Conflict with latest `varfish-cli` release
eudesbarbosa opened this issue · comments
Eudes Barbosa commented
Issue
Latest varfish-cli
release (v0.3.0) leads to conflicts with biomedsheets
installation. Attempts to install biomedsheets
versions earlier than v0.5.4 will crash as it is not meant to work with newer versions of pip (>v10).
External issue: bihealth/snappy-pipeline#126
Suggestion
Update dependencies to make it compatible with latest varfish-cli
release.
Eudes Barbosa commented
Further, it is incompatible with snakemake
version 7.3.8 (latest):
Installing collected packages: cubi-tk, MarkupSafe, Jinja2, jsonschema
Attempting uninstall: cubi-tk
Found existing installation: cubi-tk 0.2.0+98.g7dd786c
Uninstalling cubi-tk-0.2.0+98.g7dd786c:
Successfully uninstalled cubi-tk-0.2.0+98.g7dd786c
Running setup.py develop for cubi-tk
Attempting uninstall: MarkupSafe
Found existing installation: MarkupSafe 2.0.1
Uninstalling MarkupSafe-2.0.1:
Successfully uninstalled MarkupSafe-2.0.1
Attempting uninstall: Jinja2
Found existing installation: Jinja2 3.1.1
Uninstalling Jinja2-3.1.1:
Successfully uninstalled Jinja2-3.1.1
Attempting uninstall: jsonschema
Found existing installation: jsonschema 4.4.0
Uninstalling jsonschema-4.4.0:
Successfully uninstalled jsonschema-4.4.0
ERROR: After October 2020 you may experience errors when installing or updating packages. This is because pip will change the way that it resolves dependency conflicts.
We recommend you use --use-feature=2020-resolver to test your packages with the new resolver before it becomes the default.
snakemake 7.3.8 requires jinja2<4.0,>=3.0, but you'll have jinja2 2.11.3 which is incompatible.
nbformat 5.3.0 requires jsonschema>=2.6, but you'll have jsonschema 2.5.1 which is incompatible.
Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 cubi-tk jsonschema-2.5.1
Eudes Barbosa commented
Further, at least python v3.7:
https://github.com/snakemake/snakemake/blob/main/setup.py#L14