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Merge master to stable v0.7.1 #287
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* initial docs for docker users * Fixes plus PR feedback
…d cluster configs (#168) * support programmatically generated credentials/cluster config * update docs for programmatically generated config * reformat code * styling fixes * combine credentials cluster config methods * fix set credentials issue and test input * do not create az_config.json * update messages * move githubAuthenticationToken from cluster config to credentials
* Implemented a more detailed verbose progress bar * Fixed infix operator spacing * Added newline for 'Tasks have completed' message
* Redone the progress bar * Added string utilities
…erminateJob (#174) * add documentation and sample for long running job * update sample file name * update long running job doc and test * update metadata code * add errorHandling to job metadata * add deleteJob to delete both job defintion and job result * styling fix * save foreach wait setting to metadata * implement retry logic in getjobresult * add terminateJob * handle various corner cases * regenerate document * add job state in getJob * do not fail getJobResult if getMetadata failed for backward compatibility * add deleteJob option to foreach, by default it is true for wait=TRUE job * styling fix * update version and changelog * address review feedback * add setJobAutoDelete function * rename jobAutoDelete to autoDeleteJob to workaround R bugs and update docs * update faq * fix styling issues * more styling fix * roll back manual update to DESCRIPTION * add namespace to api call
* initial changes to support auth * Temp changes to pull install scripts from local branch * Updated docs to expose dockerAuth field * Minor tweaks to doc language * revert change to setup scripts back to master * fix linter line too long error * add links to cluster configuration docs * remove whitespace * PR feedback * write and read docker password from disk
#190) * address issue where empty docker auth credentials are used to create the cluster * remove unnecessary null check
* Collasping the R package installations for pool installation * Renamed script variable * Fixed pool installation test * Fixed length test
* Improve UI experience * Added verbose mode to deleteJob and deleteStorageContainer * Refactor print method
* Added task id range * Removed upload blob methods * Removed upload blob * Fixed trailing whitespace * Discarded job id on merge task id name * Adding chunk logic for argsList * Added check for args containing data sets * Removed container name for docker run command for all tasks * Added test for hasDataSet * Fix travis yml * Adding before_install for R * Removed before install, added github package of nycflights13
* support for async cluster creation * fix lintr bot errors * remove test files * use private function for duplicate code * update change log * Feature/asynccluster1 (#200) * show node status in getCluster * workaround error * minor fixes * add getClusterList api * add metadata to pool indicating pool is created by doAzureParallel * add test for getClusterList(), add 'other' state for nodes for getCluster()
* update documentation for private docker registry * update docs to be less confusing
renamed a misnamed azure options variable
* use paste() instead of + * use paste0
* Get job result locally * Get job result locally * preserve task sequence in getjobresult * keep task result sequence * keep task result in sequence and as a flat list * fix lintr error * fix typo in error message * delete cluster after test is done * add retry to getJobResultLocal, resolve xml2 issue * fix typo, lintr and missing variable
* allow local session info to be loaded * update line lengths
* Added zip file extraction * Fixed cluster setup * Added cluster script and quiet zip function * Replaced url name with correct zip file name * Removed startup folder name * Added apt-get install on job prep * Fixed branch names
The file format change over the year so only use the first 6 so the sample is consistent. This also has the added benefit that the sample runs a bit faster so users can get a feel for the tooling a bit more easily.
* Added doParallel support * Renamed txt file * Fixed lintr * Restructured merger script * Removed some error handling cases * Fixed syntax * Renamed error handling test * Added accumulator * Using filter on function * Proper filtering of tasks * Fixed merge naming * Added error handling for worker, separate merge task function * Added buckets * Added addSubMergeTask * Added merge sub task functions * Fixing file names * Fixed sorting order for merger * Added space * Merger in R * Clean up merger worker script * Added mergeSize option * By default one bucket * Removed merge size flag * Fixed test * Fixed lint code * Fixed more lintr issues * Fixed lintr * Fixed the added comments * Fixed the if statement * Add list combine function validation * Removed verification * Fixed lintr
* resubmit sas resource files example * fixed typos and grammar * remove unnecessary github reference
* merge package management doc * merge packagement docs * address review feedback (#232) * address review feedback * add reference to github and bioconductor packages in worker * update package management sample * update package management doc (#233) * address review feedback * add reference to github and bioconductor packages in worker * update package management sample * update package management doc * remove cluster.json * remove package installation
* get started script * add account_setup.sh * fix typo * fix typo * support shared key * fix typos * retrieve batch/storage account keys * fix bug * typo * fix if logic * fix typo * bug * retrieve batch primary key * storage list_keys * storage keys * storage key exceptin * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key\ * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key * storage key\ * storage key * storage key * storage key * delete resource group * print * print * print * exit from delete rg * delete resource group * aad auth * resource group name * add docs for get started script * update python script location * update doc * update doc * update doc * fix credential setting names * fix credential setting names * address review feedback
* Added config property for service principal * Fixed property names for service principal * Added makeBatchClient and makeStorageClient functions * Added ARM calls * Fixed configuration * Added more working features for AAD auth * Switched sas token generator * Added storage client generate sas tokens into doAzureParallel * basic foreach loop works * Long running jobs with AAD validated * Removed credentials output * Added docs for vnets * Fixed network configurations for doazp * Replaced rAzureBatch namespace with batchClient * Fixed url auth for storage * Changed cluster parameter naming * Renamed helper file and fixed lintr * Wrong file name * Removed new line * Removed lowerCamelCase for R6 classes * Fixed sas token * Fixed createBlobUrl * Fixed configuration endpoint suffix * Fixed endpoint suffix for download merge results * Added environment parameter in setCredentials * Added default for endpoint suffix for svp * Changed default credentials file to shared key * Updated docs for sharedkey/serviceprincipal * Updated documentation * Broken test for doc example * Fixed lintr for docs * Updated version to 0.7.0
Parameter name looks to have changed. Fixing. There are still some issues that I will open a separate ticket for.
* fix AAD credential config field names * fix json format
* Removed rAzureBatch from storage api calls * Fixed quota documentation * Added job and core quota limits
* Added custom package script * Added feature custom download * Fixed typo * Fixed directory for installation * Fixed full folder directory * Add dependencies and fix pattern * Fix pattern not found * Added repo * Switching to devtools * Fixing devtools install with directory * Fix in for merger.R * Working cluster custom packages * Removed printed statements * Working on custom docs * Custom packages sample docs * Fixed typo in azure files typo * Fixed typos based on PR
* Renamed operations * Fixing docs * Removed stuff from README.md * Fixed links for TOC * Added descriptions for TOC * Major renaming of files * Added TOC to main README.md * Added low pri link * Added link to vm priority * Fix broken links * Added Notable features
* Added install R
* Added devtools build
* devtools build and test
* Clean up rscript
* Added line breaks
* Added devtools('.')
* Added testthat package
* Added roxygen
* Replaced rscript
* Test live
* Added environment variables to test
* Fixed test
* Removed
* Fixed tests
* makeClusters to makeCluster
* Error handling to stop exit
* Added params to setup function
* Removed pool names
* Get / Get Cluster List
* Added utility R source
* Fixed tests
* Fixed remove error handling with combine test
* Forgot \ lines
* Switched to R6 sas client * Added storage endpoint suffix
* Added comment on maxTasksPerNode * Added bolded note * After comments
* Switched to R6 client * Replaced createContainer function
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0.7.1 (2018-07-13)