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- Add noqa: F401 to intentional re-exports in __init__.py files - Fix F821 undefined names: add missing imports (os, subprocess, shlex, tempfile, Namespace, utils, genomicranges), fix dst_fname->dst_path bug in region_shuffling.py, fix Scenario1/2 file->path_simfile bug in visualization.py, add lazy import for genomicranges in io.py - Fix E741 ambiguous variable names: rename l->line, l->last, l->idx - Fix E712: replace == True with truthiness check - Fix E722 bare except: add Exception to all bare excepts - Fix F841 unused variables: remove unused assignments in eval/, bedspace/, universe/ - Fix F403/F405 star imports: replace with explicit imports in bedspace/, region2vec/, scembed/ - Fix E402 module level imports: add noqa comments in visualization.py - Fix F821 in atacformer: replace unused imports in try block
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