Rename XPalm into XPalmModel

PalmStudio · Feb 6, 2025 · ea404db · ea404db · VEZY · Feb 6, 2025
1 parent b921f97
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -65,6 +65,6 @@ jobs:
         shell: julia --project=docs --color=yes {0}
         run: |
           using Documenter: DocMeta, doctest
-          using XPalm
-          DocMeta.setdocmeta!(XPalm, :DocTestSetup, :(using XPalm); recursive=true)
-          doctest(XPalm)
+          using XPalmModel
+          DocMeta.setdocmeta!(XPalmModel, :DocTestSetup, :(using XPalmModel); recursive=true)
+          doctest(XPalmModel)
diff --git a/CITATION.bib b/CITATION.bib
@@ -1,7 +1,7 @@
-@misc{XPalm.jl,
+@misc{XPalmModel.jl,
 	author  = {Rémi Vezy <VEZY@users.noreply.github.com> and contributors},
-	title   = {XPalm.jl},
-	url     = {https://github.com/PalmStudio/XPalm.jl},
+	title   = {XPalmModel.jl},
+	url     = {https://github.com/PalmStudio/XPalmModel.jl},
 	version = {v0.1.0},
 	year    = {2022},
 	month   = {11}

diff --git a/Project.toml b/Project.toml
@@ -1,4 +1,4 @@
-name = "XPalm"
+name = "XPalmModel"
 uuid = "6b523e1e-d512-416c-8e51-a8fbef0064e7"
 authors = ["Rémi Vezy <[email protected]> and contributors"]
 version = "0.1.0"

diff --git a/README.md b/README.md
@@ -1,9 +1,9 @@
-# XPalm - Growth and yield model for oil palm <img src="https://commons.wikimedia.org/wiki/File:Elaeis_guineensis_-_K%C3%B6hler%E2%80%93s_Medizinal-Pflanzen-056.jpg#/media/Fichier:Elaeis_guineensis_-_K%C3%B6hler%E2%80%93s_Medizinal-Pflanzen-056.jpg" alt="" width="300" align="right" />
+# XPalm - A Growth and Yield Model for Oil Palm <img src="https://commons.wikimedia.org/wiki/File:Elaeis_guineensis_-_K%C3%B6hler%E2%80%93s_Medizinal-Pflanzen-056.jpg#/media/Fichier:Elaeis_guineensis_-_K%C3%B6hler%E2%80%93s_Medizinal-Pflanzen-056.jpg" alt="" width="300" align="right" />
 
-<!-- [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://PalmStudio.github.io/XPalm.jl/stable/) -->
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://PalmStudio.github.io/XPalm.jl/dev/)
-[![Build Status](https://github.com/PalmStudio/XPalm.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/PalmStudio/XPalm.jl/actions/workflows/CI.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/PalmStudio/XPalm.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/PalmStudio/XPalm.jl)
+<!-- [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://PalmStudio.github.io/XPalmModel.jl/stable/) -->
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://PalmStudio.github.io/XPalmModel.jl/dev/)
+[![Build Status](https://github.com/PalmStudio/XPalmModel.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/PalmStudio/XPalmModel.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/PalmStudio/XPalmModel.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/PalmStudio/XPalmModel.jl)
 [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
 
 ## Overview
@@ -60,30 +60,30 @@ Fraction of transpirable soil water (FTSW) over time:
 The package can be installed using the Julia package manager. From the Julia REPL, type `]` to enter the Pkg REPL mode and run:
 
 ```julia
-pkg> add XPalm
+pkg> add XPalmModel
 ```
 
 To use the package, type the following in the Julia REPL:
 
 ```julia
-using XPalm
+using XPalmModel
 ```
 
 ## Quick Start
 
 From the Julia REPL, load the package:
 
 ```julia
-using XPalm
+using XPalmModel
 ```
 
 ### The easiest way of running the model
 
 The easiest way to run the model is to use the template notebook provided by the package. To run the notebook, you need to install the Pluto package first by running `] add Pluto`. Then, you can run the notebook using the following commands in the Julia REPL:
 
 ```julia
-using Pluto, XPalm
-XPalm.notebook("xpalm_notebook.jl")
+using Pluto, XPalmModel
+XPalmModel.notebook("xpalm_notebook.jl")
 ```
 
 This command will create a new Pluto notebook (named "xpalm_notebook.jl") in the current directory, and open it automatically for you.
@@ -97,10 +97,10 @@ Once closed, you can re-open this notebook by running the same command again. If
 Run a simple simulation using default parameters and meteorological data:
 
 ```julia
-using XPalm, CSV, DataFrames
+using XPalmModel, CSV, DataFrames
 
 # Load example meteorological data
-meteo = CSV.read(joinpath(dirname(dirname(pathof(XPalm))), "0-data/meteo.csv"), DataFrame)
+meteo = CSV.read(joinpath(dirname(dirname(pathof(XPalmModel))), "0-data/meteo.csv"), DataFrame)
 
 # Run simulation
 df = xpalm(meteo; 
@@ -119,13 +119,13 @@ Customize palm parameters and request multiple outputs:
 ```julia
 # Read the parameters from a YAML file (provided in the example folder of the package):
 using YAML
-parameters = YAML.load_file(joinpath(dirname(dirname(pathof(XPalm))), "examples/xpalm_parameters.yml"); dicttype=Dict{Symbol,Any})
+parameters = YAML.load_file(joinpath(dirname(dirname(pathof(XPalmModel))), "examples/xpalm_parameters.yml"); dicttype=Dict{Symbol,Any})
 
 # Load example meteorological data
-meteo = CSV.read(joinpath(dirname(dirname(pathof(XPalm))), "0-data/meteo.csv"), DataFrame)
+meteo = CSV.read(joinpath(dirname(dirname(pathof(XPalmModel))), "0-data/meteo.csv"), DataFrame)
 
 # Create palm with custom parameters
-p = XPalm.Palm(parameters=parameters)
+p = XPalmModel.Palm(parameters=parameters)
 
 # Run simulation with multiple outputs
 results = xpalm(
@@ -144,7 +144,7 @@ You can also import the parameters from a JSON file using the `JSON` package:
 
 ```julia
 using JSON # You first need to install the JSON package by running `] add JSON`
-params = open(joinpath(dirname(dirname(pathof(XPalm))), "examples/xpalm_parameters.json"), "r") do io
+params = open(joinpath(dirname(dirname(pathof(XPalmModel))), "examples/xpalm_parameters.json"), "r") do io
     JSON.parse(io; dicttype=Dict{Symbol,Any}, inttype=Int64)
 end
 ```
@@ -157,8 +157,8 @@ end
 The models are available from the `Models` submodule. To import all models, you can use the following command:
 
 ```julia
-using XPalm
-using XPalm.Models
+using XPalmModel
+using XPalmModel.Models
 ```
 
 #### More examples

diff --git a/docs/Manifest.toml b/docs/Manifest.toml
@@ -859,16 +859,16 @@ git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6"
 uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
 version = "2.13.5+0"
 
-[[deps.XPalm]]
+[[deps.XPalmModel]]
 deps = ["Dates", "MultiScaleTreeGraph", "PlantMeteo", "PlantSimEngine", "Random", "Statistics", "Tables"]
 path = ".."
 uuid = "6b523e1e-d512-416c-8e51-a8fbef0064e7"
 version = "0.1.0"
 
-    [deps.XPalm.extensions]
-    XPalmPluto = "Pluto"
+    [deps.XPalmModel.extensions]
+    XPalmModelPluto = "Pluto"
 
-    [deps.XPalm.weakdeps]
+    [deps.XPalmModel.weakdeps]
     Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
 
 [[deps.YAML]]

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,3 +1,3 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-XPalm = "6b523e1e-d512-416c-8e51-a8fbef0064e7"
+XPalmModel = "6b523e1e-d512-416c-8e51-a8fbef0064e7"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,16 +1,16 @@
-using XPalm
+using XPalmModel
 using Documenter
 
-DocMeta.setdocmeta!(XPalm, :DocTestSetup, :(using XPalm); recursive=true)
+DocMeta.setdocmeta!(XPalmModel, :DocTestSetup, :(using XPalmModel); recursive=true)
 
 makedocs(;
-    modules=[XPalm],
+    modules=[XPalmModel],
     authors="Rémi Vezy <[email protected]> and contributors",
-    repo=Documenter.Remotes.GitHub("PalmStudio", "XPalm.jl"),
-    sitename="XPalm.jl",
+    repo=Documenter.Remotes.GitHub("PalmStudio", "XPalmModel.jl"),
+    sitename="XPalmModel.jl",
     format=Documenter.HTML(;
         prettyurls=get(ENV, "CI", "false") == "true",
-        canonical="https://PalmStudio.github.io/XPalm.jl",
+        canonical="https://PalmStudio.github.io/XPalmModel.jl",
         edit_link="main",
         assets=String[]
     ),
@@ -20,6 +20,6 @@ makedocs(;
 )
 
 deploydocs(;
-    repo="github.com/PalmStudio/XPalm.jl",
+    repo="github.com/PalmStudio/XPalmModel.jl",
     devbranch="main"
 )
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,19 +1,19 @@
 ```@meta
-CurrentModule = XPalm
+CurrentModule = XPalmModel
 ```
 
-# XPalm - A growth and yield model for oil palm
+# XPalm - A Growth and Yield Model for Oil Palm
 
 ```@raw html
-<!-- [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://PalmStudio.github.io/XPalm.jl/stable/) -->
+<!-- [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://PalmStudio.github.io/XPalmModel.jl/stable/) -->
 ```
 
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://PalmStudio.github.io/XPalm.jl/dev/)
-[![Build Status](https://github.com/PalmStudio/XPalm.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/PalmStudio/XPalm.jl/actions/workflows/CI.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/PalmStudio/XPalm.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/PalmStudio/XPalm.jl)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://PalmStudio.github.io/XPalmModel.jl/dev/)
+[![Build Status](https://github.com/PalmStudio/XPalmModel.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/PalmStudio/XPalmModel.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/PalmStudio/XPalmModel.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/PalmStudio/XPalmModel.jl)
 [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
 
-[XPalm](https://github.com/PalmStudio/XPalm.jl) is a growth and yield model for oil palm (*Elaeis guineensis*).
+[XPalmModel](https://github.com/PalmStudio/XPalmModel.jl) is a growth and yield model for oil palm (*Elaeis guineensis*).
 
 ```@contents
 Pages = ["index.md"]
@@ -75,24 +75,24 @@ Fraction of transpirable soil water (FTSW) over time:
 Install XPalm using Julia's package manager, typing `]` in the Julia REPL (*i.e.* the console) to enter the Pkg REPL mode and then typing:
 
 ```julia
-add XPalm
+add XPalmModel
 ```
 
 ## Quick Start
 
 From the Julia REPL, load the package:
 
 ```julia
-using XPalm
+using XPalmModel
 ```
 
 ### The easiest way of running the model
 
 The easiest way to run the model is to use the template notebook provided by the package. To run the notebook, you need to install the Pluto package first by running `] add Pluto`. Then, you can run the notebook using the following commands in the Julia REPL:
 
 ```julia
-using Pluto, XPalm
-XPalm.notebook("xpalm_notebook.jl")
+using Pluto, XPalmModel
+XPalmModel.notebook("xpalm_notebook.jl")
 ```
 
 This command will create a new Pluto notebook (named "xpalm_notebook.jl") in the current directory, and open it automatically for you.
@@ -106,10 +106,10 @@ Once closed, you can re-open this notebook by running the same command again. If
 Run a simple simulation using default parameters and meteorological data:
 
 ```julia
-using XPalm, CSV, DataFrames
+using XPalmModel, CSV, DataFrames
 
 # Load example meteorological data
-meteo = CSV.read(joinpath(dirname(dirname(pathof(XPalm))), "0-data/meteo.csv"), DataFrame)
+meteo = CSV.read(joinpath(dirname(dirname(pathof(XPalmModel))), "0-data/meteo.csv"), DataFrame)
 
 # Run simulation
 df = xpalm(meteo, DataFrame;
@@ -127,13 +127,13 @@ Customize palm parameters and request multiple outputs:
 ```julia
 # Read the parameters from a YAML file (provided in the example folder of the package). Note that parameter keys should be imported as `Symbol`s
 using YAML
-parameters = YAML.load_file(joinpath(dirname(dirname(pathof(XPalm))), "examples/xpalm_parameters.yml"); dicttype=Dict{Symbol,Any})
+parameters = YAML.load_file(joinpath(dirname(dirname(pathof(XPalmModel))), "examples/xpalm_parameters.yml"); dicttype=Dict{Symbol,Any})
 
 # Load example meteorological data
-meteo = CSV.read(joinpath(dirname(dirname(pathof(XPalm))), "0-data/meteo.csv"), DataFrame)
+meteo = CSV.read(joinpath(dirname(dirname(pathof(XPalmModel))), "0-data/meteo.csv"), DataFrame)
 
 # Create palm with custom parameters
-p = XPalm.Palm(parameters=parameters)
+p = XPalmModel.Palm(parameters=parameters)
 
 # Run simulation with multiple outputs
 results = xpalm(
@@ -165,8 +165,8 @@ end
 The models are available from the `Models` submodule. To import all models, you can use the following command:
 
 ```julia
-using XPalm
-using XPalm.Models
+using XPalmModel
+using XPalmModel.Models
 ```
 
 #### More examples
@@ -191,13 +191,13 @@ This work is supported by the PalmStudio research project, funded by the [SMART
 Documentation for the main functions of the XPalm package.
 
 ```@autodocs
-Modules = [XPalm]
+Modules = [XPalmModel]
 ```
 
 ### Models
 
 Documentation for the models available in XPalm.
 
 ```@autodocs
-Modules = [XPalm.Models]
+Modules = [XPalmModel.Models]
 ```
diff --git a/examples/Manifest.toml b/examples/Manifest.toml
@@ -1863,16 +1863,16 @@ git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6"
 uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
 version = "2.13.5+0"
 
-[[deps.XPalm]]
+[[deps.XPalmModel]]
 deps = ["Dates", "MultiScaleTreeGraph", "PlantMeteo", "PlantSimEngine", "Random", "Statistics", "Tables"]
 path = ".."
 uuid = "6b523e1e-d512-416c-8e51-a8fbef0064e7"
 version = "0.1.0"
 
-    [deps.XPalm.extensions]
+    [deps.XPalmModel.extensions]
     XPalmPluto = "Pluto"
 
-    [deps.XPalm.weakdeps]
+    [deps.XPalmModel.weakdeps]
     Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
 
 [[deps.XSLT_jll]]

diff --git a/examples/Project.toml b/examples/Project.toml
@@ -11,5 +11,5 @@ PlantMeteo = "4630fe09-e0fb-4da5-a846-781cb73437b6"
 PlantSimEngine = "9a576370-710b-4269-adf9-4f603a9c6423"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-XPalm = "6b523e1e-d512-416c-8e51-a8fbef0064e7"
+XPalmModel = "6b523e1e-d512-416c-8e51-a8fbef0064e7"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
diff --git a/examples/run_XPalm.jl b/examples/run_XPalm.jl
@@ -6,7 +6,7 @@ using PlantMeteo, PlantSimEngine, MultiScaleTreeGraph
 using CairoMakie, AlgebraOfGraphics
 using DataFrames, CSV, Statistics
 using Dates
-using XPalm
+using XPalmModel
 
 meteo = CSV.read("0-data/meteo", DataFrame)
 meteo.duration = [Dates.Day(i[1:1]) for i in meteo.duration]
@@ -27,9 +27,9 @@ df = xpalm(m, DataFrame; vars=out_vars)
 
 # Example 2.1: Run the model with custom parameter values from a YAML file:
 using YAML, OrderedCollections
-params = YAML.load_file(joinpath(dirname(dirname(pathof(XPalm))), "examples/xpalm_parameters.yml"), dicttype=OrderedDict{Symbol,Any})
+params = YAML.load_file(joinpath(dirname(dirname(pathof(XPalmModel))), "examples/xpalm_parameters.yml"), dicttype=OrderedDict{Symbol,Any})
 params[:k] = 0.6
-p = XPalm.Palm(parameters=params)
+p = XPalmModel.Palm(parameters=params)
 df = xpalm(m, DataFrame; palm=p, vars=out_vars)
 
 # Example 2.2: Run the model with custom parameter values from a JSON file:
@@ -38,7 +38,7 @@ params = open("examples/xpalm_parameters.json", "r") do io
     JSON.parse(io; dicttype=OrderedDict{Symbol,Any}, inttype=Int64)
 end
 params[:k] = 0.6
-p = XPalm.Palm(parameters=params)
+p = XPalmModel.Palm(parameters=params)
 df = xpalm(m, DataFrame; palm=p, vars=out_vars)
 
 # Making some plots with the results:

diff --git a/ext/XPalmPluto.jl b/ext/XPalmPluto.jl
@@ -1,6 +1,6 @@
 module XPalmPluto
 
-import XPalm: notebook
+import XPalmModel: notebook
 import Pluto
 
 
@@ -10,7 +10,7 @@ function template_pluto_notebook(copyto; force=false)
     else
         cp(joinpath(@__DIR__, "template_notebook.jl"), copyto; force=force)
         chmod(copyto, 0o777)
-        @info "New XPalm notebook created at $copyto"
+        @info "New XPalmModel notebook created at $copyto"
     end
 
     Pluto.run(notebook=copyto)