preparing new release and submission (#82)

* removed man for internal func, adapted comput_day_from_date for a vector of dates, tests added

* update man: for dates vector

* added rhub workflow for rhub

* news update, site, description

* Update CITATION.cff

---------

Co-authored-by: plecharpent <[email protected]>

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

CITATION.cff

@@ -1,14 +1,14 @@
-# -----------------------------------------------------------
-# CITATION file created with {cffr} R package, v1.0.0
+# --------------------------------------------
+# CITATION file created with {cffr} R package
 # See also: https://docs.ropensci.org/cffr/
-# -----------------------------------------------------------
+# --------------------------------------------
 
 cff-version: 1.2.0
 message: 'To cite package "SticsRFiles" in publications use:'
 type: software
 license: LGPL-3.0-or-later
 title: 'SticsRFiles: Read and Modify ''STICS'' Input/Output Files'
-version: 1.2.0
+version: 1.3.0
 abstract: Manipulating input and output files of the 'STICS' crop model. Files are
   either 'JavaSTICS' XML files or text files used by the model 'fortran' executable.
   Most basic functionalities are reading or writing parameter names and values in
@@ -35,7 +35,7 @@ authors:
 repository: https://CRAN.R-project.org/package=SticsRFiles
 repository-code: https://github.com/SticsRPacks/SticsRFiles
 url: https://doi.org/10.5281/zenodo.4443206
-date-released: '2024-02-23'
+date-released: '2024-04-10'
 contact:
 - family-names: Lecharpentier
   given-names: Patrice
@@ -468,3 +468,4 @@ references:
     given-names: Hadley
     email: [email protected]
   year: '2024'
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SticsRFiles
 Title: Read and Modify 'STICS' Input/Output Files
-Version: 1.2.0
-Date: 2024-02-23
+Version: 1.3.0
+Date: 2024-04-10
 Authors@R: c(
     person("Patrice", "Lecharpentier", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4044-4322")),
@@ -11,6 +11,7 @@ Authors@R: c(
            comment = c(ORCID = "0000-0002-8676-5447")),
     person("Michel", "Giner", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0002-9310-2377")),
+    person("Timothee", "Flutre", ,"[email protected]", role = "ctb"),
     person("Thomas", "Robine", role = "ctb"),
     person("Amine", "Barkaoui", role = "ctb"),
     person("Patrick", "Chabrier", role = "ctb"),

NEWS.md

@@ -1,3 +1,24 @@
+# SticsRFiles 1.3.0 _2024-04-10_
+
+* FUNCTIONS
+   * Message improvement for missing xml files detected before text files
+   generation
+   * New functions for computing days numbers from dates with reference to
+   starting dates
+
+* FIXES
+   * Updating STICS versions information 
+   * get_file using usm names (regex pattern)
+   * upgrade _ini.xml file (magrain0 parameter position)
+   * xml files generation: missing data management when loading xls/csv 
+   files
+   * text files generation: plant and tec files were not generated in
+   intercropping usms for the associated crop
+
+* DOC
+   * added license file
+
+
 # SticsRFiles 1.2.0 _2024-02-21_
 
 * FUNCTIONS

_pkgdown.yml

@@ -4,6 +4,7 @@ url: https://sticsrpacks.github.io/SticsRFiles/
     c(person(given = "Patrice", family = "Lecharpentier", role = c("aut", "cre"), email = "[email protected]"),
       person(given = "Remi",family = "Vezy", role = c("aut"), email = "[email protected]"),
       person(given = "SticsRPacks", role = c("aut","cph")),
+      person("Timothee", "Flutre", ,"[email protected]", role = "ctb"),
       person(given = "Julie", family = "Constantin", email = "[email protected]", role = c("rev")),
       person(given = "Dominique", family = "Ripoche", email = "[email protected]", role = c("rev")),
       person(given = "Marie", family = "Launay", email = "[email protected]", role = c("rev")),
@@ -115,3 +116,4 @@ reference:
       - is_unix
       - is_windows
       - "`[.cropr_simulation`"
+      - compute_day_from_date

cran-comments.md

@@ -21,19 +21,9 @@
 0 errors ✔ | 0 warnings ✔ | 3 notes ✖
 
 
-> revdepcheck::revdep_check(num_workers = 4)
-── INSTALL ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── 2 versions ──
-Installing CRAN version of SticsRFiles
-installation des dépendances ‘pillar’, ‘tidyselect’, ‘vctrs’, ‘timechange’, ‘stringi’, ‘fansi’, ‘pkgconfig’, ‘purrr’, ‘cpp11’, ‘Rcpp’, ‘cli’, ‘crayon’, ‘curl’, ‘data.table’, ‘dplyr’, ‘lifecycle’, ‘lubridate’, ‘rlang’, ‘rstudioapi’, ‘stringr’, ‘tibble’, ‘tidyr’, ‘XML’, ‘xml2’, ‘xslt’
-
-Installing DEV version of SticsRFiles
-Installing 31 packages: rlang, cli, vctrs, stringi, magrittr, lifecycle, glue, withr, pkgconfig, utf8, fansi, tidyselect, tibble, R6, pillar, generics, cpp11, Rcpp, xml2, stringr, purrr, dplyr, timechange, xslt, XML, tidyr, rstudioapi, lubridate, data.table, curl, crayon
-── CHECK ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── 0 packages ──
-OK: 0
-BROKEN: 0
-Total time: <1 min
-── REPORT ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
-Writing summary to 'revdep/README.md'
-Writing problems to 'revdep/problems.md'
-Writing failures to 'revdep/failures.md'
-Writing CRAN report to 'revdep/cran.md'
+## revdepcheck results
+
+We checked 0 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 0 packages