commit 65723d2a3f8d8728b7b67db7013999a799364847 Merge: 6def6f6 504ac66 Date: Thu Jan 8 08:21:50 2015 -0800 Merge pull request #256 from RosettaCommons/kalekundert/fix_integration_tests Fix the instability in the loop_creation integration test. I decided to do this because I already spent a day figuring out how to run valgrind for my own unstable integration test, and it turned out to be a really easy process. So I thought I might as well fix the other unstable test while I still remembered how. The problem in this case was related to the prevent_nonloop_modifications_ variable being declared in the parent class and the child class, but only defined in the child class. I fixed this by removing the child class declaration and forcing everything through the parent class. commit 6def6f61d18a6ea2c9c860efd393bb4929ed8f9d Merge: 99d6043 8b881c7 Date: Thu Jan 8 11:56:21 2015 +0200 Merge pull request #254 from RosettaCommons/sjf/AddChainFix appending poses in AddChainMover for some reason did not update the chai... commit 99d6043d2a1d03dd4761b8eff1f19a560a22b812 Merge: d373281 d92519d Date: Wed Jan 7 15:40:29 2015 -0500 Increasing speed tolerance for performance benchmark to 7%. Adding separate option for PyRosetta unit tests memory requirements. commit d373281bd118ca15791d7ffdb350a33d6af8d750 Merge: ef39b24 c6f4270 Date: Wed Jan 7 11:20:13 2015 +0100 Merge pull request #244 from RosettaCommons/zhezhang1986/restricted_wte_refine Zhezhang1986/restricted wte refine commit ef39b24c891b2a612c7904157612446cb2e3406b Merge: 823aeed 273b577 Date: Tue Jan 6 19:51:46 2015 -0800 Merge pull request #245 from RosettaCommons/vmullig/for_chris This creates a new mover, BundleGridSampler, which samples Crick parameter space in user-defined ranges and returns the parameters corresponding to the lowest-energy pose, along with that low-energy pose. The mover can also dump out PDB files for all structures sampled. Tasks completed: Update protocols_c.5.src.settings and the MoverCreators/MoverRegistrators init files. Create the BundleGridSampler mover. Add RosettaScripts support. Let the mover parse all options accessible to the MakeBundle mover (using parsing code that dwells in that mover), and additionally let the user specify custom parameter ranges. Add PDB output support for all states sampled. Add a sample low / sample high option, and let the user specify a custom scorefunction. Let the user specify a custom mover for the grid sampler to apply at each grid point before final scoring. Possibly add warnings for unreasonably high numbers of samples? Select lowest-energy structure sampled, and return this as the output pose. Documentation. Integration test. I expect very minor cosmetic changes to the helical_bundle, helical_bundle_nonideal, and perturb_helical_bundle integration tests (I think one line of output, related to delta_t, will now occur slightly later or earlier in sequence than it did before). The newly-added bundlegridsampler and bundlegridsampler_design integration tests should also fail, because they're new. Note that the KIC_with_fragments integration test has been failing consistently, and the Linux PyRosetta unit tests have intermittently been failing with memory errors (all independent of this merge). I didn't wait for the Windows PyRosetta build test since it completed successfully on a slightly earlier version of this branch, and since there is a major backlog with that test. commit 823aeedcaea091d6049364d5bbcddf188a096037 Merge: e21a7cc 8403aae Date: Tue Jan 6 16:06:56 2015 -0800 Fix an uninitialized variable in the loop modeling code. I think this bug has been responsible for the instabilities in the KIC_with_fragments test, but it shouldn't have had any real effect on loop modeling performance. commit e21a7ccdc613ed374627b1154f6fbb2182dcbfd9 Merge: db21bd0 51b2422 Date: Tue Jan 6 10:36:18 2015 -0500 Merge pull request #250 from RosettaCommons/jkleman/fix_mpsymdock_integration fixing failing integration test for mpsymdock commit db21bd0273dd9eabfe569517629d93c473331900 Merge: c7b0243 961336a Date: Tue Jan 6 08:06:26 2015 -0500 Merge pull request #253 from RosettaCommons/rfalford12/fix-symdock-bug Fixing a small bug in the membrane symmetric docking protocol commit c7b0243bdc54d9f12ee37064b9102914d611a557 Merge: b808d75 f932082 Date: Tue Jan 6 00:19:26 2015 -0800 Merge pull request #251 from RosettaCommons/kalekundert/fix_integration_tests Fix three integration tests that I accidentally broke a while back: favor_native_residue, hotspot_graft, and place_simultaneously. Three tests remain broken: antibody_graft, pocket_suggest_targets, and mpframework_syndock. The former two were broken before my original commit and the latter one was broken after, so I won't be doing anything about those. The instabilities in the KIC_with_fragments test are also probably related to my original commit, since the instabilities started around then and my commit made a lot of changes to that code. So my next goal will be to track down that bug. commit b808d757ec4c4b60de7dcff1bcf6c4029a930372 Merge: 2e9e79b c51e0f9 Date: Mon Jan 5 10:23:14 2015 -0800 Merge pull request #249 from RosettaCommons/rhiju/inner_score_delta_clarification renaming inner_score_temperature_delta to inner_score_delta_over_tempera... commit 2e9e79bfd3a5126ce0e77038aa6bb04270c37ec7 Merge: e440ff1 6333441 Date: Sun Jan 4 10:41:08 2015 -0800 Merge pull request #248 from RosettaCommons/daslab Daslab -- proper docking in stepwise modeling all tests confirmed OK (except windows_pyrosetta_build -- seems to be a big backlog in that build queue...) commit e440ff12f2566c0549966648fb593af2284ac4af Date: Fri Jan 2 20:16:23 2015 -0600 added missing app from apps.src.settings to resolve pocket_sugggest... integration test failures commit 778734adc5ba18420a5475b493549e98261975f1 Merge: d07f868 ae88343 Date: Thu Jan 1 11:26:15 2015 -0800 Merge pull request #246 from RosettaCommons/rhiju/fix_default_for_sampler_perform_phosphate_pack Rhiju/fix default for sampler perform phosphate pack setting allow_internal_local_moves (erraser-style moves) to true in step... test changes are in 3 expected stepwise tests, and rest are 'usual suspects'. windows pyrosetta build not queued yet, but I'll keep an eye on master after this merge. commit d07f8682e192a5afa5a8479767d92fa988660627 Merge: bd534a3 d0a467d Date: Thu Jan 1 11:25:34 2015 -0800 Merge pull request #247 from RosettaCommons/rhiju/allow_internal_local_moves_true setting allow_internal_local_moves (erraser-style moves) to true in step... test changes are acceptable (and minimal). windows pyrosetta build not queued yet, but I'll keep an eye on master after this merge. commit bd534a3e9f82c5bca795e1ab388edde66ac66aa3 Merge: 20140b1 95db035 Date: Wed Dec 31 10:35:42 2014 -0800 Merge pull request #242 from RosettaCommons/daslab Daslab -- minor updates Merging! A few integration test changes in stepwise tests: • Test changes other than stepwise are 'usual suspects' -- broken tests or kic_fragments • cosmetic changes: getting rid of NativeRMSDScreener in cases without native. • in SWA, score offset from the way rna_bulge is computed; use of ftol vs. atol leads to some differences in minimization. • RMSD computation fixed in SWA. cosmetic changes. • cosmetic changes from reducing number of etable instantiations. commit 20140b1472a1b65560c61c0f633f046130bed5de Merge: 97af5d6 f59f518 Date: Tue Dec 30 11:42:38 2014 -0800 Merge pull request #243 from RosettaCommons/justinrporter/env_release Integrating two bug fixes (18dde7b and f59f518) to master. No integration or unit test breakages expected, other than the usual suspects. commit 97af5d6fba96bf4fa283c496db4a3babc6f66ad4 Merge: 0d81dd2 8f06c20 Date: Sat Dec 27 09:10:20 2014 -0800 Merge pull request #241 from RosettaCommons/justinrporter/env_release Merging several bug fixes to the environment. No expected unit test changes, no expected integration or performance test failures except the usual suspects. commit 0d81dd2e31a3bf91fe6c1161ec8591dff9ca6410 Merge: ce60b79 69bc694 Date: Thu Dec 25 09:16:41 2014 +0200 Merge pull request #238 from RosettaCommons/sjf/short_circuit_hairpin2 Sjf/fix_seqprof_cons_for_covalent_modifications