Changelog#

Name

PR

User

Date

Patch

๐Ÿš‘ Fix version key type

166

sunnyosun

2023-01-18

0.6.4

๐Ÿšš Rename species common_name to name

165

sunnyosun

2023-01-17

0.6.3

๐ŸŽจ Changed version filename separator from

to ___

164

sunnyosun

2023-01-16

๐Ÿ› Fix docs

162

sunnyosun

2023-01-12

0.6.1

๐Ÿ‘ท Expand CI to python 3.7-3.10

161

sunnyosun

2023-01-12

0.6.0

โœจ Pull species table dynamically from Ensembl

160

sunnyosun

2023-01-05

Add progressbar to downloads

159

Zethson

2023-01-05

๐Ÿ› Fixed id=name bug

157

sunnyosun

2022-12-09

0.5.7

โ™ป๏ธ Refactor version files

156

sunnyosun

2022-12-08

0.5.6

โœจ Added ontology_info

155

sunnyosun

2022-12-01

โœจ Add readout to lookup

153

sunnyosun

2022-11-24

0.5.5

โœจ Write most recent versions to _current.yaml

152

sunnyosun

2022-11-23

๐ŸŽจ Fetch the latest ontology from ols

151

sunnyosun

2022-11-22

๐Ÿšš Moved readout from bioreadout into bionty

150

sunnyosun

2022-11-19

โœจ Added a local versions tracking file

149

sunnyosun

2022-11-18

๐Ÿ› Fixed column id in curate

148

sunnyosun

2022-11-16

0.5.4

๐Ÿฉน Removed prefix in ontology df

147

sunnyosun

2022-11-15

0.5.3

๐ŸŽจ Default id to ontology_id

146

sunnyosun

2022-11-15

๐Ÿšš Rename id to ontology_id for ontology df

145

sunnyosun

2022-11-11

0.5.2

โšก Cache id and name for ontology

144

sunnyosun

2022-11-10

๐ŸŽจ Simplified ontology

143

sunnyosun

2022-11-10

๐Ÿ› Fixed bug in tissue id

142

sunnyosun

2022-11-10

โšก Switch to cloudpath for caching

141

sunnyosun

2022-11-09

โšก Cache species table

140

sunnyosun

2022-11-06

0.5.1

๐Ÿ“ Link the species df to bionty-assets

139

sunnyosun

2022-10-25

0.5.0

๐Ÿฑ Updated protein table

138

sunnyosun

2022-10-25

๐Ÿฑ Updated cell marker link

137

sunnyosun

2022-10-25

๐Ÿฑ Updated the species df path to use s3

136

sunnyosun

2022-10-25

0.4.3

๐Ÿฑ Updated gene table

135

sunnyosun

2022-10-25

๐Ÿšš Migrated the tables to the new ids

134

sunnyosun

2022-10-24

0.4.2

๐Ÿ”ฅ Removed feature_model lookups

133

sunnyosun

2022-10-20

0.4.1

๐Ÿ’ฅ Redefine lookup in EntityTable

132

sunnyosun

2022-10-12

0.4.0

๐ŸŽจ Improve todict(), added to EntityTable

131

sunnyosun

2022-10-11

0.3.2

๐Ÿ› Fix duplicated cell marker names

130

sunnyosun

2022-10-03

0.3.1

๐Ÿฑ Added description and version columns to the gene table

128

sunnyosun

2022-09-27

0.3.0

๐Ÿšš Migrated dfs of gene, protein, cell marker to the lndb version

127

sunnyosun

2022-09-26

0.2.5

๐Ÿšš Rename guides to FAQ, tutorials to guide

125

falexwolf

2022-09-05

๐Ÿ”ฅ Remove cell_type, disease from lookup

123

sunnyosun

2022-08-29

0.2.4

๐Ÿšš Rename cell_marker column to name to fit schema

122

sunnyosun

2022-08-28

0.2.3

๐Ÿšš Rename gene_symbol to symbol

121

sunnyosun

2022-08-28

0.2.2

๐Ÿ”ฅ Remove lookup.cell_marker

120

sunnyosun

2022-08-28

๐ŸŽจ Fixed bugs in ontology class

119

sunnyosun

2022-08-28

0.2.1

๐Ÿšš Moved .entity to the base class

118

sunnyosun

2022-08-27

๐Ÿ“ Updated docs etc

117

sunnyosun

2022-08-27

โœ… Added more tests

116

sunnyosun

2022-08-27

โœจ Added Tissue entity

115

sunnyosun

2022-08-27

โœจ Added CellMarker entity

114

sunnyosun

2022-08-26

0.2.0

๐Ÿšš Updated protein df, rename name to gene_symbol

113

sunnyosun

2022-08-26

๐Ÿ“ Added lookup to the API ref

112

sunnyosun

2022-08-25

๐Ÿ”Š Added n_mapped to logging

111

sunnyosun

2022-08-18

0.1.11

๐Ÿšš Rename gene_ids to gene_id

110

sunnyosun

2022-08-18

0.1.10

๐ŸŽจ Migrate to ensembl gene reference

109

sunnyosun

2022-08-18

๐ŸŽจ Ensure entrez_gene_id is int

108

sunnyosun

2022-08-16

โšก Use display_name as common_name so that its unique

107

sunnyosun

2022-08-15

๐Ÿฉน Increased timeout

106

sunnyosun

2022-08-11

0.1.9

๐Ÿฉน Modify get_term

104

sunnyosun

2022-08-10

0.1.8

โœจ Use pronto to access cell type ontology

103

sunnyosun

2022-08-08

0.1.7

๐Ÿ› Fixed duplicated index during curate

100

sunnyosun

2022-07-31

0.1.6

โœจ Added lookup module for lookups

98

sunnyosun

2022-07-31

0.1.5

๐Ÿ”ฅ Removed duplicated code in lookup

97

sunnyosun

2022-07-28

0.1.4

โœจ Added shortcuts for looking up static sets

96

sunnyosun

2022-07-28

0.1.3

๐Ÿ”ฅ Switched logger to use lamin-logger

95

sunnyosun

2022-07-23

โœจ Allow to input columns with non-standard names

93

sunnyosun

2022-07-11

0.1.2

โœจ Maps alias when using gene symbols

92

sunnyosun

2022-07-06

๐ŸŽจ Added a developer API

89

falexwolf

2022-07-02

0.1.1

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

88

falexwolf

2022-07-02

โ™ป๏ธ Refactor curation

87

falexwolf

2022-07-02

๐Ÿ“ Prototype index standardization

86

falexwolf

2022-07-02

๐ŸŽจ Polish APIs and tutorials

85

sunnyosun

2022-06-30

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

84

sunnyosun

2022-06-29

๐Ÿฑ Added back the Protein entity

83

sunnyosun

2022-06-29

๐Ÿšš Move hard-to-test code from bionty into asset curation

82

falexwolf

2022-06-28

๐Ÿ—๏ธ Simplify Bionty

81

falexwolf

2022-06-28

๐Ÿšธ Pull disease data from bionty-assets

80

falexwolf

2022-06-27

๐Ÿšธ Replace HGNC file access with our S3 bucket

79

falexwolf

2022-06-26

โœ… Added disease and tissue to quickstart

78

sunnyosun

2022-06-26

๐Ÿ‘ท Update coverage setup

77

sunnyosun

2022-06-26

โœ… Collect coverage from test nbs

76

sunnyosun

2022-06-26

๐Ÿ’„ Added badges for build, codecov, pypi, pre-commit

75

sunnyosun

2022-06-25

๐Ÿ‘ท Added Codecov to the build.yml

73

sunnyosun

2022-06-25

๐Ÿ“ Iterate quickstart for better readability

71

falexwolf

2022-06-24

๐Ÿ’ฅ Improved quickstart, implemented .dataclass everywhere

67

sunnyosun

2022-06-22

0.1.0

๐Ÿ”ฅ Remove versioneer

66

falexwolf

2022-06-22

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

65

sunnyosun

2022-06-22

0.1a3

๐Ÿšš Renamed Celltype to CellType, fixed gene Entry fields

62

sunnyosun

2022-06-17

0.1a2

๐Ÿ“ Rewrite landing page and rename tasks

61

falexwolf

2022-06-17

โœจ Added static class gene

59

sunnyosun

2022-06-16

๐Ÿ’„ Prettified ontology docstring

58

sunnyosun

2022-06-15

๐Ÿ”จ Species class by default taks a common_name

56

sunnyosun

2022-06-13

โ™ป๏ธ Refactored species

55

sunnyosun

2022-06-13

0.1a1

โ™ป๏ธ Refactored species

54

sunnyosun

2022-06-13

โšก Speed up requests with async

53

sunnyosun

2022-06-12

๐Ÿ’š Fix docs build warnings/errors

52

falexwolf

2022-06-10

โ™ป๏ธ Refactored species for dual usage

51

sunnyosun

2022-06-10

๐Ÿšš Rename taxon to species

50

sunnyosun

2022-06-10

๐ŸŽจ Made Ensembl its own class

45

sunnyosun

2022-06-09

โœจ Propose new design of the entity APIs

44

sunnyosun

2022-06-07

๐Ÿ› Fix gene.id fields

43

sunnyosun

2022-06-03

๐Ÿ› Fix standardize to work on any iterables

41

sunnyosun

2022-06-03

๐ŸŽจ Implement an initial .standardize() in the Ontology manager

40

sunnyosun

2022-06-02

โœจ Introduce tissue

38

sunnyosun

2022-06-01

โœจ Introduce disease

36

sunnyosun

2022-06-01

โœจ Introduce celltype

34

sunnyosun

2022-05-30