Changelog

  • 🐛 Fix trailing slash in upload_from source PR @Koncopd

  • 🚸 Make upload_from(), download_to(), and view_tree() more user friendly PR @falexwolf

  • 🚸 More intuitive version updating dialogue PR @falexwolf

  • :sparkles: Improve coverage of annotate PR @Zethson

  • 🔊 Fix annotate logging PR @sunnyosun

  • 🐛 Actually add tracking run for entities beyond Artifact & Collection PR @falexwolf

Note

If using LaminHub, please use the latest version of lamindb.

LaminDB implements “migration-based versioning”. When upgrading your LaminDB installation to a new minor version in major.minor.patch, you also migrate your database by calling lamin migrate deploy.

0.72

0.72.1 2024-05-19

0.72.0 2024-05-19

  • ✨ Extend managed access for AWS S3 to arbitrary paths PR @Koncopd @fredericenard

  • ✨ Extended data lineage tracking PR @falexwolf

    • Now store all creating runs and all updating runs for any entity, not just for Artifact & Collection, e.g., runs can now have CellType record outputs

    • Code is simpler through inheritance from two new base classes: TracksRun and TracksUpdates

  • ♻️ Briefer and richer syntax for denoting feature types, renamed Feature.type to Feature.dtype, e.g., for categorical features, a valid type can be: cat[ULabel|bionty.Drug] PR @falexwolf

  • ✨ Support non-categorical metadata PR @falexwolf

    • Track non-categorical features: int, float, bool, datetime, lists & dictionaries stored in a FeatureValue registry

    • Track arbitrary typed parameters for runs through a Param registry analogous to the Feature registry: this replaces the hard-to-validate, hard-to-migrate, and hard-to-query json field of Run

  • 🏗️ Refactor link models PR PR @falexwolf

    • All annotation-related links are now stratified by Feature: what held for ULabel now also holds CellType and all other Bionty registries

    • Indicate whether semantic keys were used during validation to enable warnings upon renames

    • Protect artifact annotations rather than cascade delete them

    • More consistent naming of link models, e.g., ulabels.artifact_links instead of ulabels.artifactulabel_set

    • Dropped linking Bionty entities directly against Collection

    • Pruned & squashed migrations for faster instance creation

0.71

0.71.3 2024-05-14

0.71.2 2024-05-07

0.71.1 2024-05-07

  • 🚸 Upload source code of scripts upon ln.finish() and no longer upon ln.track() PR @falexwolf

  • 🎨 Make features.add_feature_set public PR @sunnyosun

  • 🎨 Use the same uid for the same feature set in transfer PR @sunnyosun

  • 🎨 Upon upload switch to virtual key PR @falexwolf

  • ⚡️ Zarr and cache improvements PR @Koncopd

  • ♻️ Extend valid suffixes to composite suffixes PR @falexwolf

  • 🔥 Remove little-used artifact.view_tree() PR @falexwolf

0.71.0 2024-05-01

0.70

0.70.4 2024-04-24

  • ✨ Allow passing path to .from_anndata PR @sunnyosun

  • 🚸 In .setup.delete(), check for data deletion & delete from hub PR @falexwolf

  • ⚡️ Speed up latest_version PR @falexwolf

  • 🚸 Better user feedback on folder-like artifacts PR @falexwolf

0.70.3 2024-04-22

  • 🚸 Update metadata like description upon re-running PR @falexwolf

  • 🐛 Fix detection of AnnData in zarr and h5ad, refactor directory upload PR @Koncopd

  • 🚸 Raise error if transforms of type notebook or script are passed manually PR @falexwolf

0.70.2 2024-04-19

  • ♻️ In Vitessce integration, separate VitessceConfig from its referenced artifacts PR @falexwolf

  • 🚸 In ln.finish(), remove flag i_saved_the_notebook PR @falexwolf

0.70.1 2024-04-18

0.70.0 2024-04-17

  • 🚸 Update data source in case transform is re-run PR @falexwolf

  • 🚸 Enable to label transforms via transform.ulabels PR @falexwolf

  • 🚚 Deprecate stage() in favor of cache() PR @falexwolf

0.69

0.69.10 2024-04-12

  • ✨ Add .obsm and .layers to MappedCollection and rename label_keys to obs_keys PR @Koncopd

  • 🚸 Eliminate kwargs PR @sunnyosun

  • ✨ Introduce Annotate.from_mudata PR @sunnyosun

0.69.9 2024-04-08

0.69.8 2024-04-04

0.69.7 2024-04-03

  • ✨ Add ability to upload arbitrary files or folders from CLI PR @falexwolf

  • 🐛 Fix anndata backed mode incompatibility with scipy 1.13.0 f

0.69.6 2024-04-02

  • 🚑️ Temp fix region for non-hosted buckets PR @sunnyosun

0.69.5 2024-03-30

0.69.4 2024-03-30

0.69.3 2024-03-28

  • ✨ Introduce annotation flow via Annotate.from_df and Annotate.from_anndata PR 1 2 3 @sunnyosun

0.69.2 2024-03-26

0.69.1 2024-03-18

✨ To try out, add lamindb.validation with the Validator class PR @sunnyosun

0.69.0 2024-03-17

Main new features:

  • ✨ Integrate lamindb with git PR PR @falexwolf

  • ✨ Introduce ln.finish(), track run finish times as run.finished_at, rename run.run_at to run.started_at, upload notebooks during ln.finish() PR @falexwolf

  • 🚸 Upload script source code and environment during ln.track() PR @falexwolf

Other changes:

0.68

0.68.2 2024-03-11

  • 🚸 Move transform & run artifacts into cache before uploading PR @falexwolf

  • 🚸 More sensible transform types PR @falexwolf

  • 🚚 Rename lnschema_lamin1 to wetlab PR @falexwolf

0.68.1 2024-03-08

  • 🚸 You can now use ln.connect() to connect to a LaminDB instance PR @falexwolf

  • 🚸 You can no longer delete data from non-default storage locations, as these might be tracked in other instances PR @sunnyosun

  • 🚸 Enable transferring data from local instances to remote instances PR @sunnyosun

0.68.0 2024-03-01

🚸 Decouple features linking from Artifact construction PR 1 2 3 @sunnyosun.

# default constructor for PathLike
artifact = ln.Artifact("mysc.h5ad", description="raw data")
# from_ constructors for other types
artifact = ln.Artifact.from_anndata(mysc_adata, description="raw data")  # no longer links features
artifact = artifact.save()

# high-level feature linking
artifact.features.add_from_anndata(var_field=bt.Gene.ensembl_gene_id)
artifact.features.add_from_df()

# low-level feature linking
meta = ln.Feature.from_values(mysc_adata.obs.columns, field="name")
genes = bt.Gene.from_values(mysc_adata.var.ensembl_gene_id, field="ensembl_gene_id")
artifact.features.add(genes, slot="obs")
artifact.features.add(genes, slot="var")

# labels linking (no change)
labels = ln.ULabel.from_values(adata.obs.donor, field=...)
ln.save(labels)
artifact.labels.add(labels)

0.67

0.67.3 2024-02-02

0.67.2 2024-01-14

  • ✨ Enable staging notebooks & code using the CLI PR @falexwolf

0.67.1 2024-01-12

0.67.0 2024-01-11

  • 🚚 Rename .bionty to .public, .from_bionty to .from_public PR @sunnyosun

0.66

0.66.1 2024-01-09

  • 🐛 Fix id matching in view_lineage PR @sunnyosun

  • ♻️ Fix connection time outs PR @Koncopd

  • ♻️ Incorporate edge cases in inner and outer join in Collection.mapped PR @Koncopd

  • 🎨 Not create organism records when calling .bionty() PR @sunnyosun

0.66.0 2024-01-07

0.65

0.65.1 2024-01-05

0.65.0 2024-01-02

0.64

0.64.2 2023-12-18

0.64.1 2023-12-13

0.64.0 2023-12-13

🏗️ Replace File with Artifact to model directories and directory-like array stores PR1345 @falexwolf.

For artifacts that are simple files, rename File to Artifact along with the word file to artifact in registry fields. Otherwise, your code will behave the same.

0.63

0.63.5 2023-12-11

0.63.4 2023-12-08

0.63.3 2023-12-05

0.63.2 2023-12-02

0.63.1 2023-11-28

  • 🚸 Enable schema packages that do not start with lnschema_ 592 falexwolf

  • 🚸 Do not rely on naming the primary key id PR1328 @falexwolf

  • ✨ Add context manager to File.backed and Dataset.mapped PR1326 @Koncopd

0.63.0 2023-11-24

0.62

0.62.0 2023-11-20

0.61

0.61.0 2023-11-15

0.60

0.60.3 2023-11-13

0.60.1 2023-11-10

0.60.0 2023-11-09

0.59

0.59.3 2023-11-04

0.59.2 2023-11-04

0.59.1 2023-11-03

0.59.0 2023-10-27

0.58

0.58.2 2023-10-26

0.58.1 2023-10-26

0.58.0 2023-10-24

0.57

0.57.2 2023-10-23

0.57.1 2023-10-20

0.57.0 2023-10-19

0.56

0.56.2 2023-10-19

0.56.1 2023-10-18

0.56.0 2023-10-17

The previous universal primary keys are now stored us unique universal ids in .uid and .id stores integer primary keys.

This leads to significantly higher storage efficiency of indexes & constraints in link tables with >10 million rows.

A dialogue guides you through the migration process.

0.55

0.55.2 2023-10-10

0.55.1 2023-10-4

0.55.0 2023-10-03

0.54

0.54.4 2023-09-29

0.54.3 2023-09-27

0.54.2 2023-09-26

0.54.1 2023-09-21

0.54.0 2023-09-17

0.53 2023-09-09

0.52

0.52.2 2023-09-05

0.52.1 2023-09-02

0.52.0 2023-09-01

0.51

0.51.3 2023-08-30

0.51.2 2023-08-28

0.51.1 2023-08-28

0.51.0 2023-08-24

0.50

0.50.1 2023-08-17

0.50.0 2023-08-07

0.49

0.49.3 2023-08-04

  • 🔧 Eliminate index files & upper bound pydantic and other core dependencies by major versions PR981 @falexwolf

0.49.2 2023-08-03

0.49.1 2023-08-01

0.49.0 2023-07-31

  • ✨ Add a progress monitoring to file.load() and file.stage() PR959 @Koncopd

  • 🚚 Rename Registry.select() to Registry.filter() PR958 @falexwolf

  • 🚚 Rename Feature.label_orms to Feature.registries PR957 @falexwolf

  • ♻️ Aggregate ref_field, ref_orm, ref_schema into ref_field PR955 @falexwolf

  • 🎨 Move feature foreignkey from label to link between label and file PR954 @falexwolf

  • 🎨 Enable file/dataset-external feature sets PR953 @falexwolf

0.48 2023-07-26

0.47 2023-07-10

0.46 2023-07-06

Features:

  • ✨ Enable hierarchical metadata, e.g., cell types, tissues, etc. PR810 @sunnyosun

  • ✨ Add Dataset & Feature ORMs, e.g., easily track column names of dataframes PR805 @falexwolf

Breaking changes:

UX:

0.45 2023-06-27

0.44

0.44.2 2023-06-23

0.44.1 2023-06-22

0.44.0 2023-06-20

Features:

  • 🚸 Idempotency across metadata records & data artifacts FAQ PR783 @falexwolf

  • ✨ add_synonym & map_synonyms to enable, e.g., add_synonym("MyGeneName") PR786 @sunnyosun

  • ✨ Backed access for general HDF5 and zarr objects PR781 @Koncopd

Refactors:

0.43.0 2023-06-15

Features:

  • ✨ Enable Registry.search() and improved Registry.lookup() PR771 @sunnyosun

  • 🎨 Consolidate lnschema_bionty and upgrade to latest Bionty PR775 @sunnyosun

  • 🚸 Introduce ln.settings.storage to switch default storage PR773 @falexwolf

  • 🚸 Return existing file if hash exists (idempotency) PR772 @falexwolf

  • 🚸 ln.settings can now change logging verbosity levels PR630 @falexwolf

Refactors:

0.42.0 2023-06-14

This is the first release after migrating from SQLModel/SQLAlchemy to Django.

With this, we’re hopeful that we get closer to a production-ready 1.0.0 API.

Highlights:

  • More robust & simpler automated migrations: lamin migrate create & lamin migrate deploy

  • Simpler query syntax (no joins anymore): ln.File.select(transform__created_by=user)

  • No need to create a session object to load relationships: access file.transform to load a Transform object

  • No need to write out link models in schemas & generally simplified schema syntax

  • Any schema package (lnschema_myschema) is now managed as minimal Django app

Breaking changes:

  • Renamed ln.Features to ln.FeatureSet and is now typically instantiated with FeatureSet.from_iterable()

  • Removed ln.Session

  • Removed .join() (replaced SelectStmt with QuerySet)

  • .all() now returns a QuerySet and no longer a list (use .list() instead)

  • Access Bionty objects within lnschema_bionty via Registry.bionty() instead of Registry.bionty

  • Removed File.stream() as all functionality is now provided through File.backed()

  • Many-to-many fields are now set with Run.inputs.set() and appended with Run.inputs.add()

Non-breaking changes:

  • Vastly simplified dependencies & introduced configurable installation

  • Auto-generated storage keys are now of the form lndb/{id}.{suffix} rather than just {id}.{suffix}

  • Renamed ln.add() to ln.save()

  • Introduced Registry.select(), Registry.save(), and Registry.delete()

  • Better tracking & linking of Bionty sources in lnschema_bionty

Additional notes:

  • Consolidated docs and auto-generate upon push events to lamindb main

  • Consolidated submodules (renamed lndb to lamindb-setup, removed lndb-storage)

The main downsides of migrating to Django are:

  • Currently only one LaminDB instance loadable per Python session

  • Type hints & constructor signatures are less pythonic (SQLModel uses less magic than Django) and lead to idiosyncrasies in model definition (nullable defaults) and validation (validation at the Registry-level is more manual as Django foresees validation at the Form level)

  • SQLAlchemy provides the more powerful Registry, and there might be future use cases that will require them

Complete list of changes below.

Name

PR

Developer

Date

Version

♻️ Use TransformType

763

falexwolf

2023-06-13

👷 Dispatch to lamin-examples & redun-lamin-fasta

762

falexwolf

2023-06-13

🔥 Remove File.stream()

761

falexwolf

2023-06-13

0.42a9

🚸 Prefix auto-storage-key with lndb/

757

falexwolf

2023-06-12

✨ Delete storage in File.delete()

754

Koncopd

2023-06-12

✅ Add more tests for File init

755

falexwolf

2023-06-12

💚 Remove test paths from pyproject.toml

753

falexwolf

2023-06-11

✨ Add to_adata() method to AnnDataAccessor

752

Koncopd

2023-06-11

🚚 Rename Featureset to FeatureSet

750

sunnyosun

2023-06-10

⚠️ Refactor save - it no longer returns records

742

falexwolf

2023-06-10

📝 Re-organize biology guides

740

falexwolf

2023-06-10

✨ Populate bionty_version in ln.parse

739

sunnyosun

2023-06-09

0.42a8

⚡ Improved multifield query in ln.parse

736

sunnyosun

2023-06-09

⬆️ First stable Django release of lnschema-bionty

733

sunnyosun

2023-06-09

🚸 Validate required fields

735

falexwolf

2023-06-09

📝 Integrate lnschema_bionty into reference

732

falexwolf

2023-06-08

0.42a7

🚸 Add select method to BaseORM

730

falexwolf

2023-06-08

📝 Overhaul README

728

falexwolf

2023-06-08

♻️ Refactored features code

731

sunnyosun

2023-06-08

📝 Add configure guide instead of setup

727

falexwolf

2023-06-08

🧪 Add tests for folder.tree()

726

sunnyosun

2023-06-08

🚚 Renamed BiontyVersions to BiontySource

725

sunnyosun

2023-06-07

🔊 folder.tree can only be used with existing folders in storage

724

sunnyosun

2023-06-07

👷 Coverage in separate job

722

falexwolf

2023-06-07

🎨 Import ORMs from .models before reload

723

sunnyosun

2023-06-07

🔥 Remove ln.nb

721

falexwolf

2023-06-07

🏗️ Re-architect transform id

720

falexwolf

2023-06-06

0.42a6

🚚 Rename ln.add to ln.save

719

falexwolf

2023-06-05

0.42a5

⬆️ Upgrade lnschema-core to 0.35a5

718

sunnyosun

2023-06-05

🚚 Migrate lnschema-bionty to Django

716

falexwolf

2023-06-05

0.42a2

♻️ Polish core schema

717

falexwolf

2023-06-05

🐛 Fix delete for File

715

Koncopd

2023-06-04

📝 Rework the stream notebook

714

Koncopd

2023-06-04

💚 Point to lamindb-setup main & fix session

713

falexwolf

2023-06-04

➖ Move nbproject to extra dependencies

711

Koncopd

2023-06-04

🔥 Delete SQLAlchemy related content

710

falexwolf

2023-06-04

➕ Pin boto3 in aws

712

Koncopd

2023-06-04

🔥 Remove SQLAlchemy tests

709

falexwolf

2023-06-04

♻️ Absorb DjangoORM.create() in DjangoORM.__init__()

707

falexwolf

2023-06-03

🐛 Disentangle keys in storage related test notebooks

708

Koncopd

2023-06-03

🚸 ln.track improvements

704

Koncopd

2023-06-03

🏗️ Enable Django backend (part 2)

702

falexwolf

2023-06-02

🎨 Simplified track sample-level metadata

705

sunnyosun

2023-06-02

🔊 Add more loggings to ln.parse

703

sunnyosun

2023-06-02

0.42a1

♻️ Refactored feature parsing and ln.parse

701

sunnyosun

2023-06-01

🚚 Move lndb-storage back into lamindb

700

falexwolf

2023-06-01

🚚 Rename lndb to lamindb_setup

699

falexwolf

2023-06-01

🏗️ Add Django backend (setup)

697

falexwolf

2023-05-31

⬆️ Update lndb to 0.45.0

698

Koncopd

2023-05-31

0.41.2

⬆️ Upgrade lnschema-bionty

696

sunnyosun

2023-05-30

0.41.1

🚑 Fix species config

695

sunnyosun

2023-05-28

0.41.0

🎨 Clean up CI more

694

falexwolf

2023-05-28

➖ Remove scanpy as test dependency

693

falexwolf

2023-05-28

👷 Fix coverage for lndb-storage

692

falexwolf

2023-05-28

➖ Do not install storage extras by default

691

Koncopd

2023-05-28

0.41a4

👷 Bring back nox session

690

falexwolf

2023-05-28

📝 Refactor guide notebooks

689

falexwolf

2023-05-28

✨ Add DataFrame support for ln.parse

688

sunnyosun

2023-05-28

👷 Refactor tests

687

falexwolf

2023-05-27

✨ Subsettable backed AnnData

668

Koncopd

2023-05-27

📝 Remove setup notebook

686

falexwolf

2023-05-27

🏗️ Remove SQL-level schema modules

685

falexwolf

2023-05-26

0.41a3

⬆️ Upgrade lnschema-bionty to 0.17.1

684

sunnyosun

2023-05-25

0.40.7

⬇️ Downgrade lnschema-bionty to 0.16.5

683

sunnyosun

2023-05-25

0.40.6

♻️ Refactor types

681

falexwolf

2023-05-23

0.40.5

♻️ Refactor BaseORM

679

falexwolf

2023-05-17

🚸 Pre-join some cheap relationships

678

falexwolf

2023-05-16

📝 Improve wording

677

Zethson

2023-05-16

✨ Added Treatment table

675

sunnyosun

2023-05-15

0.40.3

🚑 Fix ln.Features table name for postgres

674

sunnyosun

2023-05-11

0.40.1

📝 Update ontology guide

673

falexwolf

2023-05-11

🎨 Deprecated data in ln.Features, replace with iterable

672

sunnyosun

2023-05-11

🎨 Replace reference with field for ln.Features Breaking

671

sunnyosun

2023-05-09

0.40.0

⬆️ Update bionty to 0.13

670

sunnyosun

2023-05-09

0.39.8

📝 Polish

667

falexwolf

2023-04-28

📝 Polish docs

666

falexwolf

2023-04-28

⬆️ Update to lndb 0.44.7

665

sunnyosun

2023-04-28

0.39.7

🚸 Do not require session for is_run_input

664

falexwolf

2023-04-28

0.39.6

⬆️ Allow load with storage

663

sunnyosun

2023-04-27

0.39.5

💥 Switch to methods bionty.df(), bionty.lookup() Breaking

662

sunnyosun

2023-04-27

0.39.4

⬆️ Upgrade lndb

661

fredericenard

2023-04-26

0.39.3

✨ Enable database entries lookup

660

sunnyosun

2023-04-24

0.39.2

✨ Introduce File.backed()

659

falexwolf

2023-04-24

✨ Introduced ln.parse()

658

sunnyosun

2023-04-24

0.39.1

🎨 Refactor ln.File

657

falexwolf

2023-04-24

0.39.0

✨ Inherit fsspec kwargs from root and move in root check

655

Koncopd

2023-04-23

📌 Check anndata version in File.subset

commit

Koncopd

2023-04-23

🐛 Fix VS Code notebook reinitialization in track

654

Koncopd

2023-04-23

🚸 Add File.subset

653

falexwolf

2023-04-22

0.39rc1

🚚 Replace lnschema-wetlab with lnbase-biolab and lnschema-lamin1

651

falexwolf

2023-04-22

📝 Add an export example for ln.schema.view()

649

falexwolf

2023-04-21

🐛 Fix population of transform_id in File in edge cases

648

falexwolf

2023-04-21

0.38.3

🚸 Allow registering local postgres instances on the hub

647

falexwolf

2023-04-21

0.38.2

🚸 Improve error message for notebook tracking

643

falexwolf

2023-04-19

van -> can

641

ThomVett

2023-04-19

⚡ Improved feature parsing speed

640

sunnyosun

2023-04-19

0.38.1

⬆️ Compatibility with new hub

639

falexwolf

2023-04-18

0.38.0

💥 New calling patterns for lnschema-bionty

633

falexwolf

2023-04-18

✅ Use nbproject-test directly

638

Koncopd

2023-04-18

🚸 Use relative path in key

636

falexwolf

2023-04-18

0.37.2

🩹 Unpack notebook_path correctly

632

Koncopd

2023-04-17

0.37.1

🚚 Better names, more relationships directly on File Breaking

631

falexwolf

2023-04-16

0.37.0

✨ Add Google Colab integration

628

falexwolf

2023-04-16

🚸 Improve notebook tracking UX

627

falexwolf

2023-04-14

🎨 Simplify ln.track() and add app transform type

624

falexwolf

2023-04-12

0.36.3

🐛 Fix initialization of new notebooks

623

Koncopd

2023-04-10

0.36.1

🚸 Filename in File.name, new File.key and Folder.key, robustness overhaul Breaking

614

falexwolf

2023-04-08

0.36.0

✨ Introduce File.stage() and File.replace()

611

Koncopd

2023-04-03

0.35.6

🚸 More robust ontology version tracking

605

Zethson

2023-04-01

🚚 Import lnschema_bionty instead of bionty

591

sunnyosun

2023-03-28

0.35.5

🚚 Move all core entities to root level

590

falexwolf

2023-03-27

0.35.4

🚸 Polish guide

589

falexwolf

2023-03-27

0.35.3

🚚 Move Readout from lnschema-wetlab to lnschema-bionty

588

sunnyosun

2023-03-27

0.35.2

♻️ Fix parsing_id

587

sunnyosun

2023-03-27

0.35.1

🚚 Rename DObject to File and DFolder to Folder Breaking

586

falexwolf

2023-03-25

0.35.0

🚚 Introduce ln.track() to replace ln.nb.header()

585

falexwolf

2023-03-24

🏗️ Combine Notebook and Pipeline into Transform Breaking

584

falexwolf

2023-03-23

🚑 Fix optional dependencies

583

sunnyosun

2023-03-22

0.34.2

🔥 Remove Usage

581

falexwolf

2023-03-22

⬆️ Updated CellMarker asset

578

sunnyosun

2023-03-21

0.34.1

⬆️ Upgrade to bionty 0.9

575

sunnyosun

2023-03-20

0.34.0

♻️ Move storage-related code to lndb-storage

560

Koncopd

2023-03-20

🚑 Fix gene id

573

sunnyosun

2023-03-17

🐛 Check if env variable exists before trying to get his value

572

fredericenard

2023-03-15

🚸 Do not yet show deprecation warning for ln.nb.header()

commit

falexwolf

2023-03-15

0.33.4

👷 Restore streaming test from cloud

569

sunnyosun

2023-03-15

0.33.3

⬇️ typeguard<3.0.0

568

sunnyosun

2023-03-15

➖ Remove typeguard dependency

567

sunnyosun

2023-03-15

0.33.2

⬆️ Update core

566

sunnyosun

2023-03-15

0.33.1

🚚 Replace ln.nb.header() with ln.Run() except in faq/nb

564

falexwolf

2023-03-14

0.33.0

🚸 Smart about global_context and load_latest when run from notebook

563

falexwolf

2023-03-14

✨ ln.Features

562

sunnyosun

2023-03-14

🏗️ Introduce lamindb.context and enable ln.Run to create contexts

561

falexwolf

2023-03-13

📝 Improve the docstrings of ln.save and ln.delete

559

sunnyosun

2023-03-10

📝 Hide CI related cells in notebooks

558

sunnyosun

2023-03-10

📝 Update docs to clarify sign up and log in

557

lawrlee

2023-03-10

📝 Prettier species query

555

falexwolf

2023-03-09

0.32.0

📝 Refactor docs sidebar

553

sunnyosun

2023-03-09

⬆️ Upgrade ln.setup

554

falexwolf

2023-03-09

🔥 Remove ln.knowledge Breaking

552

sunnyosun

2023-03-09

➖ Remove bionty as a dependency

551

sunnyosun

2023-03-09

0.32.0rc1

📝 Replace ln.knowledge with bionty in docs

547

falexwolf

2023-03-07

0.31.1

📝 Link FAQ and guide to session and notebook API

550

falexwolf

2023-03-07

⬆️ Upgrade lndb

549

fredericenard

2023-03-07

0.31.0

⬆️ Upgrade lndb

548

fredericenard

2023-03-07

📝 Move ingest-folder back to faq

545

falexwolf

2023-03-06

🚸 Improve clarity of no_source error message

543

falexwolf

2023-03-06

💚 Fix CI

542

sunnyosun

2023-03-06

🚚 Rename data objects to data or datasets in titles

541

sunnyosun

2023-03-06

📝 Duplicate README to the guide landing page

540

sunnyosun

2023-03-06

✨ Allow uploading zarr from local paths

539

Koncopd

2023-03-05

📝 Prettify guide landing page

537

sunnyosun

2023-03-05

🚑 Fix upsert for dobject and CI

535

sunnyosun

2023-03-03

0.30.3

💄 Simplify docs

534

falexwolf

2023-03-03

🚸 Do not error, just warn upon installation of lamin

533

falexwolf

2023-03-02

0.30.2

🚑 Fix iterdir to not list itself

532

sunnyosun

2023-03-02

🔥 Remove lamin dependency

531

falexwolf

2023-03-01

0.30.1

🚑 Fix for listing cloud dir

528

sunnyosun

2023-03-01

0.30.0

🎨 Add lamindb.setup API as an alternative for the CLI

530

falexwolf

2023-03-01

🚚 Rename dfolder.get_dobject to get, allow passing a subdirectory

527

sunnyosun

2023-03-01

🚑 Ensure filepath is absolute

526

sunnyosun

2023-03-01

🎨 Allow passing a list of relpaths to dfolder.get_dobject

524

sunnyosun

2023-02-28

✨ Infer filesystem for anndata read and write

522

Koncopd

2023-02-25

📝 Replace lndb with lamin in docs

521

falexwolf

2023-02-25

0.29.1

📝 Add nbproject note box to ingest guide

520

bpenteado

2023-02-24

🍱 DFolder.get_dobject

519

sunnyosun

2023-02-24

⬆️ Upgrade lnschema-core to 0.28.6

517

bpenteado

2023-02-23

0.29.0

💥 Move lns.DFolder to ln.DFolder

510

sunnyosun

2023-02-23

🐛 Fix trailing slash within lamindb

516

falexwolf

2023-02-22

0.28.5

👷 Fix CI config

515

falexwolf

2023-02-22

0.28.4

🐛 Fix version check

514

falexwolf

2023-02-22

0.28.3

👷 Collect docs artifacts

513

falexwolf

2023-02-22

0.28.2

🐛 Fix trailing slash in storage root

512

falexwolf

2023-02-22

0.28.1

🚚 Rename DObject.run_id to DObject.source_id

509

falexwolf

2023-02-21

0.28.0

🐛 Another occurance of local filepath

508

falexwolf

2023-02-21

👷 Better CI and better arg validation

505

falexwolf

2023-02-21

🐛 Fix tracking local existing data

506

falexwolf

2023-02-21

🚑 Fix parents for existing data ingestion

504

sunnyosun

2023-02-21

🎨 Disable multiple select results for .add and .delete by fields

502

sunnyosun

2023-02-20

0.28rc1

⚡️ Replace CloudPath with UPath

501

Koncopd

2023-02-19

👷 Move fixtures from nox to conftest

500

falexwolf

2023-02-17

📝 Simplify output for dfolder faq

499

sunnyosun

2023-02-17

📝 Guide to ingest a folder

496

sunnyosun

2023-02-17

🚑 Fix determination of sqlite vs postgres

497

falexwolf

2023-02-17

0.27.2

🎨 Improve lndb (lamindb manager) architecture

495

falexwolf

2023-02-16

0.27.1

🚸 Add relationship between DFolder and DObject

494

bpenteado

2023-02-16

✨ Confirm dialog for deleting data from storage

493

sunnyosun

2023-02-16

✨ Ingest existing data from configured local storage

491

sunnyosun

2023-02-16

🚸 Proper client server check for lndb

492

falexwolf

2023-02-16

⬆️ Upgrade nbproject to 0.8.2

490

bpenteado

2023-02-16

⬆️ Upgrade and rename lndb_setup to lndb (v0.32.4) Breaking

487

bpenteado

2023-02-14

0.27.0

🚑 Fix tracking of added records during ln.save()

489

bpenteado

2023-02-13

✨ Added is_run_input param to DObject.load()

488

sunnyosun

2023-02-13

🎨 Added ln.settings.track_run_inputs_upon_load

486

sunnyosun

2023-02-13

🎨 Added zarr tests back and cleaned up faq

485

sunnyosun

2023-02-13

🔥 Drop populating runin and tracking usage upon load

484

sunnyosun

2023-02-13

🚸 Better ln.nb.header() auto-retrieval error message

483

falexwolf

2023-02-09

🚸 Make DObject upload ACID

476

bpenteado

2023-02-08

📝 Add notebook on Registry lazy loading behavior to FAQ

472

bpenteado

2023-02-06

🎨 Robust generation of DObject._filekey

481

sunnyosun

2023-02-06

0.26.1

🎨 Added erroring behavior when file doesn’t exist for ln.delete

480

sunnyosun

2023-02-06

📝 Removed extra fields in dev.datasets.pbmc68k

479

sunnyosun

2023-02-06

➖ Removed lnbfx and fix CI

478

sunnyosun

2023-02-06

📝 Query book

470

sunnyosun

2023-02-06

🩹 Print dobject name for zarr upload

475

Koncopd

2023-02-02

🐛 Fix load

474

Koncopd

2023-02-02

🔥 Disable Registry relationship preview

473

bpenteado

2023-02-02

✨ Allow ingesting existing data in the cloud

471

sunnyosun

2023-02-02

🐛 Correct filepath in header

469

Koncopd

2023-02-01

🚸 Add post-setup settings manager, error on duplicate insert Breaking

466

falexwolf

2023-02-01

0.26.0

🐛 Fix fallback for notebook name

463

falexwolf

2023-01-30

0.25.7

🔥 Remove lns.DObject Breaking

462

sunnyosun

2023-01-30

⬆️ Upgrade lndb-setup 0.30.11

461

sunnyosun

2023-01-30

0.25.6

⬆️ Cleaned up dependencies so that it’s not as redundant to lndb-setup

460

sunnyosun

2023-01-27

➕ Bring back lnfbx

459

falexwolf

2023-01-26

0.25.5

📝 Prettier section headings in the docs

456

sunnyosun

2023-01-26

📌 Pin s3fs and gcsfs to the latest versions

458

falexwolf

2023-01-26

0.25.4

🚸 Auto-populate relationship-associated foreign key fields

457

bpenteado

2023-01-26

0.25.3

🐛 Fix strict type checking for relationships

455

bpenteado

2023-01-24

0.25.2

🩺 Increase migrations testing robustness postgres

454

falexwolf

2023-01-24

📝 Remove linked-select notebook

453

falexwolf

2023-01-24

⬆️ Upgrade lnschema-core to 0.25.1

452

bpenteado

2023-01-23

0.25.1

✨ Add explicit remote sqlite instance locking to write operations

447

Koncopd

2023-01-23

♻️ Refactored FAQ

448

sunnyosun

2023-01-23

📝 Create data validation FAQ

451

bpenteado

2023-01-23

➖ Remove s3fs dependency

450

fredericenard

2023-01-23

⬆️ Upgrade lndb-setup to 0.30.8

449

fredericenard

2023-01-23

🩹 Better treat edge cases upon signup, login, failed instance loading

446

falexwolf

2023-01-20

0.25.0

🚸 Introduce data validation on the Registry level

445

bpenteado

2023-01-20

♻️ Reorganize quickstart and get-started

444

sunnyosun

2023-01-20

📝 Refactor init guide and show bionty versions in guide

443

sunnyosun

2023-01-18

0.24.6

⬆️ Upgrade wetlab schema to 0.13.3

442

sunnyosun

2023-01-17

0.24.5

🐛 Fix taxon_id type and upgrade bionty

441

sunnyosun

2023-01-17

0.24.4

⬆️ Upgrade to lnschema-bionty 0.6.7

440

sunnyosun

2023-01-17

⬆️ Upgrade to lndb-setup 0.30.6

439

sunnyosun

2023-01-16

0.24.3

⬆️ Upgrade to lndb_setup==0.30.5

438

sunnyosun

2023-01-16

0.24.2

⬆️ Upgrade lndb-setup to 0.30.4

437

sunnyosun

2023-01-16

0.24.1

⬆️ Upgrade to lndb-setup 0.30.2

436

falexwolf

2023-01-16

0.24.0

🚸 Better hash exception

434

falexwolf

2023-01-12

🚸 Safer session behavior 2/2 Breaking

432

falexwolf

2023-01-12

0.23.0

👷 Extend CI to py3.8-3.10

431

sunnyosun

2023-01-12

0.22.5

🚸 Safer session behavior 1/2

430

falexwolf

2023-01-11

⬆️ Upgrade lndb-setup

428

fredericenard

2023-01-10

📝 Re-arrange notebooks

427

falexwolf

2023-01-09

🚸 Make ln.nb.header() more robust

426

falexwolf

2023-01-09

0.22.4

📝 Improving wording of definitions

424

falexwolf

2023-01-08

📝 Fixes for lndocs upgrade

423

falexwolf

2023-01-08

♻️ Refactor guide

422

sunnyosun

2023-01-08

⬆️ Upgrade lnschema-bionty to 0.6.5

421

falexwolf

2023-01-05

0.22.3

⬆️ Upgrade to lndb-setup 0.28.1

420

falexwolf

2023-01-05

Fix typos

418

Zethson

2023-01-02

🐛 Fix bugs in lndb set & lndb info

415

falexwolf

2022-12-22

0.22.2

✅ Error behavior for ingest

414

falexwolf

2022-12-20

🎨 Simplify

413

sunnyosun

2022-12-16

⬆️ Upgrade lndb-setup

412

falexwolf

2022-12-16

0.22.1

🚸 Better CLI & logging

411

falexwolf

2022-12-15

0.22.0

⬆️ Updated setup

409

sunnyosun

2022-12-15

0.21.5

🚸 Make nb.run and nb.notebook public

408

falexwolf

2022-12-14

⬆️ Upgrade wetlab

407

bpenteado

2022-12-13

0.21.4

⬆️ Upgrade lndb-setup

405

falexwolf

2022-12-13

0.21.3

⬆️ Upgrade lndb-setup

404

sunnyosun

2022-12-13

0.21.2

⬆️ Upgrade lndb-setup

403

falexwolf

2022-12-12

0.21.1

📝 Fix docs

402

falexwolf

2022-12-09

🎨 Integrate ln.record into lns.DObject → ln.DObject

400

sunnyosun

2022-12-09

0.21.0

⬆️ Upgrade setup, core & wetlab schema

398

falexwolf

2022-12-08

0.20.0

🔥 Drop all logic related to dynamic settings

397

fredericenard

2022-12-08

⬆️ Upgrade wetlab

395

bpenteado

2022-12-06

0.19.4

⬆️ Upgrade wetlab

394

bpenteado

2022-12-06

0.19.3

⬆️ Upgrade wetlab

393

sunnyosun

2022-12-06

0.19.2

🐛 Fix view

392

falexwolf

2022-12-05

0.19.1

🎨 Enable inheriting wetlab schemas

391

falexwolf

2022-12-05

0.19.0

✅ Better tests for features hashing

390

falexwolf

2022-12-04

⬆️ Upgrade lndb-setup

389

fredericenard

2022-12-04

0.18.9

✨ Check duplication before inserting records

387

sunnyosun

2022-11-30

0.18.8

🚸 Do not autoflush upon select

386

falexwolf

2022-11-30

0.18.7

🐛 Fix bug in schema module name lookup

384

falexwolf

2022-11-29

⬆️ Updated wetlab

383

sunnyosun

2022-11-29

0.18.6

⬆️ Upgrade lnschema-core and lndb-setup

382

falexwolf

2022-11-28

0.18.5

✨ Improve lazy selectors

375

Koncopd

2022-11-28

⬆️ Update wetlab schema

381

sunnyosun

2022-11-28

0.18.4

⬆️ Upgrade wetlab schema

380

sunnyosun

2022-11-28

0.18.3

⬆️ Upgrade lndb-setup & lnschema-core

379

fredericenard

2022-11-28

0.18.2

⬆️ Upgrade lndb-setup to 0.18.1

378

falexwolf

2022-11-25

🔥 Removed bioreadout

373

sunnyosun

2022-11-24

0.18.1

✨ Add lazy selectors to ln.subset

370

Koncopd

2022-11-23

🏗️ Persist the session

372

falexwolf

2022-11-23

⬆️ Upgrade lndb-setup

371

fredericenard

2022-11-23

✨ Add subset function for dobjects

368

Koncopd

2022-11-23

0.18.0

🎨 Drop Biometa

369

falexwolf

2022-11-22

🎨 Simplify schema module handling

367

falexwolf

2022-11-22

📝 Bring back guide to linking sample-level metadata

365

falexwolf

2022-11-21

0.17.0

📝 Add flow example back to main guide

363

falexwolf

2022-11-21

📝 Update schema

362

falexwolf

2022-11-21

🩹 Restore default fsspec for upload

361

Koncopd

2022-11-20

🎨 Prettify API

359

falexwolf

2022-11-18

🐛 Also return existing features

358

falexwolf

2022-11-18

📝 Fix select gene doc

357

falexwolf

2022-11-18

🏗️ Refactor ingest

356

falexwolf

2022-11-17

✨ Knowledge guide

353

sunnyosun

2022-11-16

🎨 Separate nb.publish from ingest.commit

355

falexwolf

2022-11-16

0.16.0

🐛 Fix data source

354

falexwolf

2022-11-15

🚚 Move storage key to core schema

352

falexwolf

2022-11-14

0.15.0

🐛 Fixed species_id in bio entity tables

351

sunnyosun

2022-11-14

✨ Initialize Jupynb run upon nb.header()

350

falexwolf

2022-11-12

0.14.0

🏗️ Aggregate Run and DTransform

349

falexwolf

2022-11-12

⬆️ Updated bionty

348

sunnyosun

2022-11-11

📝 Make notebook for link_features

347

falexwolf

2022-11-11

0.13.0

✨ Join dataframes

345

falexwolf

2022-11-10

✨ Fields in join

344

falexwolf

2022-11-10

✅ Add tests for zarr ingest and load

342

Koncopd

2022-11-10

🚚 Rename PipelineRun to Run

343

falexwolf

2022-11-10

🐛 Fix view

341

falexwolf

2022-11-09

0.12.1

🚚 Rename view arg

340

falexwolf

2022-11-09

0.12.0

📝 Refactor select notebooks

339

falexwolf

2022-11-08

📝 Simplify arg in link

338

falexwolf

2022-11-08

♻️ Refactor select

337

falexwolf

2022-11-08

⬆️ Update to bionty==0.5.3

334

sunnyosun

2022-11-06

🚚 Rename entries to records in link

333

sunnyosun

2022-11-04

📝 Improve guide

332

falexwolf

2022-11-04

🎨 Migrate to the new schema modules

331

falexwolf

2022-11-04

0.11.0

🔥 Removed link_biometa

330

sunnyosun

2022-11-03

🎨 Removed get, re-organized API docs

329

sunnyosun

2022-11-03

🚚 Move .db API to root level

328

sunnyosun

2022-11-03

🚚 Remove A prefix from notebooks

327

falexwolf

2022-11-03

✨ Storage related features

322

Koncopd

2022-11-03

🎨 Simplify generating records

326

sunnyosun

2022-11-02

🐛 Fixed bug in linking features

325

sunnyosun

2022-11-01

🍱 Added anndata_mouse_sc_lymph_node

324

sunnyosun

2022-11-01

🚚 Rename schema._table.Table to table_meta

323

sunnyosun

2022-11-01

🎨 Added LinkFeatureToKnowledgeTable

320

sunnyosun

2022-10-31

⬆️ Update lndb setup

321

fredericenard

2022-10-27

0.10.0

⬆️ Pinned bionty version

319

sunnyosun

2022-10-26

⬆️ Updated to lnschema_bionty 0.4.4

317

sunnyosun

2022-10-24

🔥 Remove lndb-hub import

318

fredericenard

2022-10-24

✨ Enable to get metadata from InstanceSettingsStore

310

fredericenard

2022-10-24

📝 Rename row to record when not yet added to the DB

316

falexwolf

2022-10-23

⬆️ Update lndb hub version

315

fredericenard

2022-10-23

🎨 Replace insert and update with add

308

falexwolf

2022-10-22

⬆️ Upgrade lnbfx to 0.4.5

311

bpenteado

2022-10-22

📝 Update postgres faq notebook

314

bpenteado

2022-10-22

🚚 Moved the rds notebooks to rnd-demo repo

309

sunnyosun

2022-10-21

✨ Added ln.link to populate link tables given two table entries

307

sunnyosun

2022-10-21

🔥 Remove hub import

301

fredericenard

2022-10-21

🎨 Overhaul select and add get

300

falexwolf

2022-10-21

🩹 Skip nc_evolutions table created by nocodb

302

sunnyosun

2022-10-21

✨ Added knowledge module

299

sunnyosun

2022-10-20

⬆️ Upgrade wetlab schema

297

sunnyosun

2022-10-20

0.9.6

⬆️ Added dset and project tables to core

296

sunnyosun

2022-10-19

0.9.5

🩹 Fixed rds nbs

295

sunnyosun

2022-10-18

📝 Add prisma examples and implementation ideas

294

fredericenard

2022-10-18

♻️ Refactor linked select

286

sunnyosun

2022-10-18

0.9.4

✏️ Fix typo in link table entry fetching

292

bpenteado

2022-10-17

🐛 Fixed link via link tables

291

sunnyosun

2022-10-15

0.9.3

✨ Add an option to use fsspec for upload

288

Koncopd

2022-10-15

✨ Load returns filepath if no in-memory format is found

287

sunnyosun

2022-10-13

0.9.2

🎨 Clean up dtransform_in

commit

falexwolf

2022-10-13

0.9.1

🎨 Continue overhaul

285

falexwolf

2022-10-13

0.9.0

🎨 Refactor linking dobjects & base64 encode checksum

283

falexwolf

2022-10-13

🐛 View only prints existing tables

284

sunnyosun

2022-10-12

✨ Added db.view, rename schema.draw to schema.view

282

sunnyosun

2022-10-12

0.8.3

⬆️ Added bioreadout lookup to guide

281

sunnyosun

2022-10-12

🚚 Rename query to select

280

falexwolf

2022-10-12

🩹 Fix out of sync db warning

279

Koncopd

2022-10-12

✨ Add streaming zarr write and streaming h5ad and zarr read

277

Koncopd

2022-10-12

💄 Cosmetics

276

falexwolf

2022-10-12

♻️ Refactor ingest & insert

273

falexwolf

2022-10-11

✨ Compute checksum during ingest

274

fredericenard

2022-10-11

🚚 Moved bfx ingestion to faq

272

sunnyosun

2022-10-11

⬆️ Upgrade to lndb_setup 0.12.0

271

falexwolf

2022-10-10

0.8.2

📝 Improved ingest guides, fixed linked entry bugs

270

sunnyosun

2022-10-10

🐛 Fixed dobject_biometa entry insertion

269

sunnyosun

2022-10-10

0.8.1

📝 Update test users in docs

268

falexwolf

2022-10-10

⬆️ Upgrade lndb_setup to 0.11.0 and nbproject to 0.7.0

267

falexwolf

2022-10-10

0.8.0

🎨 insert.from_list accepts entries

266

sunnyosun

2022-10-10

⬆️ Upgrade nbproject version to 0.5.5

265

Koncopd

2022-10-10

⬆️ Upgrade lndb_setup version to 0.10.1

264

fredericenard

2022-10-10

📝 Improved docs of ingest, reorganized file structure

262

sunnyosun

2022-10-10

0.7.2

💥 Refactor ingest, new pipeline ingestion logic, postgres test

257

sunnyosun

2022-10-08

0.7.1

📝 Overhauled get-started

259

falexwolf

2022-10-07

🚸 Check for existence before deletion

258

falexwolf

2022-10-07

🎨 Make ingest a static class

256

sunnyosun

2022-10-07

0.7.0

⬆️ Upgrade to core schema 0.10.0

255

falexwolf

2022-10-07

✨ New ingest API

254

sunnyosun

2022-10-05

0.6.0

📝 Overhaul documentation

253

falexwolf

2022-10-05

🔧 Update lndb setup to 0.9.4

252

fredericenard

2022-10-04

🔧 Enable setup outside cli

250

fredericenard

2022-10-04

⬆️ Upgrade lndb_setup and bionty

249

falexwolf

2022-10-03

0.5.0 0.5.0

🚸 Check for migrations upon import

247

falexwolf

2022-10-03

🔊 Raise warnings for unpopulated columns from insert.from_df

248

sunnyosun

2022-10-03

⬆️ Upgrade lndb_setup to 0.8.3

246

fredericenard

2022-10-03

♻️ Inherit IngestObject and IngestPipelineRun from IngestEntity

243

bpenteado

2022-10-01

0.4.1

⬆️ Upgrade to lnschema_core 0.9.0

241

falexwolf

2022-09-30

🎨 Add type annotation to ingest

240

sunnyosun

2022-09-30

♻️ Generalize pipeline ingestion

237

bpenteado

2022-09-30

✨ Added one_or_none, fixed api links

238

sunnyosun

2022-09-29

🎨 Get db metadata as a dictionary

233

fredericenard

2022-09-29

🎨 Added .df() as an option to return select results

236

sunnyosun

2022-09-29

⬆️ Upgrade pkg versions

234

sunnyosun

2022-09-29

🚸 Test notebook integrity before anything else

232

falexwolf

2022-09-26

📝 Add a quickstart & update ingest

231

falexwolf

2022-09-26

📝 Update bfx ingestion demo

227

bpenteado

2022-09-26

🚚 Rename insert.features to insert.featureset_from_features

230

sunnyosun

2022-09-26

📝 Polish documentation

229

falexwolf

2022-09-26

✨ Populate dobject size

228

falexwolf

2022-09-26

🚸 Sort select results in DataFrame by source

226

falexwolf

2022-09-25

⬆️ Upgrade to core schema 0.7.3

223

falexwolf

2022-09-25

🩹 Removed logging for inserting link tables

221

sunnyosun

2022-09-24

✨ Ingest bfx outputs with sample metadata

215

bpenteado

2022-09-24

👷 Improve notebook test function

218

falexwolf

2022-09-23

🧱 Improved code infra

216

sunnyosun

2022-09-23

0.4.0

✨ Account for multiple filepath suffixes

214

falexwolf

2022-09-23

♻️ Refactored feature model ingestion

213

sunnyosun

2022-09-23

♻️ Refactored insert

211

sunnyosun

2022-09-22

⬆️ Upgrade lndb_setup and lnschema_bionty

212

falexwolf

2022-09-22

⬆️ Upgrade to core schema 0.7.2

208

falexwolf

2022-09-21

🚑 dtransform is either pipeline_run or jupynb

207

sunnyosun

2022-09-21

0.3.11

🐛 Fixed column mapping

206

sunnyosun

2022-09-19

0.3.10

✨ Allow batch insertion

205

sunnyosun

2022-09-19

♻️ Refactored linked queries

204

sunnyosun

2022-09-15

⬆️ Update lnbfx to 0.3.5

199

bpenteado

2022-09-14

0.3.9

🔊 Refactor pipeline logging

197

bpenteado

2022-09-14

0.3.8

✨ Insert unmapped features

198

sunnyosun

2022-09-14

♻️ Refactored linked queries

196

sunnyosun

2022-09-13

⬆️ Updated wetlab schema

195

sunnyosun

2022-09-13

♻️ Refactor pipeline logging

193

bpenteado

2022-09-13

0.3.7

⬆️ Updated lnbfx version

194

sunnyosun

2022-09-12

0.3.6

🍱 Updated cell ranger test dir

192

sunnyosun

2022-09-12

🐛 Fix synchronization error in load

191

Koncopd

2022-09-12

⬆️ Updated setup version

189

sunnyosun

2022-09-08

0.3.5

♻️ Split ingestion logic into IngestObject and IngestPipeline

188

bpenteado

2022-09-06

📝 Add flow data ingestion example

186

sunnyosun

2022-09-06

💄 Added sidebar to guide

185

sunnyosun

2022-09-06

♻️ Split pipeline ingestion from non-pipeline ingestion

183

bpenteado

2022-09-06

⬆️ Updated schema module versions

184

sunnyosun

2022-09-06

♻️ Refactored select

182

sunnyosun

2022-09-05

🚚 Rename return_df to as_df in select

181

sunnyosun

2022-09-05

🚚 Rename guides to faq & tutorials to guide

180

falexwolf

2022-09-05

♻️ Refactored guide

179

sunnyosun

2022-09-03

📝 Prettify documentation

178

falexwolf

2022-09-02

Update lndb_hub version

176

fredericenard

2022-09-01

✨ Allow selecting dobjects by biological entities

175

sunnyosun

2022-09-01

0.3.4

⬆️ Update to sqm 0.0.8 to silence the warnings

174

sunnyosun

2022-08-30

🤡 R&D team simulation

172

sunnyosun

2022-08-30

🚸 Fix pipeline ingestion logging

158

bpenteado

2022-08-30

🚚 Move problems page to lamin-profile

171

falexwolf

2022-08-30

🩹 Uncomment out sharing tests

168

fredericenard

2022-08-30

🔥 Removed examples dir

170

sunnyosun

2022-08-30

🚸 Improve delete function

169

falexwolf

2022-08-30

🎨 Remove track submodule, move session, rename biogram to erdiagram

167

falexwolf

2022-08-29

🚚 Rename .do to .db

166

falexwolf

2022-08-29

🎨 Move header call to nb, re-export all of nbproject

165

falexwolf

2022-08-29

👷 Get rid of sqm warnings

164

falexwolf

2022-08-29

🎨 Simplify loading data

163

falexwolf

2022-08-29

👷 Allow stripping notebooks, upgrade nbproject_test

162

falexwolf

2022-08-29

0.3.3

✨ Use cell_marker feature model for flow data

161

sunnyosun

2022-08-28

⬆️ Updated to bionty 0.2.2

160

sunnyosun

2022-08-28

⬆️ Updated to sqm 0.0.7

159

sunnyosun

2022-08-28

⬆️ Updated dependencies

157

sunnyosun

2022-08-28

⬆️ Upgrade to lnschema_core 0.5.1

156

falexwolf

2022-08-26

♻️ Update pipeline ingestion to lnschema_core 0.5.0

154

bpenteado

2022-08-26

🍱 Add scrnaseq cellranger dataset

151

bpenteado

2022-08-26

🐛 Fix population of dtransform

155

falexwolf

2022-08-26

✨ Populate dtransform_in

153

falexwolf

2022-08-26

⬆️ Updated dependencies

152

sunnyosun

2022-08-26

0.3.2

♻️ Refactor lnbfx integration

149

bpenteado

2022-08-26

🚧 Temporary solution to extend modules

150

sunnyosun

2022-08-25

0.3.1

🏗️ Make tables within schema modules configurable

148

falexwolf

2022-08-25

0.3.0

✏️ Fixed typo in check versions

147

sunnyosun

2022-08-24

🏗️ Use id to reference storage

146

fredericenard

2022-08-23

🚚 Renamed FeatureModel to LinkFeatureModel

145

sunnyosun

2022-08-23

⬆️ Upgrade to lnbfx 0.2.0

144

falexwolf

2022-08-23

🚚 Renamed id to key in update and delete APIs

143

sunnyosun

2022-08-23

♻️ Cleaned up and added a mouse dataset

142

sunnyosun

2022-08-23

⬆️ Upgrade lndb-hub to v0.5.0

140

fredericenard

2022-08-23

💄 Added logging to update and delete

141

sunnyosun

2022-08-22

✨ Autogenerate select, update and delete

139

sunnyosun

2022-08-22

⬆️ Upgrade core schema to v0.4.0

138

falexwolf

2022-08-22

✨ Track storage root location

137

fredericenard

2022-08-22

🚚 Rename schema modules and bioinformatics module

136

falexwolf

2022-08-19

✨ Integrate bioinformatics pipline runs

133

bpenteado

2022-08-18

📝 Updated docs

135

sunnyosun

2022-08-18

👽 Adapt to lnschema-bionty 0.1.4

134

sunnyosun

2022-08-18

⚡ Ingest genes properly

131

sunnyosun

2022-08-16

✨ New readout table, registered species

130

sunnyosun

2022-08-12

🚚 Migrate bioreader to bioreadout

129

sunnyosun

2022-08-04

⬆️ Upgrade to lndb_setup 0.5.0

128

falexwolf

2022-08-03

⬆️ Upgrade to lnschema_core 0.3.0

127

falexwolf

2022-08-03

🚚 Renamed meta.annotate to db.link

126

sunnyosun

2022-08-03

👷 Cleaner CI environment switching

125

falexwolf

2022-08-02

0.2.1

⬆️ Upgrade to lndb_setup 0.4.2

123

falexwolf

2022-08-02

0.2.0

📝 Polish the introspect tutorial

122

falexwolf

2022-08-02

📝 Polish the 4 key tutorial pages

121

falexwolf

2022-08-02

📝 Polish get-started & select-data

119

falexwolf

2022-08-01

✨ Allow ingesting fcs files and selecting genes

118

sunnyosun

2022-08-01

📝 Prettify user mentions in guide & faq

117

falexwolf

2022-08-01

⬆️ Upgrade to lndb_setup 0.4.0

116

falexwolf

2022-08-01

🎨 Overhauled guide, renamed load to select.table_as_df

115

sunnyosun

2022-08-01

🩹 Some fixes of ingesting in-memory dobjects and an analysis draft

114

falexwolf

2022-07-31

✨ Select and update metadata

113

sunnyosun

2022-07-31

📝 Add a problem statement

112

falexwolf

2022-07-31

⬆️ Upgrade to lamindb-schema 0.3.1

111

falexwolf

2022-07-31

🚧 Annotate features during ingestion

110

sunnyosun

2022-07-31

📝 Re-write landing page

109

falexwolf

2022-07-30

📝 Improve get-started and collaborate guide

108

falexwolf

2022-07-30

⬆️ Upgrade to lnschema_core 0.2.0

106

falexwolf

2022-07-29

🚚 Move out lndb_hub

105

falexwolf

2022-07-29

♻️ Refactor sharing on the hub

104

falexwolf

2022-07-29

✨ Enable sharing dobjects & instances in the hub

69

fredericenard

2022-07-29

🔥 Moved readout vocab to bioreader

103

sunnyosun

2022-07-28

⬆️ Upgrade lndb_setup to 0.3.0

102

falexwolf

2022-07-26

⬆️ Upgrade to lndb-cli 0.2.0

101

falexwolf

2022-07-25

🚚 Account for table construction in lndb-cli

99

falexwolf

2022-07-25

🚚 Move CLI code to lndb-cli

98

falexwolf

2022-07-24

🍱 Adapted to lnschema-biology 0.1.1

97

sunnyosun

2022-07-24

🚸 Let the CLI have actual subcommands

96

falexwolf

2022-07-24

👷 Add time out to GitHub Actions

93

Koncopd

2022-07-23

🔥 Switched logger to use lamin-utils

92

sunnyosun

2022-07-23

✨ Annotate biometa when annotating genes

90

sunnyosun

2022-07-23

🔼 Upgrade to schema 0.2.1

89

falexwolf

2022-07-23

🎨 Use modular schema structure

88

falexwolf

2022-07-22

🚚 Move db API from admin to dev

87

falexwolf

2022-07-22

✨ Enable annotating features of dobjects

81

sunnyosun

2022-07-22

🚸 Offer manual way of completing a migration

86

falexwolf

2022-07-22

🏗️ Separate settings into user vs. instance and one file per instance

83

fredericenard

2022-07-22

🐛 Fix loading of multi-index and non-id tables

85

falexwolf

2022-07-21

0.1.2

🚚 Rename table interface to jupynb: migrate to schema v0.1.1

84

falexwolf

2022-07-21

🚚 Move version check into correct init

82

falexwolf

2022-07-20

⬆️ Fix the publishing call by upgrading to nbproject 0.4.3

80

falexwolf

2022-07-19

0.1.1

✨ Add schema_version check

79

falexwolf

2022-07-19

0.1.0

🚚 Rename lamindb.model to laminln.schema

77

falexwolf

2022-07-17

🚚 Migrate schema out to lamindb-schema

76

falexwolf

2022-07-17

✨ Version dobjects and interfaces

75

falexwolf

2022-07-16

💄 Pretty logging

74

sunnyosun

2022-07-15

✨ Add ingest.add and ingest.commit

73

sunnyosun

2022-07-14

📝 Add an example of ingesting images

72

sunnyosun

2022-07-12

⬆️ Upgrade to nbproject 0.2.1

71

falexwolf

2022-07-12

🐛 Fix bug

70

falexwolf

2022-07-12

📝 Added example notebook for ingesting fcs files

66

sunnyosun

2022-07-11

⬆️ Migrate to nbproject 0.2.0

68

falexwolf

2022-07-11

🚸 Auto-check integrity upon data ingestion only on Jupyter Lab

65

falexwolf

2022-07-09

0.0.9

🚚 Renamelndb config to lndb init and rewrite get-started

64

falexwolf

2022-07-09

🚸 Raise error upon multiple sign ups with same unconfirmed email

63

falexwolf

2022-07-09

✨ Allow sharing instances with other users

62

falexwolf

2022-07-08

🏗️ Improve configuration logic, flow, logging & testing

61

falexwolf

2022-07-08

✨ Populate user metadata at sign up

60

fredericenard

2022-07-07

✨ Unique user identity across instances

59

falexwolf

2022-07-06

🚧 Enable storing sqlite on S3

58

falexwolf

2022-07-04

0.0.8

🚚 Rename table file to dobject

57

falexwolf

2022-07-04

🚚 Rename CLI from lamindb to lndb

56

falexwolf

2022-07-04

✨ Add instance_name to settings and instance to setup

55

falexwolf

2022-07-03

0.0.7

♻️ Refactor file storage

54

falexwolf

2022-07-03

0.0.6

♻️ Refactor settings

52

falexwolf

2022-07-02

0.0.5

👷 Switch to nbproject tests & clean up logging

51

falexwolf

2022-07-01

✨ Use nbproject publish functionality

50

falexwolf

2022-07-01

🚚 Rename tutorial to guide

49

falexwolf

2022-06-29

👷 Measure coverage

48

sunnyosun

2022-06-26

🏗️ Settings: From pydantic BaseModel to custom class

46

falexwolf

2022-06-25

🏗️ Complete refactor of setup, settings & storage management

45

falexwolf

2022-06-25

⬆️ Upgrade to nbproject 0.1a3

43

falexwolf

2022-06-23

📝 One-page layout for data models

42

falexwolf

2022-06-14

♻️ More explicit _id name for such fields

41

falexwolf

2022-06-14

♻️ Migrate from sql to sqm everywhere

40

falexwolf

2022-06-14

✨ Implement data access log track.do

39

falexwolf

2022-06-12

0.0.4

🏗️ Re-organize API

38

falexwolf

2022-06-12

🏗️ Set up db with sqlmodel, test int ids

37

falexwolf

2022-06-11

🏗️ Re-designed entire API

36

falexwolf

2022-06-10

🔥 Remove notion integration up to CLI

35

falexwolf

2022-06-10

📝 Rename from lamindb to LaminDB & rewrite the landing page

34

falexwolf

2022-06-10

0.0.3

🏗️ Introduce field interface.type

31

falexwolf

2022-06-09

🚚 Rename global source table to interface

30

falexwolf

2022-06-09

✨ Track python package dependencies in source.dependency

27

falexwolf

2022-06-09

✨ Track title of ingesting notebook in source.name

26

falexwolf

2022-06-09

🐛 Fix user & notebook ingestion, add another test dataset

24

falexwolf

2022-06-08

✅ Fix pandas load, add tests

23

falexwolf

✨ Add introspection: db.diagram(), db.entities(), db.load()

22

falexwolf

✨ Add entity user

21

falexwolf

🚸 Auto-create local storage dir & cache dir

20

falexwolf

✅ Add a test for db creation & file ingestion

18

falexwolf

🏗️ Name the database file like the storage root directory

17

falexwolf

♻️ Refactor lndb.db

16

falexwolf

🔧 Refactor lndb.settings

15

falexwolf

🔥 Remove versioneer

14

falexwolf

👷 Track changes as in cookiecutter-py 0.3.0

13

falexwolf

2022-06-07

🏗️ Basic file ingestion from a notebook

9

falexwolf

2022-06-06

🔥 Remove sqlmodel dependency

8

falexwolf

2022-06-04

📄 Change format of license file

7

falexwolf

2022-05-23

📝 Fix faq link

6

falexwolf

2022-05-26

♻️ Update to cookiecutter 0.2.0

5

falexwolf

2022-05-23

💄 More narrow sidebar

4

falexwolf

2022-05-11

💄 Switch faq and api

3

falexwolf

2022-05-11

📝 Polish the documentation

2

falexwolf

2022-05-11

🚚 Migrated from lamin repository

1

falexwolf