NEWS.md

In Sage-Bionetworks/synapser: R Language Bindings for Synapse API

synapser 2.0.0

Improvements

• Python synapsePythonClient dependency updated to 4.0.0
• You can only login via a Synapse Personal Access token now. All other forms of authentication have been disabled for security purposes.
• synSetAnnotations removed as it is not working as expected due to implementation in the Python API.
• For more changes, please view the 3.2.0 and 4.0.0 changes on the Python client documentation.

synapser 1.3.0

Improvements

• Python synapsePythonClient dependency updated to 3.1.1

synapser 1.2.0

Improvements

• Python synapsePythonClient dependency updated to 3.0.0
• Use virtualenv to install Python dependencies

synapser 1.1.0

Improvements

• Python synapsePythonClient dependency updated to 2.7.2

synapser 1.0.0

Improvements

Special thanks to genUI for their work to push out this major release!

• PythonEmbedInR dependency has been replaced by Reticulate (SYNR-1310)
• Raised R dependency to 4.0 in DESCRIPTION
• Python synapsePythonClient dependency updated to 2.7.0
• Validated working with R >= 4.1.3, Python >= 3.8
• Python dependencies should install automatically in most instances
• Streamlined build.yml replacing custom steps with standard actions where practical
• Brought abbreviateStackTrace.py, patchStdoutStdErr.py, pyPkgInfo.py, stdouterrCapture.py, PythonPkgWrapperUtils.R file over from PythonEmbedInR for R-wrapper generation
• Brought /templates directory for auto-generating Rd files over from PythonEmbedInR
• Removed disused installPythonClient.py interruptCheck.py files
• Updated /man with latest auto-generated Rd files from /auto-man
• Removed empty sections from man/*.Rd files to resolve R CMD check WARNINGs
• Updated tests

Python synapsePythonClient release notes for 2.5.0+

• 2.7.0
• 2.6.0
• 2.5.1
• 2.5.0

synapser 0.11

Improvements

• Added ability to authenticate from a SYNAPSE_AUTH_TOKEN environment variable set with a valid personal access token, e.g.:

# set environment variable prior to using synapser
export SYNAPSE_AUTH_TOKEN='<my_personal_access_token>'

The environment variable will take priority over credentials in the user’s .synapseConfig file or any credentials saved in a prior login using the remember me option.

Deprecation

• R >= 4.0 is required for this and future versions of synapser.

synapser 0.10

Improvements

• Login using an access token is now supported, e.g. synLogin(authToken="token"). See Manage Synapse Credentials for more details.
• The following additional functions are exposed:
  • synCreateExternalS3FileHandle
  • synCreateS3StorageLocation
  • synCreateSnapshotVersion
  • synGetStsStorageToken
  • synIsCertified

Bug fixes

• Expose (additional) Python commands in the synapser package (SYNR-1474)
• Python cryptography installation can fail due to Rust compiler dependency (SYNR-1475)

synapser 0.9

Bug fixes

• Markupsafe version incompatibility resolved (SYNR-1466)
• Fixed incomaptibility with source compile R 4.0.3 on Mac (SYNR-1471)

synapser 0.8

Bug fixes

• Implicit gettext dependency removed on Macs (SYNR-1463)

Improvements

• Formal arguments defined on most Synapse methods (SYNR-1243

synapser 0.7

Bug fixes

• Internet connection no longer required to load synapser package (SYNR-1233)

Improvements

• R-4.0 compatible (SYNR-1445)

synapser 0.6

New Features

• New method set_entity_views in EntityViewSchema allows replacing the entity types that will appears in a view.
• New message on package load notifies users when a new synapser version is available on Sage's RAN.

Improvements

• synSetAnnotations() documentation now clearly states that the function will replace the existing annotations. (SYNR-1361)
• The Table() reference documentation now has a link to the Table vignette. (SYNR-1365)
• The synapser vignette now has a link to the Manage Synapse Credentials vignette. (SYNR-1382)
• The Manage Synapse Credentials vignette now has instructions on how to login using Synapse API key. (SYNR-1383)
• Table vignettes has new examples using synGetTableColumns. (SYNR-1384)
• synBuild_table() no longer shows up in the synapser package's namespace. (SYNR-1387)
• synapser installation instructions now has a link to System Dependencies vignette. (SYNR-1393)

synapser 0.5

New Features

• New parameter includeEntityTypes in EntityViewSchema allows configuring Synapse Views with all available Entity types. (SYNR-1350)

Bug Fixes

• In synapser 0.5, we locked down the version of the Python package keyring.alt to ensure stable installation in the Linux environment. (SYNR-1375)
• as.data.frame(synTableQuery(...)) now correctly returns R data.frame with column types matching the Table column types. (SYNR-1275, SYNR-1322, and SYNR-1325)

Improvements

• New Troubleshooting vignette with more information about package installation on Windows with network drive configuration. (SYNR-1248)
• New File Upload vignette with more information about uploading a new version of a file. (SYNR-1360)
• New Manage Synapse Credentials vignette with more ways to login to Synapse. (SYNR-1367)
• Improve synGetChildren() documentation. (SYNR-1280, and SYNR-1374)
• Improve synSetAnnotations() documentation. (SYNR-1165)
• Simplify docs for deleting Table rows. (SYNR-1340)
• Document accessing md5 with synGet(). (SYNR-1359)
• Document synSendMessage() for one receipient. (SYNR-1362)
• Improve Table() documentation. (SYNR-1365)

synapser 0.4

Deprecation

• synQuery() and synChunkedQuery() are deprecated and removed. To query for entities filter by annotations, please use EntityViewSchema feature.
• synUploadFileHandle() and synUploadSynapseManagedFileHandle() are deprecated in synapser 0.4, and will be removed in synapser 0.5.

Bug Fixes

• In synapser 0.4, we locked down the version of the Python package keyring to ensure stable installation on Linux environment. (SYNR-1345)

synapser 0.3

New Features

• New convenience function synBuildTable creates a Table Schema based on the given data, and returns a Table object that can be stored in Synapse using synStore.
• New convenience function synMove allows users to move entities to a different parent.

Minor Bug Fixes and Improvements

• synStore now uses a single thread to avoid the C stack limit error (SYNR-1323).
• Create 50 or more Links at a time (SYNR-1276).
• Python warning messages are no longer printed.
• synapser namespace no longer contains PythonEmbedInR and other R package functions (SYNR-1274).
• New NEWS.md provides the change log for each released version (SYNR-1315).
• New System Dependencies vignette explains what dependencies are required and how to install them (SYNR-1328).
• New examples on how to move a file shows how synMove can be used (SYNR-1296).
• New example R packages that depends on synapser showcases two R packages developed by Sage Bionetworks' scientists (SYNR-1317).
• New section Synapse Utilities links to synapserutils package for high level utilities functions (SYNR-1314).

Sage-Bionetworks/synapser documentation built on Feb. 7, 2024, 12:26 p.m.