* 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
* 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 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
* 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
* 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
* 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
* 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()
* 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
* 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
* 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
* force add PATH to current user
* checkin docker setup script
* Update cluster_setup.sh
* install docker and start container on cluster setup
* WIP: Run task in container
* fix merge conflict
* run tasks and merge task from within container
* refactor code to proper docker commands and make a single R container per job
* refactor command line utils into its own file
* refactor job utilities into its own file
* move cluster setup script to inst folder
* remove unnecessary curl installs
* remove starting container from setup script
* check in WIP
* add apt_install file
* make required directories
* update cluster setup files as needed
* include libxml2 packages in apt installs
* working cluster create with cran and github dependencies
* update job prep to install apt-get and not each task
* use rocker containers instead of r-base
* remove unused & commented code
* remove unused install function
* address several lintr issues
* initial test dockerfile
* add spacing between commands
* temporarily point wget to feature branch
* update bioconductor install for non-jobPrep installs
* Delete Dockerfile
* minor changes to install bioc
* resolve merge conflicts
* update cluster to correctly install BioC packages using install_bioconductor
* fix issue where some packages were not getting installed
* add missing BioConductorCommand initializer
* remove print lines
* initial dockerfile implementations
* update docker files
* Only install packages if they are required
* Remove requirement on bioconductor installer script on start task
* remove duplicate environment variable entry
* update docs for container support
* update version to 0.6.0
* refactor changes updates
* remove poorly formatted whitespaces
* add full path to pacakges directory
* fix docker command line
* update file share sample
* update azure files cluster name
* update mandelbrot sample
* update package management sample
* update plyr samples
* make montecarlo sample more consistent
* update montecarlo sample
* remove plyr example
* fix bad environment pointer
* fix linter issues
* more linter fixes
* more linter issues
* use latest rAzureBatch version
* update resource files example
* remove reference to deleted sample
* pr feedback
* PR docs feedback
* Print errors from worker (#154)
* Fixed pool package command line lintr test
* Package installation tests fixed - too long lines
* Fixed json in customize cluster docs
* Fix: Typos in customize cluster docs
* Cleaning up files
* Feature/githubbiopackage (#150)
* install github package worked for foreach loop
* fix lintr error
* tests for github and bioc packages installation
* lintr fix
* add back lost code due to merge and update docs
* The Travis CI build failed for feature/githubbiopackage
* remove incorrect parameter for install_github
* Updated job prep task to have default command
* Use the latest version of rAzureBatch
* Updated description + Generate cluster config
* Fix: Bioconductor and Github packages installation (#155)
* Added multiple package install test and fix obj reading args
* Fixed naming for packages install
* Replaced validation exclusion for linter
* Fixed test validate test
* Fixing all interactive tests with skip
* Fixed renaming validation
* Removed default test - cannot be tested
* Removed in validation
* Added cluster package install tests (#156)
* fix bioconductor package install docs for multi-task race condition
* fix typos
* remove docs on updating an existing cluster's packages from within the foreach loop
* support an install_bioconductor.R script
* update docs with working sample
* treat warnings as failures and fail the creation of the cluster (#91)
* treat warnings as failures and fail the creation of the cluster
* fix unit tests
* fix lintr lines too long issue
* escape single quotes
* Check if existing pool is deleted when makeCluster is called (#99)
* Added deleting pool check for makeCluster
* Fixed double quotes
* cluster logs renamed from pool to cluster
* Added correct imports and fix range
* Feature/bio conductor docs (#106)
* initial command line instructions for bioconductor
* initial startup scripts for installing bioconductor
* fix if then syntax
* force update node environment with update path for R runtime
* install bioconductor
* wrap bioconductor install command in Rscript
* bioconductor sample docs
* update bioC docs
* remove .gitignore rule for .json files
* add pointer to BioC cluster config from docs
* Feature/cluster logs (#98)
* download merge result gets content raw
* Added setHttpTraffic and logging functions docs
* Fixed broken links
* Shorten lines down to 120 characters
* download merge result gets content raw
* Added setHttpTraffic and logging functions docs
* Fixed broken links
* Shorten lines down to 120 characters
* Renamed function names from past discussion
* Fixed log documentation
* Added new operations for storage management
* Added dont run examples
* Fixed unused arg for running example
* Updated docs for storage management
* Added a new doc dedicated for managing storage
* Added attribute for container name in data frame
* Fixed downloadBlob to work with new rAzureBatch function
* Updated docs based on PR comments
* Changed dependency version to razurebatch 0.5.0
* Feature/add azure files cluster config (#108)
* initial command line instructions for bioconductor
* initial startup scripts for installing bioconductor
* fix if then syntax
* force update node environment with update path for R runtime
* install bioconductor
* wrap bioconductor install command in Rscript
* bioconductor sample docs
* update bioC docs
* remove .gitignore rule for .json files
* add pointer to BioC cluster config from docs
* add missing azureFiles cluster config to samples
* Add 0.4.2 CHANGELOG comments (#111)
* Added live scenario test (#107)
* Added live scenario test so users do not have to write their own sample code to test
* Added file names for test live
* Removed single quote linter
* Added comment about the reason for this test
* Wait for job preparation task function (#109)
* Fixed verbose for getDoParWorkers (#112)
* Feature/faq (#110)
* initial FAQ
* rename faq to FAQ
* merge FAQ and Troubleshooting docs
* add info on how to reboot a node
* refrence TSG and FAQ from main docs index page
* add more info as per PR feedback
* PR feedback
* point raw scripts at master branch (#118)
* Update DESCRIPTION (#117)
Update version for new milestone.
* Fix: Removed anaconda from path (#119)
* Removed anaconda from environment path
* Line is too long for blobxfer command
* For BioConductor install, force remove MRO 3.3 prior to installing MRO 3.4 (#120)
* force add PATH to current user
* Update bioc_setup.sh
* Check verbose null case (#121)
* Change True/False to TRUE/FALSE in README example (#124)
* add .gitiattrributes file to track line endings
* True and False are not valid in R; changed to TRUE and FALSE
* Fixed worker and merger scripts (#116)
* Fixed worker and merger scripts
* Fixed verbose logs based on PR comments
* Added documentation on error handling
* Fixed header on table markdown
* Fixed based on PR comments
* v0.4.3 Release (#131)
* Upgraded description to use rAzureBatch v0.5.1
* Updated change log for job failure
* readme.md update
* Merge from feature/getjobresult for long running job support (#130)
* Added set chunk size
* Added cluster configuration validation function (#30)
* Added pool config test validation
* Added a fix for validation
* Added if checks for null tests and more validation tests
* Install R packages at job run time (#29)
* Added cran/github installation scripts
* Added package installation tests
* Upgraded package version to 0.3.2
* Output file support (#40)
* Output files support
* Added createOutputFile method
* output files readme documentation
* added tests and find container sas
* Added more detailed variable names
* Enable/disable merge task (#39)
* Merge task pass params
* Fixed enableMerge cases
* Merge task documentation on README.md
* Fixed typo on merge task description
* Update doAzureParallel.R
* Changed enableMerge to enableCloudCombine
* convert getJobResult output from binary to text
* Only write vector to temp file
* save cloud merge enabled, chunk size and packages as job metadata
* update cloudMergeEnabled to cloudCombineEnabled
* Fix/backwards compatible (#68)
* Added backwards compatible in make cluster
* Added deprecated config validator
* Added mismatch label
* Added validation for quota limits and bad getPool requests in waitForNodesToComplete (#52)
* Added validation for quota limits and bad getPool requests
* Fixed based on PR
* Fixed progress bar layout to use switch statements instead of if statements
* Changed clusterId to poolId
* Added comments and fixed messages
* Added running state to the node status
* Reformatted lines for function
* Added end statement for node completion
* Feature/custom script and reduce (#70)
* Added custom scripts and removed dependencies parameter
* Updated roxygen tool version
* Added parallelThreads support
* Added test coverage
* Removed verbose message on command line
* Added Reduce function for group of tasks
* Fix build because of doc semantics mismatch with function
* Removed unused function
* Added command line arg
* Added docs for custom script
* Moved customize cluster to separate doc for future usage
* Fixed typo
* Bug - Waiting for tasks to completion function ends too early (#69)
* Moved wait for tasks to complete to doAzureParallel utility
* Removed unneeded variables and progress
* Fixed camel case for skiptoken
* Travis/lintr (#72)
* Added lintr config file
* Added travis github package installation
* Removed snake case rule
* Fixed documents on doAzureParallel
* Based on lintr default_settins docs, correctly added default rules
* Updated lintr package to use object_name_style
* Added package :: operator
* Reformatted after merge
* Fixed command line tests
* Upgraded roxygen to 6.0.1
* Cluster config docs
* Removed additional delete job
* add getJob api (#84)
* add getJob api
* reformat code
* update styling in utility file
* fix code styling
* update chunksize to chunkSize and remove unused code
* handle job metadata in getJob api
* fix styling issue
* update getJobList parameter from list of job ids to filter object, and output jobs status in data frame (#128)
long running job support, getJob, getJobList and getJobResult implementation
* reformat code
* update styling in utility file
* fix code styling
* update chunksize to chunkSize and remove unused code
* handle job metadata in getJob api
* fix styling issue
* use counting service api in getJobList
* fix coding style
* return data frame from getJobList
* update getJobList parameter from job id list to filter by state
* reformat code
* update description for getJobList
* remove dup code
* address review feedback
* jobId parameter check for getJobResult
* update documentation for long run job
* update version to 0.5.0
* update version
* address review feedback
* update chunkSizeValue to chunkSizeKeyValuePair
* Validate job names and pool names (#129)
* Added validator class
* Added validators for lintr
* Added exclusion list for validators
* fix bug in metadata handling for packages and enableCloudCombine (#133)
* fix bug in metadata handling for packages and enableCloudCombine
* call long running job api in test
* update test
* add test for long running job feature
* code style fix
* update job state description in readme
* use list for job state filter
* address review feedback
* fix bug in metadata handling for packages and enableCloudCombine
* call long running job api in test
* update test
* add test for long running job feature
* code style fix
* update job state description in readme
* use list for job state filter
* Added set chunk size
* Added cluster configuration validation function (#30)
* Added pool config test validation
* Added a fix for validation
* Added if checks for null tests and more validation tests
* Install R packages at job run time (#29)
* Added cran/github installation scripts
* Added package installation tests
* Upgraded package version to 0.3.2
* Output file support (#40)
* Output files support
* Added createOutputFile method
* output files readme documentation
* added tests and find container sas
* Added more detailed variable names
* Enable/disable merge task (#39)
* Merge task pass params
* Fixed enableMerge cases
* Merge task documentation on README.md
* Fixed typo on merge task description
* Update doAzureParallel.R
* Changed enableMerge to enableCloudCombine
* convert getJobResult output from binary to text
* Only write vector to temp file
* save cloud merge enabled, chunk size and packages as job metadata
* update cloudMergeEnabled to cloudCombineEnabled
* Fix/backwards compatible (#68)
* Added backwards compatible in make cluster
* Added deprecated config validator
* Added mismatch label
* Added validation for quota limits and bad getPool requests in waitForNodesToComplete (#52)
* Added validation for quota limits and bad getPool requests
* Fixed based on PR
* Fixed progress bar layout to use switch statements instead of if statements
* Changed clusterId to poolId
* Added comments and fixed messages
* Added running state to the node status
* Reformatted lines for function
* Added end statement for node completion
* Feature/custom script and reduce (#70)
* Added custom scripts and removed dependencies parameter
* Updated roxygen tool version
* Added parallelThreads support
* Added test coverage
* Removed verbose message on command line
* Added Reduce function for group of tasks
* Fix build because of doc semantics mismatch with function
* Removed unused function
* Added command line arg
* Added docs for custom script
* Moved customize cluster to separate doc for future usage
* Fixed typo
* Bug - Waiting for tasks to completion function ends too early (#69)
* Moved wait for tasks to complete to doAzureParallel utility
* Removed unneeded variables and progress
* Fixed camel case for skiptoken
* Travis/lintr (#72)
* Added lintr config file
* Added travis github package installation
* Removed snake case rule
* Fixed documents on doAzureParallel
* Based on lintr default_settins docs, correctly added default rules
* Updated lintr package to use object_name_style
* Added package :: operator
* Reformatted after merge
* Fixed command line tests
* Upgraded roxygen to 6.0.1
* Cluster config docs
* Removed additional delete job
* add getJob api (#84)
* add getJob api
* reformat code
* update styling in utility file
* fix code styling
* update chunksize to chunkSize and remove unused code
* handle job metadata in getJob api
* fix styling issue
* update getJobList parameter from list of job ids to filter object, and output jobs status in data frame (#128)
long running job support, getJob, getJobList and getJobResult implementation
* reformat code
* update styling in utility file
* fix code styling
* update chunksize to chunkSize and remove unused code
* handle job metadata in getJob api
* fix styling issue
* use counting service api in getJobList
* fix coding style
* return data frame from getJobList
* update getJobList parameter from job id list to filter by state
* reformat code
* update description for getJobList
* remove dup code
* address review feedback
* jobId parameter check for getJobResult
* update documentation for long run job
* update version to 0.5.0
* update version
* address review feedback
* update chunkSizeValue to chunkSizeKeyValuePair
* treat warnings as failures and fail the creation of the cluster (#91)
* treat warnings as failures and fail the creation of the cluster
* fix unit tests
* fix lintr lines too long issue
* escape single quotes
* Check if existing pool is deleted when makeCluster is called (#99)
* Added deleting pool check for makeCluster
* Fixed double quotes
* cluster logs renamed from pool to cluster
* Added correct imports and fix range
* Feature/bio conductor docs (#106)
* initial command line instructions for bioconductor
* initial startup scripts for installing bioconductor
* fix if then syntax
* force update node environment with update path for R runtime
* install bioconductor
* wrap bioconductor install command in Rscript
* bioconductor sample docs
* update bioC docs
* remove .gitignore rule for .json files
* add pointer to BioC cluster config from docs
* Feature/cluster logs (#98)
* download merge result gets content raw
* Added setHttpTraffic and logging functions docs
* Fixed broken links
* Shorten lines down to 120 characters
* download merge result gets content raw
* Added setHttpTraffic and logging functions docs
* Fixed broken links
* Shorten lines down to 120 characters
* Renamed function names from past discussion
* Fixed log documentation
* Added new operations for storage management
* Added dont run examples
* Fixed unused arg for running example
* Updated docs for storage management
* Added a new doc dedicated for managing storage
* Added attribute for container name in data frame
* Fixed downloadBlob to work with new rAzureBatch function
* Updated docs based on PR comments
* Changed dependency version to razurebatch 0.5.0
* Feature/add azure files cluster config (#108)
* initial command line instructions for bioconductor
* initial startup scripts for installing bioconductor
* fix if then syntax
* force update node environment with update path for R runtime
* install bioconductor
* wrap bioconductor install command in Rscript
* bioconductor sample docs
* update bioC docs
* remove .gitignore rule for .json files
* add pointer to BioC cluster config from docs
* add missing azureFiles cluster config to samples
* Add 0.4.2 CHANGELOG comments (#111)
* Added live scenario test (#107)
* Added live scenario test so users do not have to write their own sample code to test
* Added file names for test live
* Removed single quote linter
* Added comment about the reason for this test
* Wait for job preparation task function (#109)
* Fixed verbose for getDoParWorkers (#112)
* Feature/faq (#110)
* initial FAQ
* rename faq to FAQ
* merge FAQ and Troubleshooting docs
* add info on how to reboot a node
* refrence TSG and FAQ from main docs index page
* add more info as per PR feedback
* PR feedback
* point raw scripts at master branch (#118)
* Update DESCRIPTION (#117)
Update version for new milestone.
* Fix: Removed anaconda from path (#119)
* Removed anaconda from environment path
* Line is too long for blobxfer command
* For BioConductor install, force remove MRO 3.3 prior to installing MRO 3.4 (#120)
* force add PATH to current user
* Update bioc_setup.sh
* Check verbose null case (#121)
* Change True/False to TRUE/FALSE in README example (#124)
* add .gitiattrributes file to track line endings
* True and False are not valid in R; changed to TRUE and FALSE
* Fixed worker and merger scripts (#116)
* Fixed worker and merger scripts
* Fixed verbose logs based on PR comments
* Added documentation on error handling
* Fixed header on table markdown
* Fixed based on PR comments
* v0.4.3 Release (#131)
* Upgraded description to use rAzureBatch v0.5.1
* Updated change log for job failure
* Fixed worker and merger scripts
* Fixed verbose logs based on PR comments
* Added documentation on error handling
* Fixed header on table markdown
* Fixed based on PR comments
Brian
zfengms
Daan Knoope
Pablo Selem