Merge pull request #4140 from RosettaCommons/roccomoretti/disable_sewing_hasher_tests
Disable continuous_sewing_hasher and discontinuous_sewing_hasher integeration tests.
Per the decision at PreRosettaCon, disable these constantly-failing tests.
We don't actually need to disable them wholesale, just the parts which take forever. We can still test the (quick) setup command portion.
Anyone should feel free to reenable them later, if they can find a way of making them run faster. The reason for disabling instead of fixing is simply because there's not much interest in spending time with these legacy protocols.
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Merge pull request #4118 from RosettaCommons/JackMaguire/cxx17functionattributes
Compilers allow for various function attributes to help annotate code functionality. Most attributes are not useful for us in Rosetta, but a few can be useful for development purposes. For example, [[unused]] makes debug-mode compilation easier/cleaner in the early stages of development.
Starting in c++17, compilers are told to ignore attributes that they do not recognize, which greatly increases portability. This PR adds a macro that allows you to write attributes that will only be applied if your version of c++ is c++17 or later, along with 4 whitelisted attributes: PURE, CONST, UNUSED, and NODISCARD
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Merge pull request #3990 from RosettaCommons/JackMaguire/MonomerDesign2019
Updating FastRelax/FastDesign to make MonomerRelax2019/MonomerDesign2019 the new default relaxscripts
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Merge pull request #4074 from RosettaCommons/roccomoretti/crash_display_change
Adjust the application signature for new crash reporter scheme.
The crash reporter PR (#2978) introduces a slight change in how exceptions should be handled in executables. Instead of the application displaying the message itself, it should call the Exception::display() function, which will handle doing the appropriate display (and any applicable crash report generation).
Most of this is just somewhat mechanical changes to the source/src/apps files. (I've also updated the code templates) But I also have changes to the JD2 & JD3 exception handling, such that errors which are caught by the JD machinery will also generate the appropriate logs.
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Merge pull request #4143 from RosettaCommons/roccomoretti/update_release_settings
Add additional info for site.settings.release.
There are a couple of common modifications end users often need. Provide stub templates for them in site.settings.release such that they're easier to describe.
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Merge pull request #4096 from RosettaCommons/roccomoretti/ignore_rna_loop_data
Ignore autogenerated loop files in the database.
There are some cached files in database/scoring/loop_close/6D_potentials/rna/ which get autogenerated (e.g. by unit tests)
Add them to a gitignore file, so they don't clutter up git status reports.
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Merge pull request #4124 from RosettaCommons/roccomoretti/gcc_9.1_fixes
Fixes for GCC 9.1 compilation
Most of the issues with compiling with GCC 9.1 are making sure that the copy constructor and the assignment operator (if both are used) are either both explicit or both implicit. Most changes are mechanical, but there are a few locations where there are copy and assignment discrepancies (or where there were but are no longer.)
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Merge pull request #4131 from RosettaCommons/vmullig/remove_code_duplication
Removing some code duplication. A function override in SymmetricRotamerSets does exactly what the base class function does.
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