Merge remote-tracking branch 'origin/develop' into fix/always-yield-wildtype-transcript

Author: axelwalter

.github/workflows/claude-code-review.yml

@@ -24,21 +24,23 @@ jobs:
       pull-requests: read
       issues: read
       id-token: write
+    env:
+      HAS_TOKEN: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN != '' }}
 
     steps:
       - name: Checkout repository
+        if: env.HAS_TOKEN == 'true'
         uses: actions/checkout@v4
         with:
           fetch-depth: 1
 
       - name: Run Claude Code Review
+        if: env.HAS_TOKEN == 'true'
         id: claude-review
         uses: anthropics/claude-code-action@v1
         with:
           claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
           plugin_marketplaces: 'https://github.com/anthropics/claude-code.git'
           plugins: 'code-review@claude-code-plugins'
           prompt: '/code-review:code-review ${{ github.repository }}/pull/${{ github.event.pull_request.number }}'
-          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
-          # or https://code.claude.com/docs/en/cli-reference for available options
 

.github/workflows/python-test-conda-external.yml

@@ -1,10 +1,8 @@
 name: Unit tests external tools
 
 on:
-  push:
-    branches: [ main, develop ]
   pull_request:
-    branches: [ main, develop ]
+    branches: [ main, master ]
 
 jobs:
   tests-external:

CHANGELOG.md

@@ -3,15 +3,21 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v4.0.0 - 2026-03-06
+## v4.0.0 - Unreleased
+
+### `Added`
+
+- [#107](https://github.com/KohlbacherLab/epytope/pull/107) Added `EnsemblRESTAdapter` and `PyEnsemblAdapter` as drop-in replacements for `MartsAdapter` [#103](https://github.com/KohlbacherLab/epytope/issues/103) [#106](https://github.com/KohlbacherLab/epytope/issues/106)
+- Added MHCFlurry 2.0 predictor class
 
 ### `Changed`
 
 - **BREAKING**: Minimum Python version raised to 3.11, build via `pyproject.toml`
 - **BREAKING**: Removed `mhcnuggets` predictors; `mhcflurry` is now optional (`pip install epytope[mhcflurry]`)
 - Full pandas 3.0 compatibility
-- Added MHCFlurry 2.0 predictor class
 - Migrated CI to `pytest` with Python 3.11/3.12 matrix
+- [#107](https://github.com/KohlbacherLab/epytope/pull/107) Switched CI tests from `MartsAdapter` (BioMart) to `EnsemblRESTAdapter` (REST API) to eliminate flaky BioMart failures
+- [#107](https://github.com/KohlbacherLab/epytope/pull/107) Restricted external tool CI tests to PRs targeting `main`/`master` only
 
 ### `Fixed`