From 84c51db20d9117d8508d6f1269b7f5e5b5f4caa1 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 8 Sep 2025 02:59:27 -0400 Subject: [PATCH 1/6] Added release notes for NodeNorm v2.3.19 and v2.3.25. --- releases/v2.3.19.md | 2 +- releases/v2.3.25.md | 37 +++++++++++++++++++++++++++++++++++++ 2 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 releases/v2.3.25.md diff --git a/releases/v2.3.19.md b/releases/v2.3.19.md index 7ba7b92..74fbbc9 100644 --- a/releases/v2.3.19.md +++ b/releases/v2.3.19.md @@ -3,7 +3,7 @@ ([Babel 2025jan23](https://github.com/TranslatorSRI/Babel/blob/master/releases/2025jan23.md)) - NodeNorm: [v2.3.19](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.19) -Next release: _None as yet_ +Next release: [v2.3.25](./v2.3.25.md) Previous release: [Translator "Hammerhead" November 2024](./TranslatorHammerheadNovember2024.md) ## New features diff --git a/releases/v2.3.25.md b/releases/v2.3.25.md new file mode 100644 index 0000000..2be3b96 --- /dev/null +++ b/releases/v2.3.25.md @@ -0,0 +1,37 @@ +# NodeNorm v2.3.25 +- Babel: [2025sep1](https://stars.renci.org/var/babel_outputs/2025sep1/) + ([Babel 2025sep1](https://github.com/TranslatorSRI/Babel/blob/master/releases/2025sep1.md)) +- NodeNorm: [v2.3.25](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.25) + +Next release: _None as yet_ +Previous release: [v2.3.19](./v2.3.19.md) + +## New features +* The Babel version is now included in the `/status` endpoint (PR #315). +* Added logging of normalization so we can benchmark NodeNorm (PR #312). +* The `/query` and `/asyncquery` endpoints are now deprecated (PR #323). + +## Updates +* Improved documentation. +* Added release notes for November 2024 and January 2025. +* Updated renci-python-image to GitHub Packages. + +## Babel updates (from [Babel 2025jan23](https://github.com/TranslatorSRI/Babel/blob/master/releases/2025jan23.md)) +- TBD + +## Releases since [NodeNorm v2.3.19](./v2.3.19.md) +* [NodeNorm v2.3.20](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.20) + * Add release info for November 2024 and January 2025 by @gaurav in #308 + * Bump gunicorn from 22.0.0 to 23.0.0 by @dependabot in #310 +* [NodeNorm v2.3.21](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.21) + * Incremented version (forgot to do that in the previous release). +* [NodeNorm v2.3.22](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.22) + * Added normalization logging by @gaurav in #312 +* [NodeNorm v2.3.23](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.23) + * Add Babel version to /status by @gaurav in #315 +* [NodeNorm v2.3.24](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.24) + * Deprecated TRAPI methods (/query and /asyncquery) by @gaurav in #323 + * Added API documentation by @gaurav in #322 + * Updated RENCI Python Image in Dockerfile. +* [NodeNorm v2.3.25](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.25) + * Removed unused/invalid imports. From b4aacafdb0c24c9adc91fee9dcd4153070cf3c85 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 8 Sep 2025 03:10:20 -0400 Subject: [PATCH 2/6] Added links to significant PRs. --- releases/v2.3.25.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/releases/v2.3.25.md b/releases/v2.3.25.md index 2be3b96..99d7386 100644 --- a/releases/v2.3.25.md +++ b/releases/v2.3.25.md @@ -7,11 +7,11 @@ Next release: _None as yet_ Previous release: [v2.3.19](./v2.3.19.md) ## New features -* The Babel version is now included in the `/status` endpoint (PR #315). -* Added logging of normalization so we can benchmark NodeNorm (PR #312). -* The `/query` and `/asyncquery` endpoints are now deprecated (PR #323). +* The Babel version is now included in the `/status` endpoint ([PR #315](https://github.com/TranslatorSRI/NodeNormalization/pull/315)). +* Added logging of normalization so we can benchmark NodeNorm ([PR #312](https://github.com/TranslatorSRI/NodeNormalization/pull/312)). ## Updates +* The `/query` and `/asyncquery` endpoints are now deprecated ([PR #323](https://github.com/TranslatorSRI/NodeNormalization/pull/323)). * Improved documentation. * Added release notes for November 2024 and January 2025. * Updated renci-python-image to GitHub Packages. From fd54e5b9930219d4c5e45f45e4521ee9dc90ed6a Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Wed, 24 Sep 2025 16:38:52 -0400 Subject: [PATCH 3/6] Added Babel release notes. --- releases/v2.3.25.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/releases/v2.3.25.md b/releases/v2.3.25.md index 99d7386..f6f3860 100644 --- a/releases/v2.3.25.md +++ b/releases/v2.3.25.md @@ -1,4 +1,4 @@ -# NodeNorm v2.3.25 +# NodeNorm v2.3.26 - Babel: [2025sep1](https://stars.renci.org/var/babel_outputs/2025sep1/) ([Babel 2025sep1](https://github.com/TranslatorSRI/Babel/blob/master/releases/2025sep1.md)) - NodeNorm: [v2.3.25](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.25) @@ -16,8 +16,11 @@ Previous release: [v2.3.19](./v2.3.19.md) * Added release notes for November 2024 and January 2025. * Updated renci-python-image to GitHub Packages. -## Babel updates (from [Babel 2025jan23](https://github.com/TranslatorSRI/Babel/blob/master/releases/2025jan23.md)) -- TBD +## Babel updates (from [Babel 2025sep1](https://github.com/TranslatorSRI/Babel/blob/master/releases/2025sep1.md)) +- [MAJOR] Information content values were incorrectly calculated as `100` for some cliques when they were in fact lower. +- [MAJOR] UMLS proteins have now been removed from chemicals so that they only appear in proteins. +- [MAJOR] Improved DrugChemical conflation order. +- [MAJOR] Added secondary identifiers for ChEBI. ## Releases since [NodeNorm v2.3.19](./v2.3.19.md) * [NodeNorm v2.3.20](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.20) @@ -35,3 +38,6 @@ Previous release: [v2.3.19](./v2.3.19.md) * Updated RENCI Python Image in Dockerfile. * [NodeNorm v2.3.25](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.25) * Removed unused/invalid imports. +* [NodeNorm v2.3.26](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.25) + * Bump deepdiff from 5.8.1 to 8.6.1 by @dependabot in #328 + * Bump requests from 2.32.0 to 2.32.4 by @dependabot in #319 From 32591a2d52698182090404343e41fadb4eece669 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Wed, 24 Sep 2025 16:39:13 -0400 Subject: [PATCH 4/6] Renamed release notes to v2.3.26. --- releases/{v2.3.25.md => v2.3.26.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename releases/{v2.3.25.md => v2.3.26.md} (100%) diff --git a/releases/v2.3.25.md b/releases/v2.3.26.md similarity index 100% rename from releases/v2.3.25.md rename to releases/v2.3.26.md From fd03b816843e5b2cfe9e7a881746fb74bb9bcf02 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Wed, 24 Sep 2025 16:39:57 -0400 Subject: [PATCH 5/6] Updated previous version. --- releases/v2.3.19.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/releases/v2.3.19.md b/releases/v2.3.19.md index 74fbbc9..fb4b6f5 100644 --- a/releases/v2.3.19.md +++ b/releases/v2.3.19.md @@ -3,7 +3,7 @@ ([Babel 2025jan23](https://github.com/TranslatorSRI/Babel/blob/master/releases/2025jan23.md)) - NodeNorm: [v2.3.19](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.19) -Next release: [v2.3.25](./v2.3.25.md) +Next release: [v2.3.26](./v2.3.26.md) Previous release: [Translator "Hammerhead" November 2024](./TranslatorHammerheadNovember2024.md) ## New features From 1219729d228b445e73904309d62851dbb1ac4e0d Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Wed, 24 Sep 2025 16:42:33 -0400 Subject: [PATCH 6/6] Updated NodeNorm version. --- releases/v2.3.26.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/releases/v2.3.26.md b/releases/v2.3.26.md index f6f3860..100b831 100644 --- a/releases/v2.3.26.md +++ b/releases/v2.3.26.md @@ -1,7 +1,7 @@ # NodeNorm v2.3.26 - Babel: [2025sep1](https://stars.renci.org/var/babel_outputs/2025sep1/) ([Babel 2025sep1](https://github.com/TranslatorSRI/Babel/blob/master/releases/2025sep1.md)) -- NodeNorm: [v2.3.25](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.25) +- NodeNorm: [v2.3.26](https://github.com/TranslatorSRI/NodeNormalization/releases/tag/v2.3.26) Next release: _None as yet_ Previous release: [v2.3.19](./v2.3.19.md)