Update benchmark scripts for Python3.12. (#51) Python 3.12 gets rid of the imp module. Moreover, it gets rid of imp.load_source() altogether. We thus need to change around how we do the magic 'import from parent directory' statement. There are also a few other things which were popping up warnings when I ran things locally.

• Summary
• integration.mpi 「1」
• integration.release_debug 「1」
• scientific.glycan_structure_prediction
• scientific.peptide_pnear_vs_ic50.debug
• scientific.peptide_pnear_vs_ic50
• scientific.simple_cycpep_predict.debug

Fix make_fragments and mp_f19_ddG_of_mutation scientific tests (#48) Attempt to fix some of the scientific tests having issues. * make_fragments - restore parameter for the install_dependencies.pl in tool submodule * mp_f19_ddG_of_mutation -- update matplotlib version (and version of python needed.)

• Summary
• integration.addsan 「1」
• integration.mpi 「1」
• scientific.antibody_h3_modeling
• scientific.make_fragments
• scientific.mp_f19_tilt_angle.debug
• scientific.mp_f19_tilt_angle
• windows.build.debug
• windows.build.release

Update benchmark.py, add how-to-fix explanation to warning message (#50)

• Summary
• integration.mpi 「1」
• integration.release_debug 「1」
• scientific.mp_f19_ddG_of_mutation.debug
• scientific.mp_f19_ddG_of_mutation
• scientific.mp_f19_decoy_discrimination.debug
• scientific.mp_f19_decoy_discrimination
• scientific.mp_lipid_acc
• windows.build.debug
• windows.build.release

Add ability to specify compiler version ranges in scons settings. (#36) The basic.settings file has had a limitation for a long while where any version-specific settings are tied to an exact version. That is, settings for gcc 9.0 can't also apply to 10.0 (or even 9.1). This makes things difficult when a potential range of different compilers need to be dealt with in the same fashion, especially in a forward-compatible way. (e.g. the lack of -ffor-scope on any GCC newer than 9.0, including ones not yet released) An adjustment to one of the build files allows us to use a pattern matching specification to add parameter blocks for ranges of compilers (e.g. cxx_ver:>9.0 for any compiler version greater than 9.0, or cxx_ver:>=5.2,<7.0 for compiler versions between 5.2 (inclusive) and 7.0 (exclusive).) Should address issue #29 and #28

• Summary
• integration.mpi 「1」
• ubuntu-20.04.clang.python310.scientific.mp_f19_ddG_of_mutation.debug
• ubuntu-20.04.clang.python311.scientific.mp_f19_ddG_of_mutation.debug
• ubuntu-20.04.clang.python312.scientific.mp_f19_ddG_of_mutation.debug
• ubuntu-20.04.clang.python310.scientific.mp_f19_ddG_of_mutation
• ubuntu-20.04.clang.python311.scientific.mp_f19_ddG_of_mutation
• ubuntu-20.04.clang.python312.scientific.mp_f19_ddG_of_mutation
• scientific.protein_data_bank_diagnostic.full
• ubuntu-22.04.gcc.python39.unit 「3」
• windows.build.debug
• windows.build.release

Update CONTRIBUTING.md (#47) Add forgotten link to the Github Workflow documentation

• Summary
• integration.mpi 「1」
• linux.gcc.cxx11thread.serialization.unit 「3」
• linux.gcc.unit 「4」
• windows.build.debug
• windows.build.release

cifparse: Debian missing unistd include (#38) Addresses Issue #31

• Summary
• integration.mpi 「1」
• integration.release_debug 「2」
• windows.build.debug
• windows.build.release

QOL update to the PerResidueEsmProbabilitiesMetric (#26) This short PR: * Adds the proper citation for ESM * Adds some checks for NaNs/Infs to the Perplexity/softmax calculation * fixes a typo in MIFST.cc * Prevents an error in SampleSequenceFromProbabilities when calling the SimpleThreadingMover without mutations * Fixes const behavior in SampleSequenceFromProbabilities --------- Co-authored-by: moritzertelt <moritz.ertelt@gmail.com>

• Summary
• integration.mpi 「2」
• integration.release_debug 「10」
• integration.tensorflow 「1」
• integration.thread 「1」
• integration 「8」

fix PyRosetta build on Ubuntu-22.04 (#45)

• Summary
• integration.mpi 「1」
• integration.release_debug 「1」
• scientific.glycan_structure_prediction
• scientific.make_fragments.debug
• scientific.make_fragments
• scientific.mp_f19_ddG_of_mutation.debug
• scientific.mp_f19_ddG_of_mutation
• scientific.mp_f19_decoy_discrimination.debug
• scientific.mp_f19_decoy_discrimination
• scientific.mp_f19_tilt_angle.debug
• scientific.mp_f19_tilt_angle
• scientific.mp_lipid_acc
• scientific.peptide_pnear_vs_ic50.debug
• scientific.peptide_pnear_vs_ic50
• scientific.simple_cycpep_predict.debug
• scientific.simple_cycpep_predict

rename torch extras and defines (#43) * rename torch extras and defines * fix integration tests

• Summary
• integration.mpi 「1」
• integration.release_debug 「1」
• scientific.protein_data_bank_diagnostic.full

Fix uninitialized variable in InterfaceScoreCalculator (#40) The native_ensemble_best_ variable was uninitialized, which could potentially cause issues for non-XML cases were it doesn't get explicitly set. Make sure we initialize it.

• Summary
• integration.mpi 「1」
• integration.release_debug 「1」

update documentation and remove deprecated scripts (#41) * Update README.md * add reference docker files * add reference Docker files readme * remove deprecated Conda setup and instructions * remove PyRosetta deprecated build option and update readme

• Summary
• integration.addsan 「1」
• integration.mpi 「1」

libxml2 build: strcasecmp needs strings.h (#39) The exact error (by clang) was that a missing declaration is no longer supported with the latest C++ standards.

• Summary
• integration.addsan 「1」
• integration.mpi 「1」
• integration.release_debug 「1」
• scientific.glycan_structure_prediction
• scientific.peptide_pnear_vs_ic50.debug
• scientific.peptide_pnear_vs_ic50
• scientific.simple_cycpep_predict.debug
• scientific.simple_cycpep_predict

fix PyRosetta license file path (#35)

• Summary
• integration.addsan 「1」
• integration.mpi 「1」
• integration.release_debug 「1」
• scientific.make_fragments.debug
• gcc-9.gcc.unit 「1」