change structure

02-cran-licenses.R

@@ -100,13 +100,6 @@ parse_license <- function(license) {
   )
 }
 
-# this list is based in the licenses.json file from the stack dataset
-# see: https://huggingface.co/datasets/bigcode/the-stack-dedup/blob/main/licenses.json
-
-allowed_license_codes <- c("MIT", "Apache", "BSD", "CC-BY", "Artistic", "CC0",
-                           "FreeBSD")
-
-
 # we now make the indirection from allowed codes to allowed License as specified
 # in the DESCRIPTION.
 license_codes <- licenses_table %>%
@@ -115,50 +108,63 @@ license_codes <- licenses_table %>%
   ) %>%
   unnest(parsed)
 
-permissive_licenses <- license_codes%>%
-  mutate(permissive = license_code %in% allowed_license_codes) %>%
-  group_by(license) %>%
-  summarise(permissive = any(permissive)) %>%
-  filter(permissive)
+# we now map license_codes to the same classification used by github
+
+gh_license_table <- license_codes %>%
+  mutate(
+    license_gh = case_when(
+      classif == "GPL (>=2)" ~ "gpl-3.0",
+      classif == "GPL (>=3)" ~ "gpl-3.0",
+      classif == "GPL (==3)" ~ "gpl-3.0",
+      classif == "GPL (==2)" ~ "gpl-2.0",
+      classif == "GPL" ~ "gpl-3.0",
+      classif %in% c("GPL (==3) | LGPL (==2.1)", "GPL (>2)", "GPL (>3)", "GPL (>=1)") ~ "gpl-3.0",
+      classif %in% c("GPL (<=2)", "GPL (==2) | LGPL (==2.1) | MPL (==1.1)") ~ "gpl-2.0",
+
+      classif == "AGPL (>=2)" ~ "agpl-3.0",
+      classif == "AGPL (>=3)" ~ "agpl-3.0",
+      classif == "AGPL (==3)" ~ "agpl-3.0",
+      classif == "AGPL (==2)" ~ "agpl-2.0",
+      classif == "AGPL" ~ "agpl-3.0",
+
+      classif == "LGPL (>=2)" ~ "lgpl-3.0",
+      classif == "LGPL (>=3)" ~ "lgpl-3.0",
+      classif %in% c("LGPL (==3)", "LGPL (>2)", "LGPL (>=2.1)") ~ "lgpl-3.0",
+      classif %in% c("LGPL (==2)", "LGPL (>=2, <3)", "LGPL (>= 2.0, < 3)", "LGPL (==2.1)", "LGPL (>= 2.0, < 3) | MPL") ~ "lgpl-2.0",
+      classif == "LGPL" ~ "lgpl-3.0",
+
+      classif == "BSD" ~ "bsd-3-clause",
+      classif == "BSD-Clause (==2)" ~ "bsd-2-clause",
+      classif == "BSD-Clause (==3)" ~ "bsd-3-clause",
+
+      classif %in% c("BSL", "BSL (==1)") ~ "bsl-1.0",
+      str_detect(classif, fixed("CC-BY (==4)")) ~ "cc-by-4.0",
+      str_detect(classif, fixed("CC-BY-SA (==4)")) ~ "cc-by-sa-4.0",
+      str_detect(classif, "CC0") ~ "cc0-1.0",
+      str_detect(classif, "FreeBSD") ~ "bsd-2-clause",
+
+      classif %in% c("MPL (==2)", "MPL (>=2)", "MPL") ~ "mpl-2.0",
+      classif %in% c("EUPL", "EUPL (==1.1)") ~ "eupl-1.1",
+      classif %in% c("EPL", "EPL (>=1)") ~ "epl-2.0",
+
+      str_detect(classif, "Apache") ~ "apache-2.0",
+      str_detect(classif, "Artistic") ~ "artistic-2.0",
+      str_detect(classif, "MIT") ~ "mit",
+      str_detect(classif, fixed("BSD-Clause (==2)")) ~ "bsd-2-clause",
+      str_detect(classif, fixed("BSD-Clause (==3)")) ~ "bsd-3-clause",
+      str_detect(classif, fixed("MPL (==2)")) ~ "mpl-2.0",
+
+      str_detect(classif, fixed("GPL (>=2")) ~ "gpl-2.0",
+      str_detect(classif, fixed("GPL (>=3")) ~ "gpl-3.0",
+      TRUE ~ "unknown"
+    )
+  )
 
 # We then filter the allowed packages.
-allowed_packages <- licenses %>%
-  filter(license %in% permissive_licenses$license)
-
-arrow::write_parquet(allowed_packages, "packages.parquet")
-
-# the distribution of packages per license code
-licenses %>%
-  left_join(license_codes, by = "license", relationship = "many-to-many") %>%
-  count(license_code) %>%
-  mutate(n / nrow(licenses)) %>%
-  arrange(desc(n)) %>%
-  print(n = 100)
-
-#  # A tibble: 24 × 3
-#  license_code     n `n/nrow(licenses)`
-#  <chr>        <int>              <dbl>
-#  1 GPL          18440          0.726
-#  2 MIT           4533          0.179
-#  3 LGPL           556          0.0219
-#  4 Apache         428          0.0169
-#  5 BSD-Clause     343          0.0135
-#  6 CC0            261          0.0103
-#  7 AGPL           232          0.00914
-#  8 Artistic       158          0.00622
-#  9 NA              96          0.00378
-# 10 Unlimited       76          0.00299
-# 11 CC-BY           56          0.00221
-# 12 MPL             52          0.00205
-# 13 EUPL            35          0.00138
-# 14 CC-BY-SA        34          0.00134
-# 15 CeCILL          34          0.00134
-# 16 BSD             33          0.00130
-# 17 CC-BY-NC-SA     27          0.00106
-# 18 FreeBSD         18          0.000709
-# 19 BSL             10          0.000394
-# 20 CC-BY-NC         6          0.000236
-# 21 EPL              6          0.000236
-# 22 ACM              5          0.000197
-# 23 CPL              3          0.000118
-# 24 CC-BY-NC-ND      1          0.0000394
+packages <- licenses %>%
+  mutate(license = stringr::str_trim(license)) %>%
+  left_join(gh_license %>% select(license, license_gh) %>% distinct(), by = "license") %>%
+  mutate(license_gh = coalesce(license_gh, "unknown"))
+
+arrow::write_parquet(packages, "packages.parquet")
+

03-cran-process.R

@@ -35,7 +35,6 @@ packages <- arrow::read_parquet("packages.parquet")
 opt_out <- readr::read_lines("optout.txt")
 
 repos <- jsonlite::read_json("repos.json") %>%
-  keep(\(repo) as.character(repo$name) %in% packages$package) %>%
   discard(\(repo) as.character(repo$name) %in% opt_out)
 
 library(future)
@@ -51,6 +50,10 @@ make_data <- function(repos, ext) {
     purrr::discard(\(x) inherits(x, "try-error")) |>
     dplyr::bind_rows()
 
+  files <- files %>%
+    select(package, path = filename, content, size = uncompressed_size) %>%
+    left_join(packages %>% select(package, license = license_gh), by = "package")
+
   arrow::write_dataset(
     files,
     path = fs::path("data", ext),

README.md

@@ -17,23 +17,22 @@ The dataset has been constructed using the following steps:
 
 - Downloaded latest version from all packages on CRAN (see last updated). The source code has been downloaded from the [GitHub mirror](https://github.com/cran).
 - Identified the licenses from each package from their DESCRIPTION file, and classified each of them into some license_code. See the licenses.csv file.
-- Extract R and Rmd source files from packages identified with permissive licenses (following the same list from [The Stack dataset](https://huggingface.co/datasets/bigcode/the-stack))
+- Extract R and Rmd source files from all packages and joined with the package LICENSES.
 
 Datasets are provided as parquet files containing the following columns:
 
 ```
-FileSystemDataset with 2 Parquet files
-126,478 rows x 9 columns
-$ filename <string> "cran-devtools-945c660/R/R.R", "cran-devtools-945c660/R/active.R"…
-$ compressed_size <double> 622, 601, 142, 428, 895, 455, 1365, 740, 329, 955, 1689, 3132, 24…
-$ uncompressed_size <double> 1099, 1385, 179, 715, 2024, 907, 3564, 1843, 664, 2096, 4696, 858…
-$ timestamp <timestamp[us, tz=UTC]> 2022-10-11 07:12:36, 2022-10-11 07:12:36, 2022-10-11 07:12:36, 20…
-$ permissions <ext<octmode>> 600, 600, 600, 600, 600, 600, 600, 600, 600, 600, 600, 600, 600, …
-$ crc32 <ext<hexmode>> 6aafc73e, 6c7082a5, b1fdeb73, 8f6a4e25, 16941e78, bdd4943b, 6d0a1…
-$ offset <double> 39452, 40140, 40812, 41023, 41528, 42500, 43030, 44474, 45288, 45…
-$ package <string> "devtools", "devtools", "devtools", "devtools", "devtools", "devt…
-$ content <string> "#' Environment variables to set when calling R\n#'\n#' Devtools …
-Call `print()` for full schema details
+FileSystemDataset with 1 Parquet file
+package: string
+path: string
+content: large_string
+size: double
+license: string
 ```
 
-Last updated: Jun 2th 2023
+Last updated: Jun 6th 2023
+
+## Changelog
+
+- v1: Initial version
+- dev: added all CRAN files and a license field that allows filtering out per license. Also removed some unused columns.

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@@ -1,3 +1,3 @@
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packages.parquet

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+size 314409