Fix missing includes, exception handing nitpicks, and add Nix support #274
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Exception handling fixes: - Fix URLRetrievalException caught by value in assembly_checker.cpp - Fix shared_ptr<Error> caught by value in record.cpp - Fix std::invalid_argument and std::out_of_range caught by value - Improves exception safety and prevents unnecessary copying Include fixes: - Add missing #include <cstdint> in src/fasta/faidx.cpp - Fixes uint64_t/uint32_t compilation errors with newer GCC versions Nix support: - Add flake.nix for reproducible development environments - Update README.md with Nix usage instructions for both users and developers - Enables running tools directly from GitHub without local installation - Provides dev shell with CMake, Boost, and C++ linters pre-configured These changes follow modern C++ best practices and improve developer experience.
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Hi! I ran into some compilation errors re: missing headers and some fiddly uint64_t/uint32_t stuff. While I was poking around I ran a couple linters and came across some exceptions being caught by value
This pull request also adds support for the functional package manager Nix by adding a flake.nix file. I've also updated the README with usage instructions for users and developers.