fixes for finding readers with format

* sometimes we were relying on the format being ignored ...

R/neuron-io.R

@@ -71,11 +71,11 @@ read.neuron<-function(f, format=NULL, class=c("neuron", "ngraph"), ...){
   # use ext as backup if format is missing
   ext=if(is.null(format)) 
     tolower(sub(".*\\.([^.]+$)","\\1",basename(f))) else ""
-  if(format=="rds" || ext=='rds')
   if(!is.null(format) && format %in% c("ply", "obj", "ngmesh")) 
     format=paste0("neuron.", format)
+  if(isTRUE(format=="rds") || ext=='rds')
     n=readRDS(f)
-  else if(format=="rda" || ext=='rda'){
+  else if(isTRUE(format=="rda") || ext=='rda'){
     objname=load(f, envir=environment())
     if(length(objname)>1) stop("More than 1 object in file:",f)
     n=get(objname,envir=environment())
@@ -185,6 +185,8 @@ read.neurons<-function(paths, pattern=NULL, neuronnames=NULL, format=NULL,
       on.exit(unlink(paths))
       download.file(url, destfile = paths)
     }
+    # the neurons inside the zip file will not have format zip
+    if(isTRUE(format=='zip')) format=NULL
     neurons_dir <- file.path(tempfile(pattern = "user_neurons"))
     on.exit(unlink(neurons_dir, recursive=TRUE), add = TRUE)
     unzip(paths, exdir=neurons_dir)

tests/testthat/test-neuron-io.R

@@ -201,14 +201,14 @@ test_that("we can read hxskel format neurons",{
 })
 
 test_that("we can read multiple neurons from a zip archive", {
-  files_to_zip <- c("testdata/neuron/testneuron_am3d.am", "testdata/neuron/testneuron_lineset.am")
+  files_to_zip <- test_path(c("testdata/neuron/testneuron_am3d.am", "testdata/neuron/testneuron_lineset.am"))
   # swallow extraneous warning
   expect_warning(neurons <- read.neurons(files_to_zip,
                                          neuronnames = function(f) tools::file_path_sans_ext(basename(f))),
                  regexp = "specifies radius")
   zip_file <- paste0(tempfile(), ".zip")
   on.exit(unlink(zip_file, recursive=TRUE))
-  zip(zip_file, files_to_zip)
+  zip(zip_file, files_to_zip, flags = "-r9Xq")
   expect_warning(zip_neurons <- read.neurons(zip_file, format="zip",
                                              neuronnames = function(f) tools::file_path_sans_ext(basename(f))),
                  regexp = "specifies radius")