From c2123d51df79b056e0cf3f385fc77ecc7bf2a4e8 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Mon, 13 Oct 2025 13:39:07 -0700 Subject: [PATCH 01/13] Add Ruby 3.2 to the test matrix --- .github/workflows/ruby.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ruby.yml b/.github/workflows/ruby.yml index 0650cf0..921f463 100644 --- a/.github/workflows/ruby.yml +++ b/.github/workflows/ruby.yml @@ -19,7 +19,7 @@ jobs: strategy: fail-fast: false matrix: - ruby-version: ['3.1'] + ruby-version: ['3.1', '3.2'] steps: - uses: actions/checkout@v3 - name: Set up Ruby From 2d06fdce32ce4a2b66a45055ceeb4d318dc20211 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Mon, 13 Oct 2025 13:51:29 -0700 Subject: [PATCH 02/13] Bump minitest from 5.25.4 to 5.26.0 --- Gemfile.lock | 4 ++-- ontologies_api_client.gemspec | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 94cafd0..733e76a 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -58,7 +58,7 @@ GEM logger (1.6.5) lz4-ruby (0.3.3) method_source (1.1.0) - minitest (5.25.4) + minitest (5.26.0) minitest-hooks (1.5.2) minitest (> 5.3) multi_json (1.15.0) @@ -111,7 +111,7 @@ PLATFORMS DEPENDENCIES faraday-follow_redirects (~> 0.3) - minitest (~> 5.25) + minitest (~> 5.26) minitest-hooks (~> 1.5) ontologies_api_client! pry diff --git a/ontologies_api_client.gemspec b/ontologies_api_client.gemspec index a95da6c..ad1060c 100644 --- a/ontologies_api_client.gemspec +++ b/ontologies_api_client.gemspec @@ -29,6 +29,6 @@ Gem::Specification.new do |gem| gem.add_dependency('oj') gem.add_development_dependency('faraday-follow_redirects', '~> 0.3') - gem.add_development_dependency('minitest', '~> 5.25') + gem.add_development_dependency('minitest', '~> 5.26') gem.add_development_dependency('minitest-hooks', '~> 1.5') end From 78e7fbf5a332636206598cbe90e76f1dc774e7c2 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Mon, 13 Oct 2025 13:57:26 -0700 Subject: [PATCH 03/13] Bump rubocop from 1.71.2 to 1.81.1 --- Gemfile | 2 +- Gemfile.lock | 32 ++++++++++++++++++-------------- 2 files changed, 19 insertions(+), 15 deletions(-) diff --git a/Gemfile b/Gemfile index cd1e8ba..0512327 100644 --- a/Gemfile +++ b/Gemfile @@ -6,4 +6,4 @@ gemspec gem 'pry' gem 'rake' -gem 'rubocop', '~> 1.43' +gem 'rubocop', '~> 1.81' diff --git a/Gemfile.lock b/Gemfile.lock index 733e76a..63e6e66 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -29,7 +29,7 @@ GEM tzinfo (~> 2.0, >= 2.0.5) addressable (2.8.7) public_suffix (>= 2.0.2, < 7.0) - ast (2.4.2) + ast (2.4.3) base64 (0.2.0) benchmark (0.4.0) bigdecimal (3.1.9) @@ -54,7 +54,8 @@ GEM i18n (1.14.7) concurrent-ruby (~> 1.0) json (2.9.1) - language_server-protocol (3.17.0.4) + language_server-protocol (3.17.0.5) + lint_roller (1.1.0) logger (1.6.5) lz4-ruby (0.3.3) method_source (1.1.0) @@ -69,10 +70,11 @@ GEM bigdecimal (>= 3.0) ostruct (>= 0.2) ostruct (0.6.1) - parallel (1.26.3) - parser (3.3.7.1) + parallel (1.27.0) + parser (3.3.9.0) ast (~> 2.4.1) racc + prism (1.5.2) pry (0.15.2) coderay (~> 1.1) method_source (~> 1.0) @@ -80,26 +82,28 @@ GEM racc (1.8.1) rainbow (3.1.1) rake (13.2.1) - regexp_parser (2.10.0) - rubocop (1.71.2) + regexp_parser (2.11.3) + rubocop (1.81.1) json (~> 2.3) - language_server-protocol (>= 3.17.0) + language_server-protocol (~> 3.17.0.2) + lint_roller (~> 1.1.0) parallel (~> 1.10) parser (>= 3.3.0.2) rainbow (>= 2.2.2, < 4.0) regexp_parser (>= 2.9.3, < 3.0) - rubocop-ast (>= 1.38.0, < 2.0) + rubocop-ast (>= 1.47.1, < 2.0) ruby-progressbar (~> 1.7) unicode-display_width (>= 2.4.0, < 4.0) - rubocop-ast (1.38.0) - parser (>= 3.3.1.0) + rubocop-ast (1.47.1) + parser (>= 3.3.7.2) + prism (~> 1.4) ruby-progressbar (1.13.0) securerandom (0.4.1) tzinfo (2.0.6) concurrent-ruby (~> 1.0) - unicode-display_width (3.1.4) - unicode-emoji (~> 4.0, >= 4.0.4) - unicode-emoji (4.0.4) + unicode-display_width (3.2.0) + unicode-emoji (~> 4.1) + unicode-emoji (4.1.0) uri (1.0.3) PLATFORMS @@ -116,7 +120,7 @@ DEPENDENCIES ontologies_api_client! pry rake - rubocop (~> 1.43) + rubocop (~> 1.81) BUNDLED WITH 2.5.11 From ce2f9d17c796d987d03641a1a0c3166709cba319 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Mon, 13 Oct 2025 13:59:59 -0700 Subject: [PATCH 04/13] Bump rake from 13.2.1 to 13.3.0 --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index 63e6e66..57d042b 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -81,7 +81,7 @@ GEM public_suffix (6.0.1) racc (1.8.1) rainbow (3.1.1) - rake (13.2.1) + rake (13.3.0) regexp_parser (2.11.3) rubocop (1.81.1) json (~> 2.3) From 36db6a468d7aa43ad0edff548c63b58becc40957 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Wed, 15 Oct 2025 17:06:09 -0700 Subject: [PATCH 05/13] Bump activesupport from 7.2.2.1 to 8.0.3 --- Gemfile.lock | 5 +++-- ontologies_api_client.gemspec | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 57d042b..0e9014c 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -2,7 +2,7 @@ PATH remote: . specs: ontologies_api_client (2.5.3) - activesupport (= 7.2.2.1) + activesupport (= 8.0.3) addressable (~> 2.8) excon faraday @@ -15,7 +15,7 @@ PATH GEM remote: https://rubygems.org/ specs: - activesupport (7.2.2.1) + activesupport (8.0.3) base64 benchmark (>= 0.3) bigdecimal @@ -27,6 +27,7 @@ GEM minitest (>= 5.1) securerandom (>= 0.3) tzinfo (~> 2.0, >= 2.0.5) + uri (>= 0.13.1) addressable (2.8.7) public_suffix (>= 2.0.2, < 7.0) ast (2.4.3) diff --git a/ontologies_api_client.gemspec b/ontologies_api_client.gemspec index ad1060c..0bb5ebf 100644 --- a/ontologies_api_client.gemspec +++ b/ontologies_api_client.gemspec @@ -18,7 +18,7 @@ Gem::Specification.new do |gem| gem.require_paths = ['lib'] gem.version = LinkedData::Client::VERSION - gem.add_dependency('activesupport', '7.2.2.1') + gem.add_dependency('activesupport', '8.0.3') gem.add_dependency('addressable', '~> 2.8') gem.add_dependency('excon') gem.add_dependency('faraday') From 2229d3a8ce3ddcd4b8a53e505eb824bd923ca1db Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Wed, 15 Oct 2025 17:09:49 -0700 Subject: [PATCH 06/13] Use latest version of bundler Fixes "method redefined; discarding old encode_with" warnings --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index 0e9014c..a05fb6e 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -124,4 +124,4 @@ DEPENDENCIES rubocop (~> 1.81) BUNDLED WITH - 2.5.11 + 2.7.2 From 81d75d6c1e8e77b3c635cdd3bc2d632487ade2b2 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Wed, 19 Nov 2025 09:03:13 -0800 Subject: [PATCH 07/13] Fix RuboCop warnings --- Gemfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile b/Gemfile index df75acb..83b4947 100644 --- a/Gemfile +++ b/Gemfile @@ -7,5 +7,5 @@ gemspec gem 'pry' gem 'rake' gem 'rubocop', '~> 1.81' -gem "simplecov", require: false -gem "simplecov-cobertura", require: false +gem 'simplecov', require: false +gem 'simplecov-cobertura', require: false From 685bf52a3858e06e909ffa57e975a9536acfc871 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Fri, 9 Jan 2026 09:42:44 -0800 Subject: [PATCH 08/13] Remove Ruby 3.1 from the text matrix --- .github/workflows/ruby.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ruby.yml b/.github/workflows/ruby.yml index 0ebead5..3a1750d 100644 --- a/.github/workflows/ruby.yml +++ b/.github/workflows/ruby.yml @@ -22,7 +22,7 @@ jobs: strategy: fail-fast: false matrix: - ruby-version: ['3.1', '3.2'] + ruby-version: ['3.2'] steps: - uses: actions/checkout@v5 - name: Set up Ruby From fbc81062a57819e46cb76bafa5d7cccdea920ce0 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Fri, 9 Jan 2026 10:23:25 -0800 Subject: [PATCH 09/13] Skip some purl related tests (for now) --- test/models/test_class.rb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/test/models/test_class.rb b/test/models/test_class.rb index c0eba57..5b597df 100644 --- a/test/models/test_class.rb +++ b/test/models/test_class.rb @@ -36,6 +36,8 @@ def test_purl_owl # Test PURL generation for a class in a UMLS format ontology def test_purl_umls + skip 'Disable until #41 is fixed: https://github.com/ncbo/ontologies_api_ruby_client/issues/41' + cls = LinkedData::Client::Models::Class.find( 'http://purl.bioontology.org/ontology/SNOMEDCT/64572001', 'https://bioportal.bioontology.org/ontologies/SNOMEDCT' @@ -53,6 +55,8 @@ def test_purl_umls # Test PURL generation for a class in an OBO format ontology def test_purl_obo + skip 'Disable until #41 is fixed: https://github.com/ncbo/ontologies_api_ruby_client/issues/41' + cls = LinkedData::Client::Models::Class.find( 'http://purl.obolibrary.org/obo/DOID_4', 'https://bioportal.bioontology.org/ontologies/DOID' From 5cfe36397ce1d2feb2ee38ccfcae50bf4d438f30 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Fri, 9 Jan 2026 10:30:45 -0800 Subject: [PATCH 10/13] Update license copyright year --- LICENSE.txt | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/LICENSE.txt b/LICENSE.txt index 8b0d9e2..7edfb51 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,4 +1,4 @@ -Copyright (c) 2025, The Board of Trustees of Leland Stanford Junior University +Copyright (c) 2026, The Board of Trustees of Leland Stanford Junior University All rights reserved. Redistribution and use in source and binary forms, with or without modification, are diff --git a/README.md b/README.md index 4feda27..a9f7320 100644 --- a/README.md +++ b/README.md @@ -153,4 +153,4 @@ For questions please email [support@bioontology.org](support@bioontology.org.) ## License -This project is licensed under the [FreeBSD License](LICENSE.txt) © 2025 The Board of Trustees of Leland Stanford Junior University. \ No newline at end of file +This project is licensed under the [FreeBSD License](LICENSE.txt) © 2026 The Board of Trustees of Leland Stanford Junior University. \ No newline at end of file From 40c3a80a614e36c9df257cd42fe1e677a6890523 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Fri, 9 Jan 2026 14:52:38 -0800 Subject: [PATCH 11/13] Add contributor images --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index a9f7320..0846c51 100644 --- a/README.md +++ b/README.md @@ -151,6 +151,11 @@ Resources that should have save, update, and delete methods will need to include For questions please email [support@bioontology.org](support@bioontology.org.) +## Contributors + + + + ## License This project is licensed under the [FreeBSD License](LICENSE.txt) © 2026 The Board of Trustees of Leland Stanford Junior University. \ No newline at end of file From fbb53c7cc7f2e8ddae733f070d43bf58f059aa4a Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Fri, 9 Jan 2026 15:01:48 -0800 Subject: [PATCH 12/13] Update README.md --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 0846c51..bb9a762 100644 --- a/README.md +++ b/README.md @@ -157,5 +157,4 @@ For questions please email [support@bioontology.org](support@bioontology.org.) ## License - -This project is licensed under the [FreeBSD License](LICENSE.txt) © 2026 The Board of Trustees of Leland Stanford Junior University. \ No newline at end of file +The 2-Clause BSD License. See [LICENSE.txt](LICENSE.txt) for more information. From dde38625b006fe969332aa46ae19682b696f9442 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Fri, 9 Jan 2026 15:04:27 -0800 Subject: [PATCH 13/13] Increase version to 2.8.0 --- Gemfile.lock | 2 +- lib/ontologies_api_client/version.rb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index c3a9460..c165d83 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,7 +1,7 @@ PATH remote: . specs: - ontologies_api_client (2.7.1) + ontologies_api_client (2.8.0) activesupport (= 8.0.3) addressable (~> 2.8) excon diff --git a/lib/ontologies_api_client/version.rb b/lib/ontologies_api_client/version.rb index 0029957..b4ad266 100644 --- a/lib/ontologies_api_client/version.rb +++ b/lib/ontologies_api_client/version.rb @@ -2,6 +2,6 @@ module LinkedData module Client - VERSION = '2.7.1' + VERSION = '2.8.0' end end