Merge pull request #7 from dklein-pik/master

Hopefully final fixes (paths)

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "goxygen: In-Code documentation for GAMS",
-  "version": "0.39.4",
+  "version": "0.39.5",
   "description": "<p>A collection of tools which extract a model documentation from GAMS code and comments. In order to use the package you need to install pandoc and pandoc-citeproc first (https://pandoc.org/).<\/p>",
   "creators": [
     {

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: goxygen
 Type: Package
 Title: In-Code documentation for GAMS
-Version: 0.39.4
+Version: 0.39.5
 Date: 2020-06-25
 Authors@R: c(person("Jan Philipp", "Dietrich", email = "[email protected]", role = c("aut","cre")),
              person("Kristine", "Karstens", email = "[email protected]", role = "aut"))
@@ -17,4 +17,4 @@ Suggests: testthat,
     knitr,
     rmarkdown
 VignetteBuilder: knitr
-ValidationKey: 7264572
+ValidationKey: 7283010

README.md

@@ -1,6 +1,6 @@
 # In-Code documentation for GAMS
 
-R package **goxygen**, version **0.39.4**
+R package **goxygen**, version **0.39.5**
 
 [![Travis build status](https://travis-ci.com/pik-piam/goxygen.svg?branch=master)](https://travis-ci.com/pik-piam/goxygen) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1411404.svg)](https://doi.org/10.5281/zenodo.1411404) [![codecov](https://codecov.io/gh/pik-piam/goxygen/branch/master/graph/badge.svg)](https://codecov.io/gh/pik-piam/goxygen)
 
@@ -46,8 +46,8 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **goxygen** in publications use:
 
-Dietrich J, Karstens K (2020). _goxygen: In-Code documentation for GAMS_. doi: 10.5281/zenodo.1411404 (URL:
-https://doi.org/10.5281/zenodo.1411404), R package version 0.39.4, <URL: https://github.com/pik-piam/goxygen>.
+Dietrich J, Karstens K (2020). _goxygen: In-Code documentation for GAMS_. doi: 10.5281/zenodo.1411404 (URL: https://doi.org/10.5281/zenodo.1411404), R
+package version 0.39.5, <URL: https://github.com/pik-piam/goxygen>.
 
 A BibTeX entry for LaTeX users is
 
@@ -56,7 +56,7 @@ A BibTeX entry for LaTeX users is
   title = {goxygen: In-Code documentation for GAMS},
   author = {Jan Philipp Dietrich and Kristine Karstens},
   year = {2020},
-  note = {R package version 0.39.4},
+  note = {R package version 0.39.5},
   doi = {10.5281/zenodo.1411404},
   url = {https://github.com/pik-piam/goxygen},
 }

vignettes/goxygen.Rmd

@@ -27,23 +27,21 @@ Goxygen can extract the documentation from plain GAMS code (see next section) or
 
 ## Running goxygen on plain GAMS code
 
-We take the GAMS code example from this package and save it to `tmp-plain.gms`:
+We take the GAMS code example from this package and save it to `dummymodel-plain`:
 
 ```{r eval=FALSE}
-# create temporary folder for the plain GAMS model
-dir.create("tmp-plain")
 # copy the folder containing a simple dummy model with goxygen comments 
-file.copy(from = system.file("dummymodel-plain",package="goxygen"), to = "tmp-plain", recursive = TRUE)
+file.copy(from = system.file("dummymodel-plain",package="goxygen"), to = ".", recursive = TRUE)
 ```
 
 and execute `goxygen` on this GAMS file to produce the documentation in html format. If you want the documentation in pdf format simply set `output = "pdf"`.
 
 ```{r eval=FALSE}
 library(goxygen)
-goxygen(path = "tmp-plain", mainfile = "0_main.gms", output = "html", cff = "HOWTOCITE.cff")
+goxygen(path = "dummymodel-plain/", mainfile = "0_main.gms", output = "html", cff = "HOWTOCITE.cff")
 ```
 
-Goxygen now searches the code for all lines starting with the goxygen tag "*'", interpretes the goxygen identifiers, and compiles the documentation into the format specified (html, tex, pdf). Please find the goxygen output in the folder `tmp-plain/doc`.
+Goxygen now searches the code for all lines starting with the goxygen tag "*'", interpretes the goxygen identifiers, and compiles the documentation into the format specified (html, tex, pdf). Please find the goxygen output in the folder `dummymodel-plain/doc`.
 
 ## Goxygen syntax
 
@@ -91,18 +89,16 @@ This was a simple example of a GAMS model in a single file with a plain structur
 Goxygen is tailored to extract the documentation from this modular structure and to compile it to a clearly arranged documentation. Goxygen identifies modules and their interfaces, generates a interface plots that depict the interactions between modules, and lists the inputs and outputs of modules. For each module goxygen creates a new chapter in the documentation. We will demonstrate this using the simple example model from the `gms` package:
 
 ```{r eval=FALSE}
-# create a temporary folder for the modularized GAMS model
-dir.create("tmp-modular")
 # copy all files and folders containing the modular dummy model
-file.copy(from = system.file("dummymodel",package="gms"), to = "tmp-modular", recursive = TRUE)
+file.copy(from = system.file("dummymodel",package="gms"), to = ".", recursive = TRUE)
 ```
 
 Now execute `goxygen` on the modular GAMS model:
 
 ```{r eval=FALSE}
-goxygen(path = "tmp-modular/dummymodel", output = "html", cff = "HOWTOCITE.cff")
+goxygen(path = "dummymodel/", output = "html", cff = "HOWTOCITE.cff")
 ```
 
-Please find the goxygen output in the folder `tmp-modular/dummymodel/doc`.
- 
+Please find the goxygen output in the folder `dummymodel/doc`.
+
 ## References