r.maxent.setup: new addon and refactoring r.maxent.predict and r.maxe…

…nt.train (#1243)

- Moved the option to copy the Maxent.jar file to the addon directory from r.maxent.train and r.maxent.predict to this new addon. When running this with the maxent parameter option, the user does not need to set the path to the file anymore when running r.maxent.train and r.maxent.predict.
- Option to create a text with the path to the java executable in the addon directory. It thus provides an alternative to setting the path to the java executable folder to the PATH. This is most useful on Windows, where the path to Java is not set in the OSGeo4W environment.
- Changes in r.maxent.train and r.maxent.predict; both functions will look for the above-mentioned text file in the grass addon directory. If it exists, it will use the path to the java executable.

src/raster/r.maxent.predict/r.maxent.predict.html

@@ -1,19 +1,39 @@
 <h2>DESCRIPTION</h2>
 
-The <em>r.maxent.predict</em> addon can be used to apply a previously
-calculated Maxent model to a new set of environmental raster data. It
-requires a <i>.lambdas</i> file describing a Maxent model, and the
-name of raster layers for all predictor variables described in the
-lambdas file. The <i>.lambdas file</i> can be created by the
-<em>r.maxent.train</em> addon, or by the Maxent software directly.
+
+The <em>r.maxent.predict</em> module is a front-end to the Maxent 
+software, providing a convenient way to run the Maxent software, and 
+create output layers in GRASS GIS. 
+
+<p>
+<div align="left" style="margin: 10px"> <a 
+href="r_maxent_predict_workflow.png"> <img 
+src="r_maxent_predict_workflow.png" alt="workflow, from data 
+preparation, training a model to model prediction" border="0"> 
+</a><br><i>A workflow, from data preparation, training a model to model 
+prediction using three GRASS GIS addons.</i> </div>
+
+<p>
+It is part of a set of three addons that can be used to prepare the 
+input data for the Maxent model (<em>v.maxent.sdm</em>), to train a 
+maxent presence only model (<em>r.maxent.train</em>), and to use the model to 
+create prediction layers (this module). 
+
+The <em>r.maxent.predict</em> modules uses the model  (the 
+<i>.lambdas</i> file) created with <em>r.maxent.train</em> (or the 
+Maxent software directly) and applies this to a set of environmental 
+raster layers. These should represent the same variables as used to 
+create the model, but can represent a different area, of future 
+conditions.
+
 
 <p>
-For convenience, <em>r.maxent.train</em> creates a file
-<i>maxent_explanatory_variable_names.csv</i>, which you can check for
-the names of the predictor variables. If these are different from the
-input raster layers, you can provide the variable names using the
-<em>variables</em> parameter. Alternatively, you can provide a CSV file
-with the names of the explanatory variables (first column) and the
+The <em>r.maxent.train</em> creates a file 
+<i>maxent_explanatory_variable_names.csv</i>, which you can check for 
+the names of the predictor variables. If these are different from the 
+input raster layers, you can provide the variable names using the 
+<em>variables</em> parameter. Alternatively, you can provide a CSV file 
+with the names of the explanatory variables (first column) and the 
 names of the corresponding raster layers (second column).
 
 <p>
@@ -28,26 +48,14 @@ <h2>DESCRIPTION</h2>
 
 <h2>NOTES</h2>
 
-This addon requires the Maxent software. You can download the software
-from the <a
-href="https://biodiversityinformatics.amnh.org/open_source/maxent">Maxent
-website</a>. The software includes a <em>Maxent.jar</em> file. The
-addon expects a copy of the executable in the GRASS GIS addon
-directory. If it is not there, you need to provide the path to the
-<i>maxent.jar</i> file using the <b>maxent</b> parameter. To avoid
-having to provide this each time again, you can use the <b>-i</b> flag.
-If set, the <i>maxent.jar</i> file will be copied to the addon/script
-directory. Note that if you already did this when running
-<em>r.maxent.train</em>, there is no need to repeat it here.
+This addon requires the Maxent software (version &ge; 3.4). You can download the software 
+from the <a 
+href="https://biodiversityinformatics.amnh.org/open_source/maxent">Maxent 
+website</a>. The <em>r.maxent.setup</em> module provides an helper 
+function to enable GRASS GIS to use the Maxent software.
 
-<p>
-If you want to update the Maxent.jar file, use the <b>-u</b> flag.
-Removing the Maxent.jar file needs to be done manually. Go to the GRASS
-GIS addon directory, and delete the Maxent.jar file. To find the addon
-directory, open GRASS GIS, and type `echo $GRASS_ADDON_BASE` on the
-command line.
 
-<h2>Examples</h2>
+<h2>EXAMPLE</h2>
 
 <p>
 The examples below use a dataset that you can download <a
@@ -82,26 +90,6 @@ <h2>Examples</h2>
 <i>sampledata</i> and open the mapset <i>model01</i>. This mapset
 should have access to the other mapsets.
 
-This addon is part of a series of three addons that can be used to
-prepare the data, train a maxent presence only model, and to use the
-model to create prediction layers.
-
-<p>
-<div align="left" style="margin: 10px"> <a
-href="r_maxent_predict_01.png"> <img src="r_maxent_predict_01.png"
-alt="workflow, from data preparation, training a model to model
-prediction" border="0"> </a><br><i>A workflow, from data preparation,
-training a model to model prediction using three GRASS GIS addons.</i>
-</div>
-
-<p>
-The examples below show how to use the three addons in sequence. Only
-the basic options are shown. For a detailed account of all options,
-check out the Maxent tutorial on the <a
-href="https://biodiversityinformatics.amnh.org/open_source/maxent">Maxent
-website</a>.
-
-
 <h3>1: Data preparation</h3>
 
 You can use the <em>v.maxent.swd</em> to create the required input
@@ -180,8 +168,8 @@ <h3>2: Train the model</h3>
 the sample and background point layers with the predicted values.
 
 <p>
-<div align="left" style="margin: 10px"> <a href="r_maxent_train.png">
-<img src="r_maxent_train.png" alt="Output layers in GRASS GIS"
+<div align="left" style="margin: 10px"> <a href="r_maxent_predict_01.png">
+<img src="r_maxent_predict_01.png" alt="Output layers in GRASS GIS"
 border="0"> </a><br><i>The example creates the prediction raster layer
 'model_1_suitability_current',  the sample point layer
 'model_1_samplepred' and the background point layer 'model_bgrdpred'
@@ -242,18 +230,17 @@ <h2>REFERENCES</h2>
 
 <h2>SEE ALSO</h2>
 
-<ul>
-<li><a href="v.maxent.swd.html">v.maxent.swd</a>, creating species and
-background swd files and prediction rasters that can be used directly
-by the <em>r.maxent.train</em> addon (or the Maxent software itself) to
-create species distribution models.</li>
-<li><a href="r.out.maxent_swd.html">r.out.maxent_swd</a>, creating
-species and background swd files based on species distribution data in
-raster format.</li>
-<li><a href="r.maxent.train.html">r.maxent.train</a>, creates a maxent
-model based on presence point data a set of environmental predictor
-layers.</li>
-</ul>
+<ul> <li><a href="v.maxent.swd.html">v.maxent.swd</a>, creating species 
+and background swd files and prediction rasters that can be used 
+directly by the <em>r.maxent.train</em> addon (or the Maxent software 
+itself) to create species distribution models.</li> <li><a 
+href="r.out.maxent_swd.html">r.out.maxent_swd</a>, creating species and 
+background swd files based on species distribution data in raster 
+format.</li> <li><a href="r.maxent.train.html">r.maxent.train</a>, 
+creates a maxent model based on presence point data a set of 
+environmental predictor layers.</li> <li><a 
+href="r.maxent.setup.html">r.maxent.setup</a>, helper function to 
+allow GRASS to use Maxent.</li> </ul>
 
 <h2>AUTHOR</h2>