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Insights: laminlabs/lamindb
November 27, 2024 – December 27, 2024
Overview
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2 Releases published by 1 person
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0.77.2 Release 0.77.2
published
Dec 2, 2024 -
0.77.3 Release 0.77.3
published
Dec 16, 2024
49 Pull requests merged by 4 people
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⬆️ Make tiledbsoma integration compatible with tiledbsoma==1.15.0
#2307 merged
Dec 20, 2024 -
⬆️ Release submodules
#2306 merged
Dec 20, 2024 -
✏️ Fix NA values in Curator.add_new_from
#2305 merged
Dec 20, 2024 -
✨ Add
SpatialDataCurator#2290 merged
Dec 19, 2024 -
🚸 Simplify installation & API overview
#2302 merged
Dec 19, 2024 -
⚡️ Make lamin_run_uid categorical in tiledbsoma stores
#2300 merged
Dec 19, 2024 -
🎨 Fix NA values in Curator.add_new_from
#2299 merged
Dec 19, 2024 -
✅ Check reading X in tiledbsoma tests
#2298 merged
Dec 18, 2024 -
🎨 Check organism parameter type in curator
#2297 merged
Dec 18, 2024 -
🎨 Raise ValueError when trying to search a None value
#2294 merged
Dec 18, 2024 -
✨ Allow to register artifacts with http urls
#2291 merged
Dec 17, 2024 -
🐛 Let
Curator.from_tiledbsoma()validate and annotate all.obscolumns#2287 merged
Dec 17, 2024 -
🎨 Proper type check of FeatureSet rename
#2289 merged
Dec 17, 2024 -
🐛 Fix feature set renaming
#2288 merged
Dec 17, 2024 -
🚸 Improve feedback on not-up-to-date notebook content
#2284 merged
Dec 16, 2024 -
📝 Safer gene mapping
#2283 merged
Dec 16, 2024 -
🩹 Enable annotating existing artifacts with
Curate.save_artifact()#2280 merged
Dec 16, 2024 -
🔊 Log tiledbsoma write path
#2278 merged
Dec 16, 2024 -
🛠️ Update wetlab
#2277 merged
Dec 16, 2024 -
🐛 Fix curator.validate from public
#2275 merged
Dec 16, 2024 -
✏️ Fix typos in describe sections
#2271 merged
Dec 16, 2024 -
⬆️ Upgrade lamin-utils to 0.13.10 (escape search string in bionty search)
#2274 merged
Dec 12, 2024 -
🐛 Fix very long runtimes for Artifact.describe
#2273 merged
Dec 11, 2024 -
🐛 Fix organism in curator.standardize
#2272 merged
Dec 10, 2024 -
🐛 Better error behavior for repeated calls of
standardize#2266 merged
Dec 10, 2024 -
✨ Add an artifact loader for .yaml
#2270 merged
Dec 10, 2024 -
🐛 Fix the error on special chars in search strings
#2261 merged
Dec 6, 2024 -
🎨 Remove quotes and rename sessions in describe
#2259 merged
Dec 6, 2024 -
🐛 Fix display of (non-categorical)
strfeatures in.describe()#2253 merged
Dec 5, 2024 -
⬆️ Upgrade lamindb-setup (unpin supabase)
#2252 merged
Dec 4, 2024 -
⬆️ Update wetlab
#2251 merged
Dec 4, 2024 -
🐛 Fix IPython import error
#2250 merged
Dec 3, 2024 -
🎨 Update describe layout
#2247 merged
Dec 3, 2024 -
🐛 Fix the error on existing cache on copy to cache in Artifact.save
#2248 merged
Dec 3, 2024 -
✨ Add Curator for tiledbsoma stores
#2228 merged
Dec 3, 2024 -
⬆️ Add a lower bound for pandas
#2242 merged
Dec 2, 2024 -
✅ More tests for Artifact.df()
#2241 merged
Dec 2, 2024 -
🐛 Fix collection describe
#2240 merged
Dec 1, 2024 -
🚸 Improve UX of
db$track()anddb$finish()#2213 merged
Dec 1, 2024 -
💄 Create a more intuitive
artifact.describe()#2236 merged
Dec 1, 2024 -
✨ Enable to easily join features onto artifacts via
Artifact.df()#2238 merged
Nov 30, 2024 -
🏷️ Fix type of var_index in MuDataCurator
#2239 merged
Nov 29, 2024 -
🎨 Centralize a small test dataset for curation & queries
#2234 merged
Nov 29, 2024 -
🎨 Let
.from_values()returnRecordListand better treat categorical#2233 merged
Nov 29, 2024 -
🏷️ Remove duplicated typing in Curator
#2232 merged
Nov 29, 2024 -
✨ Enable features with
dtype = 'str'#2226 merged
Nov 28, 2024 -
🎨 Fix EHRCurator warning & validation
#2230 merged
Nov 28, 2024 -
🎨 Separate labels fetching from printing
#2225 merged
Nov 28, 2024 -
⬆️ Update custom schema submodules
#2223 merged
Nov 27, 2024
1 Pull request opened by 1 person
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🎨 Isolate curator tests
#2304 opened
Dec 20, 2024
26 Issues closed by 5 people
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🚸 Creating a local instance for the cwd
#2180 closed
Dec 23, 2024 -
update tiledbsoma integration to tiledbsoma==1.15.0
#2296 closed
Dec 20, 2024 -
AnnData automatically converts int index to str, therefore matching some Gene synonyms
#2124 closed
Dec 20, 2024 -
🚸 Shall we make `aws` and `ourprojects` default dependencies?
#2301 closed
Dec 19, 2024 -
Make lamin_run_id categorical in save_tiledbsoma_experiment
#2279 closed
Dec 19, 2024 -
Searching for a `None` value leads to `AttributeError: 'NoneType' object has no attribute 'strip'`
#2292 closed
Dec 18, 2024 -
🐛 `Curator.from_tiledbsoma()` omits simple feature dtypes in the dataset
#2285 closed
Dec 17, 2024 -
🐛 `ln.finish` shows RStudio message
#2257 closed
Dec 16, 2024 -
`add_validated_from_var_index` is suggested but it doesn't even exist anymore
#2108 closed
Dec 13, 2024 -
Unable to pin Compound source when it has chebi source attached
#2078 closed
Dec 11, 2024 -
How to correctly call an S3 instance from another server?
#1936 closed
Dec 10, 2024 -
standardize KeyError output looks bad and should likely not get thrown on rerun
#2262 closed
Dec 10, 2024 -
Enhancement issue template no longer autolabels the issue
#2264 closed
Dec 9, 2024 -
Improve documentation of Curator
#2109 closed
Dec 9, 2024 -
`Curator.validate()` should not validate against synonyms and run `standardize()` under the hood
#2147 closed
Dec 9, 2024 -
Reduce verbosity of `.describe()`
#2112 closed
Dec 9, 2024 -
search queries are not properly sanitized
#2260 closed
Dec 6, 2024 -
Unable to create FeatureSets from features like specified in the docstring
#2246 closed
Dec 3, 2024 -
Add a lower bound on pandas for curation
#2227 closed
Dec 2, 2024 -
💄 Create a more intuitive `artifact.describe()`
#2221 closed
Dec 1, 2024 -
📝 Duplicated type annotations in Curator
#2231 closed
Nov 29, 2024 -
🚸 Improve the "pass a dtype" message for Feature constructor
#2212 closed
Nov 28, 2024 -
🚸 Whole bunch of ugly warnings in ehrcurator
#2229 closed
Nov 28, 2024
19 Issues opened by 3 people
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Reorganize Curators and Curator CI
#2303 opened
Dec 19, 2024 -
`.standardize()` does not warn about non-validated values
#2286 opened
Dec 16, 2024 -
🐛 `lookup(return_field="name")` throws error if multiple values exist
#2282 opened
Dec 16, 2024 -
🚸 Seeing ahead of time which features I'll get
#2281 opened
Dec 16, 2024 -
Describe text coloring inconsistent
#2276 opened
Dec 13, 2024 -
🚸 Unique contraint on `name` field of most registries
#2269 opened
Dec 10, 2024 -
♻️ Improve implementation of `describe()`
#2268 opened
Dec 10, 2024 -
Updating the dtype of feature
#2267 opened
Dec 10, 2024 -
🚸 ln.track should prompt to enter any key instead of y or n with an error
#2265 opened
Dec 6, 2024 -
Disabling searching for similar names should be a context manager
#2263 opened
Dec 6, 2024 -
Shorter "none of your storage locations were found in your environment"
#2258 opened
Dec 5, 2024 -
bionty Ontology .from_values behaves strangely
#2255 opened
Dec 4, 2024 -
Deleting Params is too difficult
#2254 opened
Dec 4, 2024 -
Remove `.from_values` from `Feature`
#2249 opened
Dec 3, 2024 -
✨ Account for `.uns` in the validation and curation flow
#2244 opened
Dec 2, 2024 -
🍱 Add an example using `wetlab.Biosample` to the `registries` guide
#2243 opened
Dec 2, 2024 -
🎨 Check logic in `save_feature_sets()`
#2237 opened
Nov 29, 2024 -
standardize errors on public ontologies if organism is passed but model has no organism
#2235 opened
Nov 29, 2024 -
unneeded new line in ln.track
#2224 opened
Nov 27, 2024
8 Unresolved conversations
Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.
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🚸 Enable deleting Transforms that are referencing artifacts & runs
#1547 commented on
Dec 5, 2024 • 0 new comments -
🚸 Catch Django errors of death
#1585 commented on
Dec 10, 2024 • 0 new comments -
finish() support for CI environments
#1851 commented on
Dec 19, 2024 • 0 new comments -
🚸 It's possible for `.from_public()` to silently return `None`
#1648 commented on
Dec 19, 2024 • 0 new comments -
IntegrityError: UNIQUE constraint failed: bionty_gene.ensembl_gene_id when repeatedly validating example dataset
#2137 commented on
Dec 19, 2024 • 0 new comments -
🎨 Integrate `nbproject` into `lamindb`
#2066 commented on
Dec 2, 2024 • 0 new comments -
✨ Add n_observations function to read n_obs from AnnData and tiledbsoma
#2097 commented on
Dec 2, 2024 • 0 new comments -
POC: Use composition instead of inheritance for user-facing Record classes
#2129 commented on
Dec 2, 2024 • 0 new comments