Changes in version 2.2.0 Improvements - Upgraded to the synapsePythonClient v4.12. - Use the latest version of rjson and reticulate Changes in version 2.1.5 Deprecation - No longer support python 3.8 Documentation Improvements - Updated documents for R and Python dependencies. Changes in version 2.1.4 Improvements - Upgraded to the synapsePythonClient v4.4.2. Documentation Improvements - Updated instructions for synLogin. Changes in version 2.1.3 Improvements - Now support R 4.5.2. Documentation Improvements - Added instruction to add string list annotation in entity view. Changes in version 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 Changes in version 2.1.1 Improvements - Pinned rjson package version to 0.2.21 to support R versions older than 4.4.0. Changes in version 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. Changes in version 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. Changes in version 1.3.0 Improvements - Python synapsePythonClient dependency updated to 3.1.1 Changes in version 1.2.0 Improvements - Python synapsePythonClient dependency updated to 3.0.0 - Use virtualenv to install Python dependencies Changes in version 1.1.0 Improvements - Python synapsePythonClient dependency updated to 2.7.2 Changes in version 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+ - 2.7.0 - 2.6.0 - 2.5.1 - 2.5.0 Changes in version 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='' 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. Changes in version 0.10 Improvements - Login using an access token is now supported, e.g. synLogin(authToken="token"). See Manage Synapse Credentials for more details. - The following additional functions are exposed: - synCreateExternalS3FileHandle - synCreateS3StorageLocation - synCreateSnapshotVersion - synGetStsStorageToken - synIsCertified Bug fixes - Expose (additional) Python commands in the synapser package (SYNR-1474) - Python cryptography installation can fail due to Rust compiler dependency (SYNR-1475) Changes in version 0.9 Bug fixes - Markupsafe version incompatibility resolved (SYNR-1466) - Fixed incomaptibility with source compile R 4.0.3 on Mac (SYNR-1471) Changes in version 0.8 Bug fixes - Implicit gettext dependency removed on Macs (SYNR-1463) Improvements - Formal arguments defined on most Synapse methods (SYNR-1243 Changes in version 0.7 Bug fixes - Internet connection no longer required to load synapser package (SYNR-1233) Improvements - R-4.0 compatible (SYNR-1445) Changes in version 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) Changes in version 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 - New Troubleshooting vignette with more information about package installation on Windows with network drive configuration. (SYNR-1248) - New File Upload vignette with more information about uploading a new version of a file. (SYNR-1360) - New Manage Synapse Credentials vignette with more ways to login to Synapse. (SYNR-1367) - Improve synGetChildren() documentation. (SYNR-1280, and SYNR-1374) - Improve synSetAnnotations() documentation. (SYNR-1165) - Simplify docs for deleting Table rows. (SYNR-1340) - Document accessing md5 with synGet(). (SYNR-1359) - Document synSendMessage() for one receipient. (SYNR-1362) - Improve Table() documentation. (SYNR-1365) Changes in version 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) Changes in version 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 - synStore now uses a single thread to avoid the C stack limit error (SYNR-1323). - Create 50 or more Links at a time (SYNR-1276). - Python warning messages are no longer printed. - synapser namespace no longer contains PythonEmbedInR and other R package functions (SYNR-1274). - New NEWS.md provides the change log for each released version (SYNR-1315). - New System Dependencies vignette explains what dependencies are required and how to install them (SYNR-1328). - New examples on how to move a file shows how synMove can be used (SYNR-1296). - New example R packages that depends on synapser showcases two R packages developed by Sage Bionetworks' scientists (SYNR-1317). - New section Synapse Utilities links to synapserutils package for high level utilities functions (SYNR-1314).