Merge pull request #5396 from RosettaCommons/roccomoretti/cleanup_fwd
Clean up forward headers.
Part of the "try to speed up compilation" series: Go through the forward headers, and clean up unneeded includes. (Under the philosophy that the forward headers should be as minimal as possible to define the existence of types.)
A number of individual deletions, but main ones:
* There were some "all" headers that really weren't being used, and probably shouldn't be used (include the individual subheaders instead) - those were deleted
* There's no appreciable difference between owning_ptr.fwd.hh and owning_ptr.hh (and corresponding access_ptr files) - delete the fwd.hh versions and just use the regular hh ones.
* Replace vector1.hh with vector1.fwd.hh in forward headers, where practical. On my machine there's about a half second of compile time difference between the two.
* Fix up some locations where APs were being defined as shared_ptr instead of weak_ptr.
Large numbers of #include additions to fix up compilation.
Additionally, I added an option to the Windows compile on the test server to increase the number of errors it reports when it fails. (Instead of just the first.) I figure this will help when people don't have a local Windows build they can run, and have to fix the errors based on the server results.
Merge pull request #4255 from RosettaCommons/roccomoretti/orbital_include
Reduce transitive inclusions of orbital headers.
Certain Orbital-related headers were contributing more than they likely should to the amount of included header lines.
We can adjust the Residue and ResidueTypeBase classes such that these headers are only in the cc files, and aren't included for everything that needs Residue.hh or ResidueType.hh.
To aid in this conversion (and to keep the deep copy semantics of the vector-of-Orbital objects), I've added a deep_copy_vector1 class, which subclasses vector1, but provides deep copy semantics for vectors-of-OPs.
Merge pull request #5346 from RosettaCommons/vmullig/more_verbose_tensorflow_error
Make a Tensorflow error message more verbose to aid debugging
Once in a while, I'm seeing a failure in the Tensorflow tests (_e.g._ https://b3.graylab.jhu.edu/sub-test/224304352), in a piece of code that combines a vector of N-tensors into an (N+1)-tensor. This _might_ be due to float-float comparisons (and I hope that's all it is), but I would have thought that `memcpy` would guarantee that float-float comparisons would be valid. For this reason, I'm going to make the error messages more verbose so that we can see for ourselves what's going wrong when this test fails on the test server.
@JackMaguire
Merge pull request #5307 from RosettaCommons/roccomoretti/fix_advanced_docking
Python3 updates in tools dir. This should hopefully fix the advanced_protein-protein_docking test on the test server.
Merge pull request #5135 from RosettaCommons/vmullig/update_docs1
Update documentation so that main repo points to current master of docs.
This is to add the page on using VSCode with RosettaScripts (https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/Using-RosettaScripts-with-VSCode).
Merge pull request #5082 from RosettaCommons/vmullig/make_helical_bundle_predict_public
Make the helical_bundle_predict app into a public app
This seems stable enough to make it public, and I've had a few requests from external Rosetta users who can see the documentation for the app but who can't access the app itself.
Tasks:
- [x] Move `helical_bundle_predict.cc` from `apps/pilot/vmullig` to `apps/public/helical_bundle`.
- [x] Update tracer output.
- [x] Add CitationManager functions.
- [x] Check that there are good integration tests. (I think I wrote some.)
- [x] Check that integration tests produce reasonable output.
- [x] Check that MPI tests produce reasonable output.
- [x] Beauty.
- [x] Check documentation and update accordingly.