From 9173158aafce0bc9b5c9656aadee661e95f0b2a6 Mon Sep 17 00:00:00 2001 From: Jake Fennick Date: Fri, 8 Dec 2023 11:51:09 -1000 Subject: [PATCH 1/2] remove galaxy-tool-util from build dependency --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0c427a7f7..34876d20d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,6 @@ requires = [ "ruamel.yaml>=0.16.0,<0.18", "schema-salad>=8.4.20230426093816,<9", "cwl-utils>=0.32", - "galaxy-tool-util>=22.1.2,<23.2,!=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5", "toml", "argcomplete>=1.12.0", ] From fea8bc122edc51d4afd831faa82e4e9ba6fcf6ed Mon Sep 17 00:00:00 2001 From: Jake Fennick Date: Fri, 8 Dec 2023 13:26:40 -1000 Subject: [PATCH 2/2] strip newline from version string; fix mypy error --- cwltool.Dockerfile | 2 +- cwltool/software_requirements.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cwltool.Dockerfile b/cwltool.Dockerfile index 4fa76b126..2b93b8d99 100644 --- a/cwltool.Dockerfile +++ b/cwltool.Dockerfile @@ -4,7 +4,7 @@ RUN apk add --no-cache git gcc python3-dev libxml2-dev libxslt-dev libc-dev linu WORKDIR /cwltool COPY . . -RUN export SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CWLTOOL=$(grep __version__ cwltool/_version.py | awk -F\' '{ print $2 }') ; \ +RUN export SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CWLTOOL=$(grep __version__ cwltool/_version.py | awk -F\' '{ print $2 }' | tr -d '\\n') ; \ CWLTOOL_USE_MYPYC=1 MYPYPATH=mypy-stubs pip wheel --no-binary schema-salad \ --wheel-dir=/wheels .[deps] # --verbose RUN rm /wheels/schema_salad* diff --git a/cwltool/software_requirements.py b/cwltool/software_requirements.py index 9360e8080..ec99bda05 100644 --- a/cwltool/software_requirements.py +++ b/cwltool/software_requirements.py @@ -159,7 +159,7 @@ def get_container_from_software_requirements( [DOCKER_CONTAINER_TYPE], tool_info ) if container_description: - return container_description.identifier + return str(container_description.identifier) return None