Update latest main

.circleci/config.yml

@@ -0,0 +1,101 @@
+version: 2.1
+
+parameters:
+  REF:
+    type: string
+    default: ''
+    description: Optional tag to build
+
+jobs:
+  arm-wheels:
+    parameters:
+      build:
+        type: string
+      image:
+        type: string
+
+    machine:
+      image: ubuntu-2404:current
+    resource_class: arm.medium  # 2 vCPUs
+
+    environment:
+      CIBW_ARCHS: "aarch64"
+      CIBW_MANYLINUX_AARCH64_IMAGE: "<< parameters.image >>"
+      CIBW_MUSLLINUX_AARCH64_IMAGE: "<< parameters.image >>"
+      CIBW_BUILD: "<< parameters.build >>"
+
+    steps:
+      - checkout
+      - when:
+          condition: << pipeline.parameters.REF >>
+          steps:
+          - run:
+              name: Checkout branch/tag << pipeline.parameters.REF >>
+              command: |
+                echo "Switching to branch/tag << pipeline.parameters.REF >> if it exists"
+                git checkout << pipeline.parameters.REF >> || true
+                git pull origin << pipeline.parameters.REF >> || true
+      - run:
+          name: install cibuildwheel and other build reqs
+          command: |
+            python3 -m pip install --upgrade pip setuptools setuptools_scm[toml]
+            python3 -m pip install -rcibw-requirements.txt
+
+      - run:
+          name: pip freeze
+          command: |
+            python3 -m pip freeze
+
+      - run:
+          name: list wheels
+          command: |
+            python3 -m cibuildwheel . --print-build-identifiers
+
+      - run:
+          name: cibuildwheel
+          command: |
+            python3 -m cibuildwheel .
+
+      - store_test_results:
+          path: test-results/
+
+      - store_artifacts:
+          path: wheelhouse/
+
+      # - when:
+      #     condition:
+      #       or:
+      #         - matches:
+      #             pattern: ".+"
+      #             value: "<< pipeline.git.tag >>"
+      #         - << pipeline.parameters.REF >>
+      #     steps:
+      #       - run:
+      #           environment:
+      #             TWINE_NONINTERACTIVE: "1"
+      #           command: |
+      #             python3 -m pip install twine
+      #             python3 -m twine upload --verbose --skip-existing wheelhouse/*
+
+workflows:
+  wheels: # This is the name of the workflow, feel free to change it to better match your workflow.
+    # Inside the workflow, you define the jobs you want to run.
+    jobs:
+      - arm-wheels:
+          name: arm-wheels-manylinux_2_28
+          filters:
+            branches:
+              only: main
+            tags:
+              only: /.*/
+          build: "*manylinux*"
+          image: quay.io/pypa/manylinux_2_28_aarch64
+      - arm-wheels:
+          name: arm-wheels-musllinux_1_2
+          filters:
+            branches:
+              only: main
+            tags:
+              only: /.*/
+          build: "*musllinux*"
+          image: quay.io/pypa/musllinux_1_2_aarch64

.github/workflows/ci-tests.yml

@@ -32,7 +32,7 @@ jobs:
     strategy:
       matrix:
         py-ver-major: [3]
-        py-ver-minor: [8, 9, 10, 11, 12, 13]
+        py-ver-minor: [9, 10, 11, 12, 13]
         step: [lint, unit, bandit, mypy]
 
     env:
@@ -44,11 +44,11 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Set up Singularity
+      - name: Set up Singularity and environment-modules
         if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
         run: |
-          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-focal_amd64.deb
-          sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb
+          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v4.2.1/singularity-ce_4.2.1-focal_amd64.deb
+          sudo apt-get install -y ./singularity-ce_4.2.1-focal_amd64.deb environment-modules
 
       - name: Give the test runner user a name to make provenance happy.
         if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
@@ -81,7 +81,7 @@ jobs:
 
       - name: Upload coverage to Codecov
         if: ${{ matrix.step == 'unit' }}
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true
         env:
@@ -132,10 +132,10 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Set up Singularity
+      - name: Set up Singularity and environment-modules
         run: |
-          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-focal_amd64.deb
-          sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb
+          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v4.2.1/singularity-ce_4.2.1-focal_amd64.deb
+          sudo apt-get install -y ./singularity-ce_4.2.1-focal_amd64.deb environment-modules
 
       - name: Give the test runner user a name to make provenance happy.
         run: sudo usermod -c 'CI Runner' "$(whoami)"
@@ -157,14 +157,15 @@ jobs:
           chmod a-w .
 
       - name: run tests
-        run: APPTAINER_TMPDIR=${RUNNER_TEMP} make test
+        run: APPTAINER_TMPDIR=${RUNNER_TEMP} make test PYTEST_EXTRA=-vvv
 
 
   conformance_tests:
     name: CWL conformance
     runs-on: ubuntu-22.04
 
     strategy:
+      fail-fast: false
       matrix:
         cwl-version: [v1.0, v1.1, v1.2]
         container: [docker, singularity, podman]
@@ -179,11 +180,11 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Singularity
+      - name: Set up Singularity and environment-modules
         if: ${{ matrix.container == 'singularity' }}
         run: |
-          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb
-          sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb
+          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v4.2.1/singularity-ce_4.2.1-focal_amd64.deb
+          sudo apt-get install -y ./singularity-ce_4.2.1-focal_amd64.deb environment-modules
 
       - name: Singularity cache
         if: ${{ matrix.container == 'singularity' }}
@@ -216,7 +217,7 @@ jobs:
           path: |
             **/cwltool_conf*.xml
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true
         env:
@@ -228,10 +229,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Singularity
+      - name: Set up Singularity and environment-modules
         run: |
-          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb
-          sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb
+          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v4.2.1/singularity-ce_4.2.1-focal_amd64.deb
+          sudo apt-get install -y ./singularity-ce_4.2.1-focal_amd64.deb environment-modules
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -301,7 +302,7 @@ jobs:
       - name: Test with tox
         run: tox
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true
         env:

.github/workflows/wheels.yml

@@ -0,0 +1,127 @@
+name: Python package build and publish
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch: {}
+  repository_dispatch: {}
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: wheels-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build_wheels:
+    name: ${{ matrix.image }} wheels
+    runs-on: ubuntu-24.04
+    strategy:
+      matrix:
+        include:
+          - image: manylinux_2_28_x86_64
+            build: "*manylinux*"
+          - image: musllinux_1_2_x86_64
+            build: "*musllinux*"
+
+    steps:
+      - uses: actions/checkout@v4
+        if: ${{ github.event_name != 'repository_dispatch' }}
+        with:
+          fetch-depth: 0  # slow, but gets all the tags
+      - uses: actions/checkout@v4
+        if: ${{ github.event_name == 'repository_dispatch' }}
+        with:
+          fetch-depth: 0  # slow, but gets all the tags
+          ref: ${{ github.event.client_payload.ref }}
+
+      # - name: Set up QEMU
+      #   if: runner.os == 'Linux'
+      #   uses: docker/setup-qemu-action@v2
+      #   with:
+      #     platforms: all
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_BUILD: ${{ matrix.build }}
+          CIBW_MANYLINUX_X86_64_IMAGE: quay.io/pypa/${{ matrix.image }}
+          CIBW_MUSLLINUX_X86_64_IMAGE: quay.io/pypa/${{ matrix.image }}
+          # configure cibuildwheel to build native 64-bit archs ('auto64'), and some
+          # emulated ones
+          # Linux arm64 wheels are built on circleci
+          CIBW_ARCHS_LINUX: auto64 # ppc64le s390x
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: artifact-${{ matrix.image }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+        if: ${{ github.event_name != 'repository_dispatch' }}
+        with:
+          fetch-depth: 0  # slow, but gets all the tags
+      - uses: actions/checkout@v4
+        if: ${{ github.event_name == 'repository_dispatch' }}
+        with:
+          fetch-depth: 0  # slow, but gets all the tags
+          ref: ${{ github.event.client_payload.ref }}
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: artifact-source
+          path: dist/*.tar.gz
+
+  build_wheels_macos:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [macos-13, macos-14]
+    steps:
+      - uses: actions/checkout@v4
+        if: ${{ github.event_name != 'repository_dispatch' }}
+        with:
+          fetch-depth: 0  # slow, but gets all the tags
+      - uses: actions/checkout@v4
+        if: ${{ github.event_name == 'repository_dispatch' }}
+        with:
+          fetch-depth: 0  # slow, but gets all the tags
+          ref: ${{ github.event.client_payload.ref }}
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: artifact-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  # upload_pypi:
+  #   needs: [build_wheels, build_sdist]
+  #   runs-on: ubuntu-24.04
+  #   environment: deploy
+  #   permissions:
+  #     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
+  #       with:
+  #         # unpacks default artifact into dist/
+  #         pattern: artifact-*
+  #         merge-multiple: true
+  #         path: dist
+
+  #     - name: Publish package distributions to PyPI
+  #       uses: pypa/gh-action-pypi-publish@release/v1
+  #       with:
+  #         skip-existing: true

.gitignore

@@ -16,6 +16,7 @@ eggs/
 *.egg
 .tox/
 .pytest_cache
+*.so
 
 # Editor Temps
 .*.sw?

MANIFEST.in

@@ -19,6 +19,7 @@ include tests/reloc/dir2/*
 include tests/checker_wf/*
 include tests/subgraph/*
 include tests/input_deps/*
+recursive-include tests/test_deps_env
 include tests/trs/*
 include tests/wf/generator/*
 include cwltool/py.typed

Makefile

@@ -24,7 +24,7 @@ MODULE=cwltool
 
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
-PYSOURCES=$(wildcard ${MODULE}/**.py cwltool/cwlprov/*.py tests/*.py) setup.py
+PYSOURCES=$(wildcard ${MODULE}/**.py cwltool/cwlprov/*.py tests/*.py tests/cwl-conformance/*.py) setup.py
 DEVPKGS=diff_cover pylint pep257 pydocstyle 'tox<4' tox-pyenv auto-walrus \
 	isort wheel autoflake pyupgrade bandit -rlint-requirements.txt\
 	-rtest-requirements.txt -rmypy-requirements.txt -rdocs/requirements.txt
@@ -190,7 +190,7 @@ shellcheck: FORCE
 		cwltool-in-docker.sh
 
 pyupgrade: $(PYSOURCES)
-	pyupgrade --exit-zero-even-if-changed --py38-plus $^
+	pyupgrade --exit-zero-even-if-changed --py39-plus $^
 	auto-walrus $^
 
 release-test: FORCE