Changelog

0.54

0.54.2 2023-09-26

• 🎨 Better implementation of dataset.view_flow PR1194 @sunnyosun

0.54.1 2023-09-21

• 🔇 Mute repetitive warning for saving parents PR1190 @sunnyosun

• 🔇 Fix warning logging upon save PR1185 @sunnyosun

• 🩹 Better suffix handling PR1181 @falexwolf

0.54.0 2023-09-17

• ✏️ Fix views for interactive terminal PR1178 @sunnyosun

• 🚸 Improve error message for conflicting storage keys PR1174 @falexwolf

• ♻️ Add string levels PR1173 @falexwolf

• ✨ Add reference and reference_type to Dataset, ULabel PR1171 @sunnyosun

• 🔒 Add client fallbacks to lamindb-setup PR1172 @falexwolf

• 🐛 Fix view_parents() when there are no parents PR1167 @sunnyosun

• 🔊 Turn on hint for tutorials PR1164 @sunnyosun

• ⚡ Speed up instance loading time & refactor lamindb-setup PR1163 @falexwolf

• ⬆️ Update fsspec to 2023.9.0 PR1162 @Koncopd

• 🎨 More validation for File creation, improve zarr backend PR1160 @Koncopd

• 🔥 Remove add_labels() & get_labels() PR1155 @falexwolf

• 🎨 Increased search threshold to 90 PR1156 @sunnyosun

0.53 2023-09-09

• ♻️ Refactor hub client PR1150 @falexwolf

• ✨ Add return_field to Lookup PR1153 @sunnyosun

• 🔇 Silence download bar for <5MB bionty files PR1151 @sunnyosun

• 🔇 Set default verbosity to warning PR1149 @sunnyosun

• 🚚 Add Data.labels accessor, rename Label to ULabel PR1148 @sunnyosun

• ✨ Allow create records from non-default bionty sources PR1147 @sunnyosun

• 🔥 Removed get_by_feature PR1145 @sunnyosun

• 🚚 Replace get_feature_set with .feature_sets.__getitem__ PR1141 @sunnyosun

0.52

0.52.2 2023-09-05

• 🎨 Add labels to describe PR1139 @sunnyosun

• 🎨 Set default field for from_values PR1137 @sunnyosun

• 📝 More comprehensive landing page PR1136 @falexwolf

• 🎨 Switch to WRatio and default to limit=20 for search PR1135 @sunnyosun

• 🚚 Rename File.tree to File.view_tree PR1133 @falexwolf

• ✨ Enable dataset versioning PR1132 @falexwolf

0.52.1 2023-09-02

• ♻️ Refactor features display PR1129 @falexwolf

• ♻️ Refactor feature set linking PR1128 @falexwolf

• ♻️ Add display of numerical features PR1127 @falexwolf

• 📝 Rewrite landing page PR1126 @falexwolf

• 🚸 Validate Run records PR1123 @falexwolf

• 🔊 Improved logging message for inspect PR1124 @sunnyosun

0.52.0 2023-09-01

• ♻️ Type features PR1121 @falexwolf

• 🚸 Enable to pass modality to from_df and from_anndata PR1116 @falexwolf

• ⬆️ Cache instance id in settings files PR1120 @bpenteado

• 🚑️ Fix map_synonyms bug PR1119 @sunnyosun

• 🐛 Fix target_label in view_parents PR1118 @sunnyosun

• ♻️ Simplify .standardize() implementation PR1117 @sunnyosun

• 🐛 Fix lookup() for QuerySet PR1115 @sunnyosun

• 🩹 Replace deprecated is_categorical_dtype PR1114 @falexwolf

0.51

0.51.3 2023-08-30

• 🚸 Better treatment of File.suffix PR1113 @falexwolf

0.51.2 2023-08-28

• ♻️ Enable typed feature sets for dataframes PR1110 @falexwolf

• ♻️ Refactor to use UPath everywhere PR1102 @Koncopd

• ⚡️ Delete cached files for local instances on File.save() PR1109 @Koncopd

• 🚚 Rename data lineage to data flow PR1108 @falexwolf

0.51.1 2023-08-28

• 📝 Added validate guide PR1104 @sunnyosun

• 🐛 Fix feature set updates & describe() if no features are present PR1098 @falexwolf

• 🎨 Make species not nullable in Gene, Protein, CellType PR1095 @sunnyosun

0.51.0 2023-08-24

• ♻️ Make suffix non-nullable and root unique PR1090 @falexwolf

• ♻️ Add view_lineage to Dataset PR1089 @falexwolf

• 🚸 Disable creating non-validated records with from_values PR1086 @sunnyosun

• ♻️ Enable passing AnnData-like File object to Dataset.from_anndata PR1085 @falexwolf

• 🔊 More consistent logging of inspect PR1081 @sunnyosun

• 🔥 Remove inherit_relations PR1079 @sunnyosun

• ♻️ Use CanValidate & HasParents PR1078 @falexwolf

• 👷 Main is the new staging, release the new production branch PR1077 @falexwolf

• ♻️ Refactor tutorial PR1076 @falexwolf

• ♻️ Add transform, run & input_of to Dataset PR1074 @falexwolf

• 🚸 Better UX of graphviz installation PR1075 @sunnyosun

• 👷 Run tutorial on anonymous worker PR1073 @falexwolf

• ♻️ Use create_path PR1072 @falexwolf

• 🎨 Make from_values synonyms aware, inspect bionty aware PR1066 @sunnyosun

• ♻️ Use principled conversion to paths with options inheritance PR1069 @Koncopd

• ♻️ Refactor storage PR1067 @falexwolf

• 🐛 Fix tree view for anonymous access PR1065 @falexwolf

• 🍱 Add the Iris images dev dataset PR1062 @falexwolf

• 🚚 Dataset.from_files replaced with default constructor PR1060 @falexwolf

• 🍱 Added populate_registries to some datasets PR1061 @sunnyosun

• ✨ Add get_feature_set to .features accessor PR1057 @sunnyosun

• 🚸 Allow reference & reference_type params in ln.track() PR1053 @falexwolf

0.50

0.50.1 2023-08-17

• ♻️ Refactor run_context PR1030 @falexwolf

• 🚸 Remove SA as a dependency and use delete dialogue PR1041 @falexwolf

• 🚚 Move data lineage to use cases PR1026 @falexwolf

• 🚸 Do not allow creating files with none of key, description and run PR1022 @falexwolf

• ♻️ Introduce ParentsAware PR1023 @sunnyosun

• ♻️ Re-enable file versioning PR1014 PR1018 @falexwolf

• 🔊 Fix validate logging PR1017 @sunnyosun

• ✨ Add InspectResult PR1012 @sunnyosun

• 🚚 Rename map_synonyms() to standardize() PR1046 @sunnyosun

• 💄 Improved logging & visualizations PR1011 @sunnyosun

0.50.0 2023-08-07

• 🚸 Introduce Label validation PR1006 @falexwolf

• 🚸 Turn File.path() into property PR1008 @falexwolf

• 🔥 Remove backward compat for auto-keyed paths PR1007 @falexwolf

• ✨ Add ValidationAware.validate() PR1000 @sunnyosun

• 🚸 Increase default verbosity to hint-level PR1005 @falexwolf

• ♻️ Better treatment of suffixes PR1004 @falexwolf

• 🍱 Add nf-core rna-seq test dataset PR1002 @falexwolf

• 🚚 Move add_labels and get_labels from FeatureManager to Data PR999 @falexwolf

• 🚚 Rename FeatureSet.ref_field to FeatureSet.registry PR997 @falexwolf

• 🚸 Ignore synonyms in from_values to incentivize explicit curation process PR993 @falexwolf

• 🚚 Move tutorial1 one level down PR989 @falexwolf

• 🚸 Only link validated features PR987 @falexwolf

• ✅ More fixes and tests for backed PR988 @Koncopd

• 🚚 Move biology notebooks to lamin-usecases PR985 @sunnyosun

• 📝 Improve API layout & description PR986 @falexwolf

• 🚚 Rename Manager to QueryManager PR984 @falexwolf

• 🚚 Rename ORM to Registry PR982 @sunnyosun

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

• ♻️ Refactor storage root management PR973 @falexwolf

• 🎨 Make add_feature_set acid PR980 @sunnyosun

• 📝 Simplify tutorial PR977 @sunnyosun

• 🐛 Account for universal_pathlib 0.1 release PR976 @Koncopd

0.49.1 2023-08-01

• 🎨 Allow passing QuerySet to .features.add_labels() PR969 @sunnyosun

• ⚡️ Speed up & remove auto-generation of feature name PR963 @falexwolf

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

• 📝 Add MuData example PR945 @sunnyosun

• 🎨 Add Modality PR940 @falexwolf

• 🎨 Describe based on provenance and features PR936 @sunnyosun

• 🚸 Add File.features accessor: FeaturesManager PR933 @falexwolf

• 📝 Add spatial data example PR930 @falexwolf

• ✨ Added with_children to view_parents PR921 @sunnyosun

• 📝 Added comprehensive lineage graph example PR919 @sunnyosun

• 🚸 File methods work prior to save() PR918 @Koncopd

• 🚚 Integrate Project and Tag into Label PR914 @falexwolf

• ♻️ Replace lamin_logger with lamin_utils PR912 @falexwolf

• ♻️ Replace Run.name with Run.reference_type and more PR910 @falexwolf

• ✨ Enable to create File outside default storage PR891 @falexwolf

• ✨ Multi-field search PR898 @sunnyosun

• ✨ Better Feature management PR897 @falexwolf

• 🎨 Make ensembl_gene_id`` unique for Gene` PR895 @sunnyosun

• ⚡ Speed up file creation PR894 @falexwolf

• 🚚 Rename Readout to ExperimentalFactor PR893 @sunnyosun

• 🎨 set_abbr adds abbr to synonyms PR892 @sunnyosun

0.47 2023-07-10

• ✨ View parents PR858 @sunnyosun

• ✨ Track parent notebooks PR859 @falexwolf

• 🚸 Improve data-lineage guide, auto-track run inputs PR869 @falexwolf

• 🚸 More reliably detect interactive environments ln.track() PR878 @Koncopd

• 🚸 Case insensitive search PR877 @falexwolf

• 🚸 Fix bug and add test for tracking multiple parent transforms PR875 @falexwolf

• ✨ Read remote h5ad in backed mode in File.from_anndata PR871 @falexwolf

• ⚡️ Speed up search PR868 @falexwolf

• ✨ Added File.inherit_relationships PR867 @sunnyosun

• ⚡️ Better cache management PR864 @Koncopd

• ✨ Added Manager.list() and allow passing field name PR863 @sunnyosun

• ✨ Added .describe() for rich repr of related objects PR862 @sunnyosun

• ✨ Track hash_type PR861 @falexwolf

• 🚸 It should be possible to use a schema module prior to importing lamindb PR852 @falexwolf

• ✨ Enable search, lookup, inspect, map_synonyms from QuerySet PR849 @sunnyosun

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:

• 🚚 Rename File.name to File.description PR824 @falexwolf

• 🚚 Rename File.featuresets to File.feature_sets PR805 @falexwolf

UX:

• ✨ Globally set species via lb.settings.species= PR142 falexwolf

• 🚚 Easy display of many-to-many fields: QuerySet.df(include=[field__name]) PR832 @falexwolf

• 🚸 Create new run if notebook is run by different user PR838 @falexwolf

• 🚸 Speed up bulk saving of records PR828 @sunnyosun

• 🚸 Hash large files faster PR836 @falexwolf

• ✨ Add from_df and from_anndata to File PR844 @falexwolf

• 🚸 Return locally backed object instead of cloud backed if available PR840 @falexwolf

• 🚸 Raise more & more user-friendly errors in setup API when instance already setup PR837 @falexwolf

• 🚸 Better error behavior when no notebook title set in ln.track() PR834 @Koncopd

• 🚸 Store hash for remote files on S3 PR808 @falexwolf

0.45 2023-06-27

• ♻️ Replaced ln.parse with Registry.from_values PR803 @sunnyosun

• 🎨 Auto-manage RunInput Registry PR802 @falexwolf

0.44

0.44.2 2023-06-23

• ♻️ Make zarr optional PR800 @falexwolf

0.44.1 2023-06-22

• ✨ Add inspect and add_synonym to Registry PR797 @sunnyosun

• 🔧 Rename extra nbproject to jupyter and add fcs extra to docs PR798 @falexwolf

• 🚚 Move default storage location from lndb/ to .lamindb/ PR796 @falexwolf

• 🚸 ln.Folder becomes ln.Tag & directories now modeled as prefixes (as on S3) PR794 @falexwolf

• ♻️ Refactor storage code PR792 @falexwolf @Koncopd

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:

• 🚸 Return records list from .from_bionty for multiple matches PR789 @sunnyosun

• 🎨 Remove lnhub-rest from lamindb-setup PR784 bpenteado

• 🔊 Move logging from stderr to stdout PR776 @falexwolf

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:

• ♻️ Refactor core schema methods and storage access PR770 @falexwolf

• 🐛 Make User.name nullable again PR769 @falexwolf

• ✅ Add integrity tests for migrations back PR768 @falexwolf

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