1st version

.github/workflows/ant.yml

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+name: Java CI
+
+on:
+  push:
+    branches: [ master ]
+    tags: [ 'v*.*' ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+        java: [ 8 ]
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-java@v1
+      with:
+        java-version: ${{ matrix.java }}
+        java-package: jdk
+    - run: |
+        WD=$PWD
+        cd ..
+        git clone https://github.com/Funz/funz-profile
+        cd $WD
+      shell: bash
+    - run: ant -noinput -buildfile build.xml test
+
+  release:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-java@v1
+      with:
+        java-version: 1.8
+        java-package: jdk
+    - run: |
+        WD=$PWD
+        cd ..
+        git clone https://github.com/Funz/funz-profile
+        cd $WD
+    - run: |
+        ant clean dist
+        cd dist; zip -r ../plugin-Rmd.zip *; cd ..
+        ant install
+        zip -r Funz-Rmd.zip Funz-Rmd
+    - uses: actions/upload-artifact@v2
+      with:
+        path: dist
+    - uses: softprops/action-gh-release@v1
+      if: startsWith(github.ref, 'refs/tags/')
+      with:
+        files: ./*-Rmd.zip
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+
+

.gitignore

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+/**/*-private
+/**/log.txt
+/**/*history
+
+/build/
+/tmp/
+/nbproject/
+/dist/
+/test/
+
+/*.png
+/*.html
+/*.log
+/*.zip
+/*.out
+/*.csv
+/*.txt
+/*.Rout
+/*.Rdata
+/*.Rmd
+/*.exec

README.md

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+[![.github/workflows/ant.yml](https://github.com/Funz/plugin-Rmd/actions/workflows/ant.yml/badge.svg)](https://github.com/Funz/plugin-Rmd/actions/workflows/ant.yml)
+
+# Funz plugin: Rmd
+
+This plugin is dedicated to launch RMarkDown rendering from Funz.
+It supports the following syntax and features:
+
+  * Input
+    * file type supported: *.Rmd, any other format for resources
+    * parameter syntax: 
+      * variable syntax: `?[...]`
+      * formula syntax: `!{...}`
+      * comment char: `/`
+    * example input file:
+        ```
+        ---
+        title: "Untitled"
+        ---
+        we set x1 to ?[x1~[1,2]]
+        we set x2 to ?x2
+        mean_speed=`r mean(cars$speed) + !{?x2 + 1.23 | #.###}`
+        ```
+      * will identify input:
+        * x1, expected to vary inside [1,2]
+        * x2, expected to vary inside [0,1] (by default)
+      * replace `!{?x2 + 1.23 | #.###}` expression by its evaluation
+
+  * Output
+    * file type supported: *.html
+    * read any named value printed with '=`r ...', like 
+    * example output file:
+        ```
+        ...
+        <p>mean_speed=15.4</p>
+        ...
+        ```
+        * will return output:
+          * mean_speed=15.4
+
+
+
+![Analytics](https://ga-beacon.appspot.com/UA-109580-20/plugin-Rmd)

build.xml

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+<project name="plugin-Rmd" default="test" basedir=".">
+
+    <property name="code.name" value="Rmd" />
+    <property name="install.dir" value="${basedir}/Funz-${code.name}" />
+
+    <property name="build_plugin.xml" location="../funz-profile/build_plugin.xml" />
+    <import file="${build_plugin.xml}"/>
+
+    <target name="dist" depends="dist-ioplugin"/> <!-- dist-ioplugin: copy just the plugin ascii files -->
+
+    <target name="test" depends="test-ioplugin"/> <!-- test-ioplugin: test the plugin ascii files -->
+
+    <target name="install" depends="install-plugin"/> <!-- test-ioplugin: test the plugin ascii files -->
+
+    <target name="super.clean" depends="clean"/>
+    <target name="super.run-reference-cases" depends="run-reference-cases"/>
+
+</project>

src/main/io/Rmd.ioplugin

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+variableStartSymbol=?
+variableLimit=[...]
+formulaStartSymbol=!
+formulaLimit={...}
+commentLineChar=#
+
+datasetFilter=contains("(.*)","cat\\(") & contains("(.*)","---")
+
+outputlist=`grep("(.*)Rmd","^(.*)=.r\\s")>>before("=")`
+
+output.???.get=lines("(.*)html") >> filter("^<p>???=(.*)</p>$") >> after("=") >> before("<")

src/main/samples/Untitled.Rmd

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+---
+title: "Untitled"
+author: "IRSN / Y. Richet"
+date: '2022-04-28'
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## R Markdown
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+```{r cars}
+summary(cars)
+```
+
+## Including Plots
+
+You can also embed plots, for example:
+
+```{r pressure, echo=FALSE}
+plot(pressure)
+```
+
+Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
+
+## Results
+
+Funz parse Rmd numerical output using the syntax of inline Rmd on a new line: 
+
+mean_speed=`r mean(cars$speed)`

src/main/scripts/Rmd.bat

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+@echo off
+
+set PATH=%PATH%;C:\Program Files\R\R-4.1.0\bin
+
+set id=%RANDOM%
+start "Rmd_%id%" cmd /c "Rscript.exe -e ""rmarkdown::render('%1', output_format = 'html_document',output_file = '%1.html', encoding='UTF-8')"" > Rmd.Rout"
+set PID_R="none"
+for /F "TOKENS=1,2,*" %%a in ('tasklist /FI "WINDOWTITLE eq Rmd_%id%"') do set PID_R=%%b
+echo %PID_R% > PID
+
+if "%PID_R%" neq "none" (
+:loop
+tasklist | findstr " %PID_R% " >nul
+if not errorlevel 1 (
+    timeout /t 1 >nul
+    goto :loop
+)
+)
+
+del /f PID
+
+if not exist "*.Rout" (
+    exit 2
+)
+findstr "Err" *.Rout
+if not errorlevel 1 (
+    exit 1
+)

src/main/scripts/Rmd.sh

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+#!/bin/bash
+
+Rscript -e "rmarkdown::render('$1', output_format = 'html_document',output_file = '$1.html', encoding='UTF-8')" > Rmd.Rout &
+PID_R=$!
+echo $PID_R >> PID #this will allow Funz to kill process if needed
+
+wait $PID_R
+
+rm -f PID
+
+ERROR=`tail -2 *.Rout | grep "Err"`
+if [ ! "$ERROR" == "" ]; then
+    echo $ERROR >&2
+    exit 1
+fi

src/test/cases/Untitled.Rmd/info.txt

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+#Thu Apr 28 18:43:15 CEST 2022
+duration=0
+output={mean_speed\=15.4}
+output.mean_speed=15.4
+code=Rmd
+input.No\ name=No value
+start=18\:43\:14
+end=
+state=running
+calc=localhost\:41909
+info=Results parsed\: {1\=1.0, mean_speed\=15.4}

src/test/cases/Untitled.Rmd/input/Untitled.Rmd

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+---
+title: "Untitled"
+author: "IRSN / Y. Richet"
+date: '2022-04-28'
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## R Markdown
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+```{r cars}
+summary(cars)
+```
+
+## Including Plots
+
+You can also embed plots, for example:
+
+```{r pressure, echo=FALSE}
+plot(pressure)
+```
+
+Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
+
+## Results
+
+Funz parse Rmd numerical output using the syntax of inline Rmd on a new line: 
+
+mean_speed=`r mean(cars$speed)`

src/test/cases/Untitled.Rmd/output/Rmd.Rout

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+  |                                                                              |                                                                      |   0%  |                                                                              |..........                                                            |  14%
+  ordinary text without R code
+
+  |                                                                              |....................                                                  |  29%
+label: setup (with options) 
+List of 1
+ $ include: logi FALSE
+
+  |                                                                              |..............................                                        |  43%
+  ordinary text without R code
+
+  |                                                                              |........................................                              |  57%
+label: cars
+  |                                                                              |..................................................                    |  71%
+  ordinary text without R code
+
+  |                                                                              |............................................................          |  86%
+label: pressure (with options) 
+List of 1
+ $ echo: logi FALSE
+
+  |                                                                              |......................................................................| 100%
+   inline R code fragments
+
+
+/usr/bin/pandoc +RTS -K512m -RTS Untitled.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output Untitled.Rmd.html --lua-filter /home/richet/R/x86_64-pc-linux-gnu-library/4.1/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/richet/R/x86_64-pc-linux-gnu-library/4.1/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --template /home/richet/R/x86_64-pc-linux-gnu-library/4.1/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --include-in-header /tmp/Rtmp8CSktq/rmarkdown-str23b5e49732e42.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' 

src/test/cases/Untitled.Rmd/output/Untitled.Rmd

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+---
+title: "Untitled"
+author: "IRSN / Y. Richet"
+date: '2022-04-28'
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## R Markdown
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+```{r cars}
+summary(cars)
+```
+
+## Including Plots
+
+You can also embed plots, for example:
+
+```{r pressure, echo=FALSE}
+plot(pressure)
+```
+
+Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
+
+## Results
+
+Funz parse Rmd numerical output using the syntax of inline Rmd on a new line: 
+
+mean_speed=`r mean(cars$speed)`

src/test/cases/Untitled.Rmd/output/err.txt

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+
+
+processing file: Untitled.Rmd
+output file: Untitled.knit.md
+
+
+Output created: Untitled.Rmd.html