NEWS.md
synSetAnnotations removed as it is not working as expected due to implementation in the Python API.Special thanks to genUI for their work to push out this major release!
build.yml replacing custom steps with standard actions where practicalabbreviateStackTrace.py, patchStdoutStdErr.py, pyPkgInfo.py, stdouterrCapture.py, PythonPkgWrapperUtils.R file over from PythonEmbedInR for R-wrapper generation/templates directory for auto-generating Rd files over from PythonEmbedInR
installPythonClient.py interruptCheck.py files/man with latest auto-generated Rd files from /auto-man
man/*.Rd files to resolve R CMD check WARNINGs# 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.
synLogin(authToken="token"). See Manage Synapse Credentials for more details.set_entity_views in EntityViewSchema allows replacing the entity types that will appears in a view.synapser version is available on Sage’s RAN.synSetAnnotations() documentation now clearly states that the function will replace the existing annotations. (SYNR-1361)Table() reference documentation now has a link to the Table vignette. (SYNR-1365)synGetTableColumns. (SYNR-1384)synBuild_table() no longer shows up in the synapser package’s namespace. (SYNR-1387)includeEntityTypes in EntityViewSchema allows configuring Synapse Views with all available Entity types. (SYNR-1350)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)synGetChildren() documentation. (SYNR-1280, and SYNR-1374)synSetAnnotations() documentation. (SYNR-1165)synGet(). (SYNR-1359)synSendMessage() for one receipient. (SYNR-1362)Table() documentation. (SYNR-1365)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.keyring to ensure stable installation on Linux environment. (SYNR-1345)synBuildTable creates a Table Schema based on the given data, and returns a Table object that can be stored in Synapse using synStore.synMove allows users to move entities to a different parent.synStore now uses a single thread to avoid the C stack limit error (SYNR-1323).synapser namespace no longer contains PythonEmbedInR and other R package functions (SYNR-1274).synMove can be used (SYNR-1296).synapser showcases two R packages developed by Sage Bionetworks’ scientists (SYNR-1317).synapserutils package for high level utilities functions (SYNR-1314).