Pushed Revisions

branch: master 「№60936」
Commited by: Julia Koehler Leman
GitHub commit link: 「2429ae1358bb1730」「№4226」
Difference from previous tested commit: code diff
Commit date: 2019-09-17 11:20:05

Merge pull request #4226 from RosettaCommons/tigerous/update-loop-modeling-scientific-tests update readme file and cutoffs - thanks Phuong!

branch: master 「№60935」
Commited by: Rocco Moretti
GitHub commit link: 「29f1d046a74a32ff」「№4224」
Difference from previous tested commit: code diff
Commit date: 2019-09-16 18:30:37

Merge pull request #4224 from RosettaCommons/roccomoretti/fix_cppcheck_for_188 Fixes for cppcheck 1.88 Sergey's interested in updating the version of cppcheck on the test server to 1.88. This version is having issues with the testing scripts (as they changed how they handle certain options.) This PR updates the command for the cppcheck test, as well as copying more logging information into the test server info. This should still work for the current 1.63 version, until we switch things over. I've augmented the "historical" list with the new 1.88 issues, but at some point we should probably clean those up.

Steven Lewis 5 years
There are a lot of weird magenta hard failures in the integration tests, but they are not replicated in the integration.release_debug version so I am inclined to ascribe them to a temporary server error. We'll want to keep an eye on it. [list]

Rocco Moretti 5 years
It looks like it's mostly .test_got_timeout_kill.log errors. This typically shows up with temporary hiccups on the test server where things take too long. -- It does look like these are no longer showing up in the most recent version of master. [list]

branch: master 「№60934」
Commited by: Shourya Sonkar Roy Burman
GitHub commit link: 「9ae8bb94f2904054」「№4112」
Difference from previous tested commit: code diff
Commit date: 2019-09-15 19:32:48

Merge pull request #4112 from RosettaCommons/ssrb19/scientific_tests_docking Scientific benchmark for protein-protein docking

branch: master 「№60933」
Commited by: Vikram K. Mulligan
GitHub commit link: 「59bbbc01e9f80046」「№4221」
Difference from previous tested commit: code diff
Commit date: 2019-09-14 16:03:43

Merge pull request #4221 from RosettaCommons/vmullig/why_the_hell_is_rosetta_still_defaulting_to_leaking_memory_when_every_developer_has_complained_about_this_at_one_point_or_another Switching default for -jd2:delete_old_poses to "true" There isn't really a reason for Rosetta to leak memory by default, to my mind.

branch: master 「№60932」
Commited by: Andy Watkins
GitHub commit link: 「470fd09fcd4f04d6」「№4219」
Difference from previous tested commit: code diff
Commit date: 2019-09-14 13:01:10

Merge pull request #4219 from RosettaCommons/everyday847/weitzner_h5py_stuff Changes to FragmentStore to patch pyrosetta functionality

branch: master 「№60931」
Commited by: Frank David Teets
GitHub commit link: 「52e9acc0f1fefe1b」「№4217」
Difference from previous tested commit: code diff
Commit date: 2019-09-13 17:43:39

branch: master 「№60930」
Commited by: Brian Coventry
GitHub commit link: 「5b299b86543fe5b4」「№4133」
Difference from previous tested commit: code diff
Commit date: 2019-09-13 17:11:24

branch: master 「№60929」
Commited by: Julia Koehler Leman
GitHub commit link: 「12de374eaab52c7a」「№4206」
Difference from previous tested commit: code diff
Commit date: 2019-09-12 15:43:55

Merge pull request #4206 from RosettaCommons/BYachnin/mhc_epitope_scitest_readmefix Minor changes to README of mhc_epitope_energy scientific test. Thanks Brahm for making these!

branch: master 「№60928」
Commited by: Julia Koehler Leman
GitHub commit link: 「f428f1b5ca0ca54f」「№4205」
Difference from previous tested commit: code diff
Commit date: 2019-09-12 15:20:54

Merge pull request #4205 from RosettaCommons/rfalford12/sci-benchmark-revision Revisions to f19 scientific benchmarks Rebecca's addressed my requested revisions to the plots and readme's of some of the MP benchmarks

branch: master 「№60927」
Commited by: Vikram K. Mulligan
GitHub commit link: 「9d2563a9f074dc75」「№4190」
Difference from previous tested commit: code diff
Commit date: 2019-09-10 14:15:42

Merge pull request #4190 from RosettaCommons/vmullig/fix_intel_cray_build Fixing Cray/icc build. For some reason, an auto-generated operator= was tripping up the Intel/Cray build. Manually implementing this fixed the build.

branch: master 「№60926」
Commited by: Jeliazko Jeliazkov
GitHub commit link: 「e1cd9f4a063d58c8」「№4196」
Difference from previous tested commit: code diff
Commit date: 2019-09-10 04:06:41

Merge pull request #4196 from RosettaCommons/lqtza/various-sci-test-fixes Fixes ensuring antibody-associated scientific tests pass

branch: master 「№60925」
Commited by: Guangfeng Zhou
GitHub commit link: 「02c3c852231bdf8a」「№4193」
Difference from previous tested commit: code diff
Commit date: 2019-09-09 12:51:31

branch: master 「№60924」
Commited by: Rocco Moretti
GitHub commit link: 「46df873d8cd9d162」「№4203」
Difference from previous tested commit: code diff
Commit date: 2019-09-07 12:26:09

Merge pull request #4203 from RosettaCommons/roccomoretti/fix_integration_tests_valgrind_count Fix integration tests logfile issues (Valgrind) The Valgrind integration test has checks to make sure the number of expected logfiles match the number of observed logfiles. (To check that we aren't missing any Valgrind error output.) There are a number of integration tests which don't pass this check. This is mostly because of accidentally overwriting log files, or otherwise dumping/ignoring the output. This also includes some updates to the heuristics themselves, to better support some use cases (running programs from within a loop), as well as to permit the testing server to track the logfile failures on a subtest-by-subtest basis.

branch: master 「№60923」
Commited by: Jack Maguire
GitHub commit link: 「5e43d5bb192c2d80」「№4192」
Difference from previous tested commit: code diff
Commit date: 2019-09-07 08:42:06

Merge pull request #4192 from RosettaCommons/JackMaguire/optE_fast_design sequel to #4184 This allows the user to pass a relax script via commandline to OptE

branch: master 「№60922」
Commited by: Jack Maguire
GitHub commit link: 「1a4cc71f63eedda5」「№4187」
Difference from previous tested commit: code diff
Commit date: 2019-09-06 12:57:07

Merge pull request #4187 from RosettaCommons/JackMaguire/ResetReferences #4184 added the 'reset_reference' command to FastRelax's list of scripting commands. This PR ensures that the final round of reference weights match the "full" scorefunction that the user is trying to optimize. This is just a simple change to a few database files. Unit and integrations tests should be enough.

branch: master 「№60921」
Commited by: Vikram K. Mulligan
GitHub commit link: 「c5ce2269a4789e96」「№3618」
Difference from previous tested commit: code diff
Commit date: 2019-09-05 20:57:03

Merge pull request #3618 from RosettaCommons/vmullig/simple_cycpep_predict_sci_benchmark Add scientific tests for the simple_cycpep_predict application. It's an awful nice peptide structure prediction and design pipeline you've got there. Be a shame if something were to happen to it. Scientific tests make sure nothing happens to it. DONE: - [x] Add a peptide to test. - [x] Set up and test-run the test. - [x] Set suitable PNear cutoffs. - [x] Finish the description. - [x] Add extra option to docs for simple_cycpep_predict and for helical_bundle_predict. - [x] Note that pull request #4046 must be merged before this one. - [x] Pull request #3593 must be merged before this one.

Legend:

queued	Queued Test
queued for comparison	Test finished running but not yet compared
running	Test is Running right now
comparing	Test results is now comparing with previous results
finished	Test is finished without errors
failed	Test failed
build Failed	Test could not be run because build failed
script failed	Test results is unknow because test-script failed
canceled	Test was canceled