Merge branch 'alice/model-grafs-spain' into alice/typologies

Author: AliceBeckmann

.Rbuildignore

@@ -1,6 +1,6 @@
 ^renv$
 ^renv\.lock$
-^WHEP.Rproj$
+^whep.Rproj$
 ^LICENSE\.md$
 ^docs$
 ^\.github$
@@ -10,3 +10,8 @@
 ^\.Rproj\.user$
 ^data-raw$
 ^README\.Rmd$
+^cran-comments\.md$
+^CRAN-SUBMISSION$
+^air.toml$
+^doc$
+^Meta$

.Renviron

@@ -1 +1,2 @@
 _R_CHECK_SYSTEM_CLOCK_=0
+RENV_CONFIG_PAK_ENABLED=TRUE

.github/workflows/format-suggest.yaml

@@ -0,0 +1,46 @@
+# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
+
+on:
+  # Using `pull_request_target` over `pull_request` for elevated `GITHUB_TOKEN`
+  # privileges, otherwise we can't set `pull-requests: write` when the pull
+  # request comes from a fork, which is our main use case (external contributors).
+  #
+  # `pull_request_target` runs in the context of the target branch (`main`, usually),
+  # rather than in the context of the pull request like `pull_request` does. Due
+  # to this, we must explicitly checkout `ref: ${{ github.event.pull_request.head.sha }}`.
+  # This is typically frowned upon by GitHub, as it exposes you to potentially running
+  # untrusted code in a context where you have elevated privileges, but they explicitly
+  # call out the use case of reformatting and committing back / commenting on the PR
+  # as a situation that should be safe (because we aren't actually running the untrusted
+  # code, we are just treating it as passive data).
+  # https://securitylab.github.com/resources/github-actions-preventing-pwn-requests/
+  pull_request_target:
+
+name: format-suggest.yaml
+
+jobs:
+  format-suggest:
+    name: format-suggest
+    runs-on: ubuntu-latest
+
+    permissions:
+      # Required to push suggestion comments to the PR
+      pull-requests: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Install
+        uses: posit-dev/setup-air@v1
+
+      - name: Format
+        run: air format .
+
+      - name: Suggest
+        uses: reviewdog/action-suggester@v1
+        with:
+          level: error
+          fail_level: error
+          tool_name: air

.github/workflows/lint.yaml

@@ -28,7 +28,13 @@ jobs:
           needs: lint
 
       - name: Lint
-        run: lintr::lint_package(linters=lintr::linters_with_defaults(object_usage_linter=NULL))
+        run: |
+          lintr::lint_package(
+            linters = lintr::linters_with_defaults(
+              object_usage_linter = NULL,
+              line_length_linter = NULL
+            )
+          )
         shell: Rscript {0}
         env:
           LINTR_ERROR_ON_LINT: true

.gitignore

@@ -9,3 +9,5 @@
 inst/google_cloud_key.json
 inst/doc
 docs
+/doc/
+/Meta/

DESCRIPTION

@@ -1,29 +1,34 @@
-Package: WHEP
-Title: Who Has Eaten the Planet
-Version: 0.0.0.9000
+Package: whep
+Title: Processing Agro-Environmental Data
+Version: 0.1.0.9000
 Authors@R: c(
     person("Catalin", "Covaci", , "catalin.covaci@csic.es", role = c("aut", "cre"), comment = c(ORCID = "0009-0005-2186-5972")),
-    person("Eduardo", "Aguilera", , "eduardo.aguilera@csic.es", role = c("aut"), comment = c(ORCID = "0000-0003-4382-124X")),
+    person("Eduardo", "Aguilera", , "eduardo.aguilera@csic.es", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-4382-124X")),
     person("João", "Serra", , "jserra@agro.au.dk", role = c("ctb"), comment = c(ORCID = "0000-0002-3561-5350")),
-    person("Alice", "Beckmann", , "alice.beckmann@cchs.csic.es", role = c("aut"), comment = c(ORCID = "0009-0009-6840-0258"))
+    person("European Research Council", role = c("fnd"))
   )
-Description: Gather historical agricultural and trade data from 1850.
+Description: A set of tools for processing and analyzing data developed in the
+    context of the "Who Has Eaten the Planet" (WHEP) project, funded by the
+    European Research Council (ERC). For more details on multi-regional
+    input–output model "Food and Agriculture Biomass Input–Output" (FABIO) see 
+    Bruckner et al. (2019) <doi:10.1021/acs.est.9b03554>.
 License: MIT + file LICENSE
 Imports:
+    cli,
     dplyr,
+    fs,
     FAOSTAT,
-    googledrive,
-    httr2,
+    httr,
     mipfp,
+    nanoparquet,
+    pins,
     purrr,
     readr,
     rlang,
     stringr,
     tidyr,
-    readxl,
-    sf,
-    stringi,
-    utils
+    withr,
+    yaml
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
@@ -38,7 +43,8 @@ Suggests:
     tibble
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-URL: https://eduaguilera.github.io/WHEP, https://github.com/eduaguilera/WHEP
-BugReports: https://github.com/eduaguilera/WHEP/issues
+URL: https://eduaguilera.github.io/whep/, https://github.com/eduaguilera/whep
+BugReports: https://github.com/eduaguilera/whep/issues
 Depends: 
     R (>= 3.5)
+LazyData: true

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2025
-COPYRIGHT HOLDER: WHEP authors
+COPYRIGHT HOLDER: whep authors

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2025 WHEP authors
+Copyright (c) 2025 whep authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

LICENSE.note

@@ -0,0 +1,8 @@
+The whep package as a whole is distributed under MIT. The whep package includes
+as part of their code some code taken from other R packages. The following is a
+list of these parts:
+
+* whep: written by package authors
+* pins: Apache 2.0
+
+A copy of the Apache 2.0 license can be found at inst/APACHE-LICENSE.md.

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(pin_fetch,pins_with_progress)
 export(add_area_code)
 export(add_area_name)
 export(add_item_cbs_code)
@@ -11,13 +12,24 @@ export(create_n_inputs_grafs_spain)
 export(create_prod_and_destiny_grafs)
 export(create_typologies_grafs_spain)
 export(create_typologies_of_josette)
+export(calculate_nue_crops)
+export(calculate_nue_livestock)
+export(calculate_system_nue)
+export(create_alfredos_typologies)
+export(create_n_production)
+export(create_n_prov_destiny)
+export(create_n_soil_inputs)
+export(create_typologies_whep)
 export(expand_trade_sources)
 export(get_bilateral_trade)
 export(get_faostat_data)
 export(get_feed_intake)
-export(get_file_path)
 export(get_primary_production)
 export(get_primary_residues)
 export(get_processing_coefs)
 export(get_wide_cbs)
+export(plot_whep_typologies)
+export(whep_list_file_versions)
+export(whep_read_file)
+importFrom(pins,pin_fetch)
 importFrom(rlang,":=")