[ARVADOS] updated: 2.1.0-1909-ge2b3ed63a

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py | 6 +++++-
 sdk/cwl/setup.py                | 5 +----
 sdk/cwl/tests/arvados-tests.yml | 5 +++++
 sdk/dev-jobs.dockerfile         | 6 ++----
 4 files changed, 13 insertions(+), 9 deletions(-)

       via  e2b3ed63a292537ec7bf37a904ad2925d6afa0bf (commit)
       via  cadf55f2a09546812a650668770249d0f23ec9a5 (commit)
      from  0494b40a03348e584dbc255d93615a4ef01afaf9 (commit)

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commit e2b3ed63a292537ec7bf37a904ad2925d6afa0bf
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Mon Feb 14 09:54:26 2022 -0500

    18723: Use setuptools console entrypoints, fix dev-jobs.dockerfile
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index c3848b262..734945c0f 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -258,7 +258,11 @@ def exit_signal_handler(sigcode, frame):
     logger.error(str(u"Caught signal {}, exiting.").format(sigcode))
     sys.exit(-sigcode)
 
-def main(args, stdout, stderr, api_client=None, keep_client=None,
+def main(args=sys.argv[1:],
+         stdout=sys.stdout,
+         stderr=sys.stderr,
+         api_client=None,
+         keep_client=None,
          install_sig_handlers=True):
     parser = arg_parser()
 
diff --git a/sdk/dev-jobs.dockerfile b/sdk/dev-jobs.dockerfile
index 1e0068ffd..b55b056b2 100644
--- a/sdk/dev-jobs.dockerfile
+++ b/sdk/dev-jobs.dockerfile
@@ -23,9 +23,7 @@ ARG pipcmd=pip3
 
 RUN apt-get update -q && apt-get install -qy --no-install-recommends \
     git ${pythoncmd}-pip ${pythoncmd}-virtualenv ${pythoncmd}-dev libcurl4-gnutls-dev \
-    libgnutls28-dev nodejs ${pythoncmd}-pyasn1-modules build-essential
-
-RUN $pipcmd install -U setuptools six requests
+    libgnutls28-dev nodejs ${pythoncmd}-pyasn1-modules build-essential ${pythoncmd}-setuptools
 
 ARG sdk
 ARG runner
@@ -39,7 +37,7 @@ ADD cwl/dist/$runner /tmp/
 
 RUN cd /tmp/arvados-python-client-* && $pipcmd install .
 RUN if test -d /tmp/schema-salad-* ; then cd /tmp/schema-salad-* && $pipcmd install . ; fi
-RUN if test -d /tmp/cwltool-* ; then cd /tmp/cwltool-* && $pipcmd install networkx==2.2 && $pipcmd install . ; fi
+RUN if test -d /tmp/cwltool-* ; then cd /tmp/cwltool-* && $pipcmd install . ; fi
 RUN cd /tmp/arvados-cwl-runner-* && $pipcmd install .
 
 # Install dependencies and set up system.

commit cadf55f2a09546812a650668770249d0f23ec9a5
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Fri Feb 11 17:12:35 2022 -0500

    18723: Use setuptools provided entry point
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index ae90df43c..e73923595 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -31,10 +31,7 @@ setup(name='arvados-cwl-runner',
       license='Apache 2.0',
       packages=find_packages(),
       package_data={'arvados_cwl': ['arv-cwl-schema-v1.0.yml', 'arv-cwl-schema-v1.1.yml', 'arv-cwl-schema-v1.2.yml']},
-      scripts=[
-          'bin/cwl-runner',
-          'bin/arvados-cwl-runner',
-      ],
+      entry_points={"console_scripts": ["cwl-runner=arvados_cwl:main", "arvados-cwl-runner=arvados_cwl:main"]},
       # Note that arvados/build/run-build-packages.sh looks at this
       # file to determine what version of cwltool and schema-salad to
       # build.
diff --git a/sdk/cwl/tests/arvados-tests.yml b/sdk/cwl/tests/arvados-tests.yml
index ae22d65f4..5282e9392 100644
--- a/sdk/cwl/tests/arvados-tests.yml
+++ b/sdk/cwl/tests/arvados-tests.yml
@@ -439,3 +439,8 @@
     "outstr": "foo woble bar"
   tool: 17879-ignore-sbg-fields.cwl
   doc: "Test issue 17879 - ignores sbg fields"
+
+- job: chipseq/chip-seq-single.json
+  output: {}
+  tool: chipseq/cwl-packed.json
+  doc: "Test issue 18723 - correctly upload two directories with the same basename"

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