include ruamel.yaml in the mypy reqs & fix/test container build (#1701)

Author: mr-c

.github/workflows/ci-tests.yml

@@ -177,3 +177,10 @@ jobs:
         env:
           RELEASE_SKIP: head
         run: ./release-test.sh
+
+  build_test_container:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: build & test cwltool_module container
+        run: ./build-cwltool-docker.sh

build-cwltool-docker.sh

@@ -3,14 +3,8 @@ set -ex
 docker build --file=cwltool.Dockerfile --tag=quay.io/commonwl/cwltool_module --target module .
 docker build --file=cwltool.Dockerfile --tag=quay.io/commonwl/cwltool .
 
-docker run -it -v /var/run/docker.sock:/var/run/docker.sock \
+docker run -t -v /var/run/docker.sock:/var/run/docker.sock \
 	-v /tmp:/tmp \
 	-v "$PWD":/tmp/cwltool \
 	quay.io/commonwl/cwltool_module /bin/sh -c \
 	"apk add gcc bash && pip install -r/tmp/cwltool/test-requirements.txt ; pytest -k 'not (test_bioconda or test_double_overwrite or test_env_filtering or test_biocontainers or test_disable_file_overwrite_without_ext or test_disable_file_creation_in_outdir_with_ext or test_write_write_conflict or test_directory_literal_with_real_inputs_inside or test_revsort_workflow or test_stdin_with_id_preset)' --ignore-glob '*test_udocker.py' -n auto -v -rs --pyargs cwltool"
-
-version=$(git describe --tags)
-if echo "$version" | grep -vq '\-' >& /dev/null ; then
-    docker tag quay.io/commonwl/cwltool_module quay.io/commonwl/cwltool_module:"$version"
-    docker tag quay.io/commonwl/cwltool quay.io/commonwl/cwltool:"$version"
-fi

cwltool.Dockerfile

@@ -5,8 +5,7 @@ RUN apk add --no-cache git gcc python3-dev libxml2-dev libxslt-dev libc-dev linu
 WORKDIR /cwltool
 COPY . .
 
-RUN pip install toml -rmypy-requirements.txt "$(grep ruamel requirements.txt)" \
-	"$(grep schema.salad requirements.txt)"
+RUN pip install toml -rmypy-requirements.txt "$(grep schema.salad requirements.txt)"
 # schema-salad is needed to be installed (this time as pure Python) for
 # cwltool + mypyc
 RUN CWLTOOL_USE_MYPYC=1 MYPYPATH=mypy-stubs pip wheel --no-binary schema-salad --wheel-dir=/wheels .[deps]

mypy-requirements.txt

@@ -1,4 +1,5 @@
 mypy==0.971
+ruamel.yaml>=0.16.0,<0.17.22
 types-requests
 types-setuptools
 types-psutil