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Convert subprocess calls for git to pygit2 #23

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@uirmaksever

Implementation on ànnotation_collection.py`still relies on subprocess calls to push changes in annotation collection to the git repo. Those changes are required to realize this:

  • CatmaProject does not keep gitlab_access_tokenas an attribute. To be able to access it from AnnotationCollection, the token should be saved.
  • Rewrite subprocess calls with appropriate methods of pygit2.

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