Changelog#
Name |
PR |
User |
Date |
Patch |
|---|---|---|---|---|
♻️ New implementation of lookup |
2023-06-13 |
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:sparkles: Renamed sources_local |
2023-06-13 |
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Add fields |
2023-06-13 |
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:bug: Fix filtering & remove bioregistry & refactoring |
2023-06-13 |
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🐛 Fixed index bug in fuzzy_match |
2023-06-12 |
0.20.0 |
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🔊 Improved inspect logging |
2023-06-12 |
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♻️ Removed curate, updated inspect guide Breaking |
2023-06-12 |
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🚑 Fixed lamindb instance error and refactored source matching |
2023-06-11 |
0.19.1 |
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🔥 No longer checks compat |
2023-06-10 |
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🎨 Always regenerate |
2023-06-10 |
0.19.0 |
||
🐛 Fix LAMINDB_INSTANCE_LOADED on Windows |
2023-06-10 |
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📝 Fix notebook execution |
2023-06-10 |
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🚚 Renamed source path variables |
2023-06-10 |
0.18.1 |
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➖ Clean up dependencies |
2023-06-10 |
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🎨 Removed environment variable for loaded lamindb instance Breaking |
2023-06-09 |
0.18.0 |
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🚚 Move img folder to guide |
2023-06-09 |
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📝 Re-organize docs |
2023-06-08 |
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📝 Fix API ref |
2023-06-08 |
0.17.0 |
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🚚 Renamed version to source everywhere possible Breaking |
2023-06-07 |
0.17a3 |
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🎨 Updated yaml parameter in parse_current_versions |
2023-06-07 |
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🎨 Harmonize names |
2023-06-07 |
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🚑 Fixed readout parsing |
2023-06-07 |
0.17a1 |
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🧪 Add tests to versions file generation |
2023-06-07 |
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🎨 Use the same code to create and update local yaml |
2023-06-06 |
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♻️ Changed yaml format to have species as keys, refactored versioning Breaking |
2023-06-04 |
0.17a1 |
||
✨ Add improved species support Breaking |
2023-06-04 |
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👷 Remove nox venv |
2023-06-01 |
0.16.0 |
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🔥 Remove global lookup Breaking |
2023-05-31 |
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🎨 Default to return df when displaying versions |
2023-05-30 |
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✨ Add GO |
2023-05-30 |
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🚸 Delete an incomplete file on an exception in s3_bionty_assets |
2023-05-29 |
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➖ Remove nbproject from production dependencies |
2023-05-29 |
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🚑 Added |
2023-05-29 |
0.15.1 |
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✨ Implemented a first |
2023-05-29 |
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🐛 Decrease refresh_per_second in the progress bar to 10 |
2023-05-28 |
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➖ Replace upath and fsspec with botocore |
2023-05-28 |
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➖ Removed unused dependencies |
2023-05-28 |
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✨ Allow |
2023-05-28 |
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✨ Include |
2023-05-27 |
0.15.0 |
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🩹 Also include the index field in |
2023-05-25 |
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💄 Prettified repr |
2023-05-25 |
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🍱 Download parquet files from |
2023-05-25 |
0.14.0 |
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✨ Implement |
2023-05-24 |
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🍱 Added |
2023-05-23 |
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✨ Add |
2023-05-15 |
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🐛 Fix DO metadata |
2023-05-13 |
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✨ Add Drug entity |
2023-05-13 |
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👷 Fix non-process safe code |
2023-05-11 |
0.13.5 |
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✏️ Fix lowercase types |
2023-05-11 |
0.13.4 |
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⬆️ Remove lndb |
2023-05-10 |
0.13.3 |
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🎨 Rename to internal UPath implementation and add s3 to ffspec |
2023-05-10 |
0.13.2 |
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🎨 Add Upath, remove lndb_storage |
2023-05-10 |
0.13.1 |
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✨ Added synonyms for CellMarker Breaking |
2023-05-09 |
0.13.0 |
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🚚 Deprecate ‘database’ parameter and replace it with ‘source’ Breaking |
2023-05-08 |
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🚚 Move s3_bionty_assets |
2023-05-08 |
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📝 Improve lookup docs |
2023-05-06 |
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🎨 Add more flexible prefixes |
2023-05-02 |
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🎨 Improve print versions |
2023-05-02 |
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📌 No pinning of lndb-storage version |
2023-04-27 |
0.12.1 |
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🎨 Update lnschema-bionty |
2023-04-27 |
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🎨 Change |
2023-04-27 |
0.12.0 |
||
🐛 Fix pathway ontology |
2023-04-26 |
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💚 Fix bionty-asset instance for file upload |
2023-04-26 |
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👷 Sync staging into main |
2023-04-25 |
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🚑 Fix lookup for empty strings |
2023-04-23 |
0.11.6 |
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⚡ Make sure no NAs present in the |
2023-04-23 |
0.11.5 |
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⬆️ Pronto>=2.5.4, removed cached_property dep for py3.7 |
2023-04-23 |
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⚡ Improve the speed loading of ontology df |
2023-04-19 |
0.11.4 |
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👷 Add staging to CI |
2023-04-04 |
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💚 Add current/lndb updating on new entities |
2023-03-30 |
0.11.3 |
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💚 Try fixing |
2023-03-27 |
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🐛 Fix field for gene and protein |
2023-03-27 |
0.11.2 |
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🚚 Renamed to field everywhere |
2023-03-27 |
0.11.1 |
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👷 Fix lnschema-bionty CI |
2023-03-27 |
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🚚 Rename property |
2023-03-24 |
0.11.0 |
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✅ Add update_defaults test |
2023-03-23 |
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👷 Test against |
2023-03-23 |
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✨ Move ID from Entity to curate Breaking |
2023-03-23 |
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🐛 Fix removeprefix 3.8 & versions pathing |
2023-03-22 |
0.10.1 |
||
📝 Updated the curation notebook for cellmarker |
2023-03-22 |
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🍱 Updated CellMarker assets Breaking |
2023-03-21 |
0.10.0 |
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🚑 Ensure version names are strings |
2023-03-20 |
0.9.0 |
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✨ Add pathway ontology |
2023-03-17 |
0.9.0rc1 |
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✨ Add compatibility functions |
2023-03-17 |
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✨ Add latest version inference if only db is passed |
2023-03-14 |
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🐛 Fix default ids |
2023-03-14 |
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Add md5 sums |
2023-03-13 |
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🎨 Fixed case sensitivity, lookup output as namedtuple |
2023-03-11 |
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💥 Lookup returns the full record Breaking |
2023-03-11 |
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💄 Actually fix image display |
2023-03-11 |
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🐛 Fix img links |
2023-03-11 |
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📝 Keep improving docs |
2023-03-11 |
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🐛 Fix version order |
2023-03-10 |
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🐛 Ensure datadir is created |
2023-03-09 |
0.8.1 |
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🐛 Fixed readout lookup |
2023-03-09 |
0.8.0 |
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📝 A take on 3 summary bullets |
2023-03-08 |
0.8rc2 |
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💚 Fix CI build |
2023-03-08 |
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📝 Improving documentation |
2023-03-08 |
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👷 Add entity tests |
2023-03-07 |
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✨ Add names/website per ontology & improve versions rich tables |
2023-03-06 |
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📝 Add better docstrings and docstring decorator |
2023-03-06 |
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🐛 Fix cellmarker ontology |
2023-03-03 |
0.8rc1 |
||
✨ Add CellLine ontology |
2023-03-03 |
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🎨 Simplify filenames |
2023-03-03 |
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🎨 Deduce filenames on the fly for non-S3 Entites |
2023-03-01 |
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📝 Simplify FAQ |
2023-02-27 |
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🎨 Simplify ontology accesses |
2023-02-27 |
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🎨 Move Species to Entity |
2023-02-27 |
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🎨 Rename EntityTable to Entity Breaking |
2023-02-26 |
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🎨 Add laminci |
2023-02-26 |
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✨ Add HCA ontology |
2023-02-21 |
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✨ Improve version handling |
2023-02-21 |
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🔥 No downloading upon import |
2023-02-20 |
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👷 Remove py3.7 from CI |
2023-02-20 |
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📝 Add better documentation & function to print currently available/active ontologies |
2023-02-17 |
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👷 Add HDO & improve support for multiple databases |
2023-02-15 |
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👷 Add GH workflow to check for version URLs |
2023-02-13 |
0.7.0 |
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⬆️ Rename |
2023-02-13 |
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✨ Add human phenotype ontology |
2023-02-06 |
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📝 Add dev APIs to docs |
2023-02-06 |
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📝 Use guide/index as landing page |
2023-02-06 |
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🔥 Removed _logger.py |
2023-02-06 |
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🐛 Fix #167 |
2023-02-05 |
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👷 Add lamindocs secret key for CI |
2023-02-05 |
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✨ Added case_sensitive to curate |
2023-01-31 |
0.6.5 |
||
🚑 Fix version key type |
2023-01-18 |
0.6.4 |
||
🚚 Rename species common_name to name |
2023-01-17 |
0.6.3 |
||
🎨 Changed version filename separator from |
to ___ |
2023-01-16 |
||
🐛 Fix docs |
2023-01-12 |
0.6.1 |
||
👷 Expand CI to python 3.7-3.10 |
2023-01-12 |
0.6.0 |
||
✨ Pull species table dynamically from Ensembl |
2023-01-05 |
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✨ Add progressbar to downloads |
2023-01-05 |
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🐛 Fixed id=name bug |
2022-12-09 |
0.5.7 |
||
♻️ Refactor version files |
2022-12-08 |
0.5.6 |
||
✨ Added ontology_info |
2022-12-01 |
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✨ Add readout to lookup |
2022-11-24 |
0.5.5 |
||
✨ Write most recent versions to |
2022-11-23 |
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🎨 Fetch the latest ontology from ols |
2022-11-22 |
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🚚 Moved readout from bioreadout into bionty |
2022-11-19 |
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✨ Added a local versions tracking file |
2022-11-18 |
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🐛 Fixed column id in curate |
2022-11-16 |
0.5.4 |
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🩹 Removed prefix in ontology df |
2022-11-15 |
0.5.3 |
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🎨 Default id to ontology_id |
2022-11-15 |
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🚚 Rename id to ontology_id for ontology df |
2022-11-11 |
0.5.2 |
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⚡ Cache id and name for ontology |
2022-11-10 |
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🎨 Simplified ontology |
2022-11-10 |
|||
🐛 Fixed bug in tissue id |
2022-11-10 |
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⚡ Switch to cloudpath for caching |
2022-11-09 |
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⚡ Cache species table |
2022-11-06 |
0.5.1 |
||
📝 Link the species df to bionty-assets |
2022-10-25 |
0.5.0 |
||
🍱 Updated protein table |
2022-10-25 |
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🍱 Updated cell marker link |
2022-10-25 |
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🍱 Updated the species df path to use s3 |
2022-10-25 |
0.4.3 |
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🍱 Updated gene table |
2022-10-25 |
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🚚 Migrated the tables to the new ids |
2022-10-24 |
0.4.2 |
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🔥 Removed |
2022-10-20 |
0.4.1 |
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💥 Redefine |
2022-10-12 |
0.4.0 |
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🎨 Improve |
2022-10-11 |
0.3.2 |
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🐛 Fix duplicated cell marker names |
2022-10-03 |
0.3.1 |
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🍱 Added |
2022-09-27 |
0.3.0 |
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🚚 Migrated dfs of gene, protein, cell marker to the lndb version |
2022-09-26 |
0.2.5 |
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🚚 Rename guides to FAQ, tutorials to guide |
2022-09-05 |
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🔥 Remove cell_type, disease from lookup |
2022-08-29 |
0.2.4 |
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🚚 Rename |
2022-08-28 |
0.2.3 |
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🚚 Rename gene_symbol to symbol |
2022-08-28 |
0.2.2 |
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🔥 Remove |
2022-08-28 |
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🎨 Fixed bugs in ontology class |
2022-08-28 |
0.2.1 |
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🚚 Moved |
2022-08-27 |
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📝 Updated docs etc |
2022-08-27 |
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✅ Added more tests |
2022-08-27 |
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✨ Added |
2022-08-27 |
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✨ Added |
2022-08-26 |
0.2.0 |
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🚚 Updated protein df, rename |
2022-08-26 |
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📝 Added lookup to the API ref |
2022-08-25 |
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🔊 Added |
2022-08-18 |
0.1.11 |
||
🚚 Rename gene_ids to gene_id |
2022-08-18 |
0.1.10 |
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🎨 Migrate to ensembl gene reference |
2022-08-18 |
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🎨 Ensure |
2022-08-16 |
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⚡ Use display_name as common_name so that its unique |
2022-08-15 |
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🩹 Increased timeout |
2022-08-11 |
0.1.9 |
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🩹 Modify |
2022-08-10 |
0.1.8 |
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✨ Use pronto to access cell type ontology |
2022-08-08 |
0.1.7 |
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🐛 Fixed duplicated index during curate |
2022-07-31 |
0.1.6 |
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✨ Added |
2022-07-31 |
0.1.5 |
||
🔥 Removed duplicated code in lookup |
2022-07-28 |
0.1.4 |
||
✨ Added shortcuts for looking up static sets |
2022-07-28 |
0.1.3 |
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🔥 Switched logger to use lamin-logger |
2022-07-23 |
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✨ Allow to input columns with non-standard names |
2022-07-11 |
0.1.2 |
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✨ Maps alias when using gene symbols |
2022-07-06 |
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🎨 Added a developer API |
2022-07-02 |
0.1.1 |
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✅ Add more tests for curation, rename |
2022-07-02 |
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♻️ Refactor curation |
2022-07-02 |
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📝 Prototype index standardization |
2022-07-02 |
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🎨 Polish APIs and tutorials |
2022-06-30 |
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✨ Added MGI for mouse genes, switched to use feather for HGNC |
2022-06-29 |
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🍱 Added back the Protein entity |
2022-06-29 |
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🚚 Move hard-to-test code from bionty into asset curation |
2022-06-28 |
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🏗️ Simplify Bionty |
2022-06-28 |
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🚸 Pull disease data from bionty-assets |
2022-06-27 |
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🚸 Replace HGNC file access with our S3 bucket |
2022-06-26 |
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✅ Added disease and tissue to quickstart |
2022-06-26 |
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👷 Update coverage setup |
2022-06-26 |
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✅ Collect coverage from test nbs |
2022-06-26 |
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💄 Added badges for build, codecov, pypi, pre-commit |
2022-06-25 |
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👷 Added Codecov to the build.yml |
2022-06-25 |
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📝 Iterate quickstart for better readability |
2022-06-24 |
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💥 Improved quickstart, implemented .dataclass everywhere |
2022-06-22 |
0.1.0 |
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🔥 Remove versioneer |
2022-06-22 |
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⚡ Implemented pickling of dataclasses, refactored static class into |
2022-06-22 |
0.1a3 |
||
🚚 Renamed Celltype to CellType, fixed gene Entry fields |
2022-06-17 |
0.1a2 |
||
📝 Rewrite landing page and rename tasks |
2022-06-17 |
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✨ Added static class |
2022-06-16 |
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💄 Prettified ontology docstring |
2022-06-15 |
|||
🔨 |
2022-06-13 |
|||
♻️ Refactored |
2022-06-13 |
0.1a1 |
||
♻️ Refactored |
2022-06-13 |
|||
⚡ Speed up requests with |
2022-06-12 |
|||
💚 Fix docs build warnings/errors |
2022-06-10 |
|||
♻️ Refactored |
2022-06-10 |
|||
🚚 Rename |
2022-06-10 |
|||
🎨 Made |
2022-06-09 |
|||
✨ Propose new design of the entity APIs |
2022-06-07 |
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🐛 Fix |
2022-06-03 |
|||
🐛 Fix |
2022-06-03 |
|||
🎨 Implement an initial |
2022-06-02 |
|||
✨ Introduce |
2022-06-01 |
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✨ Introduce |
2022-06-01 |
|||
✨ Introduce |
2022-05-30 |