v0.2.7

What's Changed

• Fixed a bug where the 'skip_annotators' option was being ignored by @daikiad in #108
• Microbial trait template by @realmarcin in #109

New Contributors

• @daikiad made their first contribution in #108

Full Changelog: v0.2.6...v0.2.7

v0.2.6

What's Changed

• Added streamlit app for spindoctor by @cmungall in #101
• Study class as tree root in environment_sample template by @sujaypatil96 in #104
• update sections in README by @sujaypatil96 in #105

New Contributors

• @sujaypatil96 made their first contribution in #104

Full Changelog: v0.2.5...v0.2.6

v0.2.5

What's Changed

• Add diagnostic_procedure template by @caufieldjh in #29
• Fix for web-ontogpt not working on new install by @caufieldjh in #85
• geneweaver format by @cmungall in #89
• re-ran notebook by @cmungall in #90
• re-ran notebooks for enrichGPT by @cmungall in #95
• Update documentation by @caufieldjh in #92
• Autogenerate docs by @caufieldjh in #98
• Fix for doc generation by @caufieldjh in #100

Full Changelog: v0.2.4...v0.2.5

v0.2.4

What's Changed

• Adding schema for ontology issues in github. refactor enrichment by @cmungall in #83
• p-value templates with edited end markers to run multiple independent… by @realmarcin in #82

Full Changelog: v0.2.3...v0.2.4

v0.2.3

What's Changed

• Added command to generate mock clinical notes by @justaddcoffee in #74
• Bump version of oaklib by @cmungall in #73
• msigdb hallmark gene sets by @realmarcin in #78
• use prompts for enrichment by @cmungall in #80
• fixing gene sets and updating analysis by @cmungall in #81

Full Changelog: v0.2.2...v0.2.3

v0.2.2

What's Changed

• Adding gene set enrichment by @cmungall in #30
• enrichment by @cmungall in #31
• README updates; add project.Makefile by @caufieldjh in #32
• allow use of different models, entailing different API endpoints. extending enrichment comparison. by @cmungall in #34
• Add CITATION and version updater by @caufieldjh in #35
• Ingest and extract things from literature about inflammatory bowel disease by @justaddcoffee in #36
• eval enrich by @cmungall in #37
• Create dental-restoration-material-composite-polymer-1.txt by @wdduncan in #53
• Create dental-restoration-material-composite-resin-1.txt by @wdduncan in #52
• Create dental-restoration-material-ceramic-composite-1.txt by @wdduncan in #51
• Create dental-restoration-material-ceramic-composite-resin-1.txt by @wdduncan in #50
• Create dental-restoration-material-ceramic-composite-polymer-2.txt by @wdduncan in #49
• Create dental-restoration-material-ceramic-composite-polymer-1.txt by @wdduncan in #48
• Create dental-restoration-material-ceramic-composite-polymer-resin-2.txt by @wdduncan in #47
• Create dental-restoration-material-ceramic-composite-polymer-resin-1.txt by @wdduncan in #46
• Create dental-restoration-material-composite-2.txt by @wdduncan in #45
• Create dental-restoration-material-composite-1.txt by @wdduncan in #44
• Create dental-restoration-material-polymer-1.txt by @wdduncan in #42
• Create dental-restoration-material-resin-2.txt by @wdduncan in #41
• Create dental-restoration-material-ceramic-2.txt by @wdduncan in #39
• Create dental-restoration-material-ceramic-1.txt by @wdduncan in #38
• Create dental-restoration-material-resin-1.txt by @wdduncan in #40
• Create dental-restoration-material-polymer-2.txt by @wdduncan in #43
• similarity by @cmungall in #57
• Add option to provide path to input file by @caufieldjh in #56
• Bicluster enrichment by @realmarcin in #62
• Added command and code for computing euclidian distances between embeddings by @justaddcoffee in #58
• Flake8 fixes + lint by @hrshdhgd in #63
• enrichment changes by @cmungall in #65
• Missed parenthesis for random.SystemRamdom() by @hrshdhgd in #67
• Change citation updater in Makefile to get_version by @caufieldjh in #68
• Raise FileNotFoundError if filepath for extract is missing by @caufieldjh in #72
• Makefile uses all templates by @caufieldjh in #69
• interactive-mode by @cmungall in #71

New Contributors

• @wdduncan made their first contribution in #53

Full Changelog: v0.2.1...v0.2.2

v0.2.1

What's Changed

• Playing around: adding a phenotype extractor by @matentzn in #14
• add unit test to makefile by @cmungall in #16
• Linted and minor flake8 edits by @hrshdhgd in #15
• Add linter to workflow by @hrshdhgd in #17
• Improve dependencies, add a web optional by @vemonet in #21
• add recipe for test by @sierra-moxon in #23
• added pad krapow recipe by @justaddcoffee in #25
• Add recipe URL by @pkalita-lbl in #24
• Add Walforf Salad URL by @caufieldjh in #26
• Add rajma pulao to recipe-urls.csv by @turbomam in #27

New Contributors

• @matentzn made their first contribution in #14
• @vemonet made their first contribution in #21
• @sierra-moxon made their first contribution in #23
• @justaddcoffee made their first contribution in #25
• @pkalita-lbl made their first contribution in #24
• @turbomam made their first contribution in #27

Full Changelog: v0.2.0...v0.2.1

v0.2.0

What's Changed

• If output is YAML, codecs not needed by @hrshdhgd in #1
• Readme updates and other doc copyedits by @caufieldjh in #2
• owl generation by @cmungall in #7
• three cases for 'environmental_sample' by @realmarcin in #8
• Env study test cases by @realmarcin in #10
• refactor tests by @cmungall in #12

New Contributors

• @hrshdhgd made their first contribution in #1
• @caufieldjh made their first contribution in #2
• @cmungall made their first contribution in #7
• @realmarcin made their first contribution in #8

Full Changelog: v0.1.0...v0.2.0

v0.1.1

Full Changelog: https://github.com/monarch-initiative/ontogpt/commits/v0.1.1

v0.1.0

Full Changelog: https://github.com/monarch-initiative/ontogpt/commits/v0.1.0