Release 0.77.3

See https://docs.lamin.ai/changelog/2024#db-0-77-3

What's Changed

• ✅ More tests for Artifact.df() by @falexwolf in #2241
• ⬆️ Add a lower bound for pandas by @Koncopd in #2242
• ✨ Add Curator for tiledbsoma stores by @Koncopd in #2228
• 🐛 Fix the error on existing cache on copy to cache in Artifact.save by @Koncopd in #2248
• 🎨 Update describe layout by @sunnyosun in #2247
• 🐛 Fix IPython import error by @Koncopd in #2250
• ⬆️ Update wetlab by @sunnyosun in #2251
• ⬆️ Upgrade lamindb-setup (unpin supabase) by @Koncopd in #2252
• 🐛 Fix display of (non-categorical) str features in .describe() by @sunnyosun in #2253
• 🎨 Remove quotes and rename sessions in describe by @sunnyosun in #2259
• 🐛 Fix the error on special chars in search strings by @Koncopd in #2261
• ✨ Add an artifact loader for .yaml by @Koncopd in #2270
• 🐛 Better error behavior for repeated calls of standardize by @Zethson in #2266
• 🐛 Fix organism in curator.standardize by @sunnyosun in #2272
• 🐛 Fix very long runtimes for Artifact.describe by @Koncopd in #2273
• ⬆️ Upgrade lamin-utils to 0.13.10 (escape search string in bionty search) by @Koncopd in #2274
• ✏️ Fix typos in describe sections by @falexwolf in #2271
• 🐛 Fix curator.validate from public by @sunnyosun in #2275
• 🛠️ Update wetlab by @Zethson in #2277
• 🔊 Log tiledbsoma write path by @Koncopd in #2278
• 🩹 Enable annotating existing artifacts with Curate.save_artifact() by @falexwolf in #2280
• 📝 Safer gene mapping by @Zethson in #2283
• 🚸 Improve feedback on not-up-to-date notebook content by @falexwolf in #2284

Full Changelog: 0.77.2...0.77.3

Release 0.77.2

See https://docs.lamin.ai/changelog/2024#db-0-77-2

What's Changed

• ⬆️ Update core by @sunnyosun in #2197
• 🩹 Make search rules the same across all systems by @Koncopd in #2199
• 🎨 Make search in bionty consistent with the lamindb implementation by @Koncopd in #2205
• ♻️ Simplify coupling of bionty and lamindb-setup by @falexwolf in #2207
• 💚 Fix tiledbsoma installation in CI by @Koncopd in #2208
• 📝 Move tutorial and tutorial2 to lamin-docs by @falexwolf in #2184
• 📝 Prettify gene symbols guide & logging by @falexwolf in #2210
• 🐛 Check protocol first in check_path_is_child_of_root by @Koncopd in #2215
• 🩹 Add a lower bound on nbconvert to avoid problems with lxml by @Koncopd in #2216
• ✨ Support dtype = 'datetime' and improve annotating with, retrieving & removing feature values by @falexwolf in #2218
• 👷 Simplify issue templates by @falexwolf in #2220
• ♻️ Add .standardize() to Curator and refactor by @sunnyosun in #2186
• ⬆️ Update custom schema submodules by @sunnyosun in #2223
• 🎨 Separate labels fetching from printing by @sunnyosun in #2225
• 🎨 Fix EHRCurator warning & validation by @Zethson in #2230
• ✨ Enable features with dtype = 'str' by @falexwolf in #2226
• 🏷️ Remove duplicated typing in Curator by @sunnyosun in #2232
• 🎨 Let .from_values() return RecordList and better treat categorical by @falexwolf in #2233
• 🎨 Centralize a small test dataset for curation & queries by @falexwolf in #2234
• 🏷️ Fix type of var_index in MuDataCurator by @Koncopd in #2239
• ✨ Enable to easily join features onto artifacts via Artifact.df() by @falexwolf in #2238
• 💄 Create a more intuitive artifact.describe() by @sunnyosun in #2236
• 🚸 Improve UX of db$track() and db$finish() by @falexwolf in #2213
• 🐛 Fix collection describe by @sunnyosun in #2240

Full Changelog: 0.77.0...0.77.2

Release 0.77.0

See https://docs.lamin.ai/changelog/2024#db-0-77-0-bionty-0-53-0

What's Changed

• ⚡️ Additional search rule for truncated searches by @Koncopd in #2183
• ✨ Enable Django field validation and Literal validation by @sunnyosun in #2177
• 🩹 Check anndata version to import read_zarr by @Koncopd in #2185
• 🔊 Prompt to use laminr on trying to load .rds files by @Koncopd in #2188
• ⬆️ Prepare release by @sunnyosun in #2189
• ⬆️ Upgrade lamindb-setup by @Koncopd in #2194
• ⬆️ Upgrade lamin-utils by @Koncopd in #2195
• 🚸 Mark .qmd & .Rmd files as notebooks, not scripts by @falexwolf in #2196

Full Changelog: 0.76.16...0.77.0

Release 0.76.16

See https://docs.lamin.ai/changelog/2024#db-0-76-16

What's Changed

• 🎨 Refactor flatten_unique by @Zethson in #2121
• ✨ Add extra groups for all schemas by @Zethson in #2123
• 📝 Recursive query of parents and children example by @Koncopd in #2126
• 🐛 Fix registering Gene columns in DataFrameCurator by @sunnyosun in #2131
• ✨ Truncate standardization output by @Zethson in #2103
• 🐛 Fix hard-coded "name" field during search by @sunnyosun in #2130
• 🐛 Fix transfering artifacts from a source instance with fewer schema modules by @sunnyosun in #2132
• ✨ Support Hugging Face paths by @Koncopd in #2128
• 📝 Explain what can be registered as Artifact and show Hugging Face integration by @Koncopd in #2136
• 📝 Add gene symbol usage and mapping FAQ by @Zethson in #2134
• ✨ Compute hash for files in Google Cloud Storage and Hugging Face by @Koncopd in #2139
• 🎨 Improve saving validated output by @Zethson in #2140
• ✨ Warn if curating against gene symbols by @Zethson in #2142
• ✨ Raise TypeError if a string is passed to var_index of AnnDataCurator by @Zethson in #2105
• 🚸 Validate minimum uid length by @falexwolf in #2144
• ✅ Test registering GCP paths by @Koncopd in #2145
• 🚚 Deprecate BioRecord.import_from_source in favor of BioRecord.import_source by @Zethson in #2146
• 🎨 Make EHRCurator immutable by @Zethson in #2149
• 🚸 Enable autocompletion for inherited methods in Jupyter by @Koncopd in #2148
• 📝 Add hide-output for some cells & links to storage engines by @Zethson in #2151
• ⬆️ Upgrade anndata to 0.11.0 by @Koncopd in #2152
• ⬆️ Upgrade fsspec to 2024.10.0 by @Koncopd in #2153
• ✨ Improve runtime formatting by @Zethson in #2157
• 🚸 Enable to query with records from a different database instance by @falexwolf in #2164
• ⬆️ Upgrade anndata to 0.11.1 by @Zethson in #2166
• ♻️ Only apply exact length uid constraint for internal entities by @falexwolf in #2167
• ⚡️ Improve speed and relevance of search by @Koncopd in #2163
• 🎨 Improve runtime formatting code by @Zethson in #2162
• ⚡️ Improve Record.search runtime by @Koncopd in #2168
• ✨ Support saving R code including .qmd and .Rmd by @falexwolf in #2169
• 🚸 Refactor ln.track() to improve logging and method signature by @falexwolf in #2176

Full Changelog: 0.76.15...0.76.16

Release 0.76.15

See https://docs.lamin.ai/changelog

What's Changed

• 💚 Fix docs by @falexwolf in #2083
• 🔇 Fix Curator logging by @sunnyosun in #2085
• 🔊 Raise ValidationError by @sunnyosun in #2086
• ⬆️ Remove the pin on scipy by @Koncopd in #2087
• 🐛 Fix TypeError by @Zethson in #2089
• ✨ Restrict stdout of validation messages of Curator to max 10 terms by @Zethson in #2094
• ✨ Recursively query parents and children by @Koncopd in #2106
• 🐛 Proper numerous for Curator stdout by @Zethson in #2107
• ⬆️ Upgrade lamindb-setup by @Koncopd in #2114
• ✨ Stream pyarrow.dataset.dataset supported formats in Artifact.open() by @Koncopd in #2115
• ♻️ Refactor imports and update upath code by @Koncopd in #2116
• ✨ Python 3.12 support by @Zethson in #2092
• 📝 Add parquet example to arrays.ipynb by @Koncopd in #2118
• 🐛 Fix list validation in Curator by @sunnyosun in #2119
• ⬆️ Release sub modules by @sunnyosun in #2120

Full Changelog: 0.76.14...0.76.15

Release 0.76.14

See https://docs.lamin.ai/changelog/2024#db-0-76-14

What's Changed

• 🐛 Return include fields when one of them is empty by @sunnyosun in #2044
• 🧪 More tests of df include by @sunnyosun in #2045
• 📝 Consistent documentation for all schema modules by @falexwolf in #2047
• 🐛 Fix loading artifact by key and give clear errors if no artifacts or transforms found by @Koncopd in #2050
• 🎨 Remove update in add_ontology_from_df by @sunnyosun in #2051
• 🍱 Add omop, cellregistry, ourprojects by @falexwolf in #2049
• 📝 Update login docs for new API key by @Koncopd in #2054
• ✨ Upon Validator, populate ref_is_name fields in link tables by @sunnyosun in #2053
• 📝 Improve save_artifact docs by @sunnyosun in #2055
• ✏️ Only register new features in add_new_from_columns by @sunnyosun in #2057
• ✏️ Fix logging integer values by @sunnyosun in #2056
• 🔥 Remove .list_source() by @sunnyosun in #2058
• 🔈 Fix add new logging by @sunnyosun in #2059
• ♻️ Move cloud_to_local to lnamindb_setup.settings by @Koncopd in #2062
• 🐛 Fix tracking of notebooks on PyCharm by @Koncopd in #2064
• 📝 Document how to subclass Curator by @Zethson in #2022
• ✨ Error when renaming internal features and labels by @sunnyosun in #2061
• ✨ Add Collection.append() by @Koncopd in #2077
• ✨ Enable curating multiple categorical features per artifact against the same label registry by @falexwolf in #2080
• 🔥 Remove Curator.add_validated_from() by @sunnyosun in #2081
• 🎨 Fix Curator.from_mudata by @sunnyosun in #2082

Full Changelog: 0.76.13...0.76.14

Release 0.76.13

See https://docs.lamin.ai/changelog/2024#db-0-76-13

What's Changed

• 🐛 Do not double track runs by @falexwolf in #2032
• 🔥 Remove __getitem__ from QuerySet by @sunnyosun in #2034
• 🐛Fix track message by @Zethson in #2036
• ♻️ Properly resolve schema mismatch by @sunnyosun in #2040
• 🎨 for circular input/outputs by @sunnyosun in #2041
• 🐛 Fix get with using_key by @sunnyosun in #2042
• 💚 Fix switch instance test by @falexwolf in #2043

Full Changelog: 0.76.12...0.76.13

Release 0.76.12

See https://docs.lamin.ai/changelog/2024#db-0-76-12-bionty-0-51-2

What's Changed

• ♻️ Move lamindb_setup.settings.storage.cache_dir to lamindb_setup.settings.cache_dir by @Koncopd in #2013
• 🎨 Remove creates one artifact per file in the directory warning by @Zethson in #2015
• 📝 Use anon=True access for UPath.view_tree() in tutorial by @Koncopd in #2016
• ♻️ Some minor improvements by @falexwolf in #2018
• 🐛 Fix walrus and duplicated updated_at by @Koncopd in #2020
• ♻️ Migrate to edge function in connect() by @Koncopd in #2017
• 🏗️ Make lamindb-setup a dependency of lamin-cli by @falexwolf in #2021
• 🚸 Query with typed labels through .features by @falexwolf in #2023
• 📝 Document how to query by dictionary-like run parameters by @falexwolf in #2024
• ✨ Overhaul save_vitessce_config() to support multiple artifacts and non-.zarr by @keller-mark in #1953
• ✅ Add more tests for querying via .features by @falexwolf in #2028
• 🔊 More logging in save_vitessce_config() by @falexwolf in #2029

New Contributors

• @keller-mark made their first contribution in #1953

Full Changelog: 0.76.11...0.76.12

Release 0.76.11

See https://docs.lamin.ai/changelog/2024#db-0-76-11

What's Changed

• 📝 Fix docs by @falexwolf in #1999
• 🐛 Fix cache paths by @Koncopd in #2000
• 📝 Prettify track guide by @falexwolf in #2003
• 🐛 Fix label name display in .describe() by @falexwolf in #2006
• 💄 Strip NotebookNotSaved from report after ln.finish() by @Koncopd in #2007
• ✨ Add a reference manager schema module: findrefs by @falexwolf in #2009

Full Changelog: 0.76.10...0.76.11

Release 0.76.10

See https://docs.lamin.ai/changelog/2024#db-0-76-10

What's Changed

• 📝 Revise advice on managing notebook templates by @falexwolf in #1981
• 🚸 Minimal ln.track() by @falexwolf in #1982
• ⚡️ Speed up describe by @sunnyosun in #1973
• ✅ Add another test for running with tracked params, logging cosmetics by @falexwolf in #1984
• ✨ Track transfers as transforms by @falexwolf in #1985
• 🚸 lamin load → lamin connect & lamin get → lamin load by @Koncopd in #1983
• 🚚 Rename hub edge functions by @falexwolf in #1988
• 📝 Document how to work with run parameters by @falexwolf in #1989
• 🎨 Move .from_values() from Record to CanValidate by @falexwolf in #1993
• 🚸 Transfer: Warn about inconsistencies between source & target instances by @falexwolf in #1992
• 🚸 Improve lamin load UX for notebooks & scripts by @falexwolf in #1994
• ⚡️ Speed up from_values by @sunnyosun in #1970
• ⚡ Improve performance of ln.connect(), lamin connect, and lamin load for a notebook by @falexwolf in #1998

Full Changelog: 0.76.9...0.76.10