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

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