Merge pull request #57 from Merck/ext-binary

Expand binary file extensions dictionary

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: pkglite
 Title: Compact Package Representations
-Version: 0.2.3.9000
+Version: 0.2.3.9001
 Authors@R: c(
     person("Nan", "Xiao", email = "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-0250-5673")),

NEWS.md

@@ -1,11 +1,13 @@
-# pkglite 0.2.3.9000
+# pkglite 0.2.3.9001
 
 ## Enhancements
 
 - Increase the default file specification coverage for `file_src()`.
   This helps identifying the correct file collections for R packages
   with `src/Makevars` or `src/Makefile`, for example, packages that
   interface with Stan via the rstan package (#56).
+- Expand the binary file extension dictionary to cover files
+  frequently used in machine learning frameworks (#57).
 
 # pkglite 0.2.3
 

R/dictionary.R

@@ -122,8 +122,9 @@ ext_binary <- function(flat = FALSE) {
     "audio" = c("wav", "mp3", "mid", "ogg", "au", "m4a"),
     "video" = c("mp4", "avi", "mov", "mkv", "webm"),
     "generic" = c(
-      "bin", "epub", "h5", "hdf5", "onnx",
-      "parquet", "feather", "pkl", "npy"
+      "bin", "epub", "hdf5", "h5", "parquet", "feather", "msgpack",
+      "pickle", "pkl", "npy", "npz", "safetensors",
+      "pt", "pth", "keras", "tfrecord", "pb", "ckpt", "onnx"
     )
   )
   if (flat) unique(unlist(x)) else x

tests/testthat/test-independent-test_dictionary.R

@@ -77,8 +77,9 @@ test_that("Test ext_binary() generate the right string list", {
     "audio" = c("wav", "mp3", "mid", "ogg", "au", "m4a"),
     "video" = c("mp4", "avi", "mov", "mkv", "webm"),
     "generic" = c(
-      "bin", "epub", "h5", "hdf5", "onnx",
-      "parquet", "feather", "pkl", "npy"
+      "bin", "epub", "hdf5", "h5", "parquet", "feather", "msgpack",
+      "pickle", "pkl", "npy", "npz", "safetensors",
+      "pt", "pth", "keras", "tfrecord", "pb", "ckpt", "onnx"
     )
   )
 

tests/testthat/test-independent-test_templates.R

@@ -187,7 +187,7 @@ test_that("file_vignettes() creates the correct 'file_spec' objects", {
       (!is_spec_binary & is_file_spec_type(
           fs_source = fs,
           path = "vignettes/",
-          pattern = "\\.rda$|\\.rds$|\\.RData$|\\.jpg$|\\.jpeg$|\\.pdf$|\\.png$|\\.bmp$|\\.gif$|\\.tif$|\\.tiff$|\\.emf$|\\.svgz$|\\.ico$|\\.webp$|\\.eps$|\\.ppm$|\\.pgm$|\\.pbm$|\\.pnm$|\\.xcf$|\\.psd$|\\.graffle$|\\.o$|\\.so$|\\.rdb$|\\.rdx$|\\.woff2$|\\.woff$|\\.otf$|\\.ttf$|\\.eot$|\\.docx$|\\.xlsx$|\\.pptx$|\\.xltx$|\\.potx$|\\.doc$|\\.xls$|\\.ppt$|\\.xlsb$|\\.xlsm$|\\.odt$|\\.ods$|\\.odp$|\\.odg$|\\.odc$|\\.odf$|\\.odi$|\\.odm$|\\.odb$|\\.sas7bdat$|\\.sas7bcat$|\\.xpt$|\\.xpt5$|\\.xpt8$|\\.zip$|\\.tar$|\\.gz$|\\.tgz$|\\.bz2$|\\.7z$|\\.xz$|\\.sqlite$|\\.sqlite3$|\\.dbf$|\\.accdb$|\\.mdb$|\\.pyc$|\\.jar$|\\.mo$|\\.shx$|\\.shp$|\\.laz$|\\.sbx$|\\.sbn$|\\.nc$|\\.gpkg$|\\.bam$|\\.bai$|\\.wav$|\\.mp3$|\\.mid$|\\.ogg$|\\.au$|\\.m4a$|\\.mp4$|\\.avi$|\\.mov$|\\.mkv$|\\.webm$|\\.bin$|\\.epub$|\\.h5$|\\.hdf5$|\\.onnx$|\\.parquet$|\\.feather$|\\.pkl$|\\.npy$",
+          pattern = "\\.rda$|\\.rds$|\\.RData$|\\.jpg$|\\.jpeg$|\\.pdf$|\\.png$|\\.bmp$|\\.gif$|\\.tif$|\\.tiff$|\\.emf$|\\.svgz$|\\.ico$|\\.webp$|\\.eps$|\\.ppm$|\\.pgm$|\\.pbm$|\\.pnm$|\\.xcf$|\\.psd$|\\.graffle$|\\.o$|\\.so$|\\.rdb$|\\.rdx$|\\.woff2$|\\.woff$|\\.otf$|\\.ttf$|\\.eot$|\\.docx$|\\.xlsx$|\\.pptx$|\\.xltx$|\\.potx$|\\.doc$|\\.xls$|\\.ppt$|\\.xlsb$|\\.xlsm$|\\.odt$|\\.ods$|\\.odp$|\\.odg$|\\.odc$|\\.odf$|\\.odi$|\\.odm$|\\.odb$|\\.sas7bdat$|\\.sas7bcat$|\\.xpt$|\\.xpt5$|\\.xpt8$|\\.zip$|\\.tar$|\\.gz$|\\.tgz$|\\.bz2$|\\.7z$|\\.xz$|\\.sqlite$|\\.sqlite3$|\\.dbf$|\\.accdb$|\\.mdb$|\\.pyc$|\\.jar$|\\.mo$|\\.shx$|\\.shp$|\\.laz$|\\.sbx$|\\.sbn$|\\.nc$|\\.gpkg$|\\.bam$|\\.bai$|\\.wav$|\\.mp3$|\\.mid$|\\.ogg$|\\.au$|\\.m4a$|\\.mp4$|\\.avi$|\\.mov$|\\.mkv$|\\.webm$|\\.bin$|\\.epub$|\\.hdf5$|\\.h5$|\\.parquet$|\\.feather$|\\.msgpack$|\\.pickle$|\\.pkl$|\\.npy$|\\.npz$|\\.safetensors$|\\.pt$|\\.pth$|\\.keras$|\\.tfrecord$|\\.pb$|\\.ckpt$|\\.onnx$",
           format = "binary",
           recursive = TRUE,
           ignore_case = TRUE,
@@ -332,7 +332,7 @@ test_that("file_default() creates the correct 'file_spec' objects", {
       (!is_spec_binary & is_file_spec_type(
           fs_source = fs,
           path = "vignettes/",
-          pattern = "\\.rda$|\\.rds$|\\.RData$|\\.jpg$|\\.jpeg$|\\.pdf$|\\.png$|\\.bmp$|\\.gif$|\\.tif$|\\.tiff$|\\.emf$|\\.svgz$|\\.ico$|\\.webp$|\\.eps$|\\.ppm$|\\.pgm$|\\.pbm$|\\.pnm$|\\.xcf$|\\.psd$|\\.graffle$|\\.o$|\\.so$|\\.rdb$|\\.rdx$|\\.woff2$|\\.woff$|\\.otf$|\\.ttf$|\\.eot$|\\.docx$|\\.xlsx$|\\.pptx$|\\.xltx$|\\.potx$|\\.doc$|\\.xls$|\\.ppt$|\\.xlsb$|\\.xlsm$|\\.odt$|\\.ods$|\\.odp$|\\.odg$|\\.odc$|\\.odf$|\\.odi$|\\.odm$|\\.odb$|\\.sas7bdat$|\\.sas7bcat$|\\.xpt$|\\.xpt5$|\\.xpt8$|\\.zip$|\\.tar$|\\.gz$|\\.tgz$|\\.bz2$|\\.7z$|\\.xz$|\\.sqlite$|\\.sqlite3$|\\.dbf$|\\.accdb$|\\.mdb$|\\.pyc$|\\.jar$|\\.mo$|\\.shx$|\\.shp$|\\.laz$|\\.sbx$|\\.sbn$|\\.nc$|\\.gpkg$|\\.bam$|\\.bai$|\\.wav$|\\.mp3$|\\.mid$|\\.ogg$|\\.au$|\\.m4a$|\\.mp4$|\\.avi$|\\.mov$|\\.mkv$|\\.webm$|\\.bin$|\\.epub$|\\.h5$|\\.hdf5$|\\.onnx$|\\.parquet$|\\.feather$|\\.pkl$|\\.npy$",
+          pattern = "\\.rda$|\\.rds$|\\.RData$|\\.jpg$|\\.jpeg$|\\.pdf$|\\.png$|\\.bmp$|\\.gif$|\\.tif$|\\.tiff$|\\.emf$|\\.svgz$|\\.ico$|\\.webp$|\\.eps$|\\.ppm$|\\.pgm$|\\.pbm$|\\.pnm$|\\.xcf$|\\.psd$|\\.graffle$|\\.o$|\\.so$|\\.rdb$|\\.rdx$|\\.woff2$|\\.woff$|\\.otf$|\\.ttf$|\\.eot$|\\.docx$|\\.xlsx$|\\.pptx$|\\.xltx$|\\.potx$|\\.doc$|\\.xls$|\\.ppt$|\\.xlsb$|\\.xlsm$|\\.odt$|\\.ods$|\\.odp$|\\.odg$|\\.odc$|\\.odf$|\\.odi$|\\.odm$|\\.odb$|\\.sas7bdat$|\\.sas7bcat$|\\.xpt$|\\.xpt5$|\\.xpt8$|\\.zip$|\\.tar$|\\.gz$|\\.tgz$|\\.bz2$|\\.7z$|\\.xz$|\\.sqlite$|\\.sqlite3$|\\.dbf$|\\.accdb$|\\.mdb$|\\.pyc$|\\.jar$|\\.mo$|\\.shx$|\\.shp$|\\.laz$|\\.sbx$|\\.sbn$|\\.nc$|\\.gpkg$|\\.bam$|\\.bai$|\\.wav$|\\.mp3$|\\.mid$|\\.ogg$|\\.au$|\\.m4a$|\\.mp4$|\\.avi$|\\.mov$|\\.mkv$|\\.webm$|\\.bin$|\\.epub$|\\.hdf5$|\\.h5$|\\.parquet$|\\.feather$|\\.msgpack$|\\.pickle$|\\.pkl$|\\.npy$|\\.npz$|\\.safetensors$|\\.pt$|\\.pth$|\\.keras$|\\.tfrecord$|\\.pb$|\\.ckpt$|\\.onnx$",
           format = "binary",
           recursive = TRUE,
           ignore_case = TRUE,
@@ -534,7 +534,7 @@ test_that("file_auto() creates the correct 'file_spec' objects", {
       (!is_spec_binary & is_file_spec_type(
           fs_source = fs,
           path = "inst/",
-          pattern = "\\.rda$|\\.rds$|\\.RData$|\\.jpg$|\\.jpeg$|\\.pdf$|\\.png$|\\.bmp$|\\.gif$|\\.tif$|\\.tiff$|\\.emf$|\\.svgz$|\\.ico$|\\.webp$|\\.eps$|\\.ppm$|\\.pgm$|\\.pbm$|\\.pnm$|\\.xcf$|\\.psd$|\\.graffle$|\\.o$|\\.so$|\\.rdb$|\\.rdx$|\\.woff2$|\\.woff$|\\.otf$|\\.ttf$|\\.eot$|\\.docx$|\\.xlsx$|\\.pptx$|\\.xltx$|\\.potx$|\\.doc$|\\.xls$|\\.ppt$|\\.xlsb$|\\.xlsm$|\\.odt$|\\.ods$|\\.odp$|\\.odg$|\\.odc$|\\.odf$|\\.odi$|\\.odm$|\\.odb$|\\.sas7bdat$|\\.sas7bcat$|\\.xpt$|\\.xpt5$|\\.xpt8$|\\.zip$|\\.tar$|\\.gz$|\\.tgz$|\\.bz2$|\\.7z$|\\.xz$|\\.sqlite$|\\.sqlite3$|\\.dbf$|\\.accdb$|\\.mdb$|\\.pyc$|\\.jar$|\\.mo$|\\.shx$|\\.shp$|\\.laz$|\\.sbx$|\\.sbn$|\\.nc$|\\.gpkg$|\\.bam$|\\.bai$|\\.wav$|\\.mp3$|\\.mid$|\\.ogg$|\\.au$|\\.m4a$|\\.mp4$|\\.avi$|\\.mov$|\\.mkv$|\\.webm$|\\.bin$|\\.epub$|\\.h5$|\\.hdf5$|\\.onnx$|\\.parquet$|\\.feather$|\\.pkl$|\\.npy$",
+          pattern = "\\.rda$|\\.rds$|\\.RData$|\\.jpg$|\\.jpeg$|\\.pdf$|\\.png$|\\.bmp$|\\.gif$|\\.tif$|\\.tiff$|\\.emf$|\\.svgz$|\\.ico$|\\.webp$|\\.eps$|\\.ppm$|\\.pgm$|\\.pbm$|\\.pnm$|\\.xcf$|\\.psd$|\\.graffle$|\\.o$|\\.so$|\\.rdb$|\\.rdx$|\\.woff2$|\\.woff$|\\.otf$|\\.ttf$|\\.eot$|\\.docx$|\\.xlsx$|\\.pptx$|\\.xltx$|\\.potx$|\\.doc$|\\.xls$|\\.ppt$|\\.xlsb$|\\.xlsm$|\\.odt$|\\.ods$|\\.odp$|\\.odg$|\\.odc$|\\.odf$|\\.odi$|\\.odm$|\\.odb$|\\.sas7bdat$|\\.sas7bcat$|\\.xpt$|\\.xpt5$|\\.xpt8$|\\.zip$|\\.tar$|\\.gz$|\\.tgz$|\\.bz2$|\\.7z$|\\.xz$|\\.sqlite$|\\.sqlite3$|\\.dbf$|\\.accdb$|\\.mdb$|\\.pyc$|\\.jar$|\\.mo$|\\.shx$|\\.shp$|\\.laz$|\\.sbx$|\\.sbn$|\\.nc$|\\.gpkg$|\\.bam$|\\.bai$|\\.wav$|\\.mp3$|\\.mid$|\\.ogg$|\\.au$|\\.m4a$|\\.mp4$|\\.avi$|\\.mov$|\\.mkv$|\\.webm$|\\.bin$|\\.epub$|\\.hdf5$|\\.h5$|\\.parquet$|\\.feather$|\\.msgpack$|\\.pickle$|\\.pkl$|\\.npy$|\\.npz$|\\.safetensors$|\\.pt$|\\.pth$|\\.keras$|\\.tfrecord$|\\.pb$|\\.ckpt$|\\.onnx$",
           format = "binary",
           recursive = TRUE,
           ignore_case = TRUE,