From 2440a8cac19a94df29c494809c22ab2bf3d88d32 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 18 Aug 2025 02:04:07 +0100
Subject: [PATCH 1/2] Python 3.14: test with newer pydantic

---
 .github/workflows/ci-tests.yml | 16 ++++++++--------
 mypy-requirements.txt          |  5 +++--
 test-requirements.txt          |  5 +++--
 tox.ini                        |  5 ++---
 4 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 87ddaa71e..3d2e22d30 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -99,8 +99,8 @@ jobs:
         step: [lintreadme, shellcheck, pydocstyle]
 
     env:
-      py-semver: "3.12"
-      TOXENV: ${{ format('py312-{0}', matrix.step) }}
+      py-semver: "3.13"
+      TOXENV: ${{ format('py313-{0}', matrix.step) }}
 
     steps:
       - uses: actions/checkout@v5
@@ -129,7 +129,7 @@ jobs:
     name: No leftovers
     runs-on: ubuntu-22.04
     env:
-      py-semver: "3.12"
+      py-semver: "3.13"
     steps:
       - uses: actions/checkout@v5
         with:
@@ -203,7 +203,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
           cache: pip
 
       - name: "Test CWL ${{ matrix.cwl-version }} conformance"
@@ -240,7 +240,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
           cache: pip
           cache-dependency-path: |
             requirements.txt
@@ -272,9 +272,9 @@ jobs:
 
   macos:
     name: Test on macos-latest
-    runs-on: macos-13  # not latest, that is now an Apple Silicon M1, for which seqtk is not yet built on bioconda
+    runs-on: macos-latest
     env:
-      TOXENV: py312-unit
+      TOXENV: py313-unit
     steps:
       - uses: actions/checkout@v5
         with:
@@ -282,7 +282,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
           cache: pip
           cache-dependency-path: |
             requirements.txt
diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index a8676ac56..8f1956886 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -6,5 +6,6 @@ types-requests
 types-setuptools
 types-psutil
 types-mock
-galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<25.1; python_version < "3.14"
-galaxy-util<25.1; python_version < "3.14"
+galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<25.1
+galaxy-util<25.1
+pydantic==2.12.0a1; python_version >= "3.14"
diff --git a/test-requirements.txt b/test-requirements.txt
index cb96a7ae1..43b1ed39a 100644
--- a/test-requirements.txt
+++ b/test-requirements.txt
@@ -9,5 +9,6 @@ pytest-mock>=1.10.0
 pytest-cov
 arcp>=0.2.0
 -r requirements.txt
-galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<25.1; python_version < "3.14"
-galaxy-util<25.1; python_version < "3.14"
+galaxy-tool-util>=22.1.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<25.1
+galaxy-util<25.1
+pydantic==2.12.0a1
diff --git a/tox.ini b/tox.ini
index aa95d5941..547d63abf 100644
--- a/tox.ini
+++ b/tox.ini
@@ -44,7 +44,7 @@ passenv =
   SINGULARITY_FAKEROOT
 
 extras =
-  py3{9,10,11,12,13}-unit: deps
+  py3{9,10,11,12,13,14}-unit: deps
 
 deps =
   py3{9,10,11,12,13,14}-{unit,lint,bandit,mypy}: -rrequirements.txt
@@ -70,8 +70,7 @@ commands =
   py3{9,10,11,12,13,14}-unit: make coverage-report coverage.xml PYTEST_EXTRA="{posargs}"
   py3{9,10,11,12,13,14}-bandit: bandit -r cwltool
   py3{9,10,11,12,13,14}-lint: make flake8 format-check codespell-check
-  py3{9,10,11,12,13}-mypy: make mypy mypyc PYTEST_EXTRA="{posargs}"
-  py314-mypy: make mypyc PYTEST_EXTRA="{posargs}"
+  py3{9,10,11,12,13,14}-mypy: make mypy mypyc PYTEST_EXTRA="{posargs}"
   py312-shellcheck: make shellcheck
   py312-pydocstyle: make diff_pydocstyle_report
   py312-lintreadme: twine check {distdir}/*

From e110a602240cafb9f447408bd527c5e19cb5466e Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 18 Aug 2025 02:06:02 +0100
Subject: [PATCH 2/2] circleci: upgrade to the larger arm instance

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index fce789feb..b780bbb6c 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -16,7 +16,7 @@ jobs:
 
     machine:
       image: ubuntu-2404:current
-    resource_class: arm.medium  # 2 vCPUs
+    resource_class: arm.large  # 4 vCPUs
 
     environment:
       CIBW_ARCHS: "aarch64"