cwlformat 2021.1.5 has requirement ruamel.yaml==0.16.12, but you'll have ruamel-yaml 0.17.21 which is incompatible.

[golharam]

After creating a Python 3.7.8 virtual environment, and running pip3 install git+https://github.com/rabix/sbpack.git

I get an error, ERROR: cwlformat 2021.1.5 has requirement ruamel.yaml==0.16.12, but you'll have ruamel-yaml 0.17.21 which is incompatible.

If I run 'pip freeze' BEFORE installing sbpack, 'pip freeze' reports no packages.

See log below:

$ pip3 install git+https://github.com/rabix/sbpack.git
Collecting git+https://github.com/rabix/sbpack.git
  Cloning https://github.com/rabix/sbpack.git to /private/var/folders/db/dq3r90hs7yn_xnm6f717bk940000gn/T/pip-req-build-9t83r9w_
  Running command git clone -q https://github.com/rabix/sbpack.git /private/var/folders/db/dq3r90hs7yn_xnm6f717bk940000gn/T/pip-req-build-9t83r9w_
Collecting ruamel.yaml>=0.16
  Using cached ruamel.yaml-0.17.21-py3-none-any.whl (109 kB)
Collecting sevenbridges-python>=2.0
  Using cached sevenbridges_python-2.8.0-py3-none-any.whl (101 kB)
Collecting cwlformat
  Using cached cwlformat-2021.1.5-py3-none-any.whl (10 kB)
Collecting packaging
  Using cached packaging-21.3-py3-none-any.whl (40 kB)
Collecting ruamel.yaml.clib>=0.2.6; platform_python_implementation == "CPython" and python_version < "3.11"
  Using cached ruamel.yaml.clib-0.2.6-cp37-cp37m-macosx_10_9_x86_64.whl (140 kB)
Collecting urllib3>=1.26.2
  Using cached urllib3-1.26.8-py2.py3-none-any.whl (138 kB)
Collecting requests>=2.25.1
  Using cached requests-2.27.1-py2.py3-none-any.whl (63 kB)
Collecting pyparsing!=3.0.5,>=2.0.2
  Using cached pyparsing-3.0.7-py3-none-any.whl (98 kB)
Collecting certifi>=2017.4.17
  Using cached certifi-2021.10.8-py2.py3-none-any.whl (149 kB)
Collecting idna<4,>=2.5; python_version >= "3"
  Using cached idna-3.3-py3-none-any.whl (61 kB)
Collecting charset-normalizer~=2.0.0; python_version >= "3"
  Using cached charset_normalizer-2.0.12-py3-none-any.whl (39 kB)
Using legacy setup.py install for sbpack, since package 'wheel' is not installed.
ERROR: cwlformat 2021.1.5 has requirement ruamel.yaml==0.16.12, but you'll have ruamel-yaml 0.17.21 which is incompatible.
Installing collected packages: ruamel.yaml.clib, ruamel.yaml, urllib3, certifi, idna, charset-normalizer, requests, sevenbridges-python, cwlformat, pyparsing, packaging, sbpack
    Running setup.py install for sbpack ... done
Successfully installed certifi-2021.10.8 charset-normalizer-2.0.12 cwlformat-2021.1.5 idna-3.3 packaging-21.3 pyparsing-3.0.7 requests-2.27.1 ruamel.yaml-0.17.21 ruamel.yaml.clib-0.2.6 sbpack-2021.10.7 sevenbridges-python-2.8.0 urllib3-1.26.8

This matter because when I try to run cwlpack, I get:

Traceback (most recent call last):
  File "/Users/golharr/workspace/NGS/RNASeq/env/lib/python3.7/site-packages/pkg_resources/__init__.py", line 584, in _build_master
    ws.require(__requires__)
  File "/Users/golharr/workspace/NGS/RNASeq/env/lib/python3.7/site-packages/pkg_resources/__init__.py", line 901, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/Users/golharr/workspace/NGS/RNASeq/env/lib/python3.7/site-packages/pkg_resources/__init__.py", line 792, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (ruamel.yaml 0.17.21 (/Users/golharr/workspace/NGS/RNASeq/env/lib/python3.7/site-packages), Requirement.parse('ruamel.yaml==0.16.12'), {'cwlformat'})

pip freeze:

$ pip freeze
certifi==2021.10.8
charset-normalizer==2.0.12
cwlformat==2021.1.5
idna==3.3
packaging==21.3
pyparsing==3.0.7
requests==2.27.1
ruamel.yaml==0.17.21
ruamel.yaml.clib==0.2.6
sbpack==2021.10.7
sevenbridges-python==2.8.0
urllib3==1.26.8

[golharam]

I need to install ruamel.yaml==0.16.12 prior to installing sbpack

[bogdang989]

Thanks @golharam . We released a new cwlformat version with a relaxed ruamel.yaml requirement to sort this out.