Merge branch 'common-workflow-language:main' into main

giuseppe998e · web-flow · commit b58ded4c5fe1 · 2025-08-12T18:40:43.000+02:00
diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
@@ -20,14 +20,14 @@ jobs:
     strategy:
       matrix:
         py-ver-major: [3]
-        py-ver-minor: [9, 10, 11, 12, 13]
+        py-ver-minor: [9, 10, 11, 12, 13, 14]
       fail-fast: false
 
     env:
       py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -76,7 +76,7 @@ jobs:
       TOXENV: ${{ matrix.step }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -102,7 +102,7 @@ jobs:
     name: Confirm that codegen typescript passes tests with CWL
     runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Node
         uses: actions/setup-node@v4
       - name: Set up Python
@@ -138,7 +138,7 @@ jobs:
     steps:
       - name: Install C++ dependencies
         run: sudo apt-get install libyaml-cpp-dev
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
@@ -166,7 +166,7 @@ jobs:
     runs-on: ubuntu-24.04
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -192,7 +192,7 @@ jobs:
   build_test_container:
     runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: record schema-salad version
         run: |
           python3 -m venv env
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -22,7 +22,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         # We must fetch at least the immediate parents so that if this is
         # a pull request then we can checkout the head.
diff --git a/.github/workflows/quay-publish.yml b/.github/workflows/quay-publish.yml
@@ -8,7 +8,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Get image tags
         id: image_tags
         run: |
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -27,11 +27,11 @@ jobs:
             build: "*musllinux*"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name != 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name == 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
@@ -44,7 +44,7 @@ jobs:
       #     platforms: all
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.2
+        uses: pypa/cibuildwheel@v3.1
         env:
           CIBW_BUILD: ${{ matrix.build }}
           CIBW_MANYLINUX_X86_64_IMAGE: quay.io/pypa/${{ matrix.image }}
@@ -63,11 +63,11 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name != 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name == 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
@@ -89,18 +89,18 @@ jobs:
         # macos-13 is an intel runner, macos-14 is apple silicon
         os: [macos-13, macos-14]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name != 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         if: ${{ github.event_name == 'repository_dispatch' }}
         with:
           fetch-depth: 0  # slow, but gets all the tags
           ref: ${{ github.event.client_payload.ref }}
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.2
+        uses: pypa/cibuildwheel@v3.1
 
       - uses: actions/upload-artifact@v4
         with:
@@ -115,7 +115,7 @@ jobs:
       id-token: write
     if: (github.event_name == 'release' && github.event.action == 'published') || (github.event_name == 'repository_dispatch' && github.event.client_payload.publish_wheel == true)
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           # unpacks default artifact into dist/
           pattern: artifact-*
diff --git a/cibw-requirements.txt b/cibw-requirements.txt
@@ -1 +1 @@
-cibuildwheel==2.23.2
+cibuildwheel==3.1.0
diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -1,6 +1,6 @@
 tox < 3.29  # until tox-pyenv is updated for tox 4.x
 tox-pyenv < 1.2
 isort > 5, < 6.1
-build < 1.2.3
+build < 1.3.1
 autoflake < 2.4
 auto-walrus
diff --git a/lint-requirements.txt b/lint-requirements.txt
@@ -1,6 +1,6 @@
-diff_cover < 9.3
+diff_cover < 9.7
 pydocstyle < 6.4
 flake8 > 4
 flake8-bugbear < 24.13
-bandit < 1.8.3
+bandit < 1.8.7
 pylint < 3.4
diff --git a/mypy-requirements.txt b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy[mypyc]==1.15.0  # update pyproject.toml as well
+mypy[mypyc]==1.17.1  # update pyproject.toml as well
 black>=23.12,<24.11
 types-requests
 types-dataclasses
diff --git a/pyproject.toml b/pyproject.toml
@@ -2,7 +2,7 @@
 requires = [
     "setuptools>=50",  # 50 is to match mypyc's minimum
     "setuptools_scm[toml]>=8.0.4,<9",
-    'mypy[mypyc]==1.15.0',  # update mypy-requirements as well
+    'mypy[mypyc]==1.17.1',  # update mypy-requirements as well
     "black>=19.10b0,<24.11",
     "types-requests",
     "types-dataclasses",
@@ -19,9 +19,10 @@ write_to = "schema_salad/_version.py"
 test-command = "python -m pytest -n 2 --junitxml={project}/test-results/junit_$(python -V | awk '{print $2}')_${AUDITWHEEL_PLAT}.xml --pyargs schema_salad"
 test-requires = "-r test-requirements.txt"
 test-extras = "pycodegen"
-skip = "pp*"
+skip = ["pp*", "cp31?t-*"]
 #      ^ skip building wheels on PyPy (any version)
-build-verbosity = "1"
+#              ^ https://mypy.readthedocs.io/en/stable/changelog.html#mypyc-partial-unsafe-support-for-free-threading
+build-verbosity = 1
 environment = { SCHEMA_SALAD_USE_MYPYC="1", MYPYPATH="$(pwd)/mypy-stubs" }
 
 [tool.black]
diff --git a/schema_salad/java/pom.xml b/schema_salad/java/pom.xml
@@ -8,7 +8,7 @@
   <description><![CDATA[${project_description}]]></description>
   <version>${version}</version>
   <properties>
-    <commonslang.version>3.12.0</commonslang.version>
+    <commonslang.version>3.18.0</commonslang.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
     <maven.compiler.source>8</maven.compiler.source>
diff --git a/schema_salad/java_codegen.py b/schema_salad/java_codegen.py
@@ -280,6 +280,9 @@ def begin_class(
   private LoadingOptions loadingOptions_ = new LoadingOptionsBuilder().build();
   private java.util.Map<String, Object> extensionFields_ =
       new java.util.HashMap<String, Object>();
+  public java.util.Map<String, Object> getExtensionFields() {{
+    return this.extensionFields_;
+  }}
 """.format(
                     package=self.package,
                     cls=cls,
diff --git a/schema_salad/schema.py b/schema_salad/schema.py
@@ -3,7 +3,7 @@
 import copy
 import hashlib
 from collections.abc import Mapping, MutableMapping, MutableSequence
-from typing import IO, Any, Optional, TypeVar, Union, cast
+from typing import IO, Any, Optional, Union, cast
 from urllib.parse import urlparse
 
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
@@ -506,7 +506,7 @@ def avro_field_name(url: str) -> str:
     return d.path.split("/")[-1]
 
 
-Avro = TypeVar("Avro", MutableMapping[str, Any], MutableSequence[Any], str)
+Avro = Union[MutableMapping[str, Any], MutableSequence[Any], str]
 
 
 def make_valid_avro(
diff --git a/setup.py b/setup.py
@@ -115,7 +115,7 @@
     download_url="https://github.com/common-workflow-language/schema_salad/releases",
     ext_modules=ext_modules,
     license="Apache 2.0",
-    python_requires=">=3.9,<3.14",
+    python_requires=">=3.9,<3.15",
     use_scm_version=True,
     setup_requires=pytest_runner + ["setuptools_scm>=8.0.4,<9"],
     packages=["schema_salad", "schema_salad.tests", "schema_salad.avro"],
diff --git a/test-requirements.txt b/test-requirements.txt
@@ -1,4 +1,4 @@
-pytest >= 6.2, < 8.4
+pytest >= 6.2, < 8.5
 pytest-cov
 pytest-xdist
 setuptools
diff --git a/tox.ini b/tox.ini
@@ -1,9 +1,9 @@
 [tox]
 envlist =
-  py3{9,10,11,12,13}-lint,
-  py3{9,10,11,12,13}-unit,
-  py3{9,10,11,12,13}-mypy,
-  py3{9,10,11,12,13}-memleak,
+  py3{9,10,11,12,13,14}-lint,
+  py3{9,10,11,12,13,14}-unit,
+  py3{9,10,11,12,13,14}-mypy,
+  py3{9,10,11,12,13,14}-memleak,
   lintreadme,
   pydocstyle
 
@@ -20,50 +20,51 @@ python =
   3.11: py311
   3.12: py312
   3.13: py313
+  3.14: py314
 
 [testenv]
 description =
-  py3{9,10,11,12,13}-unit: Run the unit tests
-  py3{9,10,11,12,13}-lint: Lint the Python code and search for common security issues
-  py3{9,10,11,12,13}-mypy: Check for type safety
-  py3{9,10,11,12,13}-memleak: Simple test for memory leaks with mypyc
+  py3{9,10,11,12,13,14}-unit: Run the unit tests
+  py3{9,10,11,12,13,14}-lint: Lint the Python code and search for common security issues
+  py3{9,10,11,12,13,14}-mypy: Check for type safety
+  py3{9,10,11,12,13,14}-memleak: Simple test for memory leaks with mypyc
   pydocstyle: docstring style checker
   lintreadme: Lint the README.rst->.md conversion
 
 passenv =
   CI
   GITHUB_*
 deps =
-  py3{9,10,11,12,13}-{unit,mypy}: -rrequirements.txt
-  py3{9,10,11,12,13}-{unit,mypy}: -rtest-requirements.txt
-  py3{9,10,11,12,13}-lint: -rlint-requirements.txt
-  py3{9,10,11,12,13}-{mypy,memleak,lint}: -rmypy-requirements.txt
-  py3{9,10,11,12,13}-memleak: cwl-utils
-  py3{9,10,11,12,13}-memleak: objgraph
+  py3{9,10,11,12,13,14}-{unit,mypy}: -rrequirements.txt
+  py3{9,10,11,12,13,14}-{unit,mypy}: -rtest-requirements.txt
+  py3{9,10,11,12,13,14}-lint: -rlint-requirements.txt
+  py3{9,10,11,12,13,14}-{mypy,memleak,lint}: -rmypy-requirements.txt
+  py3{9,10,11,12,13,14}-memleak: cwl-utils
+  py3{9,10,11,12,13,14}-memleak: objgraph
 # don't forget to update dev-requirements.txt as well
 
 setenv =
   py3{8,9,10,11,12,13}-unit: LC_ALL = C.UTF-8
 
 commands =
-  py3{9,10,11,12,13}-unit: python -m pip install -U pip setuptools wheel
-  py3{9,10,11,12,13}-unit: make --always-make coverage-report coverage.xml PYTEST_EXTRA="{posargs}"
-  py3{9,10,11,12,13}-lint: make bandit flake8 format-check diff_pylint_report diff_pydocstyle_report
-  py3{9,10,11,12,13}-mypy: make mypy mypyc
-  py3{9,10,11,12,13}-memleak: make mypyi
-  py3{9,10,11,12,13}-memleak: python schema_salad/tests/memory-leak-check.py schema_salad/tests/test_real_cwl/ICGC-TCGA-PanCancer/complete/preprocess_vcf.cwl
+  py3{9,10,11,12,13,14}-unit: python -m pip install -U pip setuptools wheel
+  py3{9,10,11,12,13,14}-unit: make --always-make coverage-report coverage.xml PYTEST_EXTRA="{posargs}"
+  py3{9,10,11,12,13,14}-lint: make bandit flake8 format-check diff_pylint_report diff_pydocstyle_report
+  py3{9,10,11,12,13,14}-mypy: make mypy mypyc
+  py3{9,10,11,12,13,14}-memleak: make mypyi
+  py3{9,10,11,12,13,14}-memleak: python schema_salad/tests/memory-leak-check.py schema_salad/tests/test_real_cwl/ICGC-TCGA-PanCancer/complete/preprocess_vcf.cwl
 
 allowlist_externals =
-  py3{9,10,11,12,13}-lint: flake8
-  py3{9,10,11,12,13}-lint: black
-  py3{9,10,11,12,13}-{mypy,memleak,shellcheck,lint,unit}: make
+  py3{9,10,11,12,13,14}-lint: flake8
+  py3{9,10,11,12,13,14}-lint: black
+  py3{9,10,11,12,13,14}-{mypy,memleak,shellcheck,lint,unit}: make
   lintreadme: make
 
 skip_install =
-  py3{9,10,11,12,13}-lint: true
+  py3{9,10,11,12,13,14}-lint: true
 
 extras =
-  py3{9,10,11,12,13}-unit: pycodegen
+  py3{9,10,11,12,13,14}-unit: pycodegen
 
 [testenv:pydocstyle]
 allowlist_externals = make

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-cibuildwheel==2.23.2`
	`1`	`+cibuildwheel==3.1.0`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-mypy[mypyc]==1.15.0 # update pyproject.toml as well`
	`1`	`+mypy[mypyc]==1.17.1 # update pyproject.toml as well`
`2`	`2`	`black>=23.12,<24.11`
`3`	`3`	`types-requests`
`4`	`4`	`types-dataclasses`