synapser refactor phase a

[anngvu]

• "Master" issue: Refactor synapse-adjacent functions to use new reticulate-based synapser #94
  • Covers about 20% of the refactor
  • Update tests and access-utils related vignette
• Also add vignette for Vignette just focused on functionality related to portal tables #172
  • 30% of the work outlined in this issue

Update:

• Currently, have to be very specific about using synapser (>= 1.0.0) and < 2.0, suggesting you use 1.3.0, see linked issue discussion regarding synSetAnnotations. However, by the time everything is refactored, I trust that synapser will have added back synSetAnnotations.
• Ignore the one failed MacOS check, I think it is a brew issue upstream that will be resolved eventually, see discussion at setup-r@master 403 error: Failed to download resource "qpdf" r-lib/actions#280
  
• Suggest @allaway can review the low-level code, @cconrad8 can be made aware of the new vignettes.

[anngvu]

There appears to be a synapser issue that has to be resolved upstream of us. So on Linux stable source build, can use synapser::synSetAnnotations just fine. On MacOs and Windows, one gets the error
Error: 'synSetAnnotations' is not an exported object from 'namespace:synapser'

[allaway]

@anngvu, should we report this on Sage-Bionetworks/synapser?

[anngvu]

Reported in Sage-Bionetworks/synapser#331. I think for now best solution is to specify synapser (>= 1.0.0) and < 2.0 and update CI workflow.

[github-actions]

PR Preview Action v1.4.7
🚀 Deployed preview to https://nf-osi.github.io/nfportalutils/pr-preview/pr-171/
on branch gh-pages at 2024-03-13 00:35 UTC

[anngvu]

Update 2:

• Add PR doc previews to CI #176, especially helpful for this PR and upcoming tutorials.
• Partial work on Additional instructions with best known working package combinations and installation for Windows #177 as another vignette.

[anngvu]

Actually do not need synapser::

[anngvu]

Merging this into develop-synapser isntead of main develop for now.