Changelog#

Name

PR

User

Date

Patch

✨ Implemented a first fuzzy_match method

380

sunnyosun

2023-05-29

πŸ› Decrease refresh_per_second in the progress bar to10

379

Koncopd

2023-05-28

βž– Replace upath and fsspec with botocore

376

Koncopd

2023-05-28

βž– Removed unused dependencies

377

sunnyosun

2023-05-28

✨ Allow map_synonyms for every entity

375

sunnyosun

2023-05-28

✨ Include synonyms, definition columns in parquet

372

sunnyosun

2023-05-27

0.15.0

🩹 Also include the index field in BiontyField

370

sunnyosun

2023-05-25

πŸ’„ Prettified repr

369

sunnyosun

2023-05-25

🍱 Download parquet files from s3://bionty-assets

365

sunnyosun

2023-05-25

0.14.0

✨ Implement map_synonyms

359

Zethson

2023-05-24

🍱 Added children column to ontology parquet files

363

sunnyosun

2023-05-23

✨ Add inspect

356

Zethson

2023-05-15

πŸ› Fix DO metadata

355

Zethson

2023-05-13

✨ Add Drug entity

352

Zethson

2023-05-13

πŸ‘· Fix non-process safe code

350

jlricon

2023-05-11

0.13.5

✏️ Fix lowercase types

348

jlricon

2023-05-11

0.13.4

⬆️ Remove lndb

347

Zethson

2023-05-10

0.13.3

🎨 Rename to internal UPath implementation and add s3 to ffspec

346

Zethson

2023-05-10

0.13.2

🎨 Add Upath, remove lndb_storage

344

Zethson

2023-05-10

0.13.1

✨ Added synonyms for CellMarker Breaking

340

sunnyosun

2023-05-09

0.13.0

🚚 Deprecate β€˜database’ parameter and replace it with β€˜source’ Breaking

341

Zethson

2023-05-08

🚚 Move s3_bionty_assets

339

Zethson

2023-05-08

πŸ“ Improve lookup docs

338

Zethson

2023-05-06

🎨 Add more flexible prefixes

337

Zethson

2023-05-02

🎨 Improve print versions

336

Zethson

2023-05-02

πŸ“Œ No pinning of lndb-storage version

333

sunnyosun

2023-04-27

0.12.1

🎨 Update lnschema-bionty

332

sunnyosun

2023-04-27

🎨 Change .df(), .lookup() to methods, move ._entity to private Breaking

326

sunnyosun

2023-04-27

0.12.0

πŸ› Fix pathway ontology

329

Zethson

2023-04-26

πŸ’š Fix bionty-asset instance for file upload

325

sunnyosun

2023-04-26

πŸ‘· Sync staging into main

316

Zethson

2023-04-25

πŸš‘ Fix lookup for empty strings

314

sunnyosun

2023-04-23

0.11.6

⚑ Make sure no NAs present in the entity.df.name

313

sunnyosun

2023-04-23

0.11.5

⬆️ Pronto>=2.5.4, removed cached_property dep for py3.7

312

sunnyosun

2023-04-23

⚑ Improve the speed loading of ontology df

305

sunnyosun

2023-04-19

0.11.4

πŸ‘· Add staging to CI

293

Zethson

2023-04-04

πŸ’š Add current/lndb updating on new entities

290

Zethson

2023-03-30

0.11.3

πŸ’š Try fixing lnschema-bionty CI

289

falexwolf

2023-03-27

πŸ› Fix reference_id for gene and protein

288

sunnyosun

2023-03-27

0.11.2

🚚 Renamed to reference_id everywhere

287

sunnyosun

2023-03-27

0.11.1

πŸ‘· Fix lnschema-bionty CI

284

sunnyosun

2023-03-27

🚚 Rename property lookup_col to lookup_field Breaking

283

sunnyosun

2023-03-24

0.11.0

βœ… Add update_defaults test

280

Zethson

2023-03-23

πŸ‘· Test against lnschema-bionty

279

falexwolf

2023-03-23

✨ Move ID from Entity to curate Breaking

268

Zethson

2023-03-23

πŸ› Fix removeprefix 3.8 & versions pathing

277

Zethson

2023-03-22

0.10.1

πŸ“ Updated the curation notebook for cellmarker

274

sunnyosun

2023-03-22

🍱 Updated CellMarker assets Breaking

271

sunnyosun

2023-03-21

0.10.0

πŸš‘ Ensure version names are strings

269

sunnyosun

2023-03-20

0.9.0

✨ Add pathway ontology

267

Zethson

2023-03-17

0.9.0rc1

✨ Add compatibility functions

264

Zethson

2023-03-17

✨ Add latest version inference if only db is passed

256

Zethson

2023-03-14

πŸ› Fix default ids

257

sunnyosun

2023-03-14

Add md5 sums

249

Zethson

2023-03-13

🎨 Fixed case sensitivity, lookup output as namedtuple

255

sunnyosun

2023-03-11

πŸ’₯ Lookup returns the full record Breaking

254

sunnyosun

2023-03-11

πŸ’„ Actually fix image display

253

sunnyosun

2023-03-11

πŸ› Fix img links

252

sunnyosun

2023-03-11

πŸ“ Keep improving docs

250

sunnyosun

2023-03-11

πŸ› Fix version order

248

Zethson

2023-03-10

πŸ› Ensure datadir is created

245

sunnyosun

2023-03-09

0.8.1

πŸ› Fixed readout lookup

244

sunnyosun

2023-03-09

0.8.0

πŸ“ A take on 3 summary bullets

240

falexwolf

2023-03-08

0.8rc2

πŸ’š Fix CI build

239

sunnyosun

2023-03-08

πŸ“ Improving documentation

220

Zethson

2023-03-08

πŸ‘· Add entity tests

234

Zethson

2023-03-07

✨ Add names/website per ontology & improve versions rich tables

232

Zethson

2023-03-06

πŸ“ Add better docstrings and docstring decorator

231

Zethson

2023-03-06

πŸ› Fix cellmarker ontology

230

Zethson

2023-03-03

0.8rc1

✨ Add CellLine ontology

229

Zethson

2023-03-03

🎨 Simplify filenames

227

Zethson

2023-03-03

🎨 Deduce filenames on the fly for non-S3 Entites

223

Zethson

2023-03-01

πŸ“ Simplify FAQ

218

Zethson

2023-02-27

🎨 Simplify ontology accesses

217

Zethson

2023-02-27

🎨 Move Species to Entity

216

Zethson

2023-02-27

🎨 Rename EntityTable to Entity Breaking

214

Zethson

2023-02-26

🎨 Add laminci

213

Zethson

2023-02-26

✨ Add HCA ontology

209

Zethson

2023-02-21

✨ Improve version handling

202

Zethson

2023-02-21

πŸ”₯ No downloading upon import

205

sunnyosun

2023-02-20

πŸ‘· Remove py3.7 from CI

206

sunnyosun

2023-02-20

πŸ“ Add better documentation & function to print currently available/active ontologies

201

Zethson

2023-02-17

πŸ‘· Add HDO & improve support for multiple databases

187

Zethson

2023-02-15

πŸ‘· Add GH workflow to check for version URLs

188

Zethson

2023-02-13

0.7.0

⬆️ Rename lndb_setup to lndb

189

bpenteado

2023-02-13

✨ Add human phenotype ontology

172

Zethson

2023-02-06

πŸ“ Add dev APIs to docs

183

sunnyosun

2023-02-06

πŸ“ Use guide/index as landing page

182

sunnyosun

2023-02-06

πŸ”₯ Removed _logger.py

176

sunnyosun

2023-02-06

πŸ› Fix #167

168

Zethson

2023-02-05

πŸ‘· Add lamindocs secret key for CI

173

Zethson

2023-02-05

✨ Added case_sensitive to curate

169

sunnyosun

2023-01-31

0.6.5

πŸš‘ Fix version key type

166

sunnyosun

2023-01-18

0.6.4

🚚 Rename species common_name to name

165

sunnyosun

2023-01-17

0.6.3

🎨 Changed version filename separator from

to ___

164

sunnyosun

2023-01-16

πŸ› Fix docs

162

sunnyosun

2023-01-12

0.6.1

πŸ‘· Expand CI to python 3.7-3.10

161

sunnyosun

2023-01-12

0.6.0

✨ Pull species table dynamically from Ensembl

160

sunnyosun

2023-01-05

✨ Add progressbar to downloads

159

Zethson

2023-01-05

πŸ› Fixed id=name bug

157

sunnyosun

2022-12-09

0.5.7

♻️ Refactor version files

156

sunnyosun

2022-12-08

0.5.6

✨ Added ontology_info

155

sunnyosun

2022-12-01

✨ Add readout to lookup

153

sunnyosun

2022-11-24

0.5.5

✨ Write most recent versions to _current.yaml

152

sunnyosun

2022-11-23

🎨 Fetch the latest ontology from ols

151

sunnyosun

2022-11-22

🚚 Moved readout from bioreadout into bionty

150

sunnyosun

2022-11-19

✨ Added a local versions tracking file

149

sunnyosun

2022-11-18

πŸ› Fixed column id in curate

148

sunnyosun

2022-11-16

0.5.4

🩹 Removed prefix in ontology df

147

sunnyosun

2022-11-15

0.5.3

🎨 Default id to ontology_id

146

sunnyosun

2022-11-15

🚚 Rename id to ontology_id for ontology df

145

sunnyosun

2022-11-11

0.5.2

⚑ Cache id and name for ontology

144

sunnyosun

2022-11-10

🎨 Simplified ontology

143

sunnyosun

2022-11-10

πŸ› Fixed bug in tissue id

142

sunnyosun

2022-11-10

⚑ Switch to cloudpath for caching

141

sunnyosun

2022-11-09

⚑ Cache species table

140

sunnyosun

2022-11-06

0.5.1

πŸ“ Link the species df to bionty-assets

139

sunnyosun

2022-10-25

0.5.0

🍱 Updated protein table

138

sunnyosun

2022-10-25

🍱 Updated cell marker link

137

sunnyosun

2022-10-25

🍱 Updated the species df path to use s3

136

sunnyosun

2022-10-25

0.4.3

🍱 Updated gene table

135

sunnyosun

2022-10-25

🚚 Migrated the tables to the new ids

134

sunnyosun

2022-10-24

0.4.2

πŸ”₯ Removed feature_model lookups

133

sunnyosun

2022-10-20

0.4.1

πŸ’₯ Redefine lookup in EntityTable

132

sunnyosun

2022-10-12

0.4.0

🎨 Improve todict(), added to EntityTable

131

sunnyosun

2022-10-11

0.3.2

πŸ› Fix duplicated cell marker names

130

sunnyosun

2022-10-03

0.3.1

🍱 Added description and version columns to the gene table

128

sunnyosun

2022-09-27

0.3.0

🚚 Migrated dfs of gene, protein, cell marker to the lndb version

127

sunnyosun

2022-09-26

0.2.5

🚚 Rename guides to FAQ, tutorials to guide

125

falexwolf

2022-09-05

πŸ”₯ Remove cell_type, disease from lookup

123

sunnyosun

2022-08-29

0.2.4

🚚 Rename cell_marker column to name to fit schema

122

sunnyosun

2022-08-28

0.2.3

🚚 Rename gene_symbol to symbol

121

sunnyosun

2022-08-28

0.2.2

πŸ”₯ Remove lookup.cell_marker

120

sunnyosun

2022-08-28

🎨 Fixed bugs in ontology class

119

sunnyosun

2022-08-28

0.2.1

🚚 Moved .entity to the base class

118

sunnyosun

2022-08-27

πŸ“ Updated docs etc

117

sunnyosun

2022-08-27

βœ… Added more tests

116

sunnyosun

2022-08-27

✨ Added Tissue entity

115

sunnyosun

2022-08-27

✨ Added CellMarker entity

114

sunnyosun

2022-08-26

0.2.0

🚚 Updated protein df, rename name to gene_symbol

113

sunnyosun

2022-08-26

πŸ“ Added lookup to the API ref

112

sunnyosun

2022-08-25

πŸ”Š Added n_mapped to logging

111

sunnyosun

2022-08-18

0.1.11

🚚 Rename gene_ids to gene_id

110

sunnyosun

2022-08-18

0.1.10

🎨 Migrate to ensembl gene reference

109

sunnyosun

2022-08-18

🎨 Ensure entrez_gene_id is int

108

sunnyosun

2022-08-16

⚑ Use display_name as common_name so that its unique

107

sunnyosun

2022-08-15

🩹 Increased timeout

106

sunnyosun

2022-08-11

0.1.9

🩹 Modify get_term

104

sunnyosun

2022-08-10

0.1.8

✨ Use pronto to access cell type ontology

103

sunnyosun

2022-08-08

0.1.7

πŸ› Fixed duplicated index during curate

100

sunnyosun

2022-07-31

0.1.6

✨ Added lookup module for lookups

98

sunnyosun

2022-07-31

0.1.5

πŸ”₯ Removed duplicated code in lookup

97

sunnyosun

2022-07-28

0.1.4

✨ Added shortcuts for looking up static sets

96

sunnyosun

2022-07-28

0.1.3

πŸ”₯ Switched logger to use lamin-logger

95

sunnyosun

2022-07-23

✨ Allow to input columns with non-standard names

93

sunnyosun

2022-07-11

0.1.2

✨ Maps alias when using gene symbols

92

sunnyosun

2022-07-06

🎨 Added a developer API

89

falexwolf

2022-07-02

0.1.1

βœ… Add more tests for curation, rename Table to EntityTable

88

falexwolf

2022-07-02

♻️ Refactor curation

87

falexwolf

2022-07-02

πŸ“ Prototype index standardization

86

falexwolf

2022-07-02

🎨 Polish APIs and tutorials

85

sunnyosun

2022-06-30

✨ Added MGI for mouse genes, switched to use feather for HGNC

84

sunnyosun

2022-06-29

🍱 Added back the Protein entity

83

sunnyosun

2022-06-29

🚚 Move hard-to-test code from bionty into asset curation

82

falexwolf

2022-06-28

πŸ—οΈ Simplify Bionty

81

falexwolf

2022-06-28

🚸 Pull disease data from bionty-assets

80

falexwolf

2022-06-27

🚸 Replace HGNC file access with our S3 bucket

79

falexwolf

2022-06-26

βœ… Added disease and tissue to quickstart

78

sunnyosun

2022-06-26

πŸ‘· Update coverage setup

77

sunnyosun

2022-06-26

βœ… Collect coverage from test nbs

76

sunnyosun

2022-06-26

πŸ’„ Added badges for build, codecov, pypi, pre-commit

75

sunnyosun

2022-06-25

πŸ‘· Added Codecov to the build.yml

73

sunnyosun

2022-06-25

πŸ“ Iterate quickstart for better readability

71

falexwolf

2022-06-24

πŸ’₯ Improved quickstart, implemented .dataclass everywhere

67

sunnyosun

2022-06-22

0.1.0

πŸ”₯ Remove versioneer

66

falexwolf

2022-06-22

⚑ Implemented pickling of dataclasses, refactored static class into .dataclass

65

sunnyosun

2022-06-22

0.1a3

🚚 Renamed Celltype to CellType, fixed gene Entry fields

62

sunnyosun

2022-06-17

0.1a2

πŸ“ Rewrite landing page and rename tasks

61

falexwolf

2022-06-17

✨ Added static class gene

59

sunnyosun

2022-06-16

πŸ’„ Prettified ontology docstring

58

sunnyosun

2022-06-15

πŸ”¨ Species class by default taks a common_name

56

sunnyosun

2022-06-13

♻️ Refactored species

55

sunnyosun

2022-06-13

0.1a1

♻️ Refactored species

54

sunnyosun

2022-06-13

⚑ Speed up requests with async

53

sunnyosun

2022-06-12

πŸ’š Fix docs build warnings/errors

52

falexwolf

2022-06-10

♻️ Refactored species for dual usage

51

sunnyosun

2022-06-10

🚚 Rename taxon to species

50

sunnyosun

2022-06-10

🎨 Made Ensembl its own class

45

sunnyosun

2022-06-09

✨ Propose new design of the entity APIs

44

sunnyosun

2022-06-07

πŸ› Fix gene.id fields

43

sunnyosun

2022-06-03

πŸ› Fix standardize to work on any iterables

41

sunnyosun

2022-06-03

🎨 Implement an initial .standardize() in the Ontology manager

40

sunnyosun

2022-06-02

✨ Introduce tissue

38

sunnyosun

2022-06-01

✨ Introduce disease

36

sunnyosun

2022-06-01

✨ Introduce celltype

34

sunnyosun

2022-05-30