NEWS.md
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).