Merge pull request #3010 from RosettaCommons/jadolfbr/fix_integration_tests
Fix 2 integration tests that were failing
Fix integration test commands for `homodimer_fnd_ref2015_memb` and `fold_from_loops` that I broke with a missing letter in the `-testing:INTEGRATION_TEST` flag.
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Merge pull request #3001 from RosettaCommons/vmullig/fix_ubsan_tests
Fixing ubsan unit tests.
Initialization of a newly-added Boolean private member variable was omitted in two of the SetupForSymmetryMover's constructors.
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Merge pull request #2982 from RosettaCommons/jadolfbr/config
Support for common Flag Config files
This PR adds the ability for rosetta to find and read common flag config (fconfig) files. This allows us to always run rosetta with a set of custom common options.
If a file named `common` is found in `$HOME/.rosetta/flags` or if it/they are in the current working directory, we use that instead. You can set any number of flag configurations with the `-fconfig` option By default, we have:
```
-fconfig common
```
This is useful if you have a set of flags for different purposes - like design, glycans, and antibody, so you could do something like:
```
-fconfig common antibody
```
That would load both the common and antibody configurations.
If you have a common flag file (which is loaded by default if present), you skip loading through an option
```
-no_config
```
* Note, `-no_fconfig` is used for both unit and integration tests.
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Merge pull request #2994 from RosettaCommons/vmullig/correct_flag_error
Promoting warning about -correct flag to an actual error.
Users have been using the `-correct` flag with `ref2015` without realizing that this results in invalid behaviour. The warning message is easily missed. This promotes it to an error, so that they can't use it accidentally.
A small handful of score12-era integration tests were also still using the `-correct` flag despite having been updated to use `ref2015`. These now correctly do _not_ use `-correct`. This will result in some integration test changes.
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Merge pull request #2986 from RosettaCommons/vmullig/fix_rotamertrials_unit_test
Correct RotamerTrials unit test
The RotamerTrials unit test was taking the sin and cos of values that were in degrees rather than in radians. Correcting.
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Merge pull request #2980 from RosettaCommons/mpacella88/print_atom_pair_energies_pyrosetta
adding print methods to supplement the etable_atom_pair_energy pyrosetta tool
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