Changelog#
Name |
PR |
Developer |
Date |
Version |
|---|---|---|---|---|
Update BFXPipeline |
2024-05-02 |
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password is deprecated |
2024-04-25 |
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Use more general ICD website as source |
2024-04-11 |
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Pandas 3.0.0 fix |
2024-04-11 |
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Remove functions from repr |
2024-04-11 |
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Add new ICD 10-CM |
2024-04-04 |
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🔇 Remove py version warning |
2024-03-27 |
0.37.1 |
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Switch to uv for CI |
2024-03-24 |
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🐛 Catch ClientError |
2024-03-14 |
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Fix reset message |
2024-03-13 |
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📝 Added validate example to docstring |
2024-03-01 |
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🚚 Rename repo to |
2024-01-29 |
0.37.0 |
||
Add ICD ontology |
2024-01-24 |
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🚚 Rename |
2024-01-12 |
0.36.0 |
||
:sparkles: Replace pre-commit with Ruff config |
2024-01-05 |
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Add mysql-connector-python requirement to EnsemblGene |
2024-01-05 |
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🚚 Move bionty search & lookup guide to lamindb |
2023-12-04 |
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✨ Enabled ID conversion via return_field |
2023-12-02 |
0.35.2 |
||
🍱 Update EFO to version 3.57.0 |
2023-11-21 |
0.35.1 |
||
🍱 Update a few sources |
2023-11-16 |
0.35.0 |
||
🚚 Relocate bionty.lock to versionsdir |
2023-11-10 |
0.34.3 |
||
🔧 Using env variables for versionsdir |
2023-11-10 |
0.34.2 |
||
🎨 Enable set versionsdir |
2023-11-09 |
0.34.1 |
||
📝 Streamline extend guide |
2023-10-24 |
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✨ Add ncbitaxon, refactored organism |
2023-10-23 |
0.34.0 |
||
🚸 Add a backward compat parser |
2023-10-19 |
0.33.1 |
||
🚚 Rename |
2023-10-19 |
0.33.0 |
||
🚸 Suggest user to reset sources |
2023-10-13 |
0.32.0 |
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:memo: Clarify definition in readme |
2023-09-27 |
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:lipstick: Prettify changelog header |
2023-09-27 |
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✨ Add |
2023-09-13 |
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🚚 Rename |
2023-09-13 |
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🍱 Cached legacy df for genes |
2023-09-12 |
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✨ Add convert_legacy_ids for ensembl genes |
2023-09-11 |
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🔇 Silence download bar for <5MB files |
2023-09-08 |
0.31.2 |
||
✨ Add |
2023-09-07 |
0.31.1 |
||
✨ Add DevelopmentalStage ontologies |
2023-09-07 |
0.31.0 |
||
✨ Allow non-default bionty sources in LaminDB |
2023-09-07 |
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✨ Add pato to Phenotype |
2023-09-05 |
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💄 Transient download bar |
2023-09-05 |
0.30.3 |
||
Add phecodes |
2023-08-22 |
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🎨 Added |
2023-08-22 |
0.30.2 |
||
✨ Relating Bionty to other tools |
2023-08-21 |
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🚑️ Fix version recognition in lamindb |
2023-08-17 |
0.30.1 |
||
🚚 Rename |
2023-08-16 |
0.30.0 |
||
🚑️ Updated inspect params |
2023-08-15 |
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✨ Add md5 for normal URLs |
2023-08-09 |
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✨ Use latest versions of tests & add updating sources |
2023-08-09 |
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💚 Fixed tests |
2023-08-09 |
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✨ Introduce validate |
2023-08-06 |
0.29.0 |
||
📝 Fix docs |
2023-08-04 |
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✨ Added EnsemblGene class |
2023-07-31 |
0.28.0 |
||
🍱 Added all ensembl species DBs |
2023-07-31 |
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🍱 Update to ensembl-110 |
2023-07-31 |
0.27.0 |
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🍱 Include obsolete terms in .df |
2023-07-23 |
0.26.0 |
||
✨ Added |
2023-07-20 |
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🍱 Added uniprot 2023-03 |
2023-07-18 |
0.25.2 |
||
🔥 Remove top_hit from search |
2023-07-17 |
0.25.1 |
||
🚚 Rename |
2023-07-17 |
0.25.0 |
||
🚸 Case insensitive search |
2023-07-10 |
0.24.2 |
||
📝 Build docs standalone again |
2023-07-09 |
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✨ Use _bt suffix instead of _bionty for Bionty objects in docs |
2023-07-09 |
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⬆️ No longer pinning lamin-logger |
2023-06-30 |
0.24.1 |
||
🏗️ Replace children with parents, migrate assets to django instance |
2023-06-28 |
0.24.0 |
||
🎨 Log=False to turn off logging in inspect |
2023-06-22 |
0.23.1 |
||
🔈 Fixed logging of inspect, added casing check |
2023-06-21 |
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🍱 Add more phenotype ontologies |
2023-06-20 |
0.23.0 |
||
✨ Add case_sensitive to inspect and search |
2023-06-19 |
0.22.0 |
||
🍱 Fetch latest ontology versions |
2023-06-19 |
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🐛 Fix passing empty strings to map_synonyms |
2023-06-17 |
0.21.4 |
||
🧪 More tests for handle sources |
2023-06-16 |
0.21.3 |
||
🚀 Fix coverage of unit tests |
2023-06-16 |
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🎨 Default to name field for map_synonyms |
2023-06-16 |
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🚚 Update tuple name of search result |
2023-06-15 |
0.21.2 |
||
🚚 Change species to vertebrte for ensembl |
2023-06-15 |
0.21.1 |
||
🔥 Remove |
2023-06-15 |
0.21.0 |
||
🚚 Rename |
2023-06-15 |
|||
♻️ Harmonize code for Gene, Protein, CellMarker |
2023-06-15 |
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🚚 Move lookup to logger |
2023-06-14 |
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🧪 Properly test ontology_to_df |
2023-06-14 |
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🍱 Drop id, version columns |
2023-06-14 |
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⚰️ Remove dead code |
2023-06-14 |
|||
🚚 Rename |
2023-06-14 |
|||
✨ Lookup refactor to return multiple records Breaking |
2023-06-14 |
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✨ New implementation of lookup |
2023-06-13 |
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🚚 Renamed sources_local |
2023-06-13 |
|||
✨ Add fields |
2023-06-13 |
|||
🐛 Fix filtering & remove bioregistry & refactoring |
2023-06-13 |
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🐛 Fixed index bug in search |
2023-06-12 |
0.20.0 |
||
🔊 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 |
||
🔥 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 |
||
➖ Clean up dependencies |
2023-06-10 |
|||
🎨 Removed environment variable for loaded lamindb instance Breaking |
2023-06-09 |
0.18.0 |
||
🚚 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 |
||
🚚 Renamed version to source everywhere possible Breaking |
2023-06-07 |
0.17a3 |
||
🎨 Updated yaml parameter in parse_current_versions |
2023-06-07 |
|||
🎨 Harmonize names |
2023-06-07 |
|||
🚑 Fixed readout parsing |
2023-06-07 |
0.17a1 |
||
🧪 Add tests to versions file generation |
2023-06-07 |
|||
🎨 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 |
|||
👷 Remove nox venv |
2023-06-01 |
0.16.0 |
||
🔥 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 |
|||
🚸 Delete an incomplete file on an exception in s3_bionty_assets |
2023-05-29 |
|||
➖ Remove nbproject from production dependencies |
2023-05-29 |
|||
🚑 Added |
2023-05-29 |
0.15.1 |
||
✨ Implemented a first |
2023-05-29 |
|||
🐛 Decrease refresh_per_second in the progress bar to 10 |
2023-05-28 |
|||
➖ Replace upath and fsspec with botocore |
2023-05-28 |
|||
➖ Removed unused dependencies |
2023-05-28 |
|||
✨ Allow |
2023-05-28 |
|||
✨ Include |
2023-05-27 |
0.15.0 |
||
🩹 Also include the index field in |
2023-05-25 |
|||
💄 Prettified repr |
2023-05-25 |
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🍱 Download parquet files from |
2023-05-25 |
0.14.0 |
||
✨ 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 |
||
✏️ Fix lowercase types |
2023-05-11 |
0.13.4 |
||
⬆️ Remove lndb |
2023-05-10 |
0.13.3 |
||
🎨 Rename to internal UPath implementation and add s3 to ffspec |
2023-05-10 |
0.13.2 |
||
🎨 Add Upath, remove lndb_storage |
2023-05-10 |
0.13.1 |
||
✨ Added synonyms for CellMarker Breaking |
2023-05-09 |
0.13.0 |
||
🚚 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 |
||
🎨 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 |
||
⚡ Make sure no NAs present in the |
2023-04-23 |
0.11.5 |
||
⬆️ 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 |
||
👷 Add staging to CI |
2023-04-04 |
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💚 Add current/lndb updating on new entities |
2023-03-30 |
0.11.3 |
||
💚 Try fixing |
2023-03-27 |
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🐛 Fix field for gene and protein |
2023-03-27 |
0.11.2 |
||
🚚 Renamed to field everywhere |
2023-03-27 |
0.11.1 |
||
👷 Fix lnschema-bionty CI |
2023-03-27 |
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🚚 Rename property |
2023-03-24 |
0.11.0 |
||
✅ Add update_defaults test |
2023-03-23 |
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👷 Test against |
2023-03-23 |
|||
✨ 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 |
||
🚑 Ensure version names are strings |
2023-03-20 |
0.9.0 |
||
✨ Add pathway ontology |
2023-03-17 |
0.9.0rc1 |
||
✨ 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 |
|||
💄 Actually fix image display |
2023-03-11 |
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🐛 Fix img links |
2023-03-11 |
|||
📝 Keep improving docs |
2023-03-11 |
|||
🐛 Fix version order |
2023-03-10 |
|||
🐛 Ensure datadir is created |
2023-03-09 |
0.8.1 |
||
🐛 Fixed readout lookup |
2023-03-09 |
0.8.0 |
||
📝 A take on 3 summary bullets |
2023-03-08 |
0.8rc2 |
||
💚 Fix CI build |
2023-03-08 |
|||
📝 Improving documentation |
2023-03-08 |
|||
👷 Add entity tests |
2023-03-07 |
|||
✨ Add names/website per ontology & improve versions rich tables |
2023-03-06 |
|||
📝 Add better docstrings and docstring decorator |
2023-03-06 |
|||
🐛 Fix cellmarker ontology |
2023-03-03 |
0.8rc1 |
||
✨ Add CellLine ontology |
2023-03-03 |
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🎨 Simplify filenames |
2023-03-03 |
|||
🎨 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 |
|||
🎨 Move Species to Entity |
2023-02-27 |
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🎨 Rename EntityTable to Entity Breaking |
2023-02-26 |
|||
🎨 Add laminci |
2023-02-26 |
|||
✨ Add HCA ontology |
2023-02-21 |
|||
✨ Improve version handling |
2023-02-21 |
|||
🔥 No downloading upon import |
2023-02-20 |
|||
👷 Remove py3.7 from CI |
2023-02-20 |
|||
📝 Add better documentation & function to print currently available/active ontologies |
2023-02-17 |
|||
👷 Add HDO & improve support for multiple databases |
2023-02-15 |
|||
👷 Add GH workflow to check for version URLs |
2023-02-13 |
0.7.0 |
||
⬆️ Rename |
2023-02-13 |
|||
✨ Add human phenotype ontology |
2023-02-06 |
|||
📝 Add dev APIs to docs |
2023-02-06 |
|||
📝 Use guide/index as landing page |
2023-02-06 |
|||
🔥 Removed _logger.py |
2023-02-06 |
|||
🐛 Fix #167 |
2023-02-05 |
|||
👷 Add lamindocs secret key for CI |
2023-02-05 |
|||
✨ 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 |
|||
✨ Add progressbar to downloads |
2023-01-05 |
|||
🐛 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 |
|||
✨ Add readout to lookup |
2022-11-24 |
0.5.5 |
||
✨ Write most recent versions to |
2022-11-23 |
|||
🎨 Fetch the latest ontology from ols |
2022-11-22 |
|||
🚚 Moved readout from bioreadout into bionty |
2022-11-19 |
|||
✨ Added a local versions tracking file |
2022-11-18 |
|||
🐛 Fixed column id in curate |
2022-11-16 |
0.5.4 |
||
🩹 Removed prefix in ontology df |
2022-11-15 |
0.5.3 |
||
🎨 Default id to ontology_id |
2022-11-15 |
|||
🚚 Rename id to ontology_id for ontology df |
2022-11-11 |
0.5.2 |
||
⚡ Cache id and name for ontology |
2022-11-10 |
|||
🎨 Simplified ontology |
2022-11-10 |
|||
🐛 Fixed bug in tissue id |
2022-11-10 |
|||
⚡ Switch to cloudpath for caching |
2022-11-09 |
|||
⚡ 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 |
|||
🍱 Updated cell marker link |
2022-10-25 |
|||
🍱 Updated the species df path to use s3 |
2022-10-25 |
0.4.3 |
||
🍱 Updated gene table |
2022-10-25 |
|||
🚚 Migrated the tables to the new ids |
2022-10-24 |
0.4.2 |
||
🔥 Removed |
2022-10-20 |
0.4.1 |
||
💥 Redefine |
2022-10-12 |
0.4.0 |
||
🎨 Improve |
2022-10-11 |
0.3.2 |
||
🐛 Fix duplicated cell marker names |
2022-10-03 |
0.3.1 |
||
🍱 Added |
2022-09-27 |
0.3.0 |
||
🚚 Migrated dfs of gene, protein, cell marker to the lndb version |
2022-09-26 |
0.2.5 |
||
🚚 Rename guides to FAQ, tutorials to guide |
2022-09-05 |
|||
🔥 Remove cell_type, disease from lookup |
2022-08-29 |
0.2.4 |
||
🚚 Rename |
2022-08-28 |
0.2.3 |
||
🚚 Rename gene_symbol to symbol |
2022-08-28 |
0.2.2 |
||
🔥 Remove |
2022-08-28 |
|||
🎨 Fixed bugs in ontology class |
2022-08-28 |
0.2.1 |
||
🚚 Moved |
2022-08-27 |
|||
📝 Updated docs etc |
2022-08-27 |
|||
✅ Added more tests |
2022-08-27 |
|||
✨ Added |
2022-08-27 |
|||
✨ Added |
2022-08-26 |
0.2.0 |
||
🚚 Updated protein df, rename |
2022-08-26 |
|||
📝 Added lookup to the API ref |
2022-08-25 |
|||
🔊 Added |
2022-08-18 |
0.1.11 |
||
🚚 Rename gene_ids to gene_id |
2022-08-18 |
0.1.10 |
||
🎨 Migrate to ensembl gene reference |
2022-08-18 |
|||
🎨 Ensure |
2022-08-16 |
|||
⚡ Use display_name as common_name so that its unique |
2022-08-15 |
|||
🩹 Increased timeout |
2022-08-11 |
0.1.9 |
||
🩹 Modify |
2022-08-10 |
0.1.8 |
||
✨ Use pronto to access cell type ontology |
2022-08-08 |
0.1.7 |
||
🐛 Fixed duplicated index during curate |
2022-07-31 |
0.1.6 |
||
✨ 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 |
||
🔥 Switched logger to use lamin-logger |
2022-07-23 |
|||
✨ Allow to input columns with non-standard names |
2022-07-11 |
0.1.2 |
||
✨ Maps alias when using gene symbols |
2022-07-06 |
|||
🎨 Added a developer API |
2022-07-02 |
0.1.1 |
||
✅ Add more tests for curation, rename |
2022-07-02 |
|||
♻️ Refactor curation |
2022-07-02 |
|||
📝 Prototype index standardization |
2022-07-02 |
|||
🎨 Polish APIs and tutorials |
2022-06-30 |
|||
✨ Added MGI for mouse genes, switched to use feather for HGNC |
2022-06-29 |
|||
🍱 Added back the Protein entity |
2022-06-29 |
|||
🚚 Move hard-to-test code from bionty into asset curation |
2022-06-28 |
|||
🏗️ Simplify Bionty |
2022-06-28 |
|||
🚸 Pull disease data from bionty-assets |
2022-06-27 |
|||
🚸 Replace HGNC file access with our S3 bucket |
2022-06-26 |
|||
✅ Added disease and tissue to quickstart |
2022-06-26 |
|||
👷 Update coverage setup |
2022-06-26 |
|||
✅ Collect coverage from test nbs |
2022-06-26 |
|||
💄 Added badges for build, codecov, pypi, pre-commit |
2022-06-25 |
|||
👷 Added Codecov to the build.yml |
2022-06-25 |
|||
📝 Iterate quickstart for better readability |
2022-06-24 |
|||
💥 Improved quickstart, implemented .dataclass everywhere |
2022-06-22 |
0.1.0 |
||
🔥 Remove versioneer |
2022-06-22 |
|||
⚡ 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 |
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📝 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 |
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🔨 |
2022-06-13 |
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♻️ Refactored |
2022-06-13 |
0.1a1 |
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♻️ Refactored |
2022-06-13 |
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⚡ Speed up requests with |
2022-06-12 |
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💚 Fix docs build warnings/errors |
2022-06-10 |
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♻️ Refactored |
2022-06-10 |
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🚚 Rename |
2022-06-10 |
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🎨 Made |
2022-06-09 |
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✨ Propose new design of the entity APIs |
2022-06-07 |
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🐛 Fix |
2022-06-03 |
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🐛 Fix |
2022-06-03 |
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🎨 Implement an initial |
2022-06-02 |
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✨ Introduce |
2022-06-01 |
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✨ Introduce |
2022-06-01 |
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✨ Introduce |
2022-05-30 |