/falexwolf)
- 🚚 Rename `File.featuresets` to `File.feature_sets` [PR805](https://github.com/laminlabs/lamindb/pull/805) [falexwolf](https://github.com/falexwolf)

UX:

- ✨ Globally set species via `lb.settings.species=` [PR142](https://github.com/laminlabs/lnschema-bionty/pull/142) [falexwolf](https://github.com/falexwolf)
- 🚚 Easy display of many-to-many fields: `QuerySet.df(include=[field__name])` [PR832](https://github.com/laminlabs/lamindb/pull/832) [falexwolf](https://github.com/falexwolf)
- 🚸 Create new run if notebook is run by different user [PR838](https://github.com/laminlabs/lamindb/pull/838) [falexwolf](https://github.com/falexwolf)
- 🚸 Speed up bulk saving of records [PR828](https://github.com/laminlabs/lamindb/pull/828) [sunnyosun](https://github.com/sunnyosun)
- 🚸 Hash large files faster [PR836](https://github.com/laminlabs/lamindb/pull/836) [falexwolf](https://github.com/falexwolf)
- ✨ Add `from_df` and `from_anndata` to `File` [PR844](https://github.com/laminlabs/lamindb/pull/844) [falexwolf](https://github.com/falexwolf)
- 🚸 Return locally backed object instead of cloud backed if available [PR840](https://github.com/laminlabs/lamindb/pull/840) [falexwolf](https://github.com/falexwolf)
- 🚸 Raise more & more user-friendly errors in setup API when instance already setup [PR837](https://github.com/laminlabs/lamindb/pull/837) [falexwolf](https://github.com/falexwolf)
- 🚸 Better error behavior when no notebook title set in `ln.track()` [PR834](https://github.com/laminlabs/lamindb/pull/834) [Koncopd](https://github.com/Koncopd)
- 🚸 Store hash for remote files on S3 [PR808](https://github.com/laminlabs/lamindb/pull/808) [falexwolf](https://github.com/falexwolf)