laminlabs lamindb issues

laminlabs / lamindb

A data framework for biology.

https://docs.lamin.ai

Apache License 2.0

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issues

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Can the Curator.validate() function be more efficient?

#2154 Zethson opened 1 week ago
0
⬆️ Upgrade fsspec to 2024.10.0

#2153 Koncopd closed 1 week ago
2
⬆️ Upgrade anndata to 0.11.0

#2152 Koncopd closed 1 week ago
2
📝 Add hide-output for some cells & links to storage engines

#2151 Zethson closed 1 week ago
2
Several "! run input wasn't tracked, call `ln.track()` and re-run in arrays guide"

#2150 Zethson closed 1 week ago
0
🎨 Make EHRCurator immutable

#2149 Zethson closed 2 weeks ago
2
🚸 Enable autocompletion for inherited methods in Jupyter

#2148 Koncopd closed 2 weeks ago
6
`Curator.validate()` should not validate against synonyms and run `standardize()` under the hood

#2147 Zethson opened 2 weeks ago
0
🚚 Deprecate `BioRecord.import_from_source` in favor of `BioRecord.import_source`

#2146 Zethson closed 2 weeks ago
2
✅ Test registering GCP paths

#2145 Koncopd closed 2 weeks ago
2
🚸 Validate minimum `uid` length

#2144 falexwolf closed 2 weeks ago
4
🚸 Validate minimum `uid` length

#2143 falexwolf closed 2 weeks ago
1
✨ Warn if curating against gene symbols

#2142 Zethson closed 2 weeks ago
2
⚗️ Benchmark search

#2141 Koncopd closed 1 week ago
4
🎨 Improve saving validated output

#2140 Zethson closed 2 weeks ago
2
✨ Compute hash for files in Google Cloud Storage and Hugging Face

#2139 Koncopd closed 2 weeks ago
2
Document annotate in query tutorial

#2138 Zethson opened 2 weeks ago
0
IntegrityError: UNIQUE constraint failed: bionty_gene.ensembl_gene_id when repeatedly validating example dataset

#2137 Zethson opened 2 weeks ago
1
📝 Explain what can be registered as Artifact and show Hugging Face integration

#2136 Koncopd closed 2 weeks ago
2
🚸 Improve search

#2135 sunnyosun closed 1 week ago
11
📝 Add gene symbol usage and mapping FAQ

#2134 Zethson closed 2 weeks ago
3
🐛 Fix transfering artifacts from a source instance with fewer schema modules

#2132 sunnyosun closed 2 weeks ago
3
🐛 Fix registering Gene columns in DataFrameCurator

#2131 sunnyosun closed 2 weeks ago
2
🐛 Fix hard-coded "name" field during search

#2130 sunnyosun closed 2 weeks ago
2
POC: Use composition instead of inheritance for user-facing Record classes

#2129 falexwolf opened 2 weeks ago
0
✨ Support Hugging Face paths

#2128 Koncopd closed 2 weeks ago
5
🚸 Rename `import_from_source()` to `import_source()`

#2127 falexwolf closed 2 weeks ago
4
📝 Recursive query of parents and children example

#2126 Koncopd closed 3 weeks ago
2
⚗️ Benchmark lamindb and bionty search

#2125 Koncopd closed 1 week ago
2
AnnData automatically converts int index to str, therefore matching some Gene synonyms

#2124 felix0097 opened 3 weeks ago
14
✨ Add extra groups for all schemas

#2123 Zethson closed 3 weeks ago
2
Inherited classmethods are not shown in autocomplete in jupyter for models

#2122 Koncopd closed 2 weeks ago
0
🎨 Refactor flatten_unique

#2121 Zethson closed 3 weeks ago
2
⬆️ Release sub modules

#2120 sunnyosun closed 3 weeks ago
2
🐛 Fix list validation in Curator

#2119 sunnyosun closed 3 weeks ago
2
📝 Add parquet example to `arrays` guide

#2118 Koncopd closed 3 weeks ago
2
Loading dataset from a different instance that does not have all schemas of the current instance errors

#2117 Zethson closed 2 weeks ago
7
♻️ Refactor imports and update upath code

#2116 Koncopd closed 3 weeks ago
2
✨ Stream `pyarrow.dataset` via `Artifact.open()`

#2115 Koncopd closed 3 weeks ago
2
⬆️ Upgrade lamindb-setup

#2114 Koncopd closed 4 weeks ago
2
Importing Curator objects without an active instance - improving gating

#2113 Zethson opened 4 weeks ago
0
Reduce verbosity of `.describe()`

#2112 Zethson opened 4 weeks ago
0
✨ Need an optional way of copying data during transfer

#2111 falexwolf opened 4 weeks ago
0
Repeated `validate()` calls result in repeated stdout of `saving validated terms of XYZ`

#2110 Zethson closed 2 weeks ago
0
Improve documentation of Curator

#2109 Zethson opened 4 weeks ago
0
`add_validated_from_var_index` is suggested but it doesn't even exist anymore

#2108 Zethson opened 4 weeks ago
1
🐛 Proper numerous for Curator stdout

#2107 Zethson closed 4 weeks ago
2
✨ Recursively query parents and children

#2106 Koncopd closed 4 weeks ago
4
✨ Raise TypeError if a string is passed to `var_index` of `AnnDataCurator`

#2105 Zethson closed 2 weeks ago
3
✨ Truncate standardization output

#2103 Zethson closed 2 weeks ago
3

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