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synapser 2.1.5

Deprecation

  • No longer support python 3.8

Documentation Improvements

  • Updated documents for R and Python dependencies.

synapser 2.1.4

Improvements

  • Upgraded to the synapsePythonClient v4.4.2.

Documentation Improvements

  • Updated instructions for synLogin.

synapser 2.1.3

Improvements

  • Now support R 4.5.2.

Documentation Improvements

  • Added instruction to add string list annotation in entity view.

synapser 2.1.2

Improvements

  • Correcting the specification for rjson and reticulate package versions allowing the remotes library to handle automatic version resolution.

Documentation Improvements

  • Enhanced installation documentation to use remotes package for better dependency management
  • Added comprehensive troubleshooting guide for rjson/reticulate version conflicts
  • Clarified Python version compatibility requirements (3.8-3.11, recommend 3.10)
  • Updated all vignettes with improved installation instructions and cross-references
  • Added detailed guidance for users experiencing dependency conflicts

synapser 2.1.1

Improvements

  • Pinned rjson package version to 0.2.21 to support R versions older than 4.4.0.

synapser 2.1.0

Improvements

  • Upgraded to the synapsePythonClient v4.4.0.
  • Now support R 4.4.1.
  • The data upload and download algorithm in synapsePythonClient have been revamped for enhanced stability, reliability, and performance.
  • Updated reference documents and code examples for both new and modified functions.

New Functions

  • synCreateTeam and synDeleteTeam have been added to manage team.
  • synRestGetAsync, synRestDeleteAsync, synRestPostAsync and synRestPutAsync have been added to allow interaction with Synapse server utilizing asynchronous models.

Minor behavior changes:

  • Credentials passed by command line argument will now be evaluated before credentials stored in the ~/.synapseConfig file.
  • Using syn123.version notation is now supported with synGet and synSetProvenance.
  • File entities will no longer have their version incremented during no-op changes. Only when file content, or fields on the file has been updated will a version number be incremented.
  • New parameters have been added to allow more features:
    • Defining the project alias used in project url is now supported in Project.
    • Setting the annotations on the entity is now supported in synStore.
    • The MD5 of the file can now be used when creating S3 file handle in synCreateExternalS3FileHandle.

For more changes, please view the Release Notes on the Python client documentation.

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.
  • rememberMe has been deprecated in synLogin.
  • 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+

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