From 99c62acfba35cd83a75f33519c89f8822d721cd9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 16 Jul 2025 03:08:59 +0000 Subject: [PATCH 1/2] Bump toil[cwl] from 8.2.0 to 9.0.0 --- updated-dependencies: - dependency-name: toil[cwl] dependency-version: 9.0.0 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 96b4578..7c84ec1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,7 +40,7 @@ Download = "https://github.com/common-workflow-language/cwltool-service/releases [project.optional-dependencies] cwltool = ["cwlref-runner"] arvados = ["arvados-cwl-runner"] -toil = ["toil[cwl]==8.2.0"] +toil = ["toil[cwl]==9.0.0"] [project.scripts] wes-server = "wes_service.wes_service_main:main" From 5d523dfca9961dfacee34b7e5d511e29cb70680d Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 16 Jul 2025 11:38:15 +0200 Subject: [PATCH 2/2] github actions: run apt-get update before installing --- .github/workflows/ci-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index 777d5d6..90eb755 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -54,7 +54,7 @@ jobs: - name: Install libcurl-dev for pycurl (needed by arvados) if: ${{ matrix.step == 'mypy' }} - run: sudo apt-get install -y --no-install-recommends libcurl4-gnutls-dev gnutls-dev + run: sudo apt-get update && sudo apt-get install -y --no-install-recommends libcurl4-gnutls-dev gnutls-dev - name: Upgrade setuptools and install tox run: |