[ARVADOS] created: 1.1.4
Git user
git at public.curoverse.com
Tue Apr 10 09:35:26 EDT 2018
at 52b5368c863d1d10777d44db37909de870383a9e (tag)
tagging ff353df24233b40612eb228a8024ea30902397e9 (commit)
replaces 1.1.3
tagged by Fernando Monserrat
on Tue Apr 10 10:33:23 2018 -0300
tag release 1.1.4
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat at veritasgenetics.com>
Fernando Monserrat (44):
13200:test new job with timestamp only removing hash
13200:test new job with timestamp only removing hash
13200:new version using git tag latest and timestamp only
13200:new version using git tag latest and timestamp only
13200:fix python package version with latest git tag and timestamp
13200:fix python gittagers version with latest git tag and timestamp
13200:fix python gittagers version with latest git tag and timestamp
13200:fix python gittagers version with latest git tag and timestamp
13200:fix python gittagers version with latest git tag and timestamp
13200:fix python gittagers version with latest git tag and timestamp
13200:fix python version with git from tag
13200:fix python version with git from tag
13200:test run library
13200:small change to output and to test if python packages are rebuilt when there is no change
13200:small change to output and to test if python packages are rebuilt when there is no change
13200:small change to output and to test if python packages are rebuilt when there is no change
13200:test changes to not build package if no change is present
13200:test changes to not build package if no change is present
13200:test changes to not build package if no change is present
13200:test changes to not build package if no change is present
13200:remove verbose bash on run-library
13200:add verbose just to test new commit behaviour on jenkins
13200:remove repo_subdir for centos
13200:fix slash on centos repo
13200:fix complete package name
13200:test to remove adding 01 to python packages
13200:test to remove prefix on python
13200:test to remove prefix on python
13200:test to remove prefix on python
13200:test update on version in gittaggers on sdk python
13200:test update on version in gittaggers on sdk python
13200:test update on version in gittaggers on sdk python
13200:test update on version in gittaggers on sdk python
13200:rollback tests
13200: format gitinfo on all the services
13200: format gitinfo on all the services
13200: Fix format gitinfo on all the services
13200: remove verbose bash on build packages
13200: remove verbose bash on run-build-packages.sh
refs #13200 Merge branch '13200-new-package-versioning-jb'
13200: Consolidate package version behavior in arvados_version for all the python packages
13200: remove_version from python packages
13200: fix SETUP_DIR on python packages
"refs #13200" "Merge branch '13200-python-pkg-version'".
Fuad Muhic (3):
Replaced README with README.Rmd
Added documentation to each public class of SDK.
Added documentation for print classes
Javier Bértoli (5):
My silly attempt
Varnames
Add functions to return the python version for packaging
Trying some str formatting
Trying some str formatting
Joshua C. Randall (1):
add ReserveExtraRAM config option to crunch-dispatch-slurm
Joshua Randall (1):
Fix CollectionCache to pass num_retries to CollectionReader
Lucas Di Pentima (69):
11454: Replace link buttons with form buttons on search results,
11454: Code cleanup. Removed local wb link on sessions page.
11454: Replaced javascript events with proper form values
11454: Removes workbench links on /sessions page.
11454: A couple of fixes/enhancements:
11454: Avoid instantiating new SessionDB before autoRedirectToHomeCluster()
Merge branch '11454-wb-federated-search'
12863: Adds column showing process status on project pages.
12863: Adds CR's state label on description cell.
13023: Replaces div with pre tags on 'Recent logs' viewer.
13023: Fixes related tests.
13023: Fix integration test.
13023: Workaround firefox copy&paste bug on jobs & pipeline log viewers.
Merge branch '13023-wb-log-newlines'
Merge branch '12863-wb-cr-status'
11454: Don't show 'Remove' session button when listed on remoteHosts.
11454: Code readability enhancement.
Merge branch '11454-remove-button-removal'
12707: Add storage classes attributes to collections.
12707: Some fixes and additions on storage classes:
12707: Adds default value setting on collection creation.
Merge branch '12707-storage-classes-columns'
12737: Fix activesupport dependency from arvados gem.
Merge branch '12737-arvados-gem-dependency'
12268: Update nodemanager dependency on libcloud 2.3.0
12268: Remove libcloud fork installation attempt on run-tests.sh
13147: Logger call fix.
Merge branch '12268-libcloud230-official'
12268: Fix merge conflict.
12268: Fix package build scripts
12268: Add comment just in case we need to use a forked libcloud again.
Merge branch '12268-build-fix'
13147: Append X-Request-Id on error & debug log messages.
12737: Update API server to rails 4.2.10
13147: X-Request-Id logging updates when running arv-put.
Merge branch '13147-arvput-request-id'
Merge branch '12737-update-rails-api'
12737: Update workbench rails to 4.1.16 (latest 4.1.x)
12737: Fix benchmark & integration tests
12737: Avoid upgrading to selenium 3.x
12737: Try pinning all testing gems
12369: Add fuse driver installation notes & update arv-mount tutorial.
12369: Grammar fix
Merge branch '12369-fuse-driver-doc-updates'
Merge branch '12737-update-rails-wb'
12167: Report request-id when receiving SIGINT on arv-put.
13166: Order slurm queue by priority
13166: Limit wishlist to (max_nodes - up_nodes)
13166: Add descriptive comments to every integration test arguments.
Merge branch '12167-arvput-log-on-signals'
13166: Sort optimization & wishlist ordering testing.
13166: Integration test fix.
Merge branch '13166-nodemanager-whishlist'
13168: Remove commented code.
13168: Use helper to avoid updating 'modified_by_user_uuid' field on CRs.
Merge branch '13168-cr-modified-user'
12414: Add project deletion (with its contents) when delete_at is past
12414: Add tests for projects (and their contents) deletion.
12414: Enhance sweep process test to ensure no unwanted deletions happen
12414: Test fixes
Merge branch '12414-delete-trashed-project-contents'
12085: Counters support for status tracker.
12085: Test actor & cloud errors counting.
12085: Boot failures counting, with tests.
12085: Idle node times tracking, with tests.
12085: Add node_quota status & count different cloud errors separately.
12085: When an idle node disappears from the cloud node list, clear its counter.
12085: Unconditionally remove the idle time counter of paired missing nodes.
Merge branch '12085-anm-metrics'
Nico Cesar (1):
13200: minor changes to make it more readable
Peter Amstutz (86):
11876: Build R SDK reference pages for doc site
11876: Arvbox support for building R docs
11876: Update install instructions to r.arvados.org
11876: Update installation instructions
11876: Improve formatting
Merge branch '11876-r-sdk' documentation, refs #11876
R SDK documentation link fix refs #11876
11876: Pin R deps that are installed from gitub.
Merge branch '11876-R-deps' refs #11876
13090: Pass through --eval-timeout to container command line.
Merge branch '13090-eval-timeout' closes #13090
13106: Ensure cache slot is reset on error
13106: Add test confirming deadlock
11645: Add support for StorageClasses in volume config.
13106: Add note about the test.
Merge branch '13106-keepclient-slot' closes #13106
11645: Add tests that StorageClasses is loaded from config
Merge branch '11645-keepstore-storageclasses' closes #11645
13064: Check has_ref before checking in_use
13064: Add __slots__ to ArvadosFile and FuseArvadosFile
13064: Explicitly precompile regexes used in manifest parsing
13064: Add comment about has_ref() and in_use() checks
Merge branch '13064-arv-mount-perf' closes #13064
Merge branch 'wtsi/13093-crunch-dispatch-slurm-add-mem' refs #13093
Merge branch 'wtsi/13113-acr-collectioncache-retries' refs #13113
12315: Add abstract show_children query parameter
12315: Propagate show_children to infinite scroll pages. Fix & add tests.
13037: Add hidden api_token to Composer button to skip extra login
Merge branch '13037-composer-link' closes #13037
13140: Bump cwltool version
13140: Fix tests
13140: Fix call to docker.get_image()
Merge branch '13140-cwl-conformance' refs #13140
12526: add --priority for --api=containers
12526: Fix tests
12526: Add constant for default priority and check range.
13078: Add --noheader to squeue invocation.
Merge branch '13078-cds-noheader' refs #13078
Merge branch '12526-cwl-priority' closes #12526
Update version of cwltest package refs #13140
Fix arvados-cwl-runner --version argument refs #12526
Fix arvados-cwl-runner --version argument (again) refs #12526
Fix packaging for python-cwltest. refs #13140
Fix "priority" KeyError in crunch1 refs #12526
13134: Support for secret mounts in crunch-run.
13134: Get secret_mounts from separate API endpoint. Update tests.
13134: Use the container token to fetch secret_mounts
13134: Check for conflicts between secret mounts and regular mounts
Merge branch '13134-secret-mounts' closes #13134
13135: Secrets support WIP
13135: Handle secrets in file literals.
13135: Remove testing workarounds
13135: Update tests for secret_mounts
13135: Secrets not supported with --api=jobs
13135: Add secrets test to arvados-tests
13135: Update docs
13135: Fix test
Fix arvbox workbench for updated passenger, refs #12737
13135: Code cleanup & comments.
Merge branch '13135-cwl-secrets' closes #13135
13138: Gather arvados API errors under "RequestError" class.
Fix 'arvbox log' to propagate terminal size, no issue #
Merge branch '13138-request-error' refs #13138
13208: Refactor permission checking to improve query performance
Merge branch '13208-permission-performance' refs #13208
13245: Sort InitialWorkDir contents to fix conflicts and redundant mounts.
13245: Bump cwltool version
Fix cwl extension doc typo. closes #13179
Fix cwl extension doc typo. refs #13179
Add cookbook examples for uploading and downloading a file from a
13212: Replace "Output data not available" with "uuid (Unavailable)"
13212: Fix tests
Merge branch '13212-unavailable-output-workunit' closes #13212
Merge branch '13245-cwl-dir-literal' closes #13245
Bump cwltool version for bugfix, refs #13245
13301: Correctly handle dynamically computed resources with RunInSingleContainer
13301: Find hints/requirements on embedded tools
13301: Add some tests, but I'm not sure the best way to hook them into
Add RunInSingleContainer dynamic resource request tests
Merge branch '13301-cwl-resource-scatter' closes #13301
Add missing file refs #13301
13200: Fix python versioning for arvados-python-client and arvados-cwl-runner
13200: Consolidate package version behavior in arvados_version
13201: disable redundant validation.
13201: Fix tests.
Merge branch '13201-less-validate' closes #13201
Tom Clegg (101):
12199: Add node size calculator.
12199: Add SlurmNodeTypeFeatureKludge.
12199: Refactor to eliminate evil globals.
12199: Pass node type to sbatch --constraint argument if configured.
12199: Refactor for more test-friendly initialization.
12199: Use node type X to run jobs with constraint instancetype=X.
12199: Rename instance type features: a1.xl => instancetype=a1.xl
12199: Update slurm features when nodes come up.
12199: Make mocks match real slurm output.
12199: Update integration tests.
12199: Log timestamps in slow integration tests.
12199: Derate advertised node sizes by 5%.
12199: Assign slot and hostname when creating/reusing a node record.
12199: Keep SLURM's node properties up to date.
12840: Differentiate "Cancelled" from "Failed" pipeline instances.
12199: Track slurm node features, avoid redundant updates.
12199: Make operator precedence more obvious.
13022: Don't abandon cleanup tasks on SIGTERM.
12991: Propagate memory and CPU limits to docker container.
13025: Add request time metrics at /metrics and /metrics.json.
12840: Report pipeline state=Failed on job creation failure.
Merge branch '13022-tmp-cleanup'
Merge branch '12991-docker-memory-limit'
Merge branch '12840-cancelled-pipeline'
13025: Lint.
13025: Revert returning WroteStatus()==200 if no header was written.
13025: Merge branch 'master' into 13025-keepstore-metrics
12199: Update integration tests.
12199: Fix errant uses of size.name that should be size.id.
12199: Improve race handling in busywait.
12199: Merge branch 'master' into 12199-dispatch-to-node-type
12199: Move services/dispatchcloud to lib/dispatchcloud.
12199: Ensure scratch space for tmp mounts when choosing node type.
12199: Fix job_uuid missing from nodes#update response.
Merge branch '13025-keepstore-metrics'
Merge branch '12199-dispatch-to-node-type'
13063: Update azure storage client library.
13063: Don't use azure default delay-and-retry loop.
Merge branch '13063-update-azure-sdk'
Add missing parameter to update call.
12552: Add SLURM niceness calculator.
12552: Adjust SLURM niceness to bring priority into desired order.
13063: Use upstream azure-sdk-for-go.
Merge branch '13063-update-azure-sdk'
13098: 12199: Fix hostname assigned but not saved.
Merge branch '13098-assign-hostname'
12315: Add "exclude child processes" checkbox to /all_processes.
12552: Add slurm-renice test cases.
12552: Skip extra lookup.
12552: Document PrioritySpread. Default to 10 if not configured.
12552: Fix accidental textile link syntax.
12315: Tidy up test params.
Merge branch '12315-exclude-child-procs'
13078: Use --test-only instead of invalid --gres to check features.
13078: Accept "no nodes" as an indication that features are OK.
12552: Improve PrioritySpread docs.
Merge branch '13078-slurm-feature-test'
Merge branch '12552-slurm-priority'
12552: Fix starvation in test case.
12552: Remove superfluous arithmetic.
13078: Ensure compute0 always has all the instancetype=X features.
13078: Remove debug log.
13078: Ignore held jobs with priority=0 (e.g., SLURM 15.x).
13078: Fix ignoring queued jobs with reason=BadConstraints.
13078: Fix jobs stuck in "held" state in old SLURM versions.
13078: Reduce "feature kludge" poll interval.
13078: Update comment.
13078: Add test case for "release job held because BadConstraints".
Merge branch '13078-badconstraints'
13143: Add secret_mounts field to containers and container requests.
13143: Do not try to select container secret_mounts column.
13143: Skip some unneeded database resets.
13143: Don't load secret_mounts from test fixtures.
13143: Don't advertise secret_* columns in discovery doc.
13143: Skip some unneeded deep_dup.
13143: Merge branch 'master' into 13143-secret-mounts
13143: Prohibit identical path in mounts + secret_mounts.
13143: Ignore secret_mounts_md5 from fixtures, too.
13143: Sort hash keys for more realistic fixture md5.
13143: Fix same/different-secret_mounts tests.
13143: Add missing "secret_mounts scrubbed" test.
13143: Remove superfluous check for null hash.
13143: Decode request body secret_mounts properly.
13143: Update find_reusable() invocation in test suite.
Merge branch '13143-secret-mounts'
12552: Prioritize containers according to top-level requests.
12552: Fix workflow parent priority test.
12552: Merge branch 'master' into 12552-wf-priority
Merge branch '12552-wf-priority'
13100: Fix memory leak (64MiB per stream in output/log collection).
11583: 13100: Fix memory leak in test suite.
Merge branch '13100-crunch-run-memory'
12167: Stop waiting for arv-put to start up when logs appear.
7931: keep-balance: use keepstore /mounts APIs instead of /index.
7931: Trash excess replicas when a server has more than one.
7931: Fix format/type mismatch.
7931: Don't bother trying to trash replicas on readonly mounts.
7931: OTBE, prefer readonly replicas; they can't be trashed anyway.
7931: Update json field tags on trash/pull requests.
7931: Merge branch 'master' into 7931-replicas-by-volume
Merge branch '7931-replicas-by-volume'
Ward Vandewege (17):
Fix typos/grammar.
The crunch-dispatch-slurm binary has a new dependency on the
Stop running sdk/R install if sdk/R is not being tested. It is
When running inside a virtualenv, pip still uses the ~/.cache/pip cache
Python sdk: do not try to do a bitwise operation on a float.
Documention: fix spelling of --tempdir argument to arv-migrate-docker19
When running inside a virtualenv, pip still uses the ~/.cache/pip cache
build scripts: only run the package tests on packages built since the
doc: consistency fix in SSO install documentation.
Add missing test for error code in keepclient test.
Update debian version in sdk/python/README.rst
Fix a whole bunch of ineffassign warnings in our golang tests.
Fix one gofmt and more ineffassign warnings in our golang tests.
keepproxy: bugfix: do not swallow error if Readall succeeds but PutB fails.
Fix more ineffassign warnings in our golang code.
api server: get_anonymous_user_token script
Fix comment.
jiayong2 (8):
Add max resource requirement in single container test and test workflow
Merge branch 'master' into 11850-singlecontainer-max-requirements
Add changes to arvworkflow.py for taking the max requirement
Merge branch 'master' into 11850-singlecontainer-max-requirements
Take sum for outdir requirement in single container
Merge branch 'master' into 11850-singlecontainer-max-requirements
Merge branch 'master' into 11850-singlecontainer-max-requirements
Merge branch '11850-singlecontainer-max-requirements'
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