Merge pull request #195 from 0UmfHxcvx5J7JoaOhFSs5mncnisTJJ6q/dev/all…

…ow_for_full_hashing

allow for fingerprint() to hash full files if a .fullhash file is present in the directory

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '7342505'
+ValidationKey: '7484100'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'madrat: May All Data be Reproducible and Transparent (MADRaT) *'
-version: 3.7.3
-date-released: '2023-11-24'
+version: 3.8.0
+date-released: '2023-12-04'
 abstract: Provides a framework which should improve reproducibility and transparency
   in data processing. It provides functionality such as automatic meta data creation
   and management, rudimentary quality management, data caching, work-flow management

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: madrat
 Title: May All Data be Reproducible and Transparent (MADRaT) *
-Version: 3.7.3
-Date: 2023-11-24
+Version: 3.8.0
+Date: 2023-12-04
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre")),
     person("Lavinia", "Baumstark", , "[email protected]", role = "aut"),

R/fingerprint.R

@@ -160,8 +160,16 @@ fingerprintFiles <- function(paths) {
     }
 
     if (!is.null(files)) {
-      # use the first 300 byte of each file and the file sizes for hashing
-      files$hash <- vapply(files$path, digest, character(1), algo = getConfig("hash"), file = TRUE, length = 300)
+      # hash the first 300 bytes of each file, or the entire file if a
+      # `.fullhash` file is present in the directory
+      files$hash <- vapply(
+        files$path,
+        digest,
+        character(1),
+        algo = getConfig("hash"),
+        file = TRUE,
+        length = ifelse(file.exists(file.path(path, ".fullhash")), Inf, 300)
+      )
       files$path <- NULL
       if (!is.null(hashCacheFile)) {
         if (!dir.exists(dirname(hashCacheFile))) {

README.md

@@ -1,6 +1,6 @@
 # May All Data be Reproducible and Transparent (MADRaT) *
 
-R package **madrat**, version **3.7.3**
+R package **madrat**, version **3.8.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/madrat)](https://cran.r-project.org/package=madrat) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1115490.svg)](https://doi.org/10.5281/zenodo.1115490) [![R build status](https://github.com/pik-piam/madrat/workflows/check/badge.svg)](https://github.com/pik-piam/madrat/actions) [![codecov](https://codecov.io/gh/pik-piam/madrat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/madrat) [![r-universe](https://pik-piam.r-universe.dev/badges/madrat)](https://pik-piam.r-universe.dev/builds)
 
@@ -55,7 +55,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **madrat** in publications use:
 
-Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Sauer P (2023). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.7.3, <https://github.com/pik-piam/madrat>.
+Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Sauer P (2023). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.8.0, <https://github.com/pik-piam/madrat>.
 
 A BibTeX entry for LaTeX users is
 
@@ -64,7 +64,7 @@ A BibTeX entry for LaTeX users is
   title = {madrat: May All Data be Reproducible and Transparent (MADRaT)},
   author = {Jan Philipp Dietrich and Lavinia Baumstark and Stephen Wirth and Anastasis Giannousakis and Renato Rodrigues and Benjamin Leon Bodirsky and Debbora Leip and Ulrich Kreidenweis and David Klein and Pascal Sauer},
   year = {2023},
-  note = {R package version 3.7.3},
+  note = {R package version 3.8.0},
   doi = {10.5281/zenodo.1115490},
   url = {https://github.com/pik-piam/madrat},
 }