Modernize build, dependencies, and core safety - #8
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Replace the pinned compiler-specific build with a portable GNU Make setup that supports BSD via gmake and adds dependency tracking. Fix PDB coordinate cache updates and Python parser edge cases, with regression tests and updated build documentation.
Add a GitHub Actions matrix for Linux and macOS compilers using the GNU Make workflow, and run the native C++ and Python test suites. Remove the obsolete Travis configuration and document the macOS gmake requirement.
Include the standard integer header where Split declares uint64_t so GCC and Clang on Ubuntu compile the complete command-line tool set consistently.
Replace the seven unbounded system sprintf calls with bounded snprintf calls while preserving the custom PDB formatter and legacy field ordering. Add coverage for all affected PDBRUN v5 user record types and include the new test in the GNU Make build.
Clear PDB object storage through a byte pointer instead of passing the non-trivial class directly to memset, preserving legacy initialization while allowing GCC warning-clean builds. Use the standard cstring declarations for the related memory comparison and clearing operations.
Document the deliberate fallback from specialized USER record parsing to the generic USER parser so GCC and Clang no longer report an implicit fallthrough warning under the C++14 build.
Pin the Catch2 submodule to v3.9.1 and compile its amalgamated test runner through GNU Make instead of relying on the removed v2 header-only main. Update test includes and assertions, validate the Catch2 dependency, and cover the zero-prediction parser limit.
Pin Eigen to the 3.4.1 release and add focused tests for constraints, multimer transforms, PDB behavior, and invalid ZDOCK input. Document each test invariant and add compact fixtures that exercise model handling and parser error paths.
Preserve final split chunks, enforce multimer and matrix bounds, and make PDB copies own independent records. Reject malformed parser input, incompatible transformations, unsafe paths, and invalid CLI numbers with tested exceptions.
Copy PDB record graphs directly so stateful filters are not re-evaluated and model records retain their shared identity. Exercise formatter boundaries, centroid values, and M-ZDOCK poses with independent or adversarial expectations. Trigger CI for the repository's master branch.
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Summary
and a Linux/macOS GitHub Actions compiler matrix
warnings and unsafe PDBRUN v5 formatting
invariant-focused regression coverage with independent numeric oracles
Testing
make clean && make -j4 allmake cpp-test— 417 assertions in 31 test casesmake python-test— 8 tests