Updated readme to give cloud-volume error fix

* Solution to update cloud-volume: fafbseg::simple_python('none', pkgs='cloud-volume~=8.32.1')

Author: alexanderbates

R/cave-tables.R

@@ -106,7 +106,7 @@ banc_nuclei <- function (rootids = NULL,
 #' @importFrom nat xyzmatrix2str
 banc_cell_info <- function(rootids = NULL, rawcoords = FALSE){
   table <- "cell_info"
-  res <- get_cave_table_data(table)
+  res <- with_banc(get_cave_table_data(table))
   if (isTRUE(rawcoords))
     res
   else {
@@ -118,27 +118,27 @@ banc_cell_info <- function(rootids = NULL, rawcoords = FALSE){
 #' @rdname banc_cave_tables
 #' @export
 banc_cell_ids <- function(rootids = NULL){
-  get_cave_table_data('cell_ids', rootids)
+  with_banc(get_cave_table_data('cell_ids', rootids))
 }
 
 #' @rdname banc_cave_tables
 #' @export
 banc_neck_connective_neurons <- function(rootids = NULL,
                                          table = c("neck_connective_y92500", "neck_connective_y121000")){
   table <- match.arg(table)
-  get_cave_table_data(table, rootids)
+  with_banc(get_cave_table_data(table, rootids))
 }
 
 #' @rdname banc_cave_tables
 #' @export
 banc_peripheral_nerves <- function(rootids = NULL){
-  get_cave_table_data("peripheral_nerves", rootids)
+  with_banc(get_cave_table_data("peripheral_nerves", rootids))
 }
 
 #' @rdname banc_cave_tables
 #' @export
 banc_backbone_proofread <- function(rootids = NULL){
-  get_cave_table_data("backbone_proofread", rootids)
+  with_banc(get_cave_table_data("backbone_proofread", rootids))
 }
 
 # hidden

R/cave.R

@@ -18,9 +18,8 @@
 #'   filter(tag2=='anterior-posterior projection pattern') %>%
 #'   count(tag)
 #' }
-banc_cave_query <- function(table, datastack_name = NULL, live=TRUE, ...) {
-  if(is.null(datastack_name)) datastack_name=banc_datastack_name()
-  fafbseg::flywire_cave_query(table = table, datastack_name = datastack_name, live=live, ...)
+banc_cave_query <- function(table, live=TRUE, ...) {
+  with_banc(fafbseg::flywire_cave_query(table = table, live=live, ...))
 }
 
 #' Low level access to banc's CAVE annotation infrastructure
@@ -35,6 +34,6 @@ banc_cave_query <- function(table, datastack_name = NULL, live=TRUE, ...) {
 #' fcc$materialize$get_table_metadata(tables[1])
 #' }
 banc_cave_client <- function() {
-  with_banc(flywire_cave_client())
+  with_banc(fafbseg::flywire_cave_client())
 }
 

README.md

@@ -61,7 +61,7 @@ To check that everything is set up properly, try:
 # diagnose issues
 dr_banc()
 
-# confirm functionality
+# confirm functionality, should return FALSE
 banc_islatest("720575941562355975")
 ```
 
@@ -71,14 +71,21 @@ called using the `reticulate` package.
 You can install full set of recommended libraries including `fafbseg-py`:
 
 ```
-simple_python("full")
+fafbseg::simple_python("full")
 ```
 
 Note that this package is designed to play nicely with `fafbseg`, which has
 been used mainly for the *FAFB-FlyWire* project, but could be used to work with
 data from many neuroglancer/CAVE based projects.
 
-Use `with_banc()` to wrap many additional fafbseg::flywire_* functions 
+If you get an error related to not finding cloud-volume or the 
+cloud-volume version, the solution may be to update cloud-volume, as so:
+
+```r
+fafbseg::simple_python('none', pkgs='cloud-volume~=8.32.1')
+```
+
+Use `with_banc()` to wrap many additional `fafbseg::flywire_*` functions 
 for use with the *BANC*. Alternatively `choose_banc()` to set all 
 `flywire_*` functions from `fafbseg` to target the *BANC*. Not all functions
 will work.
@@ -95,7 +102,7 @@ remotes::install_github('flyconnectome/bancr')
 If you need to update a specific Python library dependent, you can do:
 
 ```r
-reticulate::py_install("fafbseg", upgrade = TRUE)
+fafbseg::simple_python(pkgs='fafbseg')
 ```
 
 Ascending Neuron Vignette
@@ -107,6 +114,7 @@ First we need to load the package, and direct ourselves to the *BANC* data set.
 
 ```r
 library(bancr)
+# choose_banc()
 ```
 
 ### Identify the neurons we care about