init : OptirrigManual initialisation repository

.Rbuildignore

+^.*\.Rproj$
+^\.Rproj\.user$
+^\.vscode$
+^\.gitlab-ci\.yml$
+^data-raw$
+^LICENSE\.md$
+^man-roxygen$
+^pkgdown$
+^\.vscode$
+^ci$
+^snippets$
+^README.rmd$
+^dev$
+^\.RDataTmp
+^\.devcontainer
+^\.png
+^_pkgdown\.yml$
+^docs$
+^reports$
+^templates$
+^public$
+

.gitignore

+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+vignettes/*.png
+
+# produced files
+inst/extdata/02_Sorties/*/*.csv
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# RStudio Connect folder
+rsconnect/
+
+/.vscode
+
+*.bak
+
+*.rds
+
+public/*
+docs

.gitlab-ci.yml

-# This file is a template, and might need editing before it works on your project.
-# This is a sample GitLab CI/CD configuration file that should run without any modifications.
-# It demonstrates a basic 3 stage CI/CD pipeline. Instead of real tests or scripts,
-# it uses echo commands to simulate the pipeline execution.
-#
-# A pipeline is composed of independent jobs that run scripts, grouped into stages.
-# Stages run in sequential order, but jobs within stages run in parallel.
-#
-# For more information, see: https://docs.gitlab.com/ee/ci/yaml/index.html#stages
-#
-# You can copy and paste this template into a new `.gitlab-ci.yml` file.
-# You should not add this template to an existing `.gitlab-ci.yml` file by using the `include:` keyword.
-#
-# To contribute improvements to CI/CD templates, please follow the Development guide at:
-# https://docs.gitlab.com/ee/development/cicd/templates.html
-# This specific template is located at:
-# https://gitlab.com/gitlab-org/gitlab/-/blob/master/lib/gitlab/ci/templates/Getting-Started.gitlab-ci.yml
-
-stages:          # List of stages for jobs, and their order of execution
-  - build
-  - test
+stages:
+  - checks
+  - pkgdown
+  - bookdown
   - deploy
 
-build-job:       # This job runs in the build stage, which runs first.
-  stage: build
+default:
+  tags: [stable]
+
+image: rocker/geospatial:4.3.1
+
+variables:
+  CI_CACHE_DIR: "$CI_PROJECT_DIR/ci"
+  R_LIBS_USER: "$CI_CACHE_DIR/lib"
+  PKG_DATA_CACHE: "$CI_CACHE_DIR/data"
+
+cache:
+  key:
+  paths:
+    - $CI_CACHE_DIR
+
+before_script:
+  - mkdir -p $R_LIBS_USER
+  - echo "R_LIBS='$R_LIBS_USER'" > .Renviron
+  - R -q -e 'if (!require(remotes)) install.packages(c("remotes", "testthat"))'
+  - R -q -e 'devtools::install_deps(dependencies = TRUE)'
+  - R -q -e 'remotes::install_git("https://forgemia.inra.fr/umr-g-eau/fairify.git")'
+
+check:
+  variables:
+    NOT_CRAN: "true"
+  stage: checks
   script:
-    - echo "Compiling the code..."
-    - echo "Compile complete."
+    - R -q -e 'remotes::update_packages("rcmdcheck")'
+    - R -q -e 'rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")'
 
-unit-test-job:   # This job runs in the test stage.
-  stage: test    # It only starts when the job in the build stage completes successfully.
+pkgdown:
+  stage: pkgdown
+  rules:
+    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
   script:
-    - echo "Running unit tests... This will take about 60 seconds."
-    - sleep 60
-    - echo "Code coverage is 90%"
+    - R -q -e 'devtools::install()'
+    - R -q -e 'remotes::update_packages("pkgdown")'
+    - R -q -e 'rmarkdown::render("README.rmd", "md_document")'
+    - R -q -e 'fairify::build_site()'
+    - mv docs/* public/
+  artifacts:
+    paths:
+      - public/
 
-lint-test-job:   # This job also runs in the test stage.
-  stage: test    # It can run at the same time as unit-test-job (in parallel).
+bookdown:
+  stage: bookdown
+  dependencies:
+    - pkgdown
   script:
-    - echo "Linting code... This will take about 10 seconds."
-    - sleep 10
-    - echo "No lint issues found."
+    - ls reports/
+    - mv reports/* public/
+  artifacts:
+    paths:
+      - public/
 
-deploy-job:      # This job runs in the deploy stage.
-  stage: deploy  # It only runs when *both* jobs in the test stage complete successfully.
-  environment: production
+pages:
+  stage: deploy
+  rules:
+    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
   script:
-    - echo "Deploying application..."
-    - echo "Application successfully deployed."
+    - ls public/
+  artifacts:
+    paths:
+      - public/
+

DESCRIPTION

+Package: OptirrigManual
+Type: Package
+Title: OptirrigManual
+Version: 0.1.0
+Authors@R: c(
+    person("UMR G-Eau Aqua Department INRAE Montpellier", "Team Optimiste", role = c("aut", "cre"), email = "florian.ricquier@inrae.fr"))
+Description: The purpose of this package is to serve as a basis for reports & documentation production.
+Encoding: UTF-8
+License: GPL (>= 3)
+LazyData: true
+Depends:
+    R (>= 2.10),
+    OptirrigCore (>= 0.4.0)
+Imports:
+    fairify,
+Suggests:
+    knitr,
+    pkgdown,
+    rmarkdown,
+    usethis,
+    testthat (>= 3.0.0)
+remotes: 
+    git::https://package_read:NypwTCoxFT6f6yDQruje@forgemia.inra.fr/optirrigdev/OptirrigCore.git,
+    git::https://forgemia.inra.fr/umr-g-eau/fairify.git
+VignetteBuilder: knitr
+RoxygenNote: 7.3.1
+Config/testthat/edition: 3

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(renderBook)
+import(fairify)

NEWS.md

+# OptirrigManual 0.1.0

OptirrigManual.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

R/renderBook.R

+#' Function to render bookdown
+#'
+#' @param path path to reports dir
+#' @param path_pub path to publish dir
+#'
+#' @import fairify
+#'
+#' @return a html bookdown
+#' @export
+#'
+renderBook <- function(path = file.path("./reports"),
+                       path_pub = file.path("../../public/reports")){
+
+  fairify::render_reports(reports_dir = path,
+                          reports = list.dirs(path,
+                                              full.names = FALSE,
+                                              recursive = FALSE),
+                          publish_dir = path_pub,
+                          clean_cache = TRUE)
+}

README.md

-# OptirrigManual
 
+# <img src="man/figures/logo_OptirrigManual.png" alt="Optirrig" align="right" style="width:200px"/> OptirrigManual: User Manual & Documentation : R Package support
 
+<!-- badges: start -->
 
-## Getting started
+[![CRAN](https://www.r-pkg.org/badges/version-ago/OptirrigManual)](https://forgemia.inra.fr/optirrigdev/OptirrigManual.git)
+[![License:
+GPL-3](https://img.shields.io/badge/license-GPL--3-orange.svg)](https://cran.r-project.org/web/licenses/GPL-3)
+[![Dev check
+status](https://forgemia.inra.fr/optirrigdev/OptirrigManual/badges/main/pipeline.svg)](forgemia.inra.fr/optirrigdev/OptirrigManual/-/pipelines)
+<!-- badges: end -->
 
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+Optirrig is a conceptual 1D model with multiple functionalities. Its
+purpose is to simulate and optimize irrigation scenarios based on the
+type of crop. It incorporates climatic forcings, and accounts for
+biological processes (plant development, leaf surface index, dry matter
+rates, water and nitrogen stress).
 
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
+The purpose of this package is to serve as a basis for developing and
+integrating functionality as required.
 
-## Add your files
+## Installation
 
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
+You can install the development version of OptirrigManual like so:
 
+``` r
+install.packages("remotes")
+remotes::install_git("https://package_read:NypwTCoxFT6f6yDQruje@forgemia.inra.fr/optirrigdev/OptirrigManual.git", build_vignettes = TRUE)
 ```
-cd existing_repo
-git remote add origin https://forgemia.inra.fr/optirrigdev/OptirrigManual.git
-git branch -M main
-git push -uf origin main
-```
-
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://forgemia.inra.fr/optirrigdev/OptirrigManual/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
 
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
+## Launch the library
 
-## Suggestions for a good README
-
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
+``` r
+library(OptirrigCore)
+library(OptirrigManual)
+```
 
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
+## Documentation
 
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
+UMR G-EAU - Gestion de l’Eau, Acteurs, Usages (Montpellier)
 
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
+<https://www.g-eau.fr/index.php/fr/>
 
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
+Equipe OPTIMISTE - Optimisation du Pilotage et des Technologies
+d’Irrigation, Minimisation des IntrantS, Transferts dans l’Environnement
 
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
+<https://www.g-eau.fr/index.php/fr/umr-geau/les-equipes/item/410-optimisation-du-pilotage-et-des-technologies-d-irrigation-minimisation-des-intrants-transferts-environnementaux-optimiste>
 
-## License
-For open source projects, say how it is licensed.
+<div style="display: flex; justify-content: space-between; align-items: center;">
 
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+<img src="man/figures/Logo-INRAE_Transparent.svg.png" alt="G-EAU" width="300"/><img src="man/figures/logo_G-EAU.jpg" alt="G-EAU" width="200"/><img src="man/figures/log_Optirrig.png" alt="G-EAU" width="200"/>

README.rmd

+---
+output: github_document
+---
+
+# <img src="man/figures/logo_OptirrigManual.png" alt="Optirrig" align="right" style="width:200px"/> OptirrigManual: User Manual & Documentation : R Package support
+
+<!-- badges: start -->
+[![CRAN](https://www.r-pkg.org/badges/version-ago/OptirrigManual)]( https://forgemia.inra.fr/optirrigdev/OptirrigManual.git)
+[![License: GPL-3](https://img.shields.io/badge/license-GPL--3-orange.svg)](https://cran.r-project.org/web/licenses/GPL-3)
+[![Dev check status](https://forgemia.inra.fr/optirrigdev/OptirrigManual/badges/main/pipeline.svg)](forgemia.inra.fr/optirrigdev/OptirrigManual/-/pipelines)
+<!-- badges: end -->
+
+```{r opts, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+Optirrig is a conceptual 1D model with multiple functionalities. Its purpose is to simulate and optimize irrigation scenarios based on the type of crop. It incorporates climatic forcings, and accounts for biological processes (plant development, leaf surface index, dry matter rates, water and nitrogen stress).
+
+The purpose of this package is to serve as a basis for developing and integrating functionality as required.
+
+## Installation
+
+You can install the development version of OptirrigManual like so:
+
+``` r
+install.packages("remotes")
+remotes::install_git("https://package_read:NypwTCoxFT6f6yDQruje@forgemia.inra.fr/optirrigdev/OptirrigManual.git", build_vignettes = TRUE)
+```
+
+## Launch the library
+
+``` r
+library(OptirrigCore)
+library(OptirrigManual)
+```
+
+## Documentation
+
+UMR G-EAU - Gestion de l'Eau, Acteurs, Usages (Montpellier)
+
+https://www.g-eau.fr/index.php/fr/
+
+Equipe OPTIMISTE - Optimisation du Pilotage et des Technologies d'Irrigation, Minimisation des IntrantS, Transferts dans l'Environnement
+
+https://www.g-eau.fr/index.php/fr/umr-geau/les-equipes/item/410-optimisation-du-pilotage-et-des-technologies-d-irrigation-minimisation-des-intrants-transferts-environnementaux-optimiste
+
+<div style="display: flex; justify-content: space-between; align-items: center;"><img src="man/figures/Logo-INRAE_Transparent.svg.png" alt="G-EAU" width="300"/><img src="man/figures/logo_G-EAU.jpg" alt="G-EAU" width="200"/><img src="man/figures/log_Optirrig.png" alt="G-EAU" width="200"/>

_pkgdown.yml

+url: https://optirrig.pages.mia.inra.fr/OptirrigManual/
+template:
+  package: pkgdown
+  params:
+    bootswatch: flatly
+    navbar:
+      type: inverse
+      background: '#0053B3'
+      text: '#ffffff'
+      border: '#004494'
+    bslib:
+      bg: '#ffffff'
+      fg: '#0053B3'
+      primary: '#0053B3'
+      success: '#4CAF50'
+      info: '#46B8DA'
+      warning: '#FFC107'
+      danger: '#D9534F'
+development:
+  mode: release
+navbar:
+  structure:
+    left:
+    - intro
+    - reports
+    - articles
+    - news
+    - reference
+    right: gitlab
+  components:
+    gitlab: ~
+    icon: fab fa-gitlab fa-lg
+    href: https://forgemia.inra.fr/optirrigdev/OptirrigManual
+    reports:
+      text: Reports
+      menu:
+      - text: User manual Optirrig method & uses
+        href: reports/User_manual_Optirrig_method_&_uses/index.html
+      - text: Livrable report for WP2 Prima MAGO project
+        href: reports/WP2_Prima_MAGO_livrable/index.html
+repo:
+  url:
+    home: https://forgemia.inra.fr/optirrigdev/OptirrigManual
+    source: https://forgemia.inra.fr/optirrigdev/OptirrigManual/-/tree/main/
+    issue: https://forgemia.inra.fr/optirrigdev/OptirrigManual/-/issues

inst/config.yml

+default:
+  Version: 0.2.0
+  data:
+    path: NULL
+    input: 01_Entrees
+    output: 02_Sorties
+    runType: NULL
+    runName: NULL
+  param: NULL
+  paramN: NULL
+  win:
+    OAD: FALSE
+    UI: FALSE
+

man/figures/Mermaid_Optirrig.txt

+flowchart TD
+    A[OptirrigCore] -->|Ex-Post| B(Usage Analytique)
+    A[OptirrigCore] -->|Ex-Ante| C(Usage Prospectif) 
+    A[OptirrigCore] -->|OAD| D(Usage en temps réel)
+
+    B --> |Reproduction de situation 
+    passées, recherche d'alternative 
+    pour les usages documentés
+    outils de compréhension| F[Calage/Simulation]
+
+    C --> |Identification de bonne 
+    stratégie d'usage future,
+    outils de planification| E[Simulation]
+
+    D --> |Prise de décision par 
+    un uttilisateur a partir des 
+    données d'observation sur la saison,
+    outils d'aide à la décision| F
+
+    G[Integration et calcule des processus bio-physique V1 à V12 :
+    - bilan hydrique 
+    - developement plantes
+    - Rendement]
+
+    I[Type de culture
+    - LSP : Légumes sur pieds; tomate, piment ...
+    - LRA : Légumes-racines; Pomme de terre, Betterave, ...
+    - GRC : Grandes Cultures; Maïs, Orgre, Soja, Blé, ...
+    - PHF : Prairie, herbes, fourrage; Gazon, Foin, Luzerne, ...
+    - CPE : Cultures pérennes; Vigne, Olivier, Fruitiers, ...
+    - VUR : Végétation Urbaines Abélia, ...]
+
+    F --> G --> H[Scenarii d'irigation]
+    E --> G
+
+    I --> G
+
+    style A fill:#669900
+    style B fill:#79A2E0
+    style C fill:#79A2E0
+    style D fill:#79A2E0
+
+    style E fill:#CC3300
+    style F fill:#CC3300
+
+    style G fill:#CC3300
+
+    style I fill:#996600
+    style I text-align:left
\ No newline at end of file

man/figures/Mermaid_Optirrig2.txt

+flowchart TD
+    A[(Données d'entrée)] --> B
+    B([Calibration/Simulation]) --> | calModel/SimModel/piloteR | C(Description processus Bio-physiques)
+    C ==> | calcPlantDev | D([Developpement Plante])
+    C ==> | calcWaterBalance | E([Bilan Hydrique]) ==> T
+    C ==> | calcFinYield | F([Rendement]) ==> T
+    C ==> | calcNitrogenMng | G([Gestion de l'Azote]) ==> T
+    
+    D --> | calcStressFactor | H(Facteur de stress) --> T
+    D --> | calcLaiTdm | I(LAI et TDM) --> T
+    D --> | calcRootGrowth | J(Developpement racinaire) --> T
+    D --> | calcDryMatter | K(Matière sèche) --> T
+
+    T[(Sorties)] ==> | plotOutputModel | U([Affichage des résultats]) ==> V(Sauvegarde Fichiers Simulations)
+
+    style B fill:#666600,stroke:#333,stroke-width:4px
+    style U fill:#666600,stroke:#333,stroke-width:4px
+
+    style D fill:#993300,stroke:#333,stroke-width:4px
+    style E fill:#993300,stroke:#333,stroke-width:4px
+    style F fill:#993300,stroke:#333,stroke-width:4px
+    style G fill:#993300,stroke:#333,stroke-width:4px
+
+    style A fill:#336666,stroke:#333,stroke-width:4px
+    style T fill:#336666,stroke:#333,stroke-width:4px
+
+

man/figures/logo_OptirrigCore.R

+createStickers <- function() {
+  # Liste des packages requis
+  packages <- c("showtext", "sysfonts", "hexSticker")
+
+  # Vérifie et installe les packages manquants
+  for(pkg in packages){
+    if(!require(pkg, character.only = TRUE)){
+      install.packages(pkg)
+      library(pkg, character.only = TRUE)
+    }
+  }
+
+  # Configuration de showtext pour utiliser les polices Google
+  sysfonts::font_add_google("Raleway", "Raleway")
+  showtext::showtext_auto()
+
+  # Création du sticker
+  hexSticker::sticker("man/figures/logo_OptirrigCore.png",
+          s_x = 1, s_y = 1, s_width = 0.85,
+          package = "",
+          p_color = "#003366",
+          h_fill = "white",
+          h_color = "#003366",
+          filename = "man/figures/logo_OptirrigCore_sticker.png")
+}
+
+createStickers()
+