Changelog 2023

0.64

0.64.2 2023-12-18

• 🚚 Deprecate view_flow in favor of view_lineage PR1367 @falexwolf

• 🐛 Account for length zero label lists PR1362 @falexwolf

• 🐛 Fix mypy PR1359 @Koncopd

• 👷 Use ruff and clean up pre-commit PR1358 @Zethson

0.64.1 2023-12-13

• 🚸 Silence the httpx logger PR1356 @falexwolf

• 🐛 Fix hash inference for cloud non-s3 objects and use stored gcs credentials PR1355 @Koncopd

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

• 🐛 Fix lamin save for scripts PR1346 @sunnyosun

0.63.4 2023-12-08

• 🚸 Parse variables upon track, do not access storage during load PR1341 @falexwolf

• 🚸 Raise error when tracking script fails PR1340 @sunnyosun

• 🚸 Literal checks for type when creating a Feature PR1339 @sunnyosun

• 🐛 Fix capitalization of feature names in describe PR1337 @sunnyosun

0.63.3 2023-12-05

• ✨ Do virtual inner join of variables in Dataset.mapped PR1334 @Koncopd

• 📝 Add a track notebooks how-to PR1333 @sunnyosun

• 🚚 Move high-level bionty docs here PR1332 @falexwolf

0.63.2 2023-12-02

• ✨ Add return_field to standardize() PR1331 @sunnyosun

• ♻️ Extend MappedDataset.get_label_weights PR1330 @Koncopd

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

• ♻️ Centralize progressbar and convert to percentage PR1322 @falexwolf

• ✨ Added view_tree for keys PR1321 @sunnyosun

• 🚚 Recode visibility to default 1, hidden 0, trash -1 PR1319 @sunnyosun

• ✨ Track Python scripts PR1318 @falexwolf

• 📝 Modify Quickstart to use File instead of Dataset PR1317 @sunnyosun

• 📝 Add an FAQ on storage keys & locations PR1253 @Zethson

0.62

0.62.0 2023-11-20

• ✨ Create dataset.mapped() for data loaders over AnnData PR1307 @Koncopd

• 🚸 Add .df() to Registry PR1313 @falexwolf

• 🐛 Fix passing organism to featureset.from_values PR1312 @sunnyosun

• 🐛 Fix idempotency of transfer files PR1311 @falexwolf

• 🍱 Updated bionty sources PR1305 @sunnyosun

• 📝 Add an annotation guide PR1302 @sunnyosun

0.61

0.61.0 2023-11-15

• 🚸 Prettify view_tree, check for ahead migrations PR1299 @sunnyosun

• 🚸 Ensure saved notebooks aren’t rerun with the same version PR1298 @falexwolf

• 🔥 Remove Modality registry PR1297 @sunnyosun

• ⬆️ More flexible versions for anndata and s3fs PR1295 @Koncopd

• ♻️ Refactor Dataset construction from directory PR1300 @falexwolf

0.60

0.60.3 2023-11-13

• 🚑 Fix visibility choices, updated intro PR1294 @sunnyosun

0.60.1 2023-11-10

• 📝 Clearer badge titles PR1291 @falexwolf

• ⏪ Fix bionty versionsdir PR1290 @sunnyosun

0.60.0 2023-11-09

• 🚸 Enable to pass metadata to dataset PR1289 @falexwolf

• 🚚 Move view_tree to UPath PR1288 @falexwolf

• ♻️ Move UPath to root-level API PR1286 @falexwolf

• 🚸 Enable to add labels without a feature PR1285 @sunnyosun

0.59

0.59.3 2023-11-04

• 💄 Show transform uid in view_lineage PR1280 @sunnyosun

• 🚸 Improve search PR1279 @sunnyosun

0.59.2 2023-11-04

• 🐛 Backed raw subset fix PR1278 @Koncopd

• 🚸 Improve connection stability PR1277 @falexwolf

• 🚸 Improve search PR1275 @sunnyosun

0.59.1 2023-11-03

• ♻️ Move CLI from lamindb-setup here PR1264 @falexwolf

• 🐛 file.replace() works with virtual keys PR1265 @Koncopd

0.59.0 2023-10-27

• 🚸 Introduce virtual keys PR1262 @falexwolf

• ♻️ Refactor visibility PR1261 @falexwolf

• ♻️ Turn using into a Registry method PR1259 @falexwolf

0.58

0.58.2 2023-10-26

• 👷 Enable to read db from env variable PR1258 @falexwolf

0.58.1 2023-10-26

• 🔒️ Re-enable read-only access for public instances PR1257 @falexwolf

• ✨ Introduce visibility to File and Dataset PR1254 @sunnyosun

• 🔒️ Enable to pass DB URLs during load PR1256 @falexwolf

• ✨ Enable passing filter expressions to lookup and search PR1255 @sunnyosun

• ♻️ Use file.uid instead of file.id in dataset.load() PR1250 @falexwolf

0.58.0 2023-10-24

• ⚡️ Speed up dataset creation in presence of millions of feature links PR1248 @falexwolf

• 📝 Add a faq for custom validator PR1249 @sunnyosun

• ✨ Add parents to Organism PR1245 @sunnyosun

0.57

0.57.2 2023-10-23

• ➕ Allow more anndata versions PR1244 @Koncopd

0.57.1 2023-10-20

• 🎨 Display uid instead of id in search result PR1239 @sunnyosun

0.57.0 2023-10-19

• 🚚 Rename Species to Organism PR1237 @sunnyosun

• 🔥 Remove email field from User registry PR1238 @falexwolf

0.56

0.56.2 2023-10-19

• 🚚 Migrate from password to apikey PR1233 @falexwolf

0.56.1 2023-10-18

• 🐛 Fix transfer of features PR1232 @sunnyosun

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.

• 🚚 Migrate to integer primary keys PR1229 @falexwolf

• ♻️ More flexible cache management PR1230 @Koncopd

0.55

0.55.2 2023-10-10

• ♻️ Keep raw in pbmc68k_reduced and human_immune_cells PR1228 @Koncopd

• ⬆️ Make backed compatible with anndata==0.10.1 PR1227 @Koncopd

• ✨ Also transfer features PR1226 @falexwolf

0.55.1 2023-10-4

• ✨ Dataset from paths aka storage PR1222 @falexwolf

• 🚸 Do not search for alternative names if id is passed PR1225 @falexwolf

• 📝 Added lamindata badge PR1223 @sunnyosun

• ♻️ Refactor data flow tracking for Dataset PR1224 @falexwolf

0.55.0 2023-10-03

• ✨ Enable to transfer data between instances PR1216 @falexwolf

• ✨ Enable saving notebook files PR1213 @falexwolf

• 💄 Display id in view_parents PR1215 @sunnyosun

0.54

0.54.4 2023-09-29

• ✨ Add labels transfer through labels.add_from PR1211 @falexwolf

• ♻️ Perform outer join during load PR1212 @falexwolf

• 🎨 Show both file and dataset in view_lineage PR1209 @sunnyosun

0.54.3 2023-09-27

• 💄 Fix double arrows for file and dataset PR1206 @sunnyosun

• 🎨 Add a members property to FeatureSet PR1205 @falexwolf

0.54.2 2023-09-26

• 🎨 Better implementation of dataset.view_lineage 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

lamindb

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

lnschema-bionty

Name	PR	Developer	Date	Version
🚚 Rename Dataset to Collection	205	falexwolf	2023-12-23	0.37.0
🚚 Rename File to Artifact	201	falexwolf	2023-12-11	0.36.0
⬆️ Enabled ID conversion via return_field	200	sunnyosun	2023-12-02
🐛 Fix save parents with bionty_source	198	sunnyosun	2023-11-23
✨ Added functions to sync bionty source	197	sunnyosun	2023-11-16	0.35.1
🚚 Rename FK organism to organisms in BiontySource	196	sunnyosun	2023-11-13	0.35.0
✨ Add parents to Organism	193	sunnyosun	2023-10-23	0.34.0
🚚 Rename Species to Organism	192	sunnyosun	2023-10-19	0.33.0
✏️ Fix uid encoder	190	sunnyosun	2023-10-18	0.32.2
🚚 Migrate to integer primary keys	188	falexwolf	2023-10-13	0.32.0
🔇 Mute repetitive warning for saving parents	187	sunnyosun	2023-09-20	0.31.2
⬆️ Silence download bar for <5MB files	186	sunnyosun	2023-09-08	0.31.1
🎨 Return None if no records are created for from_bionty	185	sunnyosun	2023-09-07	0.31.0
✨ Allow non-default bionty sources in LaminDB	184	sunnyosun	2023-09-07
♻️ Add DB-facing constructor	180	falexwolf	2023-08-28	0.30.1
🎨 Make species not nullable in Gene, Protein, CellType	179	sunnyosun	2023-08-24
♻️ Use CanValidate & HasParents	176	falexwolf	2023-08-23	0.30.0
🚚 Rename map_synonyms to standardize	173	sunnyosun	2023-08-16	0.29.5
🚚 Rename ORM to Registry	167	sunnyosun	2023-08-05
🎇 Added stable_id to Gene	166	sunnyosun	2023-07-31	0.29.0
🚚 Rename select to filter	164	falexwolf	2023-07-31
🎨 Switch biontysource id to hash id	163	sunnyosun	2023-07-25	0.28.2
🚸 New settings auto_save_parents	162	falexwolf	2023-07-25	0.28.1
🎨 Link all entities to files and datasets	160	sunnyosun	2023-07-24	0.28.0
🚚 Replace lamin_logger with lamin_utils	161	falexwolf	2023-07-24
✏️ Fix docstrings	159	sunnyosun	2023-07-21	0.27.4
🎨 Make species name unique	158	sunnyosun	2023-07-21
🎨 Gene table unique on ensembl id	152	sunnyosun	2023-07-18	0.27.0
🎨 Fix migration	150	sunnyosun	2023-07-18
🚚 Rename Readout to ExperimentalFactor	149	sunnyosun	2023-07-17
🚸 Trigger instance loading for users	147	falexwolf	2023-07-06	0.26.2
⚡️ Speed up parents ingestion	146	falexwolf	2023-07-04	0.26.1
🚸 Add settings	142	falexwolf	2023-06-30	0.25.4
🚑️ Allow bulk saving parents without causing conflicts	141	sunnyosun	2023-06-30	0.25.2
✨ Added self-referential parents, renamed abbr and description	139	sunnyosun	2023-06-29	0.25.0
♻️ Replaced ln.parse with orm.from_values	138	sunnyosun	2023-06-27	0.24.0
🚚 Move add_synonym to BaseORM	137	sunnyosun	2023-06-22	0.23.5
⬆️ Fix synonyms duplication check	136	sunnyosun	2023-06-22
🚑️ Do not check existing synonyms when db table is empty	134	sunnyosun	2023-06-20
🎨 Create multiple records with .from_bionty	133	sunnyosun	2023-06-20	0.23.3
📈 Save to DB if record already exists for add_synonyms	132	sunnyosun	2023-06-20	0.23.2
🚚 Fixed all related_names	131	sunnyosun	2023-06-20	0.23.1
🏷️ Change name to a required field for ontology tables	130	sunnyosun	2023-06-19	0.23.0
🎨 Consolidate schema, remove non-crucial fields	127	sunnyosun	2023-06-16	0.22.0
🚚 Rename source_key to source in BiontySource table	125	sunnyosun	2023-06-10	0.21.3
🚚 Rename Featureset to FeatureSet	124	sunnyosun	2023-06-10	0.21.2
⏪ Change species uid to 4 char	122	sunnyosun	2023-06-09	0.21.1
🎨 Change on_delete to PROTECT	121	sunnyosun	2023-06-09	0.21.0
🎨 Remove unnecessary null=True, blank=True	118	sunnyosun	2023-06-08	0.19a6
♻️ Simplified species code	116	sunnyosun	2023-06-08	0.19a4
🚚 Rename BiontyVersions to BiontySources	115	sunnyosun	2023-06-07	0.19a3
🚚 Migrate lnschema-bionty to Django	112	sunnyosun	2023-06-05	0.19a1
✨ Added Features.pathways	111	sunnyosun	2023-06-02	0.18.3
✨ Add add_synonym method	109	sunnyosun	2023-06-01
🚑 Must pass a species when creating record from lookup	108	sunnyosun	2023-05-30	0.18.2
✨ Added Pathway.genes	107	sunnyosun	2023-05-30	0.18.1
🚑 Fix created_by_id in Readout	106	sunnyosun	2023-05-28	0.18.0
🎨 Change .bionty to a method	105	sunnyosun	2023-05-28
🚑 Default species to None and not pass to Bionty	104	sunnyosun	2023-05-27	0.18a6
🚑 Fix 0.18.0 sqlite migration script	103	sunnyosun	2023-05-27
✨ Add synonyms, definition, short_name columns	102	sunnyosun	2023-05-27	0.18a5
🚑 Fix table name for id_encoder	101	sunnyosun	2023-05-27
⬆️ Update lamindb and bionty versions	100	sunnyosun	2023-05-27
🏷️ Restored Optional type annotation	99	sunnyosun	2023-05-26
🏗️ Remove SQL-level schema modules	96	falexwolf	2023-05-25	0.18a2
🚑 Fix last migration	98	falexwolf	2023-05-25	0.17.1
🍱 Add CreatedBy and CreatedAt to all entities	95	sunnyosun	2023-05-25	0.17.0
🚚 Rename bt.Entity to bt.Bionty	94	sunnyosun	2023-05-25
⬆️ Upgrade to bionty 0.13	92	sunnyosun	2023-05-09	0.16.4
✨ Added synonyms field to CellMarker	91	sunnyosun	2023-05-09	0.16.3
💚 Fix dependencies	90	sunnyosun	2023-04-27	0.16.2
🎨 Move ._entity to private	89	sunnyosun	2023-04-27	0.16.1
💥 Enable .bionty for accessing bionty functionalities	87	sunnyosun	2023-04-24	0.16.0
⚡ Fix adding species	84	sunnyosun	2023-04-19	0.15.2
✨ Add ._entity to knowledge class for features parsing	83	sunnyosun	2023-04-18	0.15.1
🎨 New design of the knowledge API	80	sunnyosun	2023-04-17	0.15.0
♻️ Refactor knowledge	77	sunnyosun	2023-03-28	0.14.0
✨ Added Readout	75	sunnyosun	2023-03-27	0.13.0
📝 Move knowledge guide from lamindb here	71	falexwolf	2023-03-27
⬆️ Updated bionty and lamindb deps	74	sunnyosun	2023-03-27	0.12.2
👷 Upgrade to latest cookiecutter	73	falexwolf	2023-03-27
🚑 Fix get_term	72	sunnyosun	2023-03-25	0.12.1
♻️ Switch to class property	70	sunnyosun	2023-03-24	0.12.0
✨ Expose bionty functions with knowledge decorator	69	sunnyosun	2023-03-24	0.11.0
🐛 Fix Readout population	68	sunnyosun	2023-03-23	0.10.1
⬆️ Update CellMarker columns for bionty 0.10	64	sunnyosun	2023-03-21	0.10.0
✨ Add CellLine, Pathway, Phenotype	63	sunnyosun	2023-03-21	0.9.0
💚 Fix CI	62	sunnyosun	2023-03-21
⬆️ Upgrade to bionty 0.9.0	61	sunnyosun	2023-03-20	0.8.1
🎨 Allow hashing external IDs	60	falexwolf	2023-03-10
⬆️ Stable release of bionty 0.8.0	59	sunnyosun	2023-03-09	0.8.0
⬆️ Bionty>=0.8rc3	58	sunnyosun	2023-03-09	0.8rc2
✨ Use ontology_id as the id for Tissue, CellType, Disease	57	sunnyosun	2023-03-07	0.8.0rc1
⬆️ Upgrade bionty	56	falexwolf	2023-03-06
🔥 Remove migration files	51	sunnyosun	2023-02-14	0.7.0
⬆️ Upgrade and rename lndb_setup to lndb (v0.32.0)	49	bpenteado	2023-02-14	0.6.9
🐛 Fixed taxon_id type	48	sunnyosun	2023-01-17	0.6.8
⬆️ Upgrade dependencies	47	sunnyosun	2023-01-17	0.6.7
⏪ Revert the last PR	46	sunnyosun	2023-01-17
🐛 Fixed typo for postgres	45	sunnyosun	2023-01-16	0.6.6
🎨 Change Species.taxon_id type to int	43	sunnyosun	2023-01-13
👷 Extend CI to py3.8-3.10	42	sunnyosun	2023-01-12
🚚 Rename Species.common_name to Species.name	41	falexwolf	2023-01-05
🐛 Fix migration for sqlite	40	falexwolf	2023-01-05	0.6.5
♻️ Treat link tables as in all other schema modules	39	falexwolf	2023-01-05	0.6.4
🚚 Move knowledge version tables into module	38	falexwolf	2023-01-05	0.6.3

bionty

Name	PR	Developer	Date	Version
🚚 Move bionty search & lookup guide to lamindb	532	falexwolf	2023-12-04
✨ Enabled ID conversion via return_field	530	sunnyosun	2023-12-02	0.35.2
🍱 Update EFO to version 3.57.0	528	sunnyosun	2023-11-21	0.35.1
🍱 Update a few sources	526	sunnyosun	2023-11-16	0.35.0
🚚 Relocate bionty.lock to versionsdir	525	sunnyosun	2023-11-10	0.34.3
🔧 Using env variables for versionsdir	524	sunnyosun	2023-11-10	0.34.2
🎨 Enable set versionsdir	523	sunnyosun	2023-11-09	0.34.1
📝 Streamline extend guide	522	falexwolf	2023-10-24
✨ Add ncbitaxon, refactored organism	521	sunnyosun	2023-10-23	0.34.0
🚸 Add a backward compat parser	520	sunnyosun	2023-10-19	0.33.1
🚚 Rename Species to Organism	519	sunnyosun	2023-10-19	0.33.0
🚸 Suggest user to reset sources	518	sunnyosun	2023-10-13	0.32.0
:memo: Clarify definition in readme	517	falexwolf	2023-09-27
:lipstick: Prettify changelog header	516	falexwolf	2023-09-27
✨ Add BioSample entity	515	sunnyosun	2023-09-13
🚚 Rename convert_legacy_ids to map_legacy_ids	514	sunnyosun	2023-09-13
🍱 Cached legacy df for genes	513	sunnyosun	2023-09-12
✨ Add convert_legacy_ids for ensembl genes	512	sunnyosun	2023-09-11
🔇 Silence download bar for <5MB files	511	sunnyosun	2023-09-08	0.31.2
✨ Add Ethnicity entity	510	sunnyosun	2023-09-07	0.31.1
✨ Add DevelopmentalStage ontologies	508	sunnyosun	2023-09-07	0.31.0
✨ Allow non-default bionty sources in LaminDB	506	sunnyosun	2023-09-07
✨ Add pato to Phenotype	505	sunnyosun	2023-09-05
💄 Transient download bar	504	sunnyosun	2023-09-05	0.30.3
Add phecodes	502	Zethson	2023-08-22
🎨 Added mute to .standardize	501	sunnyosun	2023-08-22	0.30.2
✨ Relating Bionty to other tools	500	Zethson	2023-08-21
🚑️ Fix version recognition in lamindb	498	sunnyosun	2023-08-17	0.30.1
🚚 Rename map_synonyms to standardize	497	sunnyosun	2023-08-16	0.30.0
🚑️ Updated inspect params	496	sunnyosun	2023-08-15
✨ Add md5 for normal URLs	495	Zethson	2023-08-09
✨ Use latest versions of tests & add updating sources	494	Zethson	2023-08-09
💚 Fixed tests	493	sunnyosun	2023-08-09
✨ Introduce validate	491	sunnyosun	2023-08-06	0.29.0
📝 Fix docs	490	falexwolf	2023-08-04
✨ Added EnsemblGene class	488	sunnyosun	2023-07-31	0.28.0
🍱 Added all ensembl species DBs	487	sunnyosun	2023-07-31
🍱 Update to ensembl-110	485	sunnyosun	2023-07-31	0.27.0
🍱 Include obsolete terms in .df	481	sunnyosun	2023-07-23	0.26.0
✨ Added .diff method	468	Zethson	2023-07-20
🍱 Added uniprot 2023-03	477	sunnyosun	2023-07-18	0.25.2
🔥 Remove top_hit from search	476	sunnyosun	2023-07-17	0.25.1
🚚 Rename Readout to ExperimentalFactor	474	sunnyosun	2023-07-17	0.25.0
🚸 Case insensitive search	466	falexwolf	2023-07-10	0.24.2
📝 Build docs standalone again	465	falexwolf	2023-07-09
✨ Use _bt suffix instead of _bionty for Bionty objects in docs	464	Zethson	2023-07-09
⬆️ No longer pinning lamin-logger	461	sunnyosun	2023-06-30	0.24.1
🏗️ Replace children with parents, migrate assets to django instance	460	sunnyosun	2023-06-28	0.24.0
🎨 Log=False to turn off logging in inspect	459	sunnyosun	2023-06-22	0.23.1
🔈 Fixed logging of inspect, added casing check	457	sunnyosun	2023-06-21
🍱 Add more phenotype ontologies	456	Zethson	2023-06-20	0.23.0
✨ Add case_sensitive to inspect and search	455	sunnyosun	2023-06-19	0.22.0
🍱 Fetch latest ontology versions	452	Zethson	2023-06-19
🐛 Fix passing empty strings to map_synonyms	451	sunnyosun	2023-06-17	0.21.4
🧪 More tests for handle sources	450	sunnyosun	2023-06-16	0.21.3
🚀 Fix coverage of unit tests	449	sunnyosun	2023-06-16
🎨 Default to name field for map_synonyms	448	sunnyosun	2023-06-16
🚚 Update tuple name of search result	447	sunnyosun	2023-06-15	0.21.2
🚚 Change species to vertebrte for ensembl	446	sunnyosun	2023-06-15	0.21.1
🔥 Remove ontology_info and NormalizeColumns	445	sunnyosun	2023-06-15	0.21.0
🚚 Rename fuzzy_match to search Breaking	444	sunnyosun	2023-06-15
♻️ Harmonize code for Gene, Protein, CellMarker	443	sunnyosun	2023-06-15
🚚 Move lookup to logger	442	falexwolf	2023-06-14
🧪 Properly test ontology_to_df	441	sunnyosun	2023-06-14
🍱 Drop id, version columns	440	sunnyosun	2023-06-14
⚰️ Remove dead code	439	sunnyosun	2023-06-14
🚚 Rename .todict() to .dict()	438	sunnyosun	2023-06-14
✨ Lookup refactor to return multiple records Breaking	436	sunnyosun	2023-06-14
✨ New implementation of lookup	434	sunnyosun	2023-06-13
🚚 Renamed sources_local	435	Zethson	2023-06-13
✨ Add fields	433	Zethson	2023-06-13
🐛 Fix filtering & remove bioregistry & refactoring	430	Zethson	2023-06-13
🐛 Fixed index bug in search	429	sunnyosun	2023-06-12	0.20.0
🔊 Improved inspect logging	428	sunnyosun	2023-06-12
♻️ Removed curate, updated inspect guide Breaking	419	sunnyosun	2023-06-12
🚑 Fixed lamindb instance error and refactored source matching	417	sunnyosun	2023-06-11	0.19.1
🔥 No longer checks compat	411	sunnyosun	2023-06-10
🎨 Always regenerate .current_sources.yaml upon import Breaking	410	sunnyosun	2023-06-10	0.19.0
🐛 Fix LAMINDB_INSTANCE_LOADED on Windows	409	Koncopd	2023-06-10
📝 Fix notebook execution	408	falexwolf	2023-06-10
🚚 Renamed source path variables	407	sunnyosun	2023-06-10	0.18.1
➖ Clean up dependencies	406	falexwolf	2023-06-10
🎨 Removed environment variable for loaded lamindb instance Breaking	405	sunnyosun	2023-06-09	0.18.0
🚚 Move img folder to guide	404	falexwolf	2023-06-09
📝 Re-organize docs	403	falexwolf	2023-06-08
📝 Fix API ref	402	sunnyosun	2023-06-08	0.17.0
🚚 Renamed version to source everywhere possible Breaking	401	sunnyosun	2023-06-07	0.17a3
🎨 Updated yaml parameter in parse_current_versions	400	sunnyosun	2023-06-07
🎨 Harmonize names	399	Zethson	2023-06-07
🚑 Fixed readout parsing	398	sunnyosun	2023-06-07	0.17a1
🧪 Add tests to versions file generation	397	sunnyosun	2023-06-07
🎨 Use the same code to create and update local yaml	396	sunnyosun	2023-06-06
♻️ Changed yaml format to have species as keys, refactored versioning Breaking	394	sunnyosun	2023-06-04	0.17a1
✨ Add improved species support Breaking	392	Zethson	2023-06-04
👷 Remove nox venv	388	falexwolf	2023-06-01	0.16.0
🔥 Remove global lookup Breaking	387	Zethson	2023-05-31
🎨 Default to return df when displaying versions	385	sunnyosun	2023-05-30
✨ Add GO	384	Zethson	2023-05-30
🚸 Delete an incomplete file on an exception in s3_bionty_assets	383	Koncopd	2023-05-29
➖ Remove nbproject from production dependencies	382	Koncopd	2023-05-29
🚑 Added Entity=Bionty backward compatibility	381	sunnyosun	2023-05-29	0.15.1
✨ Implemented a first search method	380	sunnyosun	2023-05-29
🐛 Decrease refresh_per_second in the progress bar to 10	379	Koncopd	2023-05-28
➖ Replace upath and fsspec with botocore	376	Koncopd	2023-05-28
➖ Removed unused dependencies	377	sunnyosun	2023-05-28
✨ Allow map_synonyms for every entity	375	sunnyosun	2023-05-28
✨ Include synonyms, definition columns in parquet	372	sunnyosun	2023-05-27	0.15.0
🩹 Also include the index field in BiontyField	370	sunnyosun	2023-05-25
💄 Prettified repr	369	sunnyosun	2023-05-25
🍱 Download parquet files from s3://bionty-assets	365	sunnyosun	2023-05-25	0.14.0
✨ Implement map_synonyms	359	Zethson	2023-05-24
🍱 Added children column to ontology parquet files	363	sunnyosun	2023-05-23
✨ Add inspect	356	Zethson	2023-05-15
🐛 Fix DO metadata	355	Zethson	2023-05-13
✨ Add Drug entity	352	Zethson	2023-05-13
👷 Fix non-process safe code	350	jlricon	2023-05-11	0.13.5
✏️ Fix lowercase types	348	jlricon	2023-05-11	0.13.4
⬆️ Remove lndb	347	Zethson	2023-05-10	0.13.3
🎨 Rename to internal UPath implementation and add s3 to ffspec	346	Zethson	2023-05-10	0.13.2
🎨 Add Upath, remove lndb_storage	344	Zethson	2023-05-10	0.13.1
✨ Added synonyms for CellMarker Breaking	340	sunnyosun	2023-05-09	0.13.0
🚚 Deprecate ‘database’ parameter and replace it with ‘source’ Breaking	341	Zethson	2023-05-08
🚚 Move s3_bionty_assets	339	Zethson	2023-05-08
📝 Improve lookup docs	338	Zethson	2023-05-06
🎨 Add more flexible prefixes	337	Zethson	2023-05-02
🎨 Improve print versions	336	Zethson	2023-05-02
📌 No pinning of lndb-storage version	333	sunnyosun	2023-04-27	0.12.1
🎨 Update lnschema-bionty	332	sunnyosun	2023-04-27
🎨 Change .df(), .lookup() to methods, move ._entity to private Breaking	326	sunnyosun	2023-04-27	0.12.0
🐛 Fix pathway ontology	329	Zethson	2023-04-26
💚 Fix bionty-asset instance for file upload	325	sunnyosun	2023-04-26
👷 Sync staging into main	316	Zethson	2023-04-25
🚑 Fix lookup for empty strings	314	sunnyosun	2023-04-23	0.11.6
⚡ Make sure no NAs present in the entity.df.name	313	sunnyosun	2023-04-23	0.11.5
⬆️ Pronto>=2.5.4, removed cached_property dep for py3.7	312	sunnyosun	2023-04-23
⚡ Improve the speed loading of ontology df	305	sunnyosun	2023-04-19	0.11.4
👷 Add staging to CI	293	Zethson	2023-04-04
💚 Add current/lndb updating on new entities	290	Zethson	2023-03-30	0.11.3
💚 Try fixing lnschema-bionty CI	289	falexwolf	2023-03-27
🐛 Fix field for gene and protein	288	sunnyosun	2023-03-27	0.11.2
🚚 Renamed to field everywhere	287	sunnyosun	2023-03-27	0.11.1
👷 Fix lnschema-bionty CI	284	sunnyosun	2023-03-27
🚚 Rename property lookup_col to lookup_field Breaking	283	sunnyosun	2023-03-24	0.11.0
✅ Add update_defaults test	280	Zethson	2023-03-23
👷 Test against lnschema-bionty	279	falexwolf	2023-03-23
✨ Move ID from Entity to curate Breaking	268	Zethson	2023-03-23
🐛 Fix removeprefix 3.8 & versions pathing	277	Zethson	2023-03-22	0.10.1
📝 Updated the curation notebook for cellmarker	274	sunnyosun	2023-03-22
🍱 Updated CellMarker assets Breaking	271	sunnyosun	2023-03-21	0.10.0
🚑 Ensure version names are strings	269	sunnyosun	2023-03-20	0.9.0
✨ Add pathway ontology	267	Zethson	2023-03-17	0.9.0rc1
✨ Add compatibility functions	264	Zethson	2023-03-17
✨ Add latest version inference if only db is passed	256	Zethson	2023-03-14
🐛 Fix default ids	257	sunnyosun	2023-03-14
Add md5 sums	249	Zethson	2023-03-13
🎨 Fixed case sensitivity, lookup output as namedtuple	255	sunnyosun	2023-03-11
💥 Lookup returns the full record Breaking	254	sunnyosun	2023-03-11
💄 Actually fix image display	253	sunnyosun	2023-03-11
🐛 Fix img links	252	sunnyosun	2023-03-11
📝 Keep improving docs	250	sunnyosun	2023-03-11
🐛 Fix version order	248	Zethson	2023-03-10
🐛 Ensure datadir is created	245	sunnyosun	2023-03-09	0.8.1
🐛 Fixed readout lookup	244	sunnyosun	2023-03-09	0.8.0
📝 A take on 3 summary bullets	240	falexwolf	2023-03-08	0.8rc2
💚 Fix CI build	239	sunnyosun	2023-03-08
📝 Improving documentation	220	Zethson	2023-03-08
👷 Add entity tests	234	Zethson	2023-03-07
✨ Add names/website per ontology & improve versions rich tables	232	Zethson	2023-03-06
📝 Add better docstrings and docstring decorator	231	Zethson	2023-03-06
🐛 Fix cellmarker ontology	230	Zethson	2023-03-03	0.8rc1
✨ Add CellLine ontology	229	Zethson	2023-03-03
🎨 Simplify filenames	227	Zethson	2023-03-03
🎨 Deduce filenames on the fly for non-S3 Entites	223	Zethson	2023-03-01
📝 Simplify FAQ	218	Zethson	2023-02-27
🎨 Simplify ontology accesses	217	Zethson	2023-02-27
🎨 Move Species to Entity	216	Zethson	2023-02-27
🎨 Rename EntityTable to Entity Breaking	214	Zethson	2023-02-26
🎨 Add laminci	213	Zethson	2023-02-26
✨ Add HCA ontology	209	Zethson	2023-02-21
✨ Improve version handling	202	Zethson	2023-02-21
🔥 No downloading upon import	205	sunnyosun	2023-02-20
👷 Remove py3.7 from CI	206	sunnyosun	2023-02-20
📝 Add better documentation & function to print currently available/active ontologies	201	Zethson	2023-02-17
👷 Add HDO & improve support for multiple databases	187	Zethson	2023-02-15
👷 Add GH workflow to check for version URLs	188	Zethson	2023-02-13	0.7.0
⬆️ Rename lndb_setup to lndb	189	bpenteado	2023-02-13
✨ Add human phenotype ontology	172	Zethson	2023-02-06
📝 Add dev APIs to docs	183	sunnyosun	2023-02-06
📝 Use guide/index as landing page	182	sunnyosun	2023-02-06
🔥 Removed _logger.py	176	sunnyosun	2023-02-06
🐛 Fix #167	168	Zethson	2023-02-05
👷 Add lamindocs secret key for CI	173	Zethson	2023-02-05
✨ Added case_sensitive to curate	169	sunnyosun	2023-01-31	0.6.5
🚑 Fix version key type	166	sunnyosun	2023-01-18	0.6.4
🚚 Rename species common_name to name	165	sunnyosun	2023-01-17	0.6.3
🎨 Changed version filename separator from	to ___	164	sunnyosun	2023-01-16
🐛 Fix docs	162	sunnyosun	2023-01-12	0.6.1
👷 Expand CI to python 3.7-3.10	161	sunnyosun	2023-01-12	0.6.0
✨ Pull species table dynamically from Ensembl	160	sunnyosun	2023-01-05
✨ Add progressbar to downloads	159	Zethson	2023-01-05

wetlab

Name	PR	Developer	Date	Version
✨ Added TreatmentTarget	21	sunnyosun	2023-07-04
✨ Added target_genes	19	sunnyosun	2023-07-03
🚚 Migrate to Django (2)	12	falexwolf	2023-06-11
🚚 Migrate to Django (1)	11	falexwolf	2023-06-09
🏗️ Remove lnbase-biolab	10	falexwolf	2023-06-01	0.18a1
🏗️ Remove SQL-level schema modules	9	falexwolf	2023-05-25	0.17.0
✨ Add Well table, File.cell_lines	8	sunnyosun	2023-05-23	0.16.3
✨ Added Treatment	3	sunnyosun	2023-05-15
🎉 Move content from lnschema-wetlab here	1	falexwolf	2023-04-22	0.15.1

nbproject

Name	PR	Developer	Date	Version
👷 Ruff and 3.11	276	Zethson	2023-12-26
🩹 Account for empty notebook in consecutiveness check	272	falexwolf	2023-10-01
📝 Fix image link	271	falexwolf	2023-09-18
🚸 More robust title parsing	270	falexwolf	2023-08-15	0.9.2
📝 Simplify docs, adopt new lamin.ai static site architecture	269	falexwolf	2023-08-04	0.9.1
♻️ Remove loguru-dependent call, expand metadata_only return signature	268	falexwolf	2023-06-15	0.9.0
📝 Position nbproject	264	falexwolf	2023-06-15
🩹 Try to get vs code path first	267	Koncopd	2023-06-10
🦺 Safer parsing during initialization	266	Koncopd	2023-06-03	0.8.7
➖ Remove nbproject-test from dependencies	262	Koncopd	2023-05-30
🐛 Safer ipylab initialization	263	Koncopd	2023-04-18	0.8.6
🐛 Fix VS Code integration for recent VS Code versions	260	Koncopd	2023-04-17	0.8.5
♻️ Replace display with metadata_only arg in header	257	Koncopd	2023-04-10	0.8.4
🚸 Allow to not display metadata	255	falexwolf	2023-03-12	0.8.3
⬆️ Observe lndb-setup rename to lndb	253	bpenteado	2023-02-16	0.8.2
✨ Safer notebook path inference and more ways to do it	251	Koncopd	2023-02-10
🐛 Check keys before accessing in notebook_path	250	Koncopd	2023-02-08