PominovaMS / denovo_benchmarks

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Benchmark cannot be run locally due to hardcoded paths #19

Closed BioGeek closed 5 days ago

BioGeek commented 2 weeks ago

Currently the benchmark cannot be run locally due to hardcoded paths.

This has partially been addressed in 23dfab458a2419db08d9ec166a812cbc7c3ddab3 with the introduction of algorithms/base/constants.py.

This solution is however unsatisfactory. When multiple users modify the same algorithms/base/constants.py file to adapt it to their local environment, they could end up with version control conflicts. Each time someone clones the repo, modifies the file, pushes their changes and accidentally includes algorithms/base/constants.py, it risks overwriting or conflicting with others' changes.

There are also still hardcoded paths in dataset_utils.py and evaluate.py.