bihealth / biomedsheets

:books: JSON/TSV sample sheets for biomedical experiments

Home Page:https://biomedsheets.readthedocs.io/en/master

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Conflict with latest `varfish-cli` release

eudesbarbosa opened this issue · comments

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.

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