## Changelog 2023 Note: Get notified by watching releases for git repositories: lamindb · laminhub · lamin-cli · laminr · nf-lamin · bionty For other years, see: 2026 · 2025 · 2024 · 2022 # 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 | 763 | falexwolf | 2023-06-13 | | "TransformType" | | --- | --- | --- | --- | --- | | 👷 Dispatch to | 762 | falexwolf | 2023-06-13 | | lamin-examples & | | redun-lamin-fasta | | --- | --- | --- | --- | --- | | 🔥 Remove | 761 | falexwolf | 2023-06-13 | 0.42a9 | | "File.stream()" | | --- | --- | --- | --- | --- | | 🚸 Prefix auto- | 757 | falexwolf | 2023-06-12 | | storage-key with | | "lndb/" | | --- | --- | --- | --- | --- | | ✨ Delete storage in | 754 | Koncopd | 2023-06-12 | | "File.delete()" | | --- | --- | --- | --- | --- | | ✅ Add more tests | 755 | falexwolf | 2023-06-12 | | for File init | | --- | --- | --- | --- | --- | | 💚 Remove test paths | 753 | falexwolf | 2023-06-11 | | from pyproject.toml | | --- | --- | --- | --- | --- | | ✨ Add "to_adata()" | 752 | Koncopd | 2023-06-11 | | method to | | "AnnDataAccessor" | | --- | --- | --- | --- | --- | | 🚚 Rename | 750 | sunnyosun | 2023-06-10 | | "Featureset" to | | "FeatureSet" | | --- | --- | --- | --- | --- | | ⚠️ Refactor save - | 742 | falexwolf | 2023-06-10 | | it no longer returns | | records | | --- | --- | --- | --- | --- | | 📝 Re-organize | 740 | falexwolf | 2023-06-10 | | biology guides | | --- | --- | --- | --- | --- | | ✨ Populate | 739 | sunnyosun | 2023-06-09 | 0.42a8 | | "bionty_version" in | | "ln.parse" | | --- | --- | --- | --- | --- | | ⚡ Improved | 736 | sunnyosun | 2023-06-09 | | multifield query in | | "ln.parse" | | --- | --- | --- | --- | --- | | ⬆️ First stable | 733 | sunnyosun | 2023-06-09 | | Django release of | | "lnschema-bionty" | | --- | --- | --- | --- | --- | | 🚸 Validate required | 735 | falexwolf | 2023-06-09 | | fields | | --- | --- | --- | --- | --- | | 📝 Integrate | 732 | falexwolf | 2023-06-08 | 0.42a7 | | "lnschema_bionty" | | into reference | | --- | --- | --- | --- | --- | | 🚸 Add "select" | 730 | falexwolf | 2023-06-08 | | method to "BaseORM" | | --- | --- | --- | --- | --- | | 📝 Overhaul README | 728 | falexwolf | 2023-06-08 | | --- | --- | --- | --- | --- | | ♻️ Refactored | 731 | sunnyosun | 2023-06-08 | | features code | | --- | --- | --- | --- | --- | | 📝 Add "configure" | 727 | falexwolf | 2023-06-08 | | guide instead of | | setup | | --- | --- | --- | --- | --- | | 🧪 Add tests for | 726 | sunnyosun | 2023-06-08 | | "folder.tree()" | | --- | --- | --- | --- | --- | | 🚚 Renamed | 725 | sunnyosun | 2023-06-07 | | "BiontyVersions" to | | "BiontySource" | | --- | --- | --- | --- | --- | | 🔊 "folder.tree" can | 724 | sunnyosun | 2023-06-07 | | only be used with | | existing folders in | | storage | | --- | --- | --- | --- | --- | | 👷 Coverage in | 722 | falexwolf | 2023-06-07 | | separate job | | --- | --- | --- | --- | --- | | 🎨 Import ORMs from | 723 | sunnyosun | 2023-06-07 | | .models before | | reload | | --- | --- | --- | --- | --- | | 🔥 Remove "ln.nb" | 721 | falexwolf | 2023-06-07 | | --- | --- | --- | --- | --- | | 🏗️ Re-architect | 720 | falexwolf | 2023-06-06 | 0.42a6 | | transform id | | --- | --- | --- | --- | --- | | 🚚 Rename "ln.add" | 719 | falexwolf | 2023-06-05 | 0.42a5 | | to "ln.save" | | --- | --- | --- | --- | --- | | ⬆️ Upgrade lnschema- | 718 | sunnyosun | 2023-06-05 | | core to 0.35a5 | | --- | --- | --- | --- | --- | | 🚚 Migrate | 716 | falexwolf | 2023-06-05 | 0.42a2 | | "lnschema-bionty" to | | Django | | --- | --- | --- | --- | --- | | ♻️ Polish core | 717 | falexwolf | 2023-06-05 | | schema | | --- | --- | --- | --- | --- | | 🐛 Fix delete for | 715 | Koncopd | 2023-06-04 | | File | | --- | --- | --- | --- | --- | | 📝 Rework the stream | 714 | Koncopd | 2023-06-04 | | notebook | | --- | --- | --- | --- | --- | | 💚 Point to lamindb- | 713 | falexwolf | 2023-06-04 | | setup main & fix | | session | | --- | --- | --- | --- | --- | | ➖ Move nbproject to | 711 | Koncopd | 2023-06-04 | | extra dependencies | | --- | --- | --- | --- | --- | | 🔥 Delete SQLAlchemy | 710 | falexwolf | 2023-06-04 | | related content | | --- | --- | --- | --- | --- | | ➕ Pin boto3 in aws | 712 | Koncopd | 2023-06-04 | | --- | --- | --- | --- | --- | | 🔥 Remove SQLAlchemy | 709 | falexwolf | 2023-06-04 | | tests | | --- | --- | --- | --- | --- | | ♻️ Absorb | 707 | falexwolf | 2023-06-03 | | "DjangoORM.create()" | | in "DjangoORM.__ini | | t__()" | | --- | --- | --- | --- | --- | | 🐛 Disentangle keys | 708 | Koncopd | 2023-06-03 | | in storage related | | test notebooks | | --- | --- | --- | --- | --- | | 🚸 ln.track | 704 | Koncopd | 2023-06-03 | | improvements | | --- | --- | --- | --- | --- | | 🏗️ Enable Django | 702 | falexwolf | 2023-06-02 | | backend (part 2) | | --- | --- | --- | --- | --- | | 🎨 Simplified track | 705 | sunnyosun | 2023-06-02 | | sample-level | | metadata | | --- | --- | --- | --- | --- | | 🔊 Add more loggings | 703 | sunnyosun | 2023-06-02 | 0.42a1 | | to "ln.parse" | | --- | --- | --- | --- | --- | | ♻️ Refactored | 701 | sunnyosun | 2023-06-01 | | feature parsing and | | "ln.parse" | | --- | --- | --- | --- | --- | | 🚚 Move lndb-storage | 700 | falexwolf | 2023-06-01 | | back into lamindb | | --- | --- | --- | --- | --- | | 🚚 Rename "lndb" to | 699 | falexwolf | 2023-06-01 | | "lamindb_setup" | | --- | --- | --- | --- | --- | | 🏗️ Add Django | 697 | falexwolf | 2023-05-31 | | backend (setup) | | --- | --- | --- | --- | --- | | ⬆️ Update lndb to | 698 | Koncopd | 2023-05-31 | 0.41.2 | | 0.45.0 | | --- | --- | --- | --- | --- | | ⬆️ Upgrade lnschema- | 696 | sunnyosun | 2023-05-30 | 0.41.1 | | bionty | | --- | --- | --- | --- | --- | | 🚑 Fix species | 695 | sunnyosun | 2023-05-28 | 0.41.0 | | config | | --- | --- | --- | --- | --- | | 🎨 Clean up CI more | 694 | falexwolf | 2023-05-28 | | --- | --- | --- | --- | --- | | ➖ Remove scanpy as | 693 | falexwolf | 2023-05-28 | | test dependency | | --- | --- | --- | --- | --- | | 👷 Fix coverage for | 692 | falexwolf | 2023-05-28 | | lndb-storage | | --- | --- | --- | --- | --- | | ➖ Do not install | 691 | Koncopd | 2023-05-28 | 0.41a4 | | storage extras by | | default | | --- | --- | --- | --- | --- | | 👷 Bring back nox | 690 | falexwolf | 2023-05-28 | | session | | --- | --- | --- | --- | --- | | 📝 Refactor guide | 689 | falexwolf | 2023-05-28 | | notebooks | | --- | --- | --- | --- | --- | | ✨ Add "DataFrame" | 688 | sunnyosun | 2023-05-28 | | support for | | "ln.parse" | | --- | --- | --- | --- | --- | | 👷 Refactor tests | 687 | falexwolf | 2023-05-27 | | --- | --- | --- | --- | --- | | ✨ Subsettable | 668 | Koncopd | 2023-05-27 | | backed "AnnData" | | --- | --- | --- | --- | --- | | 📝 Remove setup | 686 | falexwolf | 2023-05-27 | | notebook | | --- | --- | --- | --- | --- | | 🏗️ Remove SQL-level | 685 | falexwolf | 2023-05-26 | 0.41a3 | | schema modules | | --- | --- | --- | --- | --- | | ⬆️ Upgrade lnschema- | 684 | sunnyosun | 2023-05-25 | 0.40.7 | | bionty to 0.17.1 | | --- | --- | --- | --- | --- | | ⬇️ Downgrade | 683 | sunnyosun | 2023-05-25 | 0.40.6 | | lnschema-bionty to | | 0.16.5 | | --- | --- | --- | --- | --- | | ♻️ Refactor types | 681 | falexwolf | 2023-05-23 | 0.40.5 | | --- | --- | --- | --- | --- | | ♻️ Refactor | 679 | falexwolf | 2023-05-17 | | "BaseORM" | | --- | --- | --- | --- | --- | | 🚸 Pre-join some | 678 | falexwolf | 2023-05-16 | | cheap relationships | | --- | --- | --- | --- | --- | | 📝 Improve wording | 677 | Zethson | 2023-05-16 | | --- | --- | --- | --- | --- | | ✨ Added Treatment | 675 | sunnyosun | 2023-05-15 | 0.40.3 | | table | | --- | --- | --- | --- | --- | | 🚑 Fix ln.Features | 674 | sunnyosun | 2023-05-11 | 0.40.1 | | table name for | | postgres | | --- | --- | --- | --- | --- | | 📝 Update ontology | 673 | falexwolf | 2023-05-11 | | guide | | --- | --- | --- | --- | --- | | 🎨 Deprecated "data" | 672 | sunnyosun | 2023-05-11 | | in "ln.Features", | | replace with | | "iterable" | | --- | --- | --- | --- | --- | | 🎨 Replace reference | 671 | sunnyosun | 2023-05-09 | 0.40.0 | | with field for | | "ln.Features" | | Breaking | | --- | --- | --- | --- | --- | | ⬆️ Update bionty to | 670 | sunnyosun | 2023-05-09 | 0.39.8 | | 0.13 | | --- | --- | --- | --- | --- | | 📝 Polish | 667 | falexwolf | 2023-04-28 | | --- | --- | --- | --- | --- | | 📝 Polish docs | 666 | falexwolf | 2023-04-28 | | --- | --- | --- | --- | --- | | ⬆️ Update to lndb | 665 | sunnyosun | 2023-04-28 | 0.39.7 | | 0.44.7 | | --- | --- | --- | --- | --- | | 🚸 Do not require | 664 | falexwolf | 2023-04-28 | 0.39.6 | | session for | | "is_run_input" | | --- | --- | --- | --- | --- | | ⬆️ Allow load with | 663 | sunnyosun | 2023-04-27 | 0.39.5 | | storage | | --- | --- | --- | --- | --- | | 💥 Switch to methods | 662 | sunnyosun | 2023-04-27 | 0.39.4 | | bionty.df(), | | bionty.lookup() | | Breaking | | --- | --- | --- | --- | --- | | ⬆️ Upgrade lndb | 661 | fredericenard | 2023-04-26 | 0.39.3 | | --- | --- | --- | --- | --- | | ✨ Enable database | 660 | sunnyosun | 2023-04-24 | 0.39.2 | | entries lookup | | --- | --- | --- | --- | --- | | ✨ Introduce | 659 | falexwolf | 2023-04-24 | | "File.backed()" | | --- | --- | --- | --- | --- | | ✨ Introduced | 658 | sunnyosun | 2023-04-24 | 0.39.1 | | "ln.parse()" | | --- | --- | --- | --- | --- | | 🎨 Refactor | 657 | falexwolf | 2023-04-24 | 0.39.0 | | "ln.File" | | --- | --- | --- | --- | --- | | ✨ Inherit fsspec | 655 | Koncopd | 2023-04-23 | | kwargs from root and | | move in root check | | --- | --- | --- | --- | --- | | 📌 Check anndata | commit | Koncopd | 2023-04-23 | | version in | | "File.subset" | | --- | --- | --- | --- | --- | | 🐛 Fix VS Code | 654 | Koncopd | 2023-04-23 | | notebook | | reinitialization in | | track | | --- | --- | --- | --- | --- | | 🚸 Add "File.subset" | 653 | falexwolf | 2023-04-22 | 0.39rc1 | | --- | --- | --- | --- | --- | | 🚚 Replace | 651 | falexwolf | 2023-04-22 | | "lnschema-wetlab" | | with "lnbase-biolab" | | and "lnschema- | | lamin1" | | --- | --- | --- | --- | --- | | 📝 Add an export | 649 | falexwolf | 2023-04-21 | | example for | | "ln.schema.view()" | | --- | --- | --- | --- | --- | | 🐛 Fix population of | 648 | falexwolf | 2023-04-21 | 0.38.3 | | "transform_id" in | | "File" in edge cases | | --- | --- | --- | --- | --- | | 🚸 Allow registering | 647 | falexwolf | 2023-04-21 | 0.38.2 | | local postgres | | instances on the hub | | --- | --- | --- | --- | --- | | 🚸 Improve error | 643 | falexwolf | 2023-04-19 | | message for notebook | | tracking | | --- | --- | --- | --- | --- | | van -> can | 641 | ThomVett | 2023-04-19 | | --- | --- | --- | --- | --- | | ⚡ Improved feature | 640 | sunnyosun | 2023-04-19 | 0.38.1 | | parsing speed | | --- | --- | --- | --- | --- | | ⬆️ Compatibility | 639 | falexwolf | 2023-04-18 | 0.38.0 | | with new hub | | --- | --- | --- | --- | --- | | 💥 New calling | 633 | falexwolf | 2023-04-18 | | patterns for | | lnschema-bionty | | --- | --- | --- | --- | --- | | ✅ Use nbproject- | 638 | Koncopd | 2023-04-18 | | test directly | | --- | --- | --- | --- | --- | | 🚸 Use relative path | 636 | falexwolf | 2023-04-18 | 0.37.2 | | in key | | --- | --- | --- | --- | --- | | 🩹 Unpack | 632 | Koncopd | 2023-04-17 | 0.37.1 | | "notebook_path" | | correctly | | --- | --- | --- | --- | --- | | 🚚 Better names, | 631 | falexwolf | 2023-04-16 | 0.37.0 | | more relationships | | directly on "File" | | Breaking | | --- | --- | --- | --- | --- | | ✨ Add Google Colab | 628 | falexwolf | 2023-04-16 | | integration | | --- | --- | --- | --- | --- | | 🚸 Improve notebook | 627 | falexwolf | 2023-04-14 | | tracking UX | | --- | --- | --- | --- | --- | | 🎨 Simplify | 624 | falexwolf | 2023-04-12 | 0.36.3 | | "ln.track()" and add | | "app" transform type | | --- | --- | --- | --- | --- | | 🐛 Fix | 623 | Koncopd | 2023-04-10 | 0.36.1 | | initialization of | | new notebooks | | --- | --- | --- | --- | --- | | 🚸 Filename in | 614 | falexwolf | 2023-04-08 | 0.36.0 | | "File.name", new | | "File.key" and | | "Folder.key", | | robustness overhaul | | Breaking | | --- | --- | --- | --- | --- | | ✨ Introduce | 611 | Koncopd | 2023-04-03 | 0.35.6 | | "File.stage()" and | | "File.replace()" | | --- | --- | --- | --- | --- | | 🚸 More robust | 605 | Zethson | 2023-04-01 | | ontology version | | tracking | | --- | --- | --- | --- | --- | | 🚚 Import | 591 | sunnyosun | 2023-03-28 | 0.35.5 | | "lnschema_bionty" | | instead of "bionty" | | --- | --- | --- | --- | --- | | 🚚 Move all core | 590 | falexwolf | 2023-03-27 | 0.35.4 | | entities to root | | level | | --- | --- | --- | --- | --- | | 🚸 Polish guide | 589 | falexwolf | 2023-03-27 | 0.35.3 | | --- | --- | --- | --- | --- | | 🚚 Move "Readout" | 588 | sunnyosun | 2023-03-27 | 0.35.2 | | from "lnschema- | | wetlab" to | | "lnschema-bionty" | | --- | --- | --- | --- | --- | | ♻️ Fix "parsing_id" | 587 | sunnyosun | 2023-03-27 | 0.35.1 | | --- | --- | --- | --- | --- | | 🚚 Rename "DObject" | 586 | falexwolf | 2023-03-25 | 0.35.0 | | to "File" and | | "DFolder" to | | "Folder" Breaking | | --- | --- | --- | --- | --- | | 🚚 Introduce | 585 | falexwolf | 2023-03-24 | | "ln.track()" to | | replace | | "ln.nb.header()" | | --- | --- | --- | --- | --- | | 🏗️ Combine | 584 | falexwolf | 2023-03-23 | | "Notebook" and | | "Pipeline" into | | "Transform" Breaking | | --- | --- | --- | --- | --- | | 🚑 Fix optional | 583 | sunnyosun | 2023-03-22 | 0.34.2 | | dependencies | | --- | --- | --- | --- | --- | | 🔥 Remove "Usage" | 581 | falexwolf | 2023-03-22 | | --- | --- | --- | --- | --- | | ⬆️ Updated | 578 | sunnyosun | 2023-03-21 | 0.34.1 | | "CellMarker" asset | | --- | --- | --- | --- | --- | | ⬆️ Upgrade to | 575 | sunnyosun | 2023-03-20 | 0.34.0 | | "bionty" 0.9 | | --- | --- | --- | --- | --- | | ♻️ Move storage- | 560 | Koncopd | 2023-03-20 | | related code to | | "lndb-storage" | | --- | --- | --- | --- | --- | | 🚑 Fix gene id | 573 | sunnyosun | 2023-03-17 | | --- | --- | --- | --- | --- | | 🐛 Check if env | 572 | fredericenard | 2023-03-15 | | variable exists | | before trying to get | | his value | | --- | --- | --- | --- | --- | | 🚸 Do not yet show | commit | falexwolf | 2023-03-15 | 0.33.4 | | deprecation warning | | for "ln.nb.header()" | | --- | --- | --- | --- | --- | | 👷 Restore streaming | 569 | sunnyosun | 2023-03-15 | 0.33.3 | | test from cloud | | --- | --- | --- | --- | --- | | ⬇️ typeguard<3.0.0 | 568 | sunnyosun | 2023-03-15 | | --- | --- | --- | --- | --- | | ➖ Remove typeguard | 567 | sunnyosun | 2023-03-15 | 0.33.2 | | dependency | | --- | --- | --- | --- | --- | | ⬆️ Update core | 566 | sunnyosun | 2023-03-15 | 0.33.1 | | --- | --- | --- | --- | --- | | 🚚 Replace | 564 | falexwolf | 2023-03-14 | 0.33.0 | | "ln.nb.header()" | | with "ln.Run()" | | except in "faq/nb" | | --- | --- | --- | --- | --- | | 🚸 Smart about | 563 | falexwolf | 2023-03-14 | | "global_context" and | | "load_latest" when | | run from notebook | | --- | --- | --- | --- | --- | | ✨ "ln.Features" | 562 | sunnyosun | 2023-03-14 | | --- | --- | --- | --- | --- | | 🏗️ Introduce | 561 | falexwolf | 2023-03-13 | | "lamindb.context" | | and enable "ln.Run" | | to create contexts | | --- | --- | --- | --- | --- | | 📝 Improve the | 559 | sunnyosun | 2023-03-10 | | docstrings of | | "ln.save" and | | "ln.delete" | | --- | --- | --- | --- | --- | | 📝 Hide CI related | 558 | sunnyosun | 2023-03-10 | | cells in notebooks | | --- | --- | --- | --- | --- | | 📝 Update docs to | 557 | lawrlee | 2023-03-10 | | clarify sign up and | | log in | | --- | --- | --- | --- | --- | | 📝 Prettier species | 555 | falexwolf | 2023-03-09 | 0.32.0 | | query | | --- | --- | --- | --- | --- | | 📝 Refactor docs | 553 | sunnyosun | 2023-03-09 | | sidebar | | --- | --- | --- | --- | --- | | ⬆️ Upgrade | 554 | falexwolf | 2023-03-09 | | "ln.setup" | | --- | --- | --- | --- | --- | | 🔥 Remove | 552 | sunnyosun | 2023-03-09 | | "ln.knowledge" | | Breaking | | --- | --- | --- | --- | --- | | ➖ Remove bionty as | 551 | sunnyosun | 2023-03-09 | 0.32.0rc1 | | a dependency | | --- | --- | --- | --- | --- | | 📝 Replace | 547 | falexwolf | 2023-03-07 | 0.31.1 | | "ln.knowledge" with | | "bionty" in docs | | --- | --- | --- | --- | --- | | 📝 Link FAQ and | 550 | falexwolf | 2023-03-07 | | guide to session and | | notebook API | | --- | --- | --- | --- | --- | | ⬆️ Upgrade lndb | 549 | fredericenard | 2023-03-07 | 0.31.0 | | --- | --- | --- | --- | --- | | ⬆️ Upgrade lndb | 548 | fredericenard | 2023-03-07 | | --- | --- | --- | --- | --- | | 📝 Move ingest- | 545 | falexwolf | 2023-03-06 | | folder back to faq | | --- | --- | --- | --- | --- | | 🚸 Improve clarity | 543 | falexwolf | 2023-03-06 | | of "no_source" error | | message | | --- | --- | --- | --- | --- | | 💚 Fix CI | 542 | sunnyosun | 2023-03-06 | | --- | --- | --- | --- | --- | | 🚚 Rename data | 541 | sunnyosun | 2023-03-06 | | objects to data or | | datasets in titles | | --- | --- | --- | --- | --- | | 📝 Duplicate README | 540 | sunnyosun | 2023-03-06 | | to the guide landing | | page | | --- | --- | --- | --- | --- | | ✨ Allow uploading | 539 | Koncopd | 2023-03-05 | | zarr from local | | paths | | --- | --- | --- | --- | --- | | 📝 Prettify guide | 537 | sunnyosun | 2023-03-05 | | landing page | | --- | --- | --- | --- | --- | | 🚑 Fix upsert for | 535 | sunnyosun | 2023-03-03 | 0.30.3 | | dobject and CI | | --- | --- | --- | --- | --- | | 💄 Simplify docs | 534 | falexwolf | 2023-03-03 | | --- | --- | --- | --- | --- | | 🚸 Do not error, | 533 | falexwolf | 2023-03-02 | 0.30.2 | | just warn upon | | installation of | | lamin | | --- | --- | --- | --- | --- | | 🚑 Fix iterdir to | 532 | sunnyosun | 2023-03-02 | | not list itself | | --- | --- | --- | --- | --- | | 🔥 Remove "lamin" | 531 | falexwolf | 2023-03-01 | 0.30.1 | | dependency | | --- | --- | --- | --- | --- | | 🚑 Fix for listing | 528 | sunnyosun | 2023-03-01 | 0.30.0 | | cloud dir | | --- | --- | --- | --- | --- | | 🎨 Add | 530 | falexwolf | 2023-03-01 | | "lamindb.setup" API | | as an alternative | | for the CLI | | --- | --- | --- | --- | --- | | 🚚 Rename "dfolder. | 527 | sunnyosun | 2023-03-01 | | get_dobject" to | | "get", allow passing | | a subdirectory | | --- | --- | --- | --- | --- | | 🚑 Ensure filepath | 526 | sunnyosun | 2023-03-01 | | is absolute | | --- | --- | --- | --- | --- | | 🎨 Allow passing a | 524 | sunnyosun | 2023-02-28 | | list of relpaths to | | "dfolder.get_dobjec | | t" | | --- | --- | --- | --- | --- | | ✨ Infer filesystem | 522 | Koncopd | 2023-02-25 | | for anndata read and | | write | | --- | --- | --- | --- | --- | | 📝 Replace "lndb" | 521 | falexwolf | 2023-02-25 | 0.29.1 | | with "lamin" in docs | | --- | --- | --- | --- | --- | | 📝 Add nbproject | 520 | bpenteado | 2023-02-24 | | note box to ingest | | guide | | --- | --- | --- | --- | --- | | 🍱 "DFolder.get_dob | 519 | sunnyosun | 2023-02-24 | | ject" | | --- | --- | --- | --- | --- | | ⬆️ Upgrade | 517 | bpenteado | 2023-02-23 | 0.29.0 | | lnschema-core to | | 0.28.6 | | --- | --- | --- | --- | --- | | 💥 Move | 510 | sunnyosun | 2023-02-23 | | "lns.DFolder" to | | "ln.DFolder" | | --- | --- | --- | --- | --- | | 🐛 Fix trailing | 516 | falexwolf | 2023-02-22 | 0.28.5 | | slash within lamindb | | --- | --- | --- | --- | --- | | 👷 Fix CI config | 515 | falexwolf | 2023-02-22 | 0.28.4 | | --- | --- | --- | --- | --- | | 🐛 Fix version check | 514 | falexwolf | 2023-02-22 | 0.28.3 | | --- | --- | --- | --- | --- | | 👷 Collect docs | 513 | falexwolf | 2023-02-22 | 0.28.2 | | artifacts | | --- | --- | --- | --- | --- | | 🐛 Fix trailing | 512 | falexwolf | 2023-02-22 | 0.28.1 | | slash in storage | | root | | --- | --- | --- | --- | --- | | 🚚 Rename | 509 | falexwolf | 2023-02-21 | 0.28.0 | | "DObject.run_id" to | | "DObject.source_id" | | --- | --- | --- | --- | --- | | 🐛 Another occurance | 508 | falexwolf | 2023-02-21 | | of local filepath | | --- | --- | --- | --- | --- | | 👷 Better CI and | 505 | falexwolf | 2023-02-21 | | better arg | | validation | | --- | --- | --- | --- | --- | | 🐛 Fix tracking | 506 | falexwolf | 2023-02-21 | | local existing data | | --- | --- | --- | --- | --- | | 🚑 Fix parents for | 504 | sunnyosun | 2023-02-21 | | existing data | | ingestion | | --- | --- | --- | --- | --- | | 🎨 Disable multiple | 502 | sunnyosun | 2023-02-20 | 0.28rc1 | | select results for | | .add and .delete by | | fields | | --- | --- | --- | --- | --- | | ⚡️ Replace | 501 | Koncopd | 2023-02-19 | | CloudPath with UPath | | --- | --- | --- | --- | --- | | 👷 Move fixtures | 500 | falexwolf | 2023-02-17 | | from nox to conftest | | --- | --- | --- | --- | --- | | 📝 Simplify output | 499 | sunnyosun | 2023-02-17 | | for dfolder faq | | --- | --- | --- | --- | --- | | 📝 Guide to ingest a | 496 | sunnyosun | 2023-02-17 | | folder | | --- | --- | --- | --- | --- | | 🚑 Fix determination | 497 | falexwolf | 2023-02-17 | 0.27.2 | | of sqlite vs | | postgres | | --- | --- | --- | --- | --- | | 🎨 Improve "lndb" | 495 | falexwolf | 2023-02-16 | 0.27.1 | | (lamindb manager) | | architecture | | --- | --- | --- | --- | --- | | 🚸 Add relationship | 494 | bpenteado | 2023-02-16 | | between "DFolder" | | and "DObject" | | --- | --- | --- | --- | --- | | ✨ Confirm dialog | 493 | sunnyosun | 2023-02-16 | | for deleting data | | from storage | | --- | --- | --- | --- | --- | | ✨ Ingest existing | 491 | sunnyosun | 2023-02-16 | | data from configured | | local storage | | --- | --- | --- | --- | --- | | 🚸 Proper client | 492 | falexwolf | 2023-02-16 | | server check for | | "lndb" | | --- | --- | --- | --- | --- | | ⬆️ Upgrade | 490 | bpenteado | 2023-02-16 | | "nbproject" to 0.8.2 | | --- | --- | --- | --- | --- | | ⬆️ Upgrade and | 487 | bpenteado | 2023-02-14 | 0.27.0 | | rename "lndb_setup" | | to "lndb" (v0.32.4) | | Breaking | | --- | --- | --- | --- | --- | | 🚑 Fix tracking of | 489 | bpenteado | 2023-02-13 | | added records during | | "ln.save()" | | --- | --- | --- | --- | --- | | ✨ Added | 488 | sunnyosun | 2023-02-13 | | "is_run_input" param | | to "DObject.load()" | | --- | --- | --- | --- | --- | | 🎨 Added "ln.settin | 486 | sunnyosun | 2023-02-13 | | gs.track_run_inputs | | _upon_load" | | --- | --- | --- | --- | --- | | 🎨 Added zarr tests | 485 | sunnyosun | 2023-02-13 | | back and cleaned up | | faq | | --- | --- | --- | --- | --- | | 🔥 Drop populating | 484 | sunnyosun | 2023-02-13 | | runin and tracking | | usage upon load | | --- | --- | --- | --- | --- | | 🚸 Better | 483 | falexwolf | 2023-02-09 | | "ln.nb.header()" | | auto-retrieval error | | message | | --- | --- | --- | --- | --- | | 🚸 Make DObject | 476 | bpenteado | 2023-02-08 | | upload ACID | | --- | --- | --- | --- | --- | | 📝 Add notebook on | 472 | bpenteado | 2023-02-06 | | Registry lazy | | loading behavior to | | FAQ | | --- | --- | --- | --- | --- | | 🎨 Robust generation | 481 | sunnyosun | 2023-02-06 | 0.26.1 | | of | | "DObject._filekey" | | --- | --- | --- | --- | --- | | 🎨 Added erroring | 480 | sunnyosun | 2023-02-06 | | behavior when file | | doesn't exist for | | "ln.delete" | | --- | --- | --- | --- | --- | | 📝 Removed extra | 479 | sunnyosun | 2023-02-06 | | fields in | | dev.datasets.pbmc68k | | --- | --- | --- | --- | --- | | ➖ Removed lnbfx and | 478 | sunnyosun | 2023-02-06 | | fix CI | | --- | --- | --- | --- | --- | | 📝 Query book | 470 | sunnyosun | 2023-02-06 | | --- | --- | --- | --- | --- | | 🩹 Print dobject | 475 | Koncopd | 2023-02-02 | | name for zarr upload | | --- | --- | --- | --- | --- | | 🐛 Fix load | 474 | Koncopd | 2023-02-02 | | --- | --- | --- | --- | --- | | 🔥 Disable Registry | 473 | bpenteado | 2023-02-02 | | relationship preview | | --- | --- | --- | --- | --- | | ✨ Allow ingesting | 471 | sunnyosun | 2023-02-02 | | existing data in the | | cloud | | --- | --- | --- | --- | --- | | 🐛 Correct filepath | 469 | Koncopd | 2023-02-01 | | in header | | --- | --- | --- | --- | --- | | 🚸 Add post-setup | 466 | falexwolf | 2023-02-01 | 0.26.0 | | settings manager, | | error on duplicate | | insert Breaking | | --- | --- | --- | --- | --- | | 🐛 Fix fallback for | 463 | falexwolf | 2023-01-30 | 0.25.7 | | notebook name | | --- | --- | --- | --- | --- | | 🔥 Remove | 462 | sunnyosun | 2023-01-30 | | "lns.DObject" | | Breaking | | --- | --- | --- | --- | --- | | ⬆️ Upgrade lndb- | 461 | sunnyosun | 2023-01-30 | 0.25.6 | | setup 0.30.11 | | --- | --- | --- | --- | --- | | ⬆️ Cleaned up | 460 | sunnyosun | 2023-01-27 | | dependencies so that | | it's not as | | redundant to lndb- | | setup | | --- | --- | --- | --- | --- | | ➕ Bring back lnfbx | 459 | falexwolf | 2023-01-26 | 0.25.5 | | --- | --- | --- | --- | --- | | 📝 Prettier section | 456 | sunnyosun | 2023-01-26 | | headings in the docs | | --- | --- | --- | --- | --- | | 📌 Pin "s3fs" and | 458 | falexwolf | 2023-01-26 | 0.25.4 | | "gcsfs" to the | | latest versions | | --- | --- | --- | --- | --- | | 🚸 Auto-populate | 457 | bpenteado | 2023-01-26 | 0.25.3 | | relationship- | | associated foreign | | key fields | | --- | --- | --- | --- | --- | | 🐛 Fix strict type | 455 | bpenteado | 2023-01-24 | 0.25.2 | | checking for | | relationships | | --- | --- | --- | --- | --- | | 🩺 Increase | 454 | falexwolf | 2023-01-24 | | migrations testing | | robustness postgres | | --- | --- | --- | --- | --- | | 📝 Remove linked- | 453 | falexwolf | 2023-01-24 | | select notebook | | --- | --- | --- | --- | --- | | ⬆️ Upgrade lnschema- | 452 | bpenteado | 2023-01-23 | 0.25.1 | | core to 0.25.1 | | --- | --- | --- | --- | --- | | ✨ Add explicit | 447 | Koncopd | 2023-01-23 | | remote sqlite | | instance locking to | | write operations | | --- | --- | --- | --- | --- | | ♻️ Refactored FAQ | 448 | sunnyosun | 2023-01-23 | | --- | --- | --- | --- | --- | | 📝 Create data | 451 | bpenteado | 2023-01-23 | | validation FAQ | | --- | --- | --- | --- | --- | | ➖ Remove s3fs | 450 | fredericenard | 2023-01-23 | | dependency | | --- | --- | --- | --- | --- | | ⬆️ Upgrade lndb- | 449 | fredericenard | 2023-01-23 | | setup to 0.30.8 | | --- | --- | --- | --- | --- | | 🩹 Better treat edge | 446 | falexwolf | 2023-01-20 | 0.25.0 | | cases upon signup, | | login, failed | | instance loading | | --- | --- | --- | --- | --- | | 🚸 Introduce data | 445 | bpenteado | 2023-01-20 | | validation on the | | Registry level | | --- | --- | --- | --- | --- | | ♻️ Reorganize | 444 | sunnyosun | 2023-01-20 | | quickstart and get- | | started | | --- | --- | --- | --- | --- | | 📝 Refactor init | 443 | sunnyosun | 2023-01-18 | 0.24.6 | | guide and show | | bionty versions in | | guide | | --- | --- | --- | --- | --- | | ⬆️ Upgrade wetlab | 442 | sunnyosun | 2023-01-17 | 0.24.5 | | schema to 0.13.3 | | --- | --- | --- | --- | --- | | 🐛 Fix taxon_id type | 441 | sunnyosun | 2023-01-17 | 0.24.4 | | and upgrade bionty | | --- | --- | --- | --- | --- | | ⬆️ Upgrade to | 440 | sunnyosun | 2023-01-17 | | lnschema-bionty | | 0.6.7 | | --- | --- | --- | --- | --- | | ⬆️ Upgrade to lndb- | 439 | sunnyosun | 2023-01-16 | 0.24.3 | | setup 0.30.6 | | --- | --- | --- | --- | --- | | ⬆️ Upgrade to | 438 | sunnyosun | 2023-01-16 | 0.24.2 | | lndb_setup==0.30.5 | | --- | --- | --- | --- | --- | | ⬆️ Upgrade lndb- | 437 | sunnyosun | 2023-01-16 | 0.24.1 | | setup to 0.30.4 | | --- | --- | --- | --- | --- | | ⬆️ Upgrade to lndb- | 436 | falexwolf | 2023-01-16 | 0.24.0 | | setup 0.30.2 | | --- | --- | --- | --- | --- | | 🚸 Better hash | 434 | falexwolf | 2023-01-12 | | exception | | --- | --- | --- | --- | --- | | 🚸 Safer session | 432 | falexwolf | 2023-01-12 | 0.23.0 | | behavior 2/2 | | Breaking | | --- | --- | --- | --- | --- | | 👷 Extend CI to | 431 | sunnyosun | 2023-01-12 | 0.22.5 | | py3.8-3.10 | | --- | --- | --- | --- | --- | | 🚸 Safer session | 430 | falexwolf | 2023-01-11 | | behavior 1/2 | | --- | --- | --- | --- | --- | | ⬆️ Upgrade lndb- | 428 | fredericenard | 2023-01-10 | | setup | | --- | --- | --- | --- | --- | | 📝 Re-arrange | 427 | falexwolf | 2023-01-09 | | notebooks | | --- | --- | --- | --- | --- | | 🚸 Make | 426 | falexwolf | 2023-01-09 | 0.22.4 | | "ln.nb.header()" | | more robust | | --- | --- | --- | --- | --- | | 📝 Improving wording | 424 | falexwolf | 2023-01-08 | | of definitions | | --- | --- | --- | --- | --- | | 📝 Fixes for lndocs | 423 | falexwolf | 2023-01-08 | | upgrade | | --- | --- | --- | --- | --- | | ♻️ Refactor guide | 422 | sunnyosun | 2023-01-08 | | --- | --- | --- | --- | --- | | ⬆️ Upgrade | 421 | falexwolf | 2023-01-05 | 0.22.3 | | "lnschema-bionty" to | | 0.6.5 | | --- | --- | --- | --- | --- | | ⬆️ Upgrade to "lndb- | 420 | falexwolf | 2023-01-05 | | setup" 0.28.1 | | --- | --- | --- | --- | --- | | 📝 Fix typos | 418 | Zethson | 2023-01-02 | | --- | --- | --- | --- | --- | # lnschema-core | --- | --- | --- | --- | --- | | Name | PR | Developer | Date | Version | | ====================== | ====================== | ====================== | ====================== | ====================== | | 🚚 Rename "Dataset" | 330 | falexwolf | 2023-12-23 | 0.60.0 | | to "Collection" | | --- | --- | --- | --- | --- | | 🚚 Add field | 329 | falexwolf | 2023-12-23 | | description to | | storage | | --- | --- | --- | --- | --- | | 🔥 Remove | 328 | falexwolf | 2023-12-23 | | initial_version_id | | --- | --- | --- | --- | --- | | 🚚 Add environment | 324 | falexwolf | 2023-12-21 | 0.59.0 | | foreign key | | --- | --- | --- | --- | --- | | ♻️ Add n_objects and | 323 | falexwolf | 2023-12-12 | 0.58.1 | | n_observations to | | Artifact and remove | | unique constraint | | for key, storage | | --- | --- | --- | --- | --- | | 🔥 Remove field | 322 | falexwolf | 2023-12-11 | 0.58.0 | | storage from dataset | | --- | --- | --- | --- | --- | | 🚚 Rename File to | 321 | falexwolf | 2023-12-11 | | Artifact | | --- | --- | --- | --- | --- | | ✨ Do virtual inner | 320 | Koncopd | 2023-12-05 | | join of variables in | | Dataset.mapped | | --- | --- | --- | --- | --- | | 💚 Fix docstring | 319 | sunnyosun | 2023-12-02 | | --- | --- | --- | --- | --- | | 📝 Enabled ID | 318 | sunnyosun | 2023-12-02 | | conversion via | | return_field | | --- | --- | --- | --- | --- | | ✨ Added view_tree | 317 | sunnyosun | 2023-11-24 | | for keys | | --- | --- | --- | --- | --- | | 🚚 Recode visibility | 316 | sunnyosun | 2023-11-23 | | --- | --- | --- | --- | --- | | 🚚 Rename indexed to | 315 | falexwolf | 2023-11-20 | 0.57.1 | | mapped | | --- | --- | --- | --- | --- | | 🚸 Add ".df()" to | 314 | falexwolf | 2023-11-20 | 0.57.0 | | "Registry" | | --- | --- | --- | --- | --- | | ✨ Initial | 313 | Koncopd | 2023-11-20 | | implementation of | | IndexedDataset | | --- | --- | --- | --- | --- | | 🔥 Remove "Modality" | 312 | sunnyosun | 2023-11-13 | | --- | --- | --- | --- | --- | | ✏️ Fix | 311 | sunnyosun | 2023-11-13 | | VisibilityChoice | | --- | --- | --- | --- | --- | | 🚚 Add | 310 | falexwolf | 2023-10-27 | 0.54.0 | | key_is_virtual field | | to File | | --- | --- | --- | --- | --- | | ♻️ Create using | 309 | falexwolf | 2023-10-27 | | method | | --- | --- | --- | --- | --- | | ✨ Add "visibility" | 307 | sunnyosun | 2023-10-26 | 0.53.0 | | to "File" and | | "Dataset" | | --- | --- | --- | --- | --- | | ✨ Enable passing | 308 | sunnyosun | 2023-10-25 | | filter expressions | | to lookup and search | | --- | --- | --- | --- | --- | | 🚚 Remove field | 306 | falexwolf | 2023-10-19 | 0.52.0 | | email from user | | --- | --- | --- | --- | --- | | 🚚 Rename "Species" | 305 | sunnyosun | 2023-10-19 | | to "Organism" | | --- | --- | --- | --- | --- | | 🚚 Migrate to | 304 | falexwolf | 2023-10-13 | 0.51.0 | | integer primary keys | | --- | --- | --- | --- | --- | | 🎨 Add path | 303 | falexwolf | 2023-10-04 | 0.50.0 | | properties & storage | | field on Dataset | | --- | --- | --- | --- | --- | | 🚚 Rename notebook | 302 | sunnyosun | 2023-10-03 | | series | | --- | --- | --- | --- | --- | | ✨ Track storage of | 301 | falexwolf | 2023-10-01 | 0.49.0 | | notebooks | | --- | --- | --- | --- | --- | | 🎨 Add a "members" | 300 | falexwolf | 2023-09-27 | 0.48.4 | | property to | | "FeatureSet" | | --- | --- | --- | --- | --- | | 📝 Document dataset | 299 | falexwolf | 2023-09-23 | 0.48.3 | | methods | | --- | --- | --- | --- | --- | | ✨ Add "reference" | 298 | sunnyosun | 2023-09-15 | | and "reference_type" | | to "Dataset", | | "ULabel" | | --- | --- | --- | --- | --- | | 🔥 Remove | 297 | falexwolf | 2023-09-09 | | "add_labels" & | | "get_labels" & | | improve | | documentation of | | "ULabel" | | --- | --- | --- | --- | --- | | 🎨 Added | 296 | sunnyosun | 2023-09-08 | | return_field to | | lookup | | --- | --- | --- | --- | --- | | 🚚 Rename "Label" to | 295 | sunnyosun | 2023-09-07 | | "ULabel" | | --- | --- | --- | --- | --- | | 🎨 Make field | 293 | sunnyosun | 2023-09-04 | | optional for | | from_values | | --- | --- | --- | --- | --- | | ⬆️ Switch to WRatio | 292 | sunnyosun | 2023-09-04 | 0.47.4 | | and default to | | limit=20 for search | | --- | --- | --- | --- | --- | | 🚚 Version dataset | 291 | falexwolf | 2023-09-02 | 0.47.0 | | --- | --- | --- | --- | --- | | 📝 Fix run signature | 289 | falexwolf | 2023-09-02 | | --- | --- | --- | --- | --- | | 📝 Prettify field | 290 | falexwolf | 2023-09-02 | | sorting, improve | | File & Dataset | | docstring | | --- | --- | --- | --- | --- | | 📝 Fix Run docs | 288 | falexwolf | 2023-09-01 | 0.46.5 | | --- | --- | --- | --- | --- | | 🚚 Add modality to | 285 | falexwolf | 2023-08-31 | 0.46.4 | | from_df and | | from_anndata | | --- | --- | --- | --- | --- | | ♻️ Type features | 287 | falexwolf | 2023-08-31 | | --- | --- | --- | --- | --- | | 🎨 Added | 284 | sunnyosun | 2023-08-29 | 0.46.2 | | include_foregin_keys | | for *repr* | | --- | --- | --- | --- | --- | | 📝 Fix docs | 283 | sunnyosun | 2023-08-24 | 0.46.1 | | --- | --- | --- | --- | --- | | 🚚 Make suffix non- | 272 | falexwolf | 2023-08-23 | 0.46.0 | | nullable | | --- | --- | --- | --- | --- | | 🎨 Make storage root | 282 | falexwolf | 2023-08-23 | | unique | | --- | --- | --- | --- | --- | | ♻️ Version transform | 279 | falexwolf | 2023-08-23 | | --- | --- | --- | --- | --- | | 🚚 from_anndata and | 280 | falexwolf | 2023-08-23 | | from_df for Dataset | | --- | --- | --- | --- | --- | | 🚚 Add "modality" to | 278 | falexwolf | 2023-08-23 | | "Feature" | | --- | --- | --- | --- | --- | | ♻️ Use CanValidate & | 277 | falexwolf | 2023-08-23 | | HasParents | | --- | --- | --- | --- | --- | | 🚚 Add "transform", | 276 | falexwolf | 2023-08-22 | | "run" & "input_of" | | fields to dataset | | --- | --- | --- | --- | --- | | 🎨 Enable default | 275 | sunnyosun | 2023-08-22 | | field for .inspect | | and .validate | | --- | --- | --- | --- | --- | | 🎨 Merge | 274 | sunnyosun | 2023-08-22 | | ValidationAware and | | SynonymsAware into | | ValidationMixin | | --- | --- | --- | --- | --- | | 📝 Updated signature | 273 | sunnyosun | 2023-08-18 | | of features.from_df | | --- | --- | --- | --- | --- | | ✏️ Fix typo of | 271 | sunnyosun | 2023-08-17 | | map_synonyms | | backward compat | | --- | --- | --- | --- | --- | | 🚚 Rename | 270 | sunnyosun | 2023-08-16 | | map_synonyms to | | standardize | | --- | --- | --- | --- | --- | | 📝 Refactored docs | 269 | falexwolf | 2023-08-12 | 0.45.3 | | --- | --- | --- | --- | --- | | 💚 Fix import | 268 | sunnyosun | 2023-08-11 | 0.45.2 | | --- | --- | --- | --- | --- | | 🚚 Move describe to | 267 | sunnyosun | 2023-08-11 | 0.45.1 | | Data | | --- | --- | --- | --- | --- | | ♻️ Add ParentsAware | 266 | sunnyosun | 2023-08-11 | | --- | --- | --- | --- | --- | | 🚚 Replace "stem_id" | 265 | falexwolf | 2023-08-10 | 0.45.0 | | on "File" with | | "initial_version" | | --- | --- | --- | --- | --- | | 📝 Updated | 264 | sunnyosun | 2023-08-08 | | "validate()" | | signature | | --- | --- | --- | --- | --- | | 🚚 Add "stem_id" and | 263 | falexwolf | 2023-08-08 | | "version" to "File" | | --- | --- | --- | --- | --- | | 📝 Remove all | 262 | falexwolf | 2023-08-08 | | duplicated type | | annotation from docs | | --- | --- | --- | --- | --- | | 📝 Document all | 261 | falexwolf | 2023-08-08 | | types | | --- | --- | --- | --- | --- | | ⬆️ Add | 260 | sunnyosun | 2023-08-07 | 0.44.3 | | "InspectResult" | | --- | --- | --- | --- | --- | | 🚸 Turn method | 259 | falexwolf | 2023-08-06 | 0.44.2 | | "path()" into | | property "path" | | --- | --- | --- | --- | --- | | ✨ Added | 257 | sunnyosun | 2023-08-06 | 0.44.0 | | "validate()" | | --- | --- | --- | --- | --- | | 🚚 Rename | 256 | falexwolf | 2023-08-06 | | "ref_field" to | | "registry" | | --- | --- | --- | --- | --- | | ♻️ Add "Data" base | 255 | falexwolf | 2023-08-05 | | class for "File" & | | "Dataset" | | --- | --- | --- | --- | --- | | 🚚 Rename "ORM" to | 254 | sunnyosun | 2023-08-05 | | "Registry" | | --- | --- | --- | --- | --- | | 🚚 Type Link ORMs | 253 | falexwolf | 2023-08-04 | 0.43.3 | | with "LinkORM" | | --- | --- | --- | --- | --- | | 🚚 Rename select to | 252 | falexwolf | 2023-07-31 | 0.43.0 | | filter | | --- | --- | --- | --- | --- | | 🚚 Rename | 251 | falexwolf | 2023-07-31 | | "Feature.label_orms" | | to | | "Feature.registries" | | --- | --- | --- | --- | --- | | ♻️ Aggregate | 250 | falexwolf | 2023-07-31 | | ref_field, ref_orm, | | ref_schema into | | ref_field | | --- | --- | --- | --- | --- | | 🚚 Move feature | 249 | falexwolf | 2023-07-31 | | foreign key from | | Label to link model | | --- | --- | --- | --- | --- | | 🚚 Allow multiple | 247 | falexwolf | 2023-07-29 | | label ORMs in | | feature | | --- | --- | --- | --- | --- | | 🚑️ Hash can be null | 246 | falexwolf | 2023-07-26 | | --- | --- | --- | --- | --- | | 📝 Add signatures to | 245 | falexwolf | 2023-07-26 | 0.42.1 | | remaining ORMs | | --- | --- | --- | --- | --- | | 🚚 Add field "hash" | 244 | falexwolf | 2023-07-26 | | to "FeatureSet" | | --- | --- | --- | --- | --- | | 🚸 Type-annotate | 243 | falexwolf | 2023-07-26 | | "FeatureManager" | | --- | --- | --- | --- | --- | | 🚚 Rename | 242 | falexwolf | 2023-07-26 | | "featureset_id" to | | "feature_set_id" in | | "FeatureSetFile" | | link table | | --- | --- | --- | --- | --- | | 🚚 Add "Modality" | 240 | falexwolf | 2023-07-25 | | --- | --- | --- | --- | --- | | 🚚 Add | 239 | falexwolf | 2023-07-25 | | "File.accessor" | | --- | --- | --- | --- | --- | | 🚚 Remove reference | 238 | falexwolf | 2023-07-24 | 0.41.0 | | Registry from Label | | and add it to | | Feature, add slot to | | FeatureSet link | | models | | --- | --- | --- | --- | --- | | 📝 Updated | 237 | sunnyosun | 2023-07-23 | 0.40.1 | | view_parents | | signature | | --- | --- | --- | --- | --- | | 🚚 More | 236 | falexwolf | 2023-07-23 | | comprehensive | | "Label" and | | "FeatureSet" fields | | --- | --- | --- | --- | --- | | 🚚 Integrate | 235 | falexwolf | 2023-07-22 | | "Category" and "Tag" | | into "Label" | | --- | --- | --- | --- | --- | | 🚚 Add "description" | 233 | falexwolf | 2023-07-21 | | and "parents" to | | "Tag", delete | | "Project", replace | | "Run.name" with "Ru | | n.reference_type", | | "Run.inputs" as | | "File.input_of" | | --- | --- | --- | --- | --- | | 🚚 Add categories to | 232 | falexwolf | 2023-07-21 | | file and dataset | | --- | --- | --- | --- | --- | | 💄 Improve docstring | 231 | sunnyosun | 2023-07-20 | 0.39.0 | | --- | --- | --- | --- | --- | | 🚚 Rename | 230 | falexwolf | 2023-07-19 | | "FeatureValue" to | | "Category" | | --- | --- | --- | --- | --- | | 📝 Add examples to | 229 | sunnyosun | 2023-07-19 | | docstring | | --- | --- | --- | --- | --- | | 🚚 Move | 228 | falexwolf | 2023-07-19 | | "feature_sets" to | | "File" instead of | | having "files" on | | "FeatureSet" | | --- | --- | --- | --- | --- | | ✨ Add | 227 | falexwolf | 2023-07-19 | | "Feature.unit" | | --- | --- | --- | --- | --- | | ♻️ Refactor | 225 | falexwolf | 2023-07-18 | | "Feature" and add | | "FeatureValue" | | --- | --- | --- | --- | --- | | 🔥 Remove top_hit | 226 | sunnyosun | 2023-07-18 | | param from search | | --- | --- | --- | --- | --- | | 🍱 Added more | 224 | sunnyosun | 2023-07-17 | | methods for | | signature | | --- | --- | --- | --- | --- | | 🚚 Add | 223 | falexwolf | 2023-07-07 | 0.38.3 | | "Transform.parents" | | and "File.hash_type" | | --- | --- | --- | --- | --- | | ✨ Add "from_df" and | 222 | falexwolf | 2023-07-05 | 0.38.2 | | "from_anndata" to | | "File" | | --- | --- | --- | --- | --- | | 💄 Do not show None | 221 | falexwolf | 2023-07-03 | 0.38.1 | | fields | | --- | --- | --- | --- | --- | | 🚚 Move "QuerySet" | 220 | falexwolf | 2023-07-03 | | to lamindb | | --- | --- | --- | --- | --- | | ✨ Allow for | 219 | falexwolf | 2023-07-02 | | annotate in ".df()" | | --- | --- | --- | --- | --- | | 🚚 Rename | 218 | falexwolf | 2023-07-02 | 0.38.0 | | "File.name" to | | "File.description" | | --- | --- | --- | --- | --- | | 🚚 Update "Feature" | 217 | falexwolf | 2023-07-01 | | and "FeatureSet" | | --- | --- | --- | --- | --- | | 💄 Prettify | 216 | falexwolf | 2023-06-30 | | dataframe display | | --- | --- | --- | --- | --- | | 📝 Fix docs | 215 | falexwolf | 2023-06-30 | 0.37.0 | | --- | --- | --- | --- | --- | | 🚚 Move "File" | 214 | falexwolf | 2023-06-29 | | docstrings and | | signatures | | --- | --- | --- | --- | --- | | 🚚 Rename "BaseORM" | 213 | falexwolf | 2023-06-29 | | to "Registry", move | | "Registry" | | signatures here | | --- | --- | --- | --- | --- | | ✨ Add "Dataset" & | 212 | falexwolf | 2023-06-29 | 0.37a1 | | "Feature" ORMs | | --- | --- | --- | --- | --- | | 💄 Denoise display | 211 | falexwolf | 2023-06-26 | | of timestamps | | --- | --- | --- | --- | --- | | 🎨 Auto-manage | 210 | falexwolf | 2023-06-26 | 0.36.1 | | "RunInput" | | relationship | | --- | --- | --- | --- | --- | | 🚚 Repurpose | 209 | falexwolf | 2023-06-22 | 0.36.0 | | "Folder" to "Tag" | | --- | --- | --- | --- | --- | | 🚚 Move | 208 | falexwolf | 2023-06-19 | 0.35.10 | | "BaseORM.__init__" | | to lamindb | | --- | --- | --- | --- | --- | | 🚚 Expand field | 207 | falexwolf | 2023-06-19 | | length "short_name" | | in transform | | --- | --- | --- | --- | --- | | 🔥 Remove "Lookup" | 206 | sunnyosun | 2023-06-15 | 0.35.9 | | --- | --- | --- | --- | --- | | 🚚 Move methods to | 205 | falexwolf | 2023-06-15 | 0.35.8 | | lamindb | | --- | --- | --- | --- | --- | | 🚚 Make "User.name" | 204 | falexwolf | 2023-06-15 | | nullable | | --- | --- | --- | --- | --- | | 🔥 Remove | 203 | falexwolf | 2023-06-14 | | unnecessary file | | --- | --- | --- | --- | --- | | ✅ Add migrations | 202 | falexwolf | 2023-06-14 | | check | | --- | --- | --- | --- | --- | | ♻️ Alter SA | 200 | falexwolf | 2023-06-12 | 0.35.7 | | migration strategy | | --- | --- | --- | --- | --- | | 🍱 Add migration | 199 | falexwolf | 2023-06-12 | 0.35.5 | | process for legacy | | SA instances | | --- | --- | --- | --- | --- | | ♻️ Less customized | 198 | falexwolf | 2023-06-12 | | IDs | | --- | --- | --- | --- | --- | | ♻️ Move logic to | 197 | falexwolf | 2023-06-12 | | lamindb | | --- | --- | --- | --- | --- | | ✨ Delete storage in | 196 | Koncopd | 2023-06-12 | | File.delete | | --- | --- | --- | --- | --- | | 🚚 Rename Featureset | 194 | sunnyosun | 2023-06-10 | 0.35.4 | | to FeatureSet | | --- | --- | --- | --- | --- | | ♻️ Move save logic | 193 | falexwolf | 2023-06-10 | 0.35.3 | | here | | --- | --- | --- | --- | --- | | 🔥 Remove | 192 | falexwolf | 2023-06-09 | 0.35.2 | | unnecessary files | | --- | --- | --- | --- | --- | | 👷 Simplify CI & | 191 | falexwolf | 2023-06-09 | | remove docs | | --- | --- | --- | --- | --- | | 🚸 Check for | 190 | falexwolf | 2023-06-09 | 0.35.1 | | required fields | | --- | --- | --- | --- | --- | | 🚸 Add select method | 189 | falexwolf | 2023-06-08 | 0.35.0 | | to "BaseORM" | | --- | --- | --- | --- | --- | | 🎨 Auto fetch | 188 | sunnyosun | 2023-06-08 | | related names for | | Featureset | | --- | --- | --- | --- | --- | | 🏗️ Re-architect | 186 | falexwolf | 2023-06-06 | 0.35a7 | | transform id | | --- | --- | --- | --- | --- | | 🎨 Adapted | 185 | sunnyosun | 2023-06-05 | 0.35a6 | | featureset | | --- | --- | --- | --- | --- | | ♻️ Polish schema | 184 | falexwolf | 2023-06-05 | | --- | --- | --- | --- | --- | | 🚸 Improve QuerySet | 182 | falexwolf | 2023-06-05 | | --- | --- | --- | --- | --- | | 🔥 Delete SQLAlchemy | 181 | falexwolf | 2023-06-04 | | related content | | --- | --- | --- | --- | --- | | ♻️ Absorb | 178 | falexwolf | 2023-06-03 | | "DjangoORM.create()" | | in "DjangoORM.__ini | | t__()" | | --- | --- | --- | --- | --- | | 🏗️ Enable Django | 177 | falexwolf | 2023-06-02 | 0.35a3 | | backend | | --- | --- | --- | --- | --- | | 🚚 Rename "lndb" to | 176 | falexwolf | 2023-06-01 | 0.35a2 | | "lamindb-setup" | | --- | --- | --- | --- | --- | | 🏗️ Add Django | 175 | falexwolf | 2023-05-31 | 0.35a1 | | backend | | --- | --- | --- | --- | --- | | 👷 Refactor CI | 174 | falexwolf | 2023-05-30 | | --- | --- | --- | --- | --- | | 🏗️ Remove SQL-level | 172 | falexwolf | 2023-05-25 | 0.34.0 | | schema modules | | --- | --- | --- | --- | --- | | 🏗️ Introduce Django | 171 | falexwolf | 2023-05-24 | | skeleton | | --- | --- | --- | --- | --- | | ♻️ Refactor types | 170 | falexwolf | 2023-05-23 | | --- | --- | --- | --- | --- | | ♻️ Refactor | 169 | falexwolf | 2023-05-17 | 0.33.8 | | "BaseORM" | | --- | --- | --- | --- | --- | | 🚸 Add | 168 | falexwolf | 2023-05-16 | 0.33.7 | | "lazy="joined"" to | | some cheap joins | | --- | --- | --- | --- | --- | | 🎨 Replace "data" in | 167 | sunnyosun | 2023-05-10 | 0.33.6 | | "Features" with | | iterable | | --- | --- | --- | --- | --- | | 🎨 Replace | 166 | sunnyosun | 2023-05-09 | 0.33.5 | | "reference" with | | "field" in | | "Features" | | --- | --- | --- | --- | --- | | ✅ Use "nbproject- | 165 | Koncopd | 2023-05-04 | | test" directly | | --- | --- | --- | --- | --- | | ✨ Enable | 164 | sunnyosun | 2023-04-24 | 0.33.4 | | ".lookup()" | | --- | --- | --- | --- | --- | | 🎨 Refactor | 163 | falexwolf | 2023-04-24 | 0.33.3 | | "ln.File" | | --- | --- | --- | --- | --- | | ⚡️ Do not change | 162 | Koncopd | 2023-04-23 | 0.33.2 | | key for in-memory | | data replace | | --- | --- | --- | --- | --- | | ✨ Change | 161 | Koncopd | 2023-04-23 | | File.replace | | handling of key | | --- | --- | --- | --- | --- | | 🚚 Move | 160 | falexwolf | 2023-04-22 | | "Folder.subset" to | | lamindb | | --- | --- | --- | --- | --- | | 🐛 Fix population of | 159 | falexwolf | 2023-04-21 | 0.33.1 | | "transform_id" in | | "File" in edge cases | | --- | --- | --- | --- | --- | | 🚚 Better names, | 157 | falexwolf | 2023-04-16 | 0.33.0 | | more relationships | | directly on "File" | | --- | --- | --- | --- | --- | | 🐛 Fix ".replace()" | 156 | falexwolf | 2023-04-13 | 0.32.2 | | for key != None | | --- | --- | --- | --- | --- | | 🎨 Set "Transform" | 154 | falexwolf | 2023-04-12 | 0.32.1 | | id upon insert, | | update "Transform" | | default | | --- | --- | --- | --- | --- | | 🚚 Add app type | 155 | falexwolf | 2023-04-12 | | --- | --- | --- | --- | --- | | 🩹 Fix name check in | 153 | Koncopd | 2023-04-10 | | replace | | --- | --- | --- | --- | --- | | ✨ Overwrite key in | 152 | Koncopd | 2023-04-10 | | replace if needed | | --- | --- | --- | --- | --- | | 🚸 Use full filename | 150 | falexwolf | 2023-04-08 | 0.32.0 | | to populate | | "File.name", | | introduce "File.key" | | and "Folder.key" | | --- | --- | --- | --- | --- | | ✨ Add | 149 | Koncopd | 2023-04-03 | 0.31.0 | | "File.replace()" and | | "File.stage()" | | --- | --- | --- | --- | --- | | ♻️ Refactor Registry | 148 | falexwolf | 2023-03-29 | 0.30.0 | | defintions | | --- | --- | --- | --- | --- | | 🚚 Add "reference" | 147 | falexwolf | 2023-03-25 | 0.30rc5 | | to "Transform" | | --- | --- | --- | --- | --- | | 💚 Add weak backward | commit | falexwolf | 2023-03-24 | 0.30rc4 | | compat | | --- | --- | --- | --- | --- | | 🚚 Rename "DObject" | 146 | falexwolf | 2023-03-24 | 0.30rc3 | | to "File" and | | "DFolder" to | | "Folder" | | --- | --- | --- | --- | --- | | 🎨 Simplify "Run" | 145 | falexwolf | 2023-03-23 | | --- | --- | --- | --- | --- | | 🏗️ Combine | 144 | falexwolf | 2023-03-23 | 0.30rc2 | | "Notebook" and | | "Pipeline" into | | "Transform" | | --- | --- | --- | --- | --- | | 🔥 Remove Usage | 143 | falexwolf | 2023-03-22 | 0.30rc1 | | Registry | | --- | --- | --- | --- | --- | | ⬆️ typeguard<3.0.0 | 141 | sunnyosun | 2023-03-15 | 0.29.7 | | and update lamindb | | --- | --- | --- | --- | --- | | 🚑 Fix **name** of | 137 | falexwolf | 2023-03-14 | 0.29.6 | | reltype | | --- | --- | --- | --- | --- | | 📝 Fix docs | commit | falexwolf | 2023-03-14 | 0.29.5 | | reference | | --- | --- | --- | --- | --- | | 🚸 Be smart about | 136 | falexwolf | 2023-03-14 | 0.29.4 | | "global_context" and | | "load_latest" | | --- | --- | --- | --- | --- | | 🚚 Rename ref to | 135 | sunnyosun | 2023-03-14 | 0.29.3 | | reference, added | | backward compat for | | features_ref | | --- | --- | --- | --- | --- | | ✨ Implement | 134 | sunnyosun | 2023-03-14 | 0.29.3rc1 | | ln.Features | | --- | --- | --- | --- | --- | | 🚚 Move track_run | 133 | falexwolf | 2023-03-13 | 0.29.2 | | logic here | | --- | --- | --- | --- | --- | | 🚚 Rename get_object | 132 | sunnyosun | 2023-03-01 | 0.29.1 | | to get | | --- | --- | --- | --- | --- | | 📝 Fix docs | 130 | falexwolf | 2023-02-24 | 0.29.0 | | references | | --- | --- | --- | --- | --- | | 📝 Use lamin instead | 129 | falexwolf | 2023-02-24 | | of lndb in guides | | --- | --- | --- | --- | --- | | 👷 Minimal docs | 128 | falexwolf | 2023-02-24 | | build | | --- | --- | --- | --- | --- | | 🚸 Change user id | 127 | falexwolf | 2023-02-24 | | back to base62 | | --- | --- | --- | --- | --- | | ✨ Added | 126 | sunnyosun | 2023-02-24 | 0.28.7 | | "get_dobject" to | | DFolder | | --- | --- | --- | --- | --- | | ✨ Added unique | 125 | sunnyosun | 2023-02-24 | | constraint uq_stora | | ge__objectkey_suffix | | --- | --- | --- | --- | --- | | 👷 Use "laminci" | 124 | falexwolf | 2023-02-23 | | --- | --- | --- | --- | --- | | ✨ Create helper | 121 | bpenteado | 2023-02-23 | 0.28.6 | | functions to add | | relationships | | --- | --- | --- | --- | --- | | ✏️ Fixed folderkey | 123 | sunnyosun | 2023-02-23 | 0.28.5 | | typo | | --- | --- | --- | --- | --- | | 🐛 Fixed getting | 122 | sunnyosun | 2023-02-23 | 0.28.4 | | objectkey | | --- | --- | --- | --- | --- | | 🚚 Rename | 120 | sunnyosun | 2023-02-23 | 0.28.3 | | dobjects_features to | | dobject_features | | --- | --- | --- | --- | --- | | 🚚 Rename _filekey | 119 | sunnyosun | 2023-02-23 | 0.28.2 | | and _folderkey to | | _objectkey | | --- | --- | --- | --- | --- | | 👷 Upload run | 116 | falexwolf | 2023-02-22 | | outputs to "lamin- | | site-assets" | | --- | --- | --- | --- | --- | | ✨ Create DFolder | 113 | sunnyosun | 2023-02-22 | 0.28.1 | | from a folder | | --- | --- | --- | --- | --- | | 🚚 Rename | 114 | falexwolf | 2023-02-21 | 0.28.0 | | "DObject.run_id" to | | "DObject.source_id" | | --- | --- | --- | --- | --- | | 🚑 Fix determination | 112 | falexwolf | 2023-02-17 | | of postgres vs | | sqlite | | --- | --- | --- | --- | --- | | ✨ Add relationship | 110 | bpenteado | 2023-02-16 | 0.27.1 | | between "DFolder" | | and "DObject" | | --- | --- | --- | --- | --- | | 🚚 Add column | 109 | falexwolf | 2023-02-14 | 0.27.0 | | "external_id" to | | "Run" | | --- | --- | --- | --- | --- | | 🔧 Ensure all id | 108 | falexwolf | 2023-02-14 | | lengths are | | multiples of 4 | | --- | --- | --- | --- | --- | | 🚚 Move "storage" | 89 | falexwolf | 2023-02-14 | 0.26.1 | | table back to "core" | | module | | --- | --- | --- | --- | --- | | 🔥 Remove migration | 107 | sunnyosun | 2023-02-14 | 0.26.0 | | files | | --- | --- | --- | --- | --- | | ⬆️ Upgrade and | 105 | bpenteado | 2023-02-13 | 0.25.12 | | rename "lndb_setup" | | to "lndb" (v0.32.0) | | --- | --- | --- | --- | --- | | 🚚 Rename | 104 | sunnyosun | 2023-02-13 | 0.25.11 | | "track_runin" to | | "is_run_input" | | --- | --- | --- | --- | --- | | ✨ Added track_runin | 103 | sunnyosun | 2023-02-13 | 0.25.10 | | to DObject.load() | | --- | --- | --- | --- | --- | | 💄 Fix Registry | 102 | bpenteado | 2023-02-07 | | preview message | | --- | --- | --- | --- | --- | | 🚸 Introduce | 101 | bpenteado | 2023-02-07 | | Registry | | relationship | | previews | | --- | --- | --- | --- | --- | | 🚚 Rename "DSet" to | 100 | sunnyosun | 2023-02-07 | 0.25.9 | | "DFolder" | | --- | --- | --- | --- | --- | | 🔥 Disable Registry | 99 | bpenteado | 2023-02-02 | 0.25.8 | | relationship preview | | --- | --- | --- | --- | --- | | 🐛 Fix assigning | 98 | sunnyosun | 2023-02-02 | 0.25.7 | | _cloud_filepath | | --- | --- | --- | --- | --- | | ✨ Added _filekey to | 97 | sunnyosun | 2023-02-02 | 0.25.6 | | DObject for custom | | file keys | | --- | --- | --- | --- | --- | | ✨ Added | 96 | sunnyosun | 2023-02-02 | 0.25.5 | | _cloud_filepath | | private attribute | | --- | --- | --- | --- | --- | | ✨ Add rich string | 95 | bpenteado | 2023-01-31 | 0.25.4 | | representation for | | Registry classes | | --- | --- | --- | --- | --- | | 🚸 Auto populate fk | 94 | bpenteado | 2023-01-26 | 0.25.3 | | constrained fields | | from "Relationship"s | | --- | --- | --- | --- | --- | | 🐛 Fix strict type | 93 | bpenteado | 2023-01-24 | 0.25.2 | | checking for | | relationships | | --- | --- | --- | --- | --- | | 🩹 Fix error message | 92 | bpenteado | 2023-01-23 | 0.25.1 | | in "Relationship" | | type checking | | --- | --- | --- | --- | --- | | ✨ Enable data | 91 | bpenteado | 2023-01-20 | 0.25.0 | | validation with | | pydantic | | --- | --- | --- | --- | --- | | 🩹 Fix "_dbconfig" | 90 | falexwolf | 2023-01-16 | 0.24.1 | | --- | --- | --- | --- | --- | | 👷 Extend CI to | 88 | sunnyosun | 2023-01-12 | | py3.8-3.10 | | --- | --- | --- | --- | --- | | 🚚 Add "title" field | 87 | falexwolf | 2023-01-09 | 0.24.0 | | to "Notebook" | | --- | --- | --- | --- | --- | | 🔥 Remove backward | 86 | falexwolf | 2023-01-05 | | compat | | --- | --- | --- | --- | --- | | 👷 Reformat to 176 | 85 | falexwolf | 2023-01-05 | | char line length | | --- | --- | --- | --- | --- | # lnschema-bionty | --- | --- | --- | --- | --- | | Name | PR | Developer | Date | Version | | ====================== | ====================== | ====================== | ====================== | ====================== | | 🚚 Rename "Dataset" | 205 | falexwolf | 2023-12-23 | 0.37.0 | | to "Collection" | | --- | --- | --- | --- | --- | | 🚚 Rename "File" to | 201 | falexwolf | 2023-12-11 | 0.36.0 | | "Artifact" | | --- | --- | --- | --- | --- | | ⬆️ Enabled ID | 200 | sunnyosun | 2023-12-02 | | conversion via | | return_field | | --- | --- | --- | --- | --- | | 🐛 Fix save parents | 198 | sunnyosun | 2023-11-23 | | with bionty_source | | --- | --- | --- | --- | --- | | ✨ Added functions | 197 | sunnyosun | 2023-11-16 | 0.35.1 | | to sync bionty | | source | | --- | --- | --- | --- | --- | | 🚚 Rename FK | 196 | sunnyosun | 2023-11-13 | 0.35.0 | | organism to | | organisms in | | BiontySource | | --- | --- | --- | --- | --- | | ✨ Add "parents" to | 193 | sunnyosun | 2023-10-23 | 0.34.0 | | "Organism" | | --- | --- | --- | --- | --- | | 🚚 Rename "Species" | 192 | sunnyosun | 2023-10-19 | 0.33.0 | | to "Organism" | | --- | --- | --- | --- | --- | | ✏️ Fix uid encoder | 190 | sunnyosun | 2023-10-18 | 0.32.2 | | --- | --- | --- | --- | --- | | 🚚 Migrate to | 188 | falexwolf | 2023-10-13 | 0.32.0 | | integer primary keys | | --- | --- | --- | --- | --- | | 🔇 Mute repetitive | 187 | sunnyosun | 2023-09-20 | 0.31.2 | | warning for saving | | parents | | --- | --- | --- | --- | --- | | ⬆️ Silence download | 186 | sunnyosun | 2023-09-08 | 0.31.1 | | bar for <5MB files | | --- | --- | --- | --- | --- | | 🎨 Return "None" if | 185 | sunnyosun | 2023-09-07 | 0.31.0 | | no records are | | created for | | from_bionty | | --- | --- | --- | --- | --- | | ✨ Allow non-default | 184 | sunnyosun | 2023-09-07 | | bionty sources in | | LaminDB | | --- | --- | --- | --- | --- | | ♻️ Add DB-facing | 180 | falexwolf | 2023-08-28 | 0.30.1 | | constructor | | --- | --- | --- | --- | --- | | 🎨 Make species not | 179 | sunnyosun | 2023-08-24 | | nullable in Gene, | | Protein, CellType | | --- | --- | --- | --- | --- | | ♻️ Use "CanValidate" | 176 | falexwolf | 2023-08-23 | 0.30.0 | | & "HasParents" | | --- | --- | --- | --- | --- | | 🚚 Rename | 173 | sunnyosun | 2023-08-16 | 0.29.5 | | map_synonyms to | | standardize | | --- | --- | --- | --- | --- | | 🚚 Rename ORM to | 167 | sunnyosun | 2023-08-05 | | Registry | | --- | --- | --- | --- | --- | | 🎇 Added stable_id | 166 | sunnyosun | 2023-07-31 | 0.29.0 | | to Gene | | --- | --- | --- | --- | --- | | 🚚 Rename select to | 164 | falexwolf | 2023-07-31 | | filter | | --- | --- | --- | --- | --- | | 🎨 Switch | 163 | sunnyosun | 2023-07-25 | 0.28.2 | | biontysource id to | | hash id | | --- | --- | --- | --- | --- | | 🚸 New settings | 162 | falexwolf | 2023-07-25 | 0.28.1 | | "auto_save_parents" | | --- | --- | --- | --- | --- | | 🎨 Link all entities | 160 | sunnyosun | 2023-07-24 | 0.28.0 | | to files and | | datasets | | --- | --- | --- | --- | --- | | 🚚 Replace | 161 | falexwolf | 2023-07-24 | | "lamin_logger" with | | "lamin_utils" | | --- | --- | --- | --- | --- | | ✏️ Fix docstrings | 159 | sunnyosun | 2023-07-21 | 0.27.4 | | --- | --- | --- | --- | --- | | 🎨 Make species name | 158 | sunnyosun | 2023-07-21 | | unique | | --- | --- | --- | --- | --- | | 🎨 Gene table unique | 152 | sunnyosun | 2023-07-18 | 0.27.0 | | on ensembl id | | --- | --- | --- | --- | --- | | 🎨 Fix migration | 150 | sunnyosun | 2023-07-18 | | --- | --- | --- | --- | --- | | 🚚 Rename Readout to | 149 | sunnyosun | 2023-07-17 | | ExperimentalFactor | | --- | --- | --- | --- | --- | | 🚸 Trigger instance | 147 | falexwolf | 2023-07-06 | 0.26.2 | | loading for users | | --- | --- | --- | --- | --- | | ⚡️ Speed up parents | 146 | falexwolf | 2023-07-04 | 0.26.1 | | ingestion | | --- | --- | --- | --- | --- | | 🚸 Add settings | 142 | falexwolf | 2023-06-30 | 0.25.4 | | --- | --- | --- | --- | --- | | 🚑️ Allow bulk | 141 | sunnyosun | 2023-06-30 | 0.25.2 | | saving parents | | without causing | | conflicts | | --- | --- | --- | --- | --- | | ✨ Added self- | 139 | sunnyosun | 2023-06-29 | 0.25.0 | | referential | | "parents", renamed | | "abbr" and | | "description" | | --- | --- | --- | --- | --- | | ♻️ Replaced ln.parse | 138 | sunnyosun | 2023-06-27 | 0.24.0 | | with orm.from_values | | --- | --- | --- | --- | --- | | 🚚 Move add_synonym | 137 | sunnyosun | 2023-06-22 | 0.23.5 | | to BaseORM | | --- | --- | --- | --- | --- | | ⬆️ Fix synonyms | 136 | sunnyosun | 2023-06-22 | | duplication check | | --- | --- | --- | --- | --- | | 🚑️ Do not check | 134 | sunnyosun | 2023-06-20 | | existing synonyms | | when db table is | | empty | | --- | --- | --- | --- | --- | | 🎨 Create multiple | 133 | sunnyosun | 2023-06-20 | 0.23.3 | | records with | | .from_bionty | | --- | --- | --- | --- | --- | | 📈 Save to DB if | 132 | sunnyosun | 2023-06-20 | 0.23.2 | | record already | | exists for | | add_synonyms | | --- | --- | --- | --- | --- | | 🚚 Fixed all | 131 | sunnyosun | 2023-06-20 | 0.23.1 | | related_names | | --- | --- | --- | --- | --- | | 🏷️ Change name to a | 130 | sunnyosun | 2023-06-19 | 0.23.0 | | required field for | | ontology tables | | --- | --- | --- | --- | --- | | 🎨 Consolidate | 127 | sunnyosun | 2023-06-16 | 0.22.0 | | schema, remove non- | | crucial fields | | --- | --- | --- | --- | --- | | 🚚 Rename | 125 | sunnyosun | 2023-06-10 | 0.21.3 | | "source_key" to | | "source" in | | BiontySource table | | --- | --- | --- | --- | --- | | 🚚 Rename Featureset | 124 | sunnyosun | 2023-06-10 | 0.21.2 | | to FeatureSet | | --- | --- | --- | --- | --- | | ⏪ Change species | 122 | sunnyosun | 2023-06-09 | 0.21.1 | | uid to 4 char | | --- | --- | --- | --- | --- | | 🎨 Change on_delete | 121 | sunnyosun | 2023-06-09 | 0.21.0 | | to PROTECT | | --- | --- | --- | --- | --- | | 🎨 Remove | 118 | sunnyosun | 2023-06-08 | 0.19a6 | | unnecessary | | null=True, | | blank=True | | --- | --- | --- | --- | --- | | ♻️ Simplified | 116 | sunnyosun | 2023-06-08 | 0.19a4 | | species code | | --- | --- | --- | --- | --- | | 🚚 Rename | 115 | sunnyosun | 2023-06-07 | 0.19a3 | | BiontyVersions to | | BiontySources | | --- | --- | --- | --- | --- | | 🚚 Migrate | 112 | sunnyosun | 2023-06-05 | 0.19a1 | | "lnschema-bionty" to | | Django | | --- | --- | --- | --- | --- | | ✨ Added | 111 | sunnyosun | 2023-06-02 | 0.18.3 | | "Features.pathways" | | --- | --- | --- | --- | --- | | ✨ Add "add_synonym" | 109 | sunnyosun | 2023-06-01 | | method | | --- | --- | --- | --- | --- | | 🚑 Must pass a | 108 | sunnyosun | 2023-05-30 | 0.18.2 | | species when | | creating record from | | lookup | | --- | --- | --- | --- | --- | | ✨ Added | 107 | sunnyosun | 2023-05-30 | 0.18.1 | | "Pathway.genes" | | --- | --- | --- | --- | --- | | 🚑 Fix created_by_id | 106 | sunnyosun | 2023-05-28 | 0.18.0 | | in Readout | | --- | --- | --- | --- | --- | | 🎨 Change .bionty to | 105 | sunnyosun | 2023-05-28 | | a method | | --- | --- | --- | --- | --- | | 🚑 Default species | 104 | sunnyosun | 2023-05-27 | 0.18a6 | | to None and not pass | | to Bionty | | --- | --- | --- | --- | --- | | 🚑 Fix 0.18.0 sqlite | 103 | sunnyosun | 2023-05-27 | | migration script | | --- | --- | --- | --- | --- | | ✨ Add "synonyms", | 102 | sunnyosun | 2023-05-27 | 0.18a5 | | "definition", | | "short_name" columns | | --- | --- | --- | --- | --- | | 🚑 Fix table name | 101 | sunnyosun | 2023-05-27 | | for id_encoder | | --- | --- | --- | --- | --- | | ⬆️ Update lamindb | 100 | sunnyosun | 2023-05-27 | | and bionty versions | | --- | --- | --- | --- | --- | | 🏷️ Restored Optional | 99 | sunnyosun | 2023-05-26 | | type annotation | | --- | --- | --- | --- | --- | | 🏗️ Remove SQL-level | 96 | falexwolf | 2023-05-25 | 0.18a2 | | schema modules | | --- | --- | --- | --- | --- | | 🚑 Fix last | 98 | falexwolf | 2023-05-25 | 0.17.1 | | migration | | --- | --- | --- | --- | --- | | 🍱 Add CreatedBy and | 95 | sunnyosun | 2023-05-25 | 0.17.0 | | CreatedAt to all | | entities | | --- | --- | --- | --- | --- | | 🚚 Rename bt.Entity | 94 | sunnyosun | 2023-05-25 | | to bt.Bionty | | --- | --- | --- | --- | --- | | ⬆️ Upgrade to bionty | 92 | sunnyosun | 2023-05-09 | 0.16.4 | | 0.13 | | --- | --- | --- | --- | --- | | ✨ Added synonyms | 91 | sunnyosun | 2023-05-09 | 0.16.3 | | field to CellMarker | | --- | --- | --- | --- | --- | | 💚 Fix dependencies | 90 | sunnyosun | 2023-04-27 | 0.16.2 | | --- | --- | --- | --- | --- | | 🎨 Move ._entity to | 89 | sunnyosun | 2023-04-27 | 0.16.1 | | private | | --- | --- | --- | --- | --- | | 💥 Enable ".bionty" | 87 | sunnyosun | 2023-04-24 | 0.16.0 | | for accessing bionty | | functionalities | | --- | --- | --- | --- | --- | | ⚡ Fix adding | 84 | sunnyosun | 2023-04-19 | 0.15.2 | | species | | --- | --- | --- | --- | --- | | ✨ Add ._entity to | 83 | sunnyosun | 2023-04-18 | 0.15.1 | | knowledge class for | | features parsing | | --- | --- | --- | --- | --- | | 🎨 New design of the | 80 | sunnyosun | 2023-04-17 | 0.15.0 | | knowledge API | | --- | --- | --- | --- | --- | | ♻️ Refactor | 77 | sunnyosun | 2023-03-28 | 0.14.0 | | knowledge | | --- | --- | --- | --- | --- | | ✨ Added Readout | 75 | sunnyosun | 2023-03-27 | 0.13.0 | | --- | --- | --- | --- | --- | | 📝 Move knowledge | 71 | falexwolf | 2023-03-27 | | guide from lamindb | | here | | --- | --- | --- | --- | --- | | ⬆️ Updated bionty | 74 | sunnyosun | 2023-03-27 | 0.12.2 | | and lamindb deps | | --- | --- | --- | --- | --- | | 👷 Upgrade to latest | 73 | falexwolf | 2023-03-27 | | cookiecutter | | --- | --- | --- | --- | --- | | 🚑 Fix "get_term" | 72 | sunnyosun | 2023-03-25 | 0.12.1 | | --- | --- | --- | --- | --- | | ♻️ Switch to class | 70 | sunnyosun | 2023-03-24 | 0.12.0 | | property | | --- | --- | --- | --- | --- | | ✨ Expose bionty | 69 | sunnyosun | 2023-03-24 | 0.11.0 | | functions with | | knowledge decorator | | --- | --- | --- | --- | --- | | 🐛 Fix Readout | 68 | sunnyosun | 2023-03-23 | 0.10.1 | | population | | --- | --- | --- | --- | --- | | ⬆️ Update CellMarker | 64 | sunnyosun | 2023-03-21 | 0.10.0 | | columns for bionty | | 0.10 | | --- | --- | --- | --- | --- | | ✨ Add CellLine, | 63 | sunnyosun | 2023-03-21 | 0.9.0 | | Pathway, Phenotype | | --- | --- | --- | --- | --- | | 💚 Fix CI | 62 | sunnyosun | 2023-03-21 | | --- | --- | --- | --- | --- | | ⬆️ Upgrade to bionty | 61 | sunnyosun | 2023-03-20 | 0.8.1 | | 0.9.0 | | --- | --- | --- | --- | --- | | 🎨 Allow hashing | 60 | falexwolf | 2023-03-10 | | external IDs | | --- | --- | --- | --- | --- | | ⬆️ Stable release of | 59 | sunnyosun | 2023-03-09 | 0.8.0 | | bionty 0.8.0 | | --- | --- | --- | --- | --- | | ⬆️ Bionty>=0.8rc3 | 58 | sunnyosun | 2023-03-09 | 0.8rc2 | | --- | --- | --- | --- | --- | | ✨ Use ontology_id | 57 | sunnyosun | 2023-03-07 | 0.8.0rc1 | | as the id for | | Tissue, CellType, | | Disease | | --- | --- | --- | --- | --- | | ⬆️ Upgrade bionty | 56 | falexwolf | 2023-03-06 | | --- | --- | --- | --- | --- | | 🔥 Remove migration | 51 | sunnyosun | 2023-02-14 | 0.7.0 | | files | | --- | --- | --- | --- | --- | | ⬆️ Upgrade and | 49 | bpenteado | 2023-02-14 | 0.6.9 | | rename "lndb_setup" | | to "lndb" (v0.32.0) | | --- | --- | --- | --- | --- | | 🐛 Fixed taxon_id | 48 | sunnyosun | 2023-01-17 | 0.6.8 | | type | | --- | --- | --- | --- | --- | | ⬆️ Upgrade | 47 | sunnyosun | 2023-01-17 | 0.6.7 | | dependencies | | --- | --- | --- | --- | --- | | ⏪ Revert the last | 46 | sunnyosun | 2023-01-17 | | PR | | --- | --- | --- | --- | --- | | 🐛 Fixed typo for | 45 | sunnyosun | 2023-01-16 | 0.6.6 | | postgres | | --- | --- | --- | --- | --- | | 🎨 Change | 43 | sunnyosun | 2023-01-13 | | "Species.taxon_id" | | type to int | | --- | --- | --- | --- | --- | | 👷 Extend CI to | 42 | sunnyosun | 2023-01-12 | | py3.8-3.10 | | --- | --- | --- | --- | --- | | 🚚 Rename "Species. | 41 | falexwolf | 2023-01-05 | | common_name" to | | "Species.name" | | --- | --- | --- | --- | --- | | 🐛 Fix migration for | 40 | falexwolf | 2023-01-05 | 0.6.5 | | sqlite | | --- | --- | --- | --- | --- | | ♻️ Treat link tables | 39 | falexwolf | 2023-01-05 | 0.6.4 | | as in all other | | schema modules | | --- | --- | --- | --- | --- | | 🚚 Move knowledge | 38 | falexwolf | 2023-01-05 | 0.6.3 | | version tables into | | module | | --- | --- | --- | --- | --- | # bionty-base | --- | --- | --- | --- | --- | | Name | PR | Developer | Date | Version | | ====================== | ====================== | ====================== | ====================== | ====================== | | 🚚 Move bionty | 532 | falexwolf | 2023-12-04 | | search & lookup | | guide to lamindb | | --- | --- | --- | --- | --- | | ✨ Enabled ID | 530 | sunnyosun | 2023-12-02 | 0.35.2 | | conversion via | | return_field | | --- | --- | --- | --- | --- | | 🍱 Update EFO to | 528 | sunnyosun | 2023-11-21 | 0.35.1 | | version 3.57.0 | | --- | --- | --- | --- | --- | | 🍱 Update a few | 526 | sunnyosun | 2023-11-16 | 0.35.0 | | sources | | --- | --- | --- | --- | --- | | 🚚 Relocate | 525 | sunnyosun | 2023-11-10 | 0.34.3 | | bionty.lock to | | versionsdir | | --- | --- | --- | --- | --- | | 🔧 Using env | 524 | sunnyosun | 2023-11-10 | 0.34.2 | | variables for | | versionsdir | | --- | --- | --- | --- | --- | | 🎨 Enable set | 523 | sunnyosun | 2023-11-09 | 0.34.1 | | versionsdir | | --- | --- | --- | --- | --- | | 📝 Streamline extend | 522 | falexwolf | 2023-10-24 | | guide | | --- | --- | --- | --- | --- | | ✨ Add ncbitaxon, | 521 | sunnyosun | 2023-10-23 | 0.34.0 | | refactored organism | | --- | --- | --- | --- | --- | | 🚸 Add a backward | 520 | sunnyosun | 2023-10-19 | 0.33.1 | | compat parser | | --- | --- | --- | --- | --- | | 🚚 Rename "Species" | 519 | sunnyosun | 2023-10-19 | 0.33.0 | | to "Organism" | | --- | --- | --- | --- | --- | | 🚸 Suggest user to | 518 | sunnyosun | 2023-10-13 | 0.32.0 | | reset sources | | --- | --- | --- | --- | --- | | :memo: Clarify | 517 | falexwolf | 2023-09-27 | | definition in readme | | --- | --- | --- | --- | --- | | :lipstick: Prettify | 516 | falexwolf | 2023-09-27 | | changelog header | | --- | --- | --- | --- | --- | | ✨ Add "BioSample" | 515 | sunnyosun | 2023-09-13 | | entity | | --- | --- | --- | --- | --- | | 🚚 Rename | 514 | sunnyosun | 2023-09-13 | | "convert_legacy_ids" | | to "map_legacy_ids" | | --- | --- | --- | --- | --- | | 🍱 Cached legacy df | 513 | sunnyosun | 2023-09-12 | | for genes | | --- | --- | --- | --- | --- | | ✨ Add | 512 | sunnyosun | 2023-09-11 | | convert_legacy_ids | | for ensembl genes | | --- | --- | --- | --- | --- | | 🔇 Silence download | 511 | sunnyosun | 2023-09-08 | 0.31.2 | | bar for <5MB files | | --- | --- | --- | --- | --- | | ✨ Add "Ethnicity" | 510 | sunnyosun | 2023-09-07 | 0.31.1 | | entity | | --- | --- | --- | --- | --- | | ✨ Add | 508 | sunnyosun | 2023-09-07 | 0.31.0 | | DevelopmentalStage | | ontologies | | --- | --- | --- | --- | --- | | ✨ Allow non-default | 506 | sunnyosun | 2023-09-07 | | bionty sources in | | LaminDB | | --- | --- | --- | --- | --- | | ✨ Add pato to | 505 | sunnyosun | 2023-09-05 | | Phenotype | | --- | --- | --- | --- | --- | | 💄 Transient | 504 | sunnyosun | 2023-09-05 | 0.30.3 | | download bar | | --- | --- | --- | --- | --- | | Add phecodes | 502 | Zethson | 2023-08-22 | | --- | --- | --- | --- | --- | | 🎨 Added "mute" to | 501 | sunnyosun | 2023-08-22 | 0.30.2 | | ".standardize" | | --- | --- | --- | --- | --- | | ✨ Relating Bionty | 500 | Zethson | 2023-08-21 | | to other tools | | --- | --- | --- | --- | --- | | 🚑️ Fix version | 498 | sunnyosun | 2023-08-17 | 0.30.1 | | recognition in | | lamindb | | --- | --- | --- | --- | --- | | 🚚 Rename | 497 | sunnyosun | 2023-08-16 | 0.30.0 | | "map_synonyms" to | | "standardize" | | --- | --- | --- | --- | --- | | 🚑️ Updated inspect | 496 | sunnyosun | 2023-08-15 | | params | | --- | --- | --- | --- | --- | | ✨ Add md5 for | 495 | Zethson | 2023-08-09 | | normal URLs | | --- | --- | --- | --- | --- | | ✨ Use latest | 494 | Zethson | 2023-08-09 | | versions of tests & | | add updating sources | | --- | --- | --- | --- | --- | | 💚 Fixed tests | 493 | sunnyosun | 2023-08-09 | | --- | --- | --- | --- | --- | | ✨ Introduce | 491 | sunnyosun | 2023-08-06 | 0.29.0 | | validate | | --- | --- | --- | --- | --- | | 📝 Fix docs | 490 | falexwolf | 2023-08-04 | | --- | --- | --- | --- | --- | | ✨ Added EnsemblGene | 488 | sunnyosun | 2023-07-31 | 0.28.0 | | class | | --- | --- | --- | --- | --- | | 🍱 Added all ensembl | 487 | sunnyosun | 2023-07-31 | | species DBs | | --- | --- | --- | --- | --- | | 🍱 Update to | 485 | sunnyosun | 2023-07-31 | 0.27.0 | | ensembl-110 | | --- | --- | --- | --- | --- | | 🍱 Include obsolete | 481 | sunnyosun | 2023-07-23 | 0.26.0 | | terms in .df | | --- | --- | --- | --- | --- | | ✨ Added ".diff" | 468 | Zethson | 2023-07-20 | | method | | --- | --- | --- | --- | --- | | 🍱 Added uniprot | 477 | sunnyosun | 2023-07-18 | 0.25.2 | | 2023-03 | | --- | --- | --- | --- | --- | | 🔥 Remove top_hit | 476 | sunnyosun | 2023-07-17 | 0.25.1 | | from search | | --- | --- | --- | --- | --- | | 🚚 Rename "Readout" | 474 | sunnyosun | 2023-07-17 | 0.25.0 | | to | | "ExperimentalFactor" | | --- | --- | --- | --- | --- | | 🚸 Case insensitive | 466 | falexwolf | 2023-07-10 | 0.24.2 | | search | | --- | --- | --- | --- | --- | | 📝 Build docs | 465 | falexwolf | 2023-07-09 | | standalone again | | --- | --- | --- | --- | --- | | ✨ Use _bt suffix | 464 | Zethson | 2023-07-09 | | instead of _bionty | | for Bionty objects | | in docs | | --- | --- | --- | --- | --- | | ⬆️ No longer pinning | 461 | sunnyosun | 2023-06-30 | 0.24.1 | | lamin-logger | | --- | --- | --- | --- | --- | | 🏗️ Replace children | 460 | sunnyosun | 2023-06-28 | 0.24.0 | | with parents, | | migrate assets to | | django instance | | --- | --- | --- | --- | --- | | 🎨 Log=False to turn | 459 | sunnyosun | 2023-06-22 | 0.23.1 | | off logging in | | inspect | | --- | --- | --- | --- | --- | | 🔈 Fixed logging of | 457 | sunnyosun | 2023-06-21 | | inspect, added | | casing check | | --- | --- | --- | --- | --- | | 🍱 Add more | 456 | Zethson | 2023-06-20 | 0.23.0 | | phenotype ontologies | | --- | --- | --- | --- | --- | | ✨ Add | 455 | sunnyosun | 2023-06-19 | 0.22.0 | | case_sensitive to | | inspect and search | | --- | --- | --- | --- | --- | | 🍱 Fetch latest | 452 | Zethson | 2023-06-19 | | ontology versions | | --- | --- | --- | --- | --- | | 🐛 Fix passing empty | 451 | sunnyosun | 2023-06-17 | 0.21.4 | | strings to | | map_synonyms | | --- | --- | --- | --- | --- | | 🧪 More tests for | 450 | sunnyosun | 2023-06-16 | 0.21.3 | | handle sources | | --- | --- | --- | --- | --- | | 🚀 Fix coverage of | 449 | sunnyosun | 2023-06-16 | | unit tests | | --- | --- | --- | --- | --- | | 🎨 Default to name | 448 | sunnyosun | 2023-06-16 | | field for | | map_synonyms | | --- | --- | --- | --- | --- | | 🚚 Update tuple name | 447 | sunnyosun | 2023-06-15 | 0.21.2 | | of search result | | --- | --- | --- | --- | --- | | 🚚 Change species to | 446 | sunnyosun | 2023-06-15 | 0.21.1 | | vertebrte for | | ensembl | | --- | --- | --- | --- | --- | | 🔥 Remove | 445 | sunnyosun | 2023-06-15 | 0.21.0 | | "ontology_info" and | | "NormalizeColumns" | | --- | --- | --- | --- | --- | | 🚚 Rename | 444 | sunnyosun | 2023-06-15 | | "fuzzy_match" to | | "search" Breaking | | --- | --- | --- | --- | --- | | ♻️ Harmonize code | 443 | sunnyosun | 2023-06-15 | | for Gene, Protein, | | CellMarker | | --- | --- | --- | --- | --- | | 🚚 Move lookup to | 442 | falexwolf | 2023-06-14 | | logger | | --- | --- | --- | --- | --- | | 🧪 Properly test | 441 | sunnyosun | 2023-06-14 | | ontology_to_df | | --- | --- | --- | --- | --- | | 🍱 Drop id, version | 440 | sunnyosun | 2023-06-14 | | columns | | --- | --- | --- | --- | --- | | ⚰️ Remove dead code | 439 | sunnyosun | 2023-06-14 | | --- | --- | --- | --- | --- | | 🚚 Rename | 438 | sunnyosun | 2023-06-14 | | ".todict()" to | | ".dict()" | | --- | --- | --- | --- | --- | | ✨ Lookup refactor | 436 | sunnyosun | 2023-06-14 | | to return multiple | | records Breaking | | --- | --- | --- | --- | --- | | ✨ New | 434 | sunnyosun | 2023-06-13 | | implementation of | | lookup | | --- | --- | --- | --- | --- | | 🚚 Renamed | 435 | Zethson | 2023-06-13 | | sources_local | | --- | --- | --- | --- | --- | | ✨ Add fields | 433 | Zethson | 2023-06-13 | | --- | --- | --- | --- | --- | | 🐛 Fix filtering & | 430 | Zethson | 2023-06-13 | | remove bioregistry & | | refactoring | | --- | --- | --- | --- | --- | | 🐛 Fixed index bug | 429 | sunnyosun | 2023-06-12 | 0.20.0 | | in search | | --- | --- | --- | --- | --- | | 🔊 Improved inspect | 428 | sunnyosun | 2023-06-12 | | logging | | --- | --- | --- | --- | --- | | ♻️ Removed curate, | 419 | sunnyosun | 2023-06-12 | | updated inspect | | guide Breaking | | --- | --- | --- | --- | --- | | 🚑 Fixed lamindb | 417 | sunnyosun | 2023-06-11 | 0.19.1 | | instance error and | | refactored source | | matching | | --- | --- | --- | --- | --- | | 🔥 No longer checks | 411 | sunnyosun | 2023-06-10 | | compat | | --- | --- | --- | --- | --- | | 🎨 Always regenerate | 410 | sunnyosun | 2023-06-10 | 0.19.0 | | ".current_sources.y | | aml" upon import | | Breaking | | --- | --- | --- | --- | --- | | 🐛 Fix LAMINDB_INST | 409 | Koncopd | 2023-06-10 | | ANCE_LOADED on | | Windows | | --- | --- | --- | --- | --- | | 📝 Fix notebook | 408 | falexwolf | 2023-06-10 | | execution | | --- | --- | --- | --- | --- | | 🚚 Renamed source | 407 | sunnyosun | 2023-06-10 | 0.18.1 | | path variables | | --- | --- | --- | --- | --- | | ➖ Clean up | 406 | falexwolf | 2023-06-10 | | dependencies | | --- | --- | --- | --- | --- | | 🎨 Removed | 405 | sunnyosun | 2023-06-09 | 0.18.0 | | environment variable | | for loaded lamindb | | instance Breaking | | --- | --- | --- | --- | --- | | 🚚 Move img folder | 404 | falexwolf | 2023-06-09 | | to guide | | --- | --- | --- | --- | --- | | 📝 Re-organize docs | 403 | falexwolf | 2023-06-08 | | --- | --- | --- | --- | --- | | 📝 Fix API ref | 402 | sunnyosun | 2023-06-08 | 0.17.0 | | --- | --- | --- | --- | --- | | 🚚 Renamed version | 401 | sunnyosun | 2023-06-07 | 0.17a3 | | to source everywhere | | possible Breaking | | --- | --- | --- | --- | --- | | 🎨 Updated yaml | 400 | sunnyosun | 2023-06-07 | | parameter in parse_ | | current_versions | | --- | --- | --- | --- | --- | | 🎨 Harmonize names | 399 | Zethson | 2023-06-07 | | --- | --- | --- | --- | --- | | 🚑 Fixed readout | 398 | sunnyosun | 2023-06-07 | 0.17a1 | | parsing | | --- | --- | --- | --- | --- | | 🧪 Add tests to | 397 | sunnyosun | 2023-06-07 | | versions file | | generation | | --- | --- | --- | --- | --- | | 🎨 Use the same code | 396 | sunnyosun | 2023-06-06 | | to create and update | | local yaml | | --- | --- | --- | --- | --- | | ♻️ Changed yaml | 394 | sunnyosun | 2023-06-04 | 0.17a1 | | format to have | | species as keys, | | refactored | | versioning Breaking | | --- | --- | --- | --- | --- | | ✨ Add improved | 392 | Zethson | 2023-06-04 | | species support | | Breaking | | --- | --- | --- | --- | --- | | 👷 Remove nox venv | 388 | falexwolf | 2023-06-01 | 0.16.0 | | --- | --- | --- | --- | --- | | 🔥 Remove global | 387 | Zethson | 2023-05-31 | | lookup Breaking | | --- | --- | --- | --- | --- | | 🎨 Default to return | 385 | sunnyosun | 2023-05-30 | | df when displaying | | versions | | --- | --- | --- | --- | --- | | ✨ Add GO | 384 | Zethson | 2023-05-30 | | --- | --- | --- | --- | --- | | 🚸 Delete an | 383 | Koncopd | 2023-05-29 | | incomplete file on | | an exception in | | s3_bionty_assets | | --- | --- | --- | --- | --- | | ➖ Remove nbproject | 382 | Koncopd | 2023-05-29 | | from production | | dependencies | | --- | --- | --- | --- | --- | | 🚑 Added | 381 | sunnyosun | 2023-05-29 | 0.15.1 | | "Entity=Bionty" | | backward | | compatibility | | --- | --- | --- | --- | --- | | ✨ Implemented a | 380 | sunnyosun | 2023-05-29 | | first "search" | | method | | --- | --- | --- | --- | --- | | 🐛 Decrease | 379 | Koncopd | 2023-05-28 | | refresh_per_second | | in the progress bar | | to 10 | | --- | --- | --- | --- | --- | | ➖ Replace upath and | 376 | Koncopd | 2023-05-28 | | fsspec with botocore | | --- | --- | --- | --- | --- | | ➖ Removed unused | 377 | sunnyosun | 2023-05-28 | | dependencies | | --- | --- | --- | --- | --- | | ✨ Allow | 375 | sunnyosun | 2023-05-28 | | "map_synonyms" for | | every entity | | --- | --- | --- | --- | --- | | ✨ Include | 372 | sunnyosun | 2023-05-27 | 0.15.0 | | "synonyms", | | "definition" columns | | in parquet | | --- | --- | --- | --- | --- | | 🩹 Also include the | 370 | sunnyosun | 2023-05-25 | | index field in | | "BiontyField" | | --- | --- | --- | --- | --- | | 💄 Prettified | 369 | sunnyosun | 2023-05-25 | | **repr** | | --- | --- | --- | --- | --- | | 🍱 Download parquet | 365 | sunnyosun | 2023-05-25 | 0.14.0 | | files from "s3 | | ://bionty-assets" | | --- | --- | --- | --- | --- | | ✨ Implement | 359 | Zethson | 2023-05-24 | | "map_synonyms" | | --- | --- | --- | --- | --- | | 🍱 Added "children" | 363 | sunnyosun | 2023-05-23 | | column to ontology | | parquet files | | --- | --- | --- | --- | --- | | ✨ 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 | 350 | jlricon | 2023-05-11 | 0.13.5 | | safe code | | --- | --- | --- | --- | --- | | ✏️ Fix lowercase | 348 | jlricon | 2023-05-11 | 0.13.4 | | types | | --- | --- | --- | --- | --- | | ⬆️ Remove lndb | 347 | Zethson | 2023-05-10 | 0.13.3 | | --- | --- | --- | --- | --- | | 🎨 Rename to | 346 | Zethson | 2023-05-10 | 0.13.2 | | internal UPath | | implementation and | | add s3 to ffspec | | --- | --- | --- | --- | --- | | 🎨 Add Upath, remove | 344 | Zethson | 2023-05-10 | 0.13.1 | | lndb_storage | | --- | --- | --- | --- | --- | | ✨ Added synonyms | 340 | sunnyosun | 2023-05-09 | 0.13.0 | | for CellMarker | | Breaking | | --- | --- | --- | --- | --- | | 🚚 Deprecate | 341 | Zethson | 2023-05-08 | | 'database' parameter | | and replace it with | | 'source' Breaking | | --- | --- | --- | --- | --- | | 🚚 Move | 339 | Zethson | 2023-05-08 | | s3_bionty_assets | | --- | --- | --- | --- | --- | | 📝 Improve lookup | 338 | Zethson | 2023-05-06 | | docs | | --- | --- | --- | --- | --- | | 🎨 Add more flexible | 337 | Zethson | 2023-05-02 | | prefixes | | --- | --- | --- | --- | --- | | 🎨 Improve print | 336 | Zethson | 2023-05-02 | | versions | | --- | --- | --- | --- | --- | | 📌 No pinning of | 333 | sunnyosun | 2023-04-27 | 0.12.1 | | lndb-storage version | | --- | --- | --- | --- | --- | | 🎨 Update lnschema- | 332 | sunnyosun | 2023-04-27 | | bionty | | --- | --- | --- | --- | --- | | 🎨 Change ".df()", | 326 | sunnyosun | 2023-04-27 | 0.12.0 | | ."lookup()" to | | methods, move | | "._entity" to | | private Breaking | | --- | --- | --- | --- | --- | | 🐛 Fix pathway | 329 | Zethson | 2023-04-26 | | ontology | | --- | --- | --- | --- | --- | | 💚 Fix bionty-asset | 325 | sunnyosun | 2023-04-26 | | instance for file | | upload | | --- | --- | --- | --- | --- | | 👷 Sync staging into | 316 | Zethson | 2023-04-25 | | main | | --- | --- | --- | --- | --- | | 🚑 Fix lookup for | 314 | sunnyosun | 2023-04-23 | 0.11.6 | | empty strings | | --- | --- | --- | --- | --- | | ⚡ Make sure no NAs | 313 | sunnyosun | 2023-04-23 | 0.11.5 | | present in the | | "entity.df.name" | | --- | --- | --- | --- | --- | | ⬆️ Pronto>=2.5.4, | 312 | sunnyosun | 2023-04-23 | | removed | | cached_property dep | | for py3.7 | | --- | --- | --- | --- | --- | | ⚡ Improve the speed | 305 | sunnyosun | 2023-04-19 | 0.11.4 | | loading of ontology | | df | | --- | --- | --- | --- | --- | | 👷 Add staging to CI | 293 | Zethson | 2023-04-04 | | --- | --- | --- | --- | --- | | 💚 Add current/lndb | 290 | Zethson | 2023-03-30 | 0.11.3 | | updating on new | | entities | | --- | --- | --- | --- | --- | | 💚 Try fixing | 289 | falexwolf | 2023-03-27 | | "lnschema-bionty" CI | | --- | --- | --- | --- | --- | | 🐛 Fix field for | 288 | sunnyosun | 2023-03-27 | 0.11.2 | | gene and protein | | --- | --- | --- | --- | --- | | 🚚 Renamed to field | 287 | sunnyosun | 2023-03-27 | 0.11.1 | | everywhere | | --- | --- | --- | --- | --- | | 👷 Fix lnschema- | 284 | sunnyosun | 2023-03-27 | | bionty CI | | --- | --- | --- | --- | --- | | 🚚 Rename property | 283 | sunnyosun | 2023-03-24 | 0.11.0 | | "lookup_col" to | | "lookup_field" | | Breaking | | --- | --- | --- | --- | --- | | ✅ Add | 280 | Zethson | 2023-03-23 | | update_defaults test | | --- | --- | --- | --- | --- | | 👷 Test against | 279 | falexwolf | 2023-03-23 | | "lnschema-bionty" | | --- | --- | --- | --- | --- | | ✨ Move ID from | 268 | Zethson | 2023-03-23 | | Entity to curate | | Breaking | | --- | --- | --- | --- | --- | | 🐛 Fix removeprefix | 277 | Zethson | 2023-03-22 | 0.10.1 | | 3.8 & versions | | pathing | | --- | --- | --- | --- | --- | | 📝 Updated the | 274 | sunnyosun | 2023-03-22 | | curation notebook | | for cellmarker | | --- | --- | --- | --- | --- | | 🍱 Updated | 271 | sunnyosun | 2023-03-21 | 0.10.0 | | CellMarker assets | | Breaking | | --- | --- | --- | --- | --- | | 🚑 Ensure version | 269 | sunnyosun | 2023-03-20 | 0.9.0 | | names are strings | | --- | --- | --- | --- | --- | | ✨ Add pathway | 267 | Zethson | 2023-03-17 | 0.9.0rc1 | | ontology | | --- | --- | --- | --- | --- | | ✨ Add compatibility | 264 | Zethson | 2023-03-17 | | functions | | --- | --- | --- | --- | --- | | ✨ Add latest | 256 | Zethson | 2023-03-14 | | version inference if | | only db is passed | | --- | --- | --- | --- | --- | | 🐛 Fix default ids | 257 | sunnyosun | 2023-03-14 | | --- | --- | --- | --- | --- | | Add md5 sums | 249 | Zethson | 2023-03-13 | | --- | --- | --- | --- | --- | | 🎨 Fixed case | 255 | sunnyosun | 2023-03-11 | | sensitivity, lookup | | output as namedtuple | | --- | --- | --- | --- | --- | | 💥 Lookup returns | 254 | sunnyosun | 2023-03-11 | | the full record | | Breaking | | --- | --- | --- | --- | --- | | 💄 Actually fix | 253 | sunnyosun | 2023-03-11 | | image display | | --- | --- | --- | --- | --- | | 🐛 Fix img links | 252 | sunnyosun | 2023-03-11 | | --- | --- | --- | --- | --- | | 📝 Keep improving | 250 | sunnyosun | 2023-03-11 | | docs | | --- | --- | --- | --- | --- | | 🐛 Fix version order | 248 | Zethson | 2023-03-10 | | --- | --- | --- | --- | --- | | 🐛 Ensure datadir is | 245 | sunnyosun | 2023-03-09 | 0.8.1 | | created | | --- | --- | --- | --- | --- | | 🐛 Fixed readout | 244 | sunnyosun | 2023-03-09 | 0.8.0 | | lookup | | --- | --- | --- | --- | --- | | 📝 A take on 3 | 240 | falexwolf | 2023-03-08 | 0.8rc2 | | summary bullets | | --- | --- | --- | --- | --- | | 💚 Fix CI build | 239 | sunnyosun | 2023-03-08 | | --- | --- | --- | --- | --- | | 📝 Improving | 220 | Zethson | 2023-03-08 | | documentation | | --- | --- | --- | --- | --- | | 👷 Add entity tests | 234 | Zethson | 2023-03-07 | | --- | --- | --- | --- | --- | | ✨ Add names/website | 232 | Zethson | 2023-03-06 | | per ontology & | | improve versions | | rich tables | | --- | --- | --- | --- | --- | | 📝 Add better | 231 | Zethson | 2023-03-06 | | docstrings and | | docstring decorator | | --- | --- | --- | --- | --- | | 🐛 Fix cellmarker | 230 | Zethson | 2023-03-03 | 0.8rc1 | | ontology | | --- | --- | --- | --- | --- | | ✨ Add CellLine | 229 | Zethson | 2023-03-03 | | ontology | | --- | --- | --- | --- | --- | | 🎨 Simplify | 227 | Zethson | 2023-03-03 | | filenames | | --- | --- | --- | --- | --- | | 🎨 Deduce filenames | 223 | Zethson | 2023-03-01 | | on the fly for | | non-S3 Entites | | --- | --- | --- | --- | --- | | 📝 Simplify FAQ | 218 | Zethson | 2023-02-27 | | --- | --- | --- | --- | --- | | 🎨 Simplify ontology | 217 | Zethson | 2023-02-27 | | accesses | | --- | --- | --- | --- | --- | | 🎨 Move Species to | 216 | Zethson | 2023-02-27 | | Entity | | --- | --- | --- | --- | --- | | 🎨 Rename | 214 | Zethson | 2023-02-26 | | EntityTable to | | Entity Breaking | | --- | --- | --- | --- | --- | | 🎨 Add laminci | 213 | Zethson | 2023-02-26 | | --- | --- | --- | --- | --- | | ✨ Add HCA ontology | 209 | Zethson | 2023-02-21 | | --- | --- | --- | --- | --- | | ✨ Improve version | 202 | Zethson | 2023-02-21 | | handling | | --- | --- | --- | --- | --- | | 🔥 No downloading | 205 | sunnyosun | 2023-02-20 | | upon import | | --- | --- | --- | --- | --- | | 👷 Remove py3.7 from | 206 | sunnyosun | 2023-02-20 | | CI | | --- | --- | --- | --- | --- | | 📝 Add better | 201 | Zethson | 2023-02-17 | | documentation & | | function to print | | currently | | available/active | | ontologies | | --- | --- | --- | --- | --- | | 👷 Add HDO & improve | 187 | Zethson | 2023-02-15 | | support for multiple | | databases | | --- | --- | --- | --- | --- | | 👷 Add GH workflow | 188 | Zethson | 2023-02-13 | 0.7.0 | | to check for version | | URLs | | --- | --- | --- | --- | --- | | ⬆️ Rename | 189 | bpenteado | 2023-02-13 | | "lndb_setup" to | | "lndb" | | --- | --- | --- | --- | --- | | ✨ Add human | 172 | Zethson | 2023-02-06 | | phenotype ontology | | --- | --- | --- | --- | --- | | 📝 Add dev APIs to | 183 | sunnyosun | 2023-02-06 | | docs | | --- | --- | --- | --- | --- | | 📝 Use guide/index | 182 | sunnyosun | 2023-02-06 | | as landing page | | --- | --- | --- | --- | --- | | 🔥 Removed | 176 | sunnyosun | 2023-02-06 | | _logger.py | | --- | --- | --- | --- | --- | | 🐛 Fix #167 | 168 | Zethson | 2023-02-05 | | --- | --- | --- | --- | --- | | 👷 Add lamindocs | 173 | Zethson | 2023-02-05 | | secret key for CI | | --- | --- | --- | --- | --- | | ✨ Added | 169 | sunnyosun | 2023-01-31 | 0.6.5 | | case_sensitive to | | curate | | --- | --- | --- | --- | --- | | 🚑 Fix version key | 166 | sunnyosun | 2023-01-18 | 0.6.4 | | type | | --- | --- | --- | --- | --- | | 🚚 Rename species | 165 | sunnyosun | 2023-01-17 | 0.6.3 | | common_name to name | | --- | --- | --- | --- | --- | | 🎨 Changed version | to ___ | 164 | sunnyosun | 2023-01-16 | | filename separator | | from | | --- | --- | --- | --- | --- | | 🐛 Fix docs | 162 | sunnyosun | 2023-01-12 | 0.6.1 | | --- | --- | --- | --- | --- | | 👷 Expand CI to | 161 | sunnyosun | 2023-01-12 | 0.6.0 | | python 3.7-3.10 | | --- | --- | --- | --- | --- | | ✨ Pull species | 160 | sunnyosun | 2023-01-05 | | table dynamically | | from Ensembl | | --- | --- | --- | --- | --- | | ✨ Add progressbar | 159 | Zethson | 2023-01-05 | | to downloads | | --- | --- | --- | --- | --- | # wetlab | --- | --- | --- | --- | --- | | Name | PR | Developer | Date | Version | | ====================== | ====================== | ====================== | ====================== | ====================== | | ✨ Added | 21 | sunnyosun | 2023-07-04 | | "TreatmentTarget" | | --- | --- | --- | --- | --- | | ✨ Added | 19 | sunnyosun | 2023-07-03 | | "target_genes" | | --- | --- | --- | --- | --- | | 🚚 Migrate to Django | 12 | falexwolf | 2023-06-11 | | (2) | | --- | --- | --- | --- | --- | | 🚚 Migrate to Django | 11 | falexwolf | 2023-06-09 | | (1) | | --- | --- | --- | --- | --- | | 🏗️ Remove "lnbase- | 10 | falexwolf | 2023-06-01 | 0.18a1 | | biolab" | | --- | --- | --- | --- | --- | | 🏗️ Remove SQL-level | 9 | falexwolf | 2023-05-25 | 0.17.0 | | schema modules | | --- | --- | --- | --- | --- | | ✨ Add "Well" table, | 8 | sunnyosun | 2023-05-23 | 0.16.3 | | "File.cell_lines" | | --- | --- | --- | --- | --- | | ✨ Added "Treatment" | 3 | sunnyosun | 2023-05-15 | | --- | --- | --- | --- | --- | | 🎉 Move content from | 1 | falexwolf | 2023-04-22 | 0.15.1 | | "lnschema-wetlab" | | here | | --- | --- | --- | --- | --- | # nbproject | --- | --- | --- | --- | --- | | Name | PR | Developer | Date | Version | | ====================== | ====================== | ====================== | ====================== | ====================== | | 👷 Ruff and 3.11 | 276 | Zethson | 2023-12-26 | | --- | --- | --- | --- | --- | | 🩹 Account for empty | 272 | falexwolf | 2023-10-01 | | notebook in | | consecutiveness | | check | | --- | --- | --- | --- | --- | | 📝 Fix image link | 271 | falexwolf | 2023-09-18 | | --- | --- | --- | --- | --- | | 🚸 More robust title | 270 | falexwolf | 2023-08-15 | 0.9.2 | | parsing | | --- | --- | --- | --- | --- | | 📝 Simplify docs, | 269 | falexwolf | 2023-08-04 | 0.9.1 | | adopt new lamin.ai | | static site | | architecture | | --- | --- | --- | --- | --- | | ♻️ Remove loguru- | 268 | falexwolf | 2023-06-15 | 0.9.0 | | dependent call, | | expand | | "metadata_only" | | return signature | | --- | --- | --- | --- | --- | | 📝 Position | 264 | falexwolf | 2023-06-15 | | nbproject | | --- | --- | --- | --- | --- | | 🩹 Try to get vs | 267 | Koncopd | 2023-06-10 | | code path first | | --- | --- | --- | --- | --- | | 🦺 Safer parsing | 266 | Koncopd | 2023-06-03 | 0.8.7 | | during | | initialization | | --- | --- | --- | --- | --- | | ➖ Remove nbproject- | 262 | Koncopd | 2023-05-30 | | test from | | dependencies | | --- | --- | --- | --- | --- | | 🐛 Safer ipylab | 263 | Koncopd | 2023-04-18 | 0.8.6 | | initialization | | --- | --- | --- | --- | --- | | 🐛 Fix VS Code | 260 | Koncopd | 2023-04-17 | 0.8.5 | | integration for | | recent VS Code | | versions | | --- | --- | --- | --- | --- | | ♻️ Replace "display" | 257 | Koncopd | 2023-04-10 | 0.8.4 | | with "metadata_only" | | arg in "header" | | --- | --- | --- | --- | --- | | 🚸 Allow to not | 255 | falexwolf | 2023-03-12 | 0.8.3 | | display metadata | | --- | --- | --- | --- | --- | | ⬆️ Observe "lndb- | 253 | bpenteado | 2023-02-16 | 0.8.2 | | setup" rename to | | "lndb" | | --- | --- | --- | --- | --- | | ✨ Safer notebook | 251 | Koncopd | 2023-02-10 | | path inference and | | more ways to do it | | --- | --- | --- | --- | --- | | 🐛 Check keys before | 250 | Koncopd | 2023-02-08 | | accessing in | | "notebook_path" | | --- | --- | --- | --- | --- |