Doc fix

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ieegio
 Title: File IO for Intracranial Electroencephalography
-Version: 0.0.1.9002
+Version: 0.0.2
 Language: en-US
 Encoding: UTF-8
 Authors@R: 
@@ -35,10 +35,10 @@ Imports:
     rpyANTs (>= 0.0.3),
     stringr,
     utils,
+    hdf5r,
     yaml
 Suggests: 
     reticulate,
-    hdf5r,
     rgl,
     rpymat (>= 0.1.7),
     RNifti (>= 1.7.0),

NEWS.md

@@ -1,3 +1,12 @@
+# ieegio 0.0.2
+
+* Added `h5py` as an alternative back-end support
+* Fixed a bug where images are not loaded correctly due to image format being ignored
+* Fixed `Torig` (index to `tkr` coordinate transform) issue
+* Fixed a global variable issue
+* Fixed a bug where file name is not respected
+
+
 # ieegio 0.0.1
 
 * Initial CRAN submission.

R/hdf5-class.R

@@ -56,7 +56,7 @@ ensure_hdf5_backend <- local({
           rpymat$import("h5py")
         },
         error = function(e) {
-          rpymat$add_packages("h5py")
+          ensure_py_package("h5py")
           rpymat$import("h5py")
         }
       )

R/nifti.R

@@ -139,6 +139,13 @@ io_read_nii <- function(file, method = c("oro", "rnifti", "ants"), header_only =
 
     },
     "ants" = {
+      if(!rpyANTs::ants_available(module = "ants")) {
+        if(dir.exists(rpymat::env_path())) {
+          rpyANTs::install_ants(python_ver = "auto")
+        } else {
+          rpyANTs::install_ants()
+        }
+      }
       volume <- rpyANTs::as_ANTsImage(file, ...)
       header <- volume
       shape <- unlist(rpymat::py_to_r(volume$shape))

R/nwb-class.R

@@ -54,6 +54,7 @@ NWBHDF5IO <- R6::R6Class(
       private$construct_params <- list(
         path = path, mode = mode, ...
       )
+      ensure_py_package("pynwb")
     },
 
     #' @description

cran-comments.md

@@ -1,58 +1,3 @@
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
-
-* This is a new release.
-
-Respond to the `CRAN` comment:
-
-```
-If there are references describing the methods in your package, please add these in the description field of your DESCRIPTION file in the form
-authors (year) <doi:...>
-authors (year, ISBN:...)
-or if those are not available: <https:...>
-with no space after 'doi:', 'https:' and angle brackets for auto-linking. (If you want to add a title as well please put it in quotes: "Title")
-```
-
-Currently I don't have any publication that can be referenced in the `DESCRIPTION` file. The scripts are mostly derived from my personal code base.
-
-```
-You have examples for unexported functions. Please either omit these examples or export these functions.
-Examples for unexported function
-  io_write_fst() in:
-     read_nwb.Rd
-```
-
-Thanks, function `io_write_fst` has been exported. There is no `io_write_fst()` call in `read_nwb.Rd` now.
-
-
-```
-Only functions which are supposed to only run interactively (e.g. shiny) should be wrapped in if(interactive()). Please replace if(interactive()){} if possible.
--> ieegio_sample_data.Rd; low-level-read-write.Rd
-```
-
-Thanks, I removed all `if(interactive()){}` (2 sites), and wrapped with `dontrun` as these examples require downloading external data or additional configurations.
-
-
-```
-Please make sure that you do not change the user's options, par or working directory. If you really have to do so within functions, please ensure with an *immediate* call of on.exit() that the settings are reset when the function is exited.
-e.g.:
-...
-oldpar <- par(no.readonly = TRUE) # code line i
-on.exit(par(oldpar)) # code line i + 1
-...
-par(mfrow=c(2,2)) # somewhere after
-...
-
-e.g.: -> R/samples.R
-If you're not familiar with the function, please check ?on.exit. This function makes it possible to restore options before exiting a function even if the function breaks. Therefore it needs to be called immediately after the option change within a function.
-```
-
-Thanks, I added `on.exit` as instructed except for `ieegio_debug()`. This function is designed to change the option `ieegio.debug`, which should be controlled by this package.
-
-```
-Please ensure that your functions do not write by default or in your examples/vignettes/tests in the user's home filespace (including the package directory and getwd()). This is not allowed by CRAN policies. Please omit any default path in writing functions. In your examples/vignettes/tests you can write to tempdir().
--> R/samples.R; R/edf.R
-```
-
-Thanks. Those code are commented out. More specifically function `update_sample_registry` was removed (commented). I don't find anything in `R/edf.R` that writes to home or working directories. Maybe I missed it. My doubt is some (already) commented code such as Line-648 triggered this warning?
+0 errors | 0 warnings | 0 notes

tests/testthat/test-hdf5.R

@@ -79,6 +79,11 @@ test_that("HDF5 IO with R backend", {
     Sys.unsetenv("IEEGIO_USE_H5PY")
   })
 
+  h5py <- ensure_hdf5_backend()
+
+  # Skip if h5py is null (no python)
+  testthat::skip_if(is.null(h5py))
+
   x <- array(1:24, c(1,2,3,1,4,1))
 
   f <- tempfile()