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Documentation rewrite #273
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wesholley
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May 15, 2018
brnleehng
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Jul 13, 2018
* Update README.md (#164) * remove unused validator file (#167) * initial docs for docker users (#166) * initial docs for docker users * Fixes plus PR feedback * Feature/configfromobj support programmatically created credentials and 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 * updated docs (#172) * Implemented progress bar with verbose details (#181) * Implemented a more detailed verbose progress bar * Fixed infix operator spacing * Added newline for 'Tasks have completed' message * Changing UI of progress bar (#183) * Redone the progress bar * Added string utilities * Feature/longrunjob, long running job improvement, add deleteJob and terminateJob (#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 * Feature/docker registry auth (#182) * 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 * Fixed based on recent feedback (#185) * Updated DESCRIPTION's reference rAzureBatch to v0.5.4 (#184) * address issue where empty docker auth credentials are used to create … (#190) * address issue where empty docker auth credentials are used to create the cluster * remove unnecessary null check * Collapsing pool package installation on start task command line (#191) * Collasping the R package installations for pool installation * Renamed script variable * Fixed pool installation test * Fixed length test * Improve R console UI experience (#193) * Improve UI experience * Added verbose mode to deleteJob and deleteStorageContainer * Refactor print method * Fixed order of package installation (#196) * Fix/add task perf (#195) * 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 * fix link to generate config doc (#199) * Feature/asynccluster (#197) * 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 on using private docker registries (#201) * update documentation for private docker registry * update docs to be less confusing * In order correction (#202) * Update long_running_job.R (#206) renamed a misnamed azure options variable * Created an issue template (#207) * Typos in README.md (#210) * list cluster should use paste() instead of + (#213) * use paste() instead of + * use paste0 * Feature/getjobresultlocal (#204) * 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 RProfile libraries to be loaded by default (#209) * allow local session info to be loaded * update line lengths * Bundling worker scripts into zip (#212) * 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 * Reverted changes (#227) * Upgraded description for fix resize cluster (#225) * Update sample to only use the first 6 files (#228) 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 optional retry count flag (#235) * Added job retry count flag * Renamed maxTaskRetryCount * Added cluster config for caret example (#237) * Added cluster config for caret * Reverted changes for installation * Reverted fit model * Changed to low priority * Added cluster submission output (#236) * Finish output for cluster * Added resource files print info * Fixed ordering * Renamed Nodes to Scale * Fixed typo * Feature/nationalcloud (#239) * support national cloud * fix hardcoded domain name in createOutputFile * update rAzureBatch version etc * auto discovery of storage account endpoint suffix * styling fix * fix test failure * add back endpointSuffix for storage account * add storage account endpoint suffix to downloadBlob call * update docs * improve error handling for create cluster (#241) * improve error handling for create cluster * remove extra space * Fixed argument validation (#244) * Fixed incorrect variable name (#243) * Reverted variable name (#245) * Improvement on merge task performance (#223) * 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 * Mapping of job results (#248) * handle addjob error 403 (#251) * Sample - Add a sample for using SAS resource files (#253) * resubmit sas resource files example * fixed typos and grammar * remove unnecessary github reference * fix sample link to sas resource files (#254) * Feature/pkgmgmtdoc (#231) * 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 * Feature/getstarted (#255) * 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 * Updated version v0.6.3 (#256) * Enable AAD and VNet Support (#252) * 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 * Fixed get workers count function (#261) * Fixing change of named parameter in makeCluster (#259) Parameter name looks to have changed. Fixing. There are still some issues that I will open a separate ticket for. * Fixed resource files docs (#262) * Added change log details (#258) * Fix/getstartdoc (#263) * fix AAD credential config field names * fix json format * add sharedKey to credentials related code and doc (#266) * Fix/storage management (#267) * Removed rAzureBatch from storage api calls * Fixed quota documentation * Added job and core quota limits * Replaced deprecated function (#269) * Fixed output (#270) * Feature/custom package (#272) * 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 * Documentation rewrite (#273) * 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 * Clarifying comment on DSVM (#274) * Tests/r (#275) * 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 (#276) * Switched to R6 sas client * Added storage endpoint suffix * Fixed package strip name (#278) * Fix: Updated MaxTasksPerNode documentation (#279) * Added comment on maxTasksPerNode * Added bolded note * After comments * Fix: Updating Persistent Storage Documentation (#283) * Switched to R6 client * Replaced createContainer function * CHANGELOG for v0.7.1 (#285) * Added 0.7.1 changelog version (#286)
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