Peter Amstutz [Fri, 4 May 2018 14:29:44 +0000 (10:29 -0400)]
13365: Add tests to confirm regressions are fixed.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 4 May 2018 14:13:05 +0000 (10:13 -0400)]
13365: clean up discover_secondary_files
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 3 May 2018 20:18:12 +0000 (16:18 -0400)]
13365: Fix state logging
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 3 May 2018 20:09:37 +0000 (16:09 -0400)]
Skip some unnecessary pip invocations.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 3 May 2018 19:48:16 +0000 (15:48 -0400)]
13365: Further fixes to ensure output callback only happens once
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 25 Apr 2018 17:31:11 +0000 (13:31 -0400)]
Fix gopath/govendor recipe.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 25 Apr 2018 17:30:27 +0000 (13:30 -0400)]
Skip explicit libcloud preinstall when not using a fork.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Sun, 8 Apr 2018 00:49:21 +0000 (20:49 -0400)]
Fix wrong temp path in govendor recipe.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Sun, 8 Apr 2018 00:48:03 +0000 (20:48 -0400)]
Use released version of llfuse for tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 3 May 2018 18:24:45 +0000 (14:24 -0400)]
12167: Test X-Request-ID headers.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 3 May 2018 18:03:40 +0000 (14:03 -0400)]
12167: Generate only one request ID per get/put.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 3 May 2018 17:46:57 +0000 (13:46 -0400)]
13365: Fix race condition between job submitted and event monitor threads
Don't call "done" if work reuse means a container request or job
immediately comes back as Completed because it might get called
twice.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 3 May 2018 17:07:31 +0000 (13:07 -0400)]
Merge branch '13365-note-bug-in-docs' refs #13365
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 3 May 2018 15:13:38 +0000 (11:13 -0400)]
13365: Add example error messages and highlight the changes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 3 May 2018 14:21:05 +0000 (10:21 -0400)]
12167: Generate a new request ID if caller explicitly uses "".
Skip invoking unique ID generator if ID is already set.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 3 May 2018 14:10:11 +0000 (10:10 -0400)]
12167: Merge branch 'master'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 3 May 2018 14:05:40 +0000 (10:05 -0400)]
12626: Log UUID of auth record (if any) instead of supplied token.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 2 May 2018 23:49:12 +0000 (19:49 -0400)]
13365: Bump cwltool, 3rd party package versions.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 2 May 2018 20:54:45 +0000 (16:54 -0400)]
12626: Check for scoped tokens.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 2 May 2018 20:12:15 +0000 (16:12 -0400)]
12626: Add arvados/v1/users/merge API.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 1 May 2018 21:37:02 +0000 (17:37 -0400)]
13365: Bump schema-salad for better error formatting.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 1 May 2018 20:30:02 +0000 (16:30 -0400)]
Bump cwltool version for secondaryFile checker support.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 1 May 2018 20:09:38 +0000 (16:09 -0400)]
13365: Reintroduce secondaryFile discovery.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 17 Apr 2018 19:23:46 +0000 (15:23 -0400)]
13365: Discover secondaryFiles associated with default files inputs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 1 May 2018 18:06:15 +0000 (14:06 -0400)]
Merge branch '13111-no-anonymous-sitefs'
refs #13111
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 1 May 2018 17:35:05 +0000 (13:35 -0400)]
Merge branch '13338-wb-run-wf-proj' refs #13338
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 1 May 2018 15:16:47 +0000 (11:16 -0400)]
12167: Pass request ID via keepclient instead of custom code.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 30 Apr 2018 14:03:11 +0000 (10:03 -0400)]
Fix #ZgotmplZ in dir listing page when filename contains a colon.
refs #8784
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 30 Apr 2018 21:31:47 +0000 (17:31 -0400)]
13365: Tweak text.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 30 Apr 2018 21:29:36 +0000 (17:29 -0400)]
13365: Update release notes about a-c-r bug in v1.1.4.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 30 Apr 2018 20:37:12 +0000 (16:37 -0400)]
Fix wrong event_type when getting buffered live logs for crunch2.
refs #12690
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 27 Apr 2018 20:45:28 +0000 (16:45 -0400)]
13111: Disable siteFS routes for anonymous requests.
This enables dav clients to use HTTP authentication even when
anonymous tokens are configured.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Ward Vandewege [Fri, 27 Apr 2018 15:46:02 +0000 (11:46 -0400)]
Documentation: update PostgreSQL installation instructions
refs #13165
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Peter Amstutz [Fri, 27 Apr 2018 15:51:51 +0000 (11:51 -0400)]
Node manager integration test writes to stderr in chunks.
Handles EAGAIN when getting pipe buffer backpressure. no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 26 Apr 2018 20:51:53 +0000 (16:51 -0400)]
Avoid dangling child procs in test suite.
In go 1.10.1, these seem to make "go test" hang sometimes.
https://github.com/golang/go/issues/24050
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 26 Apr 2018 20:45:01 +0000 (16:45 -0400)]
13338: Running workflow from workbench puts collections in correct project.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 26 Apr 2018 20:11:37 +0000 (16:11 -0400)]
Merge branch '13377-block-sig-time' refs #13377
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 26 Apr 2018 20:00:11 +0000 (16:00 -0400)]
13377: Ensure that collection fetched by PDH has longest available lifetime.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 26 Apr 2018 19:34:06 +0000 (15:34 -0400)]
Merge branch '12708-balance-storage-classes'
refs #12708
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 26 Apr 2018 19:30:03 +0000 (15:30 -0400)]
Merge branch '13399-log-low-priority'
refs #13399
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 26 Apr 2018 18:54:24 +0000 (14:54 -0400)]
13399: Log when a slurm job's priority is unrealistically low.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 26 Apr 2018 18:30:29 +0000 (14:30 -0400)]
Merge branch '13282-admin-docs' refs #13282
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 26 Apr 2018 18:13:27 +0000 (14:13 -0400)]
13282: doc updates
* Improve presentation of R SDK
* Move obsolete crunch1 documentation to "Obsolete" section.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 26 Apr 2018 17:14:38 +0000 (13:14 -0400)]
12708: Merge branch 'master' into 12708-balance-storage-classes
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 26 Apr 2018 17:10:04 +0000 (13:10 -0400)]
12708: TODO notes about memory use and class combinations.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 10 Apr 2018 15:22:11 +0000 (11:22 -0400)]
13282: Add note about supported platforms to install guide.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 10 Apr 2018 14:24:12 +0000 (10:24 -0400)]
13282: Remove some obsolete crunchv1 documenation from python sdk.
Fix formatting of "websocket events" page.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 10 Apr 2018 14:19:45 +0000 (10:19 -0400)]
13282: Add architecture section
Also commented out obsolete documentation pages about using
crunchv1 (which have already been marked deprecated for a long time).
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 28 Mar 2018 19:06:58 +0000 (15:06 -0400)]
13282: First pass at reorganizing
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 26 Apr 2018 17:09:29 +0000 (13:09 -0400)]
12708: Precompute len(slots) to reduce mallocs. Rename setupCaches.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 26 Apr 2018 15:59:25 +0000 (11:59 -0400)]
Add tag to secrets test so it is recognized by new cwltest as "optional".
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 26 Apr 2018 15:42:28 +0000 (11:42 -0400)]
Merge branch '13111-projects-by-id'
refs #13111
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 26 Apr 2018 15:34:38 +0000 (11:34 -0400)]
13111: Update to Go 1.10.1.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 25 Apr 2018 15:01:36 +0000 (11:01 -0400)]
13111: Merge branch 'master'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 25 Apr 2018 14:58:06 +0000 (10:58 -0400)]
12167: Propagate X-Request-Id in API calls.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 25 Apr 2018 04:34:19 +0000 (00:34 -0400)]
12167: Propagate X-Request-Id in keep requests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 25 Apr 2018 04:20:47 +0000 (00:20 -0400)]
12167: Fix impossible fixture.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 25 Apr 2018 04:14:16 +0000 (00:14 -0400)]
12167: Log keep-web requests and responses as JSON.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Ward Vandewege [Wed, 25 Apr 2018 03:23:08 +0000 (23:23 -0400)]
libcloud 2.3.0 now requires python-requests 2.4.3 or higher, otherwise
it throws
ImportError: No module named packages.urllib3.poolmanager
when loaded. We only see this problem on ubuntu1404, because that is our
only supported distribution that ships with a python-requests older than
2.4.3. This issue was caught by our automated package testing, yay!
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 25 Apr 2018 03:21:16 +0000 (23:21 -0400)]
Remove remaining build script references to ubuntu1204, which we do not
build packages for anymore.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Fernando Monserrat [Wed, 25 Apr 2018 01:09:31 +0000 (22:09 -0300)]
refs #13369 rollback packages install on ubuntu1404 Dockerfile for builds
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Tue, 24 Apr 2018 22:31:25 +0000 (19:31 -0300)]
refs #13369 remove added packages install. rollback
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Peter Amstutz [Tue, 24 Apr 2018 21:44:44 +0000 (17:44 -0400)]
login-sync test fix also make docker group optional refs #13385
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 24 Apr 2018 20:15:53 +0000 (16:15 -0400)]
Merge branch '13385-login-sync-test' refs #13385
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 24 Apr 2018 03:17:41 +0000 (23:17 -0400)]
12167: Propagate X-Request-Id in API calls.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 24 Apr 2018 20:11:18 +0000 (16:11 -0400)]
13385: login-sync test works even if there is no fuse group
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 24 Apr 2018 15:07:15 +0000 (11:07 -0400)]
Update mock to match new arvados.File interface.
refs #13111
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 24 Apr 2018 03:23:00 +0000 (23:23 -0400)]
13111: Update arvbox and package-build images to Go 1.9.5.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fernando Monserrat [Mon, 23 Apr 2018 21:25:13 +0000 (18:25 -0300)]
refs #13369 "Merge branch '13369-update-ubuntu1404-dockerfile'".
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Mon, 23 Apr 2018 21:24:12 +0000 (18:24 -0300)]
13369: add ulimit to the docker run fixing slowness bug on ubuntu1404
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Mon, 23 Apr 2018 21:16:44 +0000 (18:16 -0300)]
Merge branch 'master' into 13369-update-ubuntu1404-dockerfile
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Mon, 23 Apr 2018 18:30:54 +0000 (15:30 -0300)]
refs #13369 "Merge branch '13369-update-ubuntu1404-dockerfile'".
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Mon, 23 Apr 2018 18:06:21 +0000 (15:06 -0300)]
13369: update ubuntu1404 test packages Dockerfile
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Peter Amstutz [Mon, 23 Apr 2018 15:29:55 +0000 (11:29 -0400)]
Fix nodemanager tests. no issue #
Stub out subprocess.check_output to avoid calling the real "scontrol".
Fixes test_failed_arvados_calls_retried, test_subscribe and
test_creation_with_arvados_node in SLURMComputeNodeSetupActorTestCase.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fernando Monserrat [Mon, 23 Apr 2018 14:38:41 +0000 (11:38 -0300)]
refs #13369 "Merge branch '13369-update-ubuntu1404-dockerfile'".
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Mon, 23 Apr 2018 14:37:31 +0000 (11:37 -0300)]
13369: update ubuntu1404 test Dockerfile
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Tom Clegg [Mon, 23 Apr 2018 13:05:39 +0000 (09:05 -0400)]
13111: Access projects via /by_id/$uuid/.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 20 Apr 2018 20:18:45 +0000 (16:18 -0400)]
Merge branch 'thehyve/master' LocalJumpError in arvados-login-sync
no issue #, github PR 65
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Fri, 20 Apr 2018 19:59:21 +0000 (15:59 -0400)]
Merge branch '13111-webdav-projects'
refs #13111
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 20 Apr 2018 19:56:12 +0000 (15:56 -0400)]
13111: Merge branch 'master' into 13111-webdav-projects
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fernando Monserrat [Fri, 20 Apr 2018 18:11:48 +0000 (15:11 -0300)]
refs #13369 "Merge branch '13369-update-ubuntu1404-dockerfile'".
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Fri, 20 Apr 2018 18:10:43 +0000 (15:10 -0300)]
13369: update ubuntu1404 Dockerfile
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Tom Clegg [Fri, 20 Apr 2018 18:08:39 +0000 (14:08 -0400)]
13111: Fix bogus form-encoding in example URL.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Pavel Mikhailovskii [Fri, 20 Apr 2018 15:08:04 +0000 (17:08 +0200)]
Fix a typo in Crunch Dispatch documentation. Arvados-DCO-1.1-Signed-off-by: Pavel Mikhailovskii <pavel@thehyve.nl>
strangepleasures [Fri, 20 Apr 2018 14:47:46 +0000 (16:47 +0200)]
Simplify filtering in arvados-login-sync. Arvados-DCO-1.1-Signed-off-by: Pavel Mikhailovskii <pavel@thehyve.nl>
strangepleasures [Fri, 20 Apr 2018 14:29:27 +0000 (16:29 +0200)]
Merge remote-tracking branch 'upstream/master'
strangepleasures [Fri, 20 Apr 2018 14:06:58 +0000 (16:06 +0200)]
Fix LocalJumpError in arvados-login-sync. Arvados-DCO-1.1-Signed-off-by: Pavel Mikhailovskii <pavel@thehyve.nl>
Peter Amstutz [Fri, 20 Apr 2018 13:44:59 +0000 (09:44 -0400)]
Fix R SDK online doc generation refs #13076
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Fri, 20 Apr 2018 08:20:12 +0000 (10:20 +0200)]
Merge branch '13076-r-autogen-api'
refs #13076
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Peter Amstutz [Thu, 19 Apr 2018 17:52:37 +0000 (13:52 -0400)]
arvbox pin pip to 9.0.3. Add LINES/COLUMNS to "arvbox shell", no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 19 Apr 2018 20:05:28 +0000 (16:05 -0400)]
Make the runin-reqs less stingy about RAM refs #13301
Tests were failing because it turns out 4 MB isn't enough to run Python!
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 19 Apr 2018 19:47:23 +0000 (15:47 -0400)]
13076: R SDK online docs include both README and method docs.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 19 Apr 2018 18:24:11 +0000 (14:24 -0400)]
13076: Get rid of pkgdown, just call knitr
Converts README.Rmd to README.html for documentation.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 19 Apr 2018 14:59:42 +0000 (10:59 -0400)]
12708: Pull blocks to desired storage classes.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 18 Apr 2018 20:26:19 +0000 (16:26 -0400)]
Bump arvados-python-client version dependency.
Set threadsafe api object to use calling command.keepdocker and
command.put.
refs #13108
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 18 Apr 2018 20:23:29 +0000 (16:23 -0400)]
arv-put: restore_signal_handlers conditional on install_sig_handlers
arv-keepdocker: accept api object to use
refs #13108
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Tue, 17 Apr 2018 15:10:04 +0000 (17:10 +0200)]
Added script to generate html doc for .Rmd files.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Peter Amstutz [Tue, 17 Apr 2018 01:26:41 +0000 (21:26 -0400)]
fix cwltest junit-xml dependency refs #13108
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Mon, 16 Apr 2018 15:03:38 +0000 (17:03 +0200)]
Updated README and small fix for Subcollection docs.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Mon, 16 Apr 2018 13:51:47 +0000 (15:51 +0200)]
Method documentation now shows headline properly.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
projects / arvados.git / log