py3.14 newer pydantic

.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"

.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
@@ -272,17 +272,17 @@ 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:
           fetch-depth: 0
       - 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

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"

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

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}/*