Changelog

Source: NEWS.md

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  • PythonEmbedInR dependency has been replaced by Reticulate (SYNR-1310)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+

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

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

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

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