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Sage-Bionetworks / synapser

An R package providing programmatic access to Synapse
Apache License 2.0
32 stars 21 forks source link

[SYN-1520] upgrade python client version and R version #336

Closed danlu1 closed 1 month ago

danlu1 commented 1 month ago

Problem:

  1. synapser is a few versions behind synapseclient
  2. infinite recursion issue caused by duplicate defining of asDataFrame
  3. numpy version was not restricted
  4. reference documents are out-of-date as functions and docstrings changed in synapseclient
  5. package build failed on ubuntu and Windows
  6. test cases failure in view and table vignettes

Solution:

  1. upgraded synapseclient version to v4.4.0
  2. fixed infinite recursion issue by calling .readCsvBasedOnSchema function directly via customized as.data.frame function
  3. restricted the version of numpy when installing dependencies for synapseclient
  4. updated reference documents for both new and modified functions
  5. utilized miniconda on ubuntu and virtualenv on Windows to resolve building failures
  6. tweaked test cases in view and table vignettes