HERON plugin (#1271)

* extraneous tracked file?

* heron as a submodule

* undoing file removal

* update with class docs

* matching remote devel

* updated to latest heron

* fixed submodule

* TESTING build

* did not work, trying again

* wip

* moved to XML library dependency lists, see raven example for instructions

* attempting to find problem with printing on testing machines

* and again, looks like we have some old pythons on the test machines

* corrected lib version, also checked others carefully

* new heron update using xml

* changed makefile ref from ini to xml

* conversion script

* removed old file

dependencies.xml

@@ -0,0 +1,67 @@
+<!--
+Structure:
+<root>
+  <install-method>
+    ...
+  </install method>
+  <next-install-method> etc
+</root>
+Note all install methods after "main" take
+  Instructions:
+
+ add library:                <library>pinned.version.number</library>
+ add with no pinned version: <library/>
+ remove a library:           <library>remove</library>
+ action for limited OS:      <library os='windows'>...
+ add library from forge:     <library source='forge'>...
+ optional:                   <library optional='True'>...
+ skip run/install check:     <library skip_check='True'>...
+
+ default OS is "all"
+ default source is "conda" meaning main conda repo
+ default optional is "false"
+
+ For more information about the command line arguments to library_handler.sh, see that module.
+ Also try
+       `python library_handler.sh -h` and
+       `python library_handler.sh conda -h`
+
+ end reading flow
+-->
+<dependencies>
+  <main>
+    <h5py>2.9.0</h5py>
+    <numpy>1.18.1</numpy>
+    <scipy>1.2.1</scipy>
+    <scikit-learn>0.21.2</scikit-learn>
+    <pandas>0.24.2</pandas>
+    <xarray>0.12.1</xarray>
+    <netcdf4>1.4.2</netcdf4>
+    <matplotlib>3.1.1</matplotlib>
+    <statsmodels>0.9.0</statsmodels>
+    <cloudpickle>1.1.1</cloudpickle>
+    <tensorflow>1.13.1</tensorflow>
+    <python skip_check='True'>3</python>
+    <hdf5 skip_check='True'/>
+    <swig skip_check='True'/>
+    <pylint/>
+    <coverage/>
+    <lxml/>
+    <psutil/>
+    <pip/>
+    <importlib_metadata/>
+    <pyside2 source='forge'/>
+    <pillow optional='True'>6.0.0</pillow>
+    <nomkl os='linux' skip_check='True'/>
+    <numexpr os='linux'/>
+    <ray os="mac,linux" source="pip"/>
+  </main>
+  <alternate name="pip">
+    <hdf5>remove</hdf5>
+    <swig>remove</swig>
+    <pip>remove</pip>
+    <python>remove</python>
+    <nomkl>remove</nomkl>
+    <numexpr>remove</numexpr>
+  </alternate>
+</dependencies>

doc/user_manual/Makefile

@@ -6,7 +6,7 @@ introduction.tex raven_user_manual.tex model.tex runInfo.tex libraries.tex DataM
 Installation/clone.tex Installation/conda.tex Installation/linux.tex Installation/macosx.tex Installation/main.tex \
 Installation/overview.tex Installation/windows.tex advanced_users_templates.tex
 LATEX_FLAGS=-interaction=nonstopmode
-LIB_FILES = ../../scripts/library_handler.py ../../dependencies.ini
+LIB_FILES = ../../scripts/library_handler.py ../../dependencies.xml
 
 all: raven_user_manual.pdf
 
@@ -43,4 +43,4 @@ conda_command.txt : $(LIB_FILES)
 	./create_command.sh
 
 pip_commands.txt : $(LIB_FILES)
-	./create_pip_commands.sh
+	./create_pip_commands.sh