Fix local test error #105
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Fix local test error #105
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- set antismash file to BGC object during loading - add SMILES parser - refactor product parser
- remove parameter `id` - rename parameter `name` to `bgc_id` - update all references to old `id` and `name`
- remove parameter `id` - update all references to old `id`
- merge methods to reimplement data parsing - add type hints - update doctrings
the method must call hash function to return an integer
- remove unused attribute `strains_lookup` - apply property to attribute `bgcs` - update method `add_bgc` logic - add docstrings - add type hints
This is a temporary solution. Loading of strains will be refactored later. See issue 104.
This is a temporary solution, will remove it later. See issue 103 #103.
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@hechth Conflicts solved and ready for review |
hechth
reviewed
Feb 22, 2023
hechth
approved these changes
Feb 23, 2023
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@CunliangGeng let's merge this and move on with the refactoring :) |
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Please review PR #101 and #102 first, then this PR (only need to review the last two commits).
The test errors of
test_nplinker.pyis caused bybgc.strainandgcf.id.This PR fixes the errors with a temporary solution (i.e. using the logics of the original codebase) to keep focusing on the refactoring of the data preparation part.
Added two issue #103 and #104 to update/change the logics later.