Merge pull request #188 from isoverse/dev

upgrade main

.Rbuildignore

@@ -11,14 +11,14 @@
 ^Makefile$
 ^NEWS$
 ^docs$
-^cache/.*
-^tests/testthat/cache/.*
+^cache
+^tests/testthat/cache
 ^inst/other$
 ^tmp.*$
 ^README-.*\.png$
 ^README\.Rmd$
 ^logo\.png$
-^vignettes/cache/.*
+^vignettes/cache
 ^vignettes/fig_output$
 ^doc$
 ^.*\.xlsx$

.github/workflows/R-CMD-check.yaml

@@ -26,6 +26,7 @@ jobs:
           - {os: ubuntu-latest,   r: 'release'}
 
     env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
@@ -45,6 +46,12 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
+      - name: enable additional tests
+        run: |
+          # include test_data by removing it from .Rbuildignore
+          cat(stringr::str_subset(readr::read_lines(".Rbuildignore"), "test_data", negate = TRUE), file = ".Rbuildignore", sep = "\n")
+        shell: Rscript {0}
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

DESCRIPTION

@@ -22,32 +22,32 @@ Authors@R:
 URL: http://isoreader.isoverse.org, https://github.com/isoverse/isoreader
 BugReports: https://github.com/isoverse/isoreader/issues
 Depends:
-    R (>= 4.0.0),
+    R (>= 4.2.0),
     stats
 Imports:
     methods,
     R.utils,
-    magrittr,
-    rlang (>= 0.4.5),
-    tidyselect (>= 1.0.0),
-    vctrs (>= 0.3.4),
+    rlang (>= 1.1.0),
+    lifecycle (>= 1.0.0),
+    tidyselect (>= 1.2.0),
+    vctrs (>= 0.6.0),
     tibble (>= 3.0.0),
-    dplyr (>= 1.0.0),
-    tidyr (>= 1.0.0),
-    glue (>= 1.4.0),
-    stringr (>= 1.4.0),
-    purrr (>= 0.3.4),
-    future (>= 1.18.0),
-    lubridate (>= 1.7.9.2),
-    readr (>= 1.4.0),
+    dplyr (>= 1.1.0),
+    tidyr (>= 1.3.0),
+    glue (>= 1.6.0),
+    stringr (>= 1.5.0),
+    purrr (>= 1.0.0),
+    future (>= 1.33.0),
+    lubridate (>= 1.9.0),
+    readr (>= 2.0.0),
     progress (>= 1.2.2)
 Suggests:
     devtools,
     testthat,
     feather (>= 0.3.5),
-    readxl (>= 1.3.1),
-    openxlsx (>= 4.1.5),
-    xml2 (>= 1.3.1),
+    readxl (>= 1.4.0),
+    openxlsx (>= 4.2.0),
+    xml2 (>= 1.3.5),
     rhdf5 (>= 2.0.0),
     knitr,
     markdown,
@@ -57,4 +57,4 @@ biocViews:
 License: GPL (>= 2)
 Encoding: UTF-8
 VignetteBuilder: knitr
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3

Makefile

@@ -7,16 +7,17 @@ all: docu check
 docu:
 	Rscript -e "devtools::document(roclets=c('rd', 'collate', 'namespace'))"
 
-# test package functionality without all example files (= as if on CRAN)
+# test package functionality without example files (= as if on CRAN)
 check:
-	R -q -e "devtools::check(env_vars = c())"
+	R -q -e "message('\nINFO: running check as if on CRAN\n'); devtools::check(env_vars = c())"
 
+# tests without file tests (= as if on CRAN)
 auto_test:
-	R -q -e "rm(list = ls()); Sys.setenv(NOT_CRAN = \"false\"); testthat::auto_test_package()"
+	R -q -e "rm(list = ls()); options("isoreader.skip_file_tests" = TRUE); message('\nINFO: running tests as if on CRAN\n'); testthat::auto_test_package()"
 
-# test with all example files (= as if not on CRAN)
+# tests with file test
 auto_test_all:
-	R -q -e "rm(list = ls()); testthat::auto_test_package()"
+	R -q -e "rm(list = ls()); message('\nINFO: running all tests (as if NOT on CRAN)\n'); testthat::auto_test_package()"
 
 # check code complexity
 count:

NAMESPACE

@@ -74,20 +74,18 @@ S3method(vec_ptype_abbr,iso_double_with_units)
 S3method(vec_ptype_full,iso_double_with_units)
 export("!!!")
 export("!!")
-export("%>%")
 export(ends_with)
 export(everything)
 export(extract_substring)
 export(extract_word)
 export(filter)
 export(iso_add_file_info)
 export(iso_as_file_list)
-export(iso_calculate_ratios)
 export(iso_cleanup_reader_cache)
-export(iso_convert_signals)
-export(iso_convert_time)
 export(iso_double_with_units)
 export(iso_expand_paths)
+export(iso_export_files_to_excel)
+export(iso_export_files_to_feather)
 export(iso_export_to_excel)
 export(iso_export_to_feather)
 export(iso_filter_files)
@@ -108,6 +106,7 @@ export(iso_get_reader_examples)
 export(iso_get_reader_examples_folder)
 export(iso_get_resistors)
 export(iso_get_resistors_info)
+export(iso_get_source_file_structure)
 export(iso_get_standards)
 export(iso_get_standards_info)
 export(iso_get_supported_file_types)
@@ -126,9 +125,6 @@ export(iso_make_units_implicit)
 export(iso_mutate_file_info)
 export(iso_omit_files_with_problems)
 export(iso_parse_file_info)
-export(iso_plot_continuous_flow_data)
-export(iso_plot_dual_inlet_data)
-export(iso_plot_raw_data)
 export(iso_print_source_file_structure)
 export(iso_read_continuous_flow)
 export(iso_read_dual_inlet)
@@ -159,7 +155,6 @@ export(iso_turn_info_messages_on)
 export(iso_turn_reader_caching_off)
 export(iso_turn_reader_caching_on)
 export(iso_with_units)
-export(isoread)
 export(matches)
 export(parse_datetime)
 export(parse_double)
@@ -208,7 +203,6 @@ importFrom(glue,glue)
 importFrom(lubridate,as_datetime)
 importFrom(lubridate,duration)
 importFrom(lubridate,interval)
-importFrom(magrittr,"%>%")
 importFrom(methods,is)
 importFrom(methods,setOldClass)
 importFrom(purrr,is_empty)

NEWS.md

@@ -1,3 +1,24 @@
+# isoreader 1.4.0
+
+## Breaking changes
+
+Several previously deprecated functions have been removed: `iso_calculate_ratios()`, `iso_convert_signals()`, `iso_convert_time()`, `iso_plot_continuous_flow_data()`, `iso_plot_dual_inlet_data()`, `iso_plot_raw_data()`, `isoread()`. Older code that still uses these functions instead of their replacements will no longer work.
+
+## New features
+
+* simpler cache file names that also removed dependency on the `UNF` package
+* faster implementation of binary file structure analysis for isodat files, accessible via the new `iso_get_source_file_structure()` function
+
+## Enhancements
+
+* ~20% performance increase in reading isodat files through code optimization
+* `iso_export_to_excel()` and `iso_export_to_feather()` renamed to `iso_export_files_to_excel()` and `iso_export_files_to_feather()`, respectively, to avoid ambiguity with other export functions.
+
+## Bug fixes
+
+* fixes to be compatible with latest tidyselect and dplyr updates
+
+
 # isoreader 1.3.0
 
 ## Major changes
@@ -40,6 +61,6 @@ This package provides the following data aggregation and data processing functio
 
 This package provides the following data export functionality for all supported data files:
 
- - export to open Excel (.xslx) with `?iso_export_to_excel`
- - export to the Python/R cross-over feather file format with `?iso_export_to_feather`
+ - export to open Excel (.xslx) with `?iso_export_files_to_excel`
+ - export to the Python/R cross-over feather file format with `?iso_export_files_to_feather`