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Checks for coding standard, code smells and typing

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Merge pull request #33 from pluskal-lab/feature/20260314_add_agents_s…
Checks for coding standard, code smells and typing #132: Commit 698ae5d pushed by segef
29s main
Merge pull request #32 from pluskal-lab/bugfix/fix_parsing_prediction…
Checks for coding standard, code smells and typing #128: Commit 499e77b pushed by SamusRam
28s main
Merge pull request #29 from pluskal-lab/feature/mmseqs-clustering-for…
Checks for coding standard, code smells and typing #126: Commit 3b7ba12 pushed by segef
32s main