Updated ISIS3 references to ISIS

.github/ISSUE_TEMPLATE/3_Support_question.md

@@ -1,13 +1,13 @@
 ---
 name: ⛔ Support Question
-about: See https://astrodiscuss.usgs.gov for questions about using ISIS3 and other Astrogeology Science Center software.
+about: See https://astrodiscuss.usgs.gov for questions about using ISIS and other Astrogeology Science Center software.
 
 ---
 
-We use Github issues solely for discussing bugs, documentation issues, and new features. 
+We use Github issues solely for discussing bugs, documentation issues, and new features.
 
 For
-questions about using ISIS3 or other ASC software, please use
+questions about using ISIS or other ASC software, please use
 any of the support alternatives: https://astrodiscuss.usgs.gov or https://gitter.im/USGS-Astrogeology/IAA
 
 A great resource about asking high quality questions that generate high quality answers is available from the StackOverflow community: [How do I ask a good question?](https://stackoverflow.com/help/how-to-ask)

README.md

@@ -91,7 +91,7 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+
 
     To use the default values for: `$ISISROOT, $ISISDATA, $ISISTESTDATA`, run the ISIS variable initialization script with default arguments.
 
-    To do this, for versions of ISIS 4.2.0 and earlier, use: 
+    To do this, for versions of ISIS 4.2.0 and earlier, use:
 
         python $CONDA_PREFIX/scripts/isis3VarInit.py
 
@@ -101,11 +101,11 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+
 
     Executing this script with no arguments will result in $ISISDATA=$CONDA\_PREFIX/data, and $ISISTESTDATA=$CONDA\_PREFIX/testdata. The user can specify different directories for both of these optional values:
 
-    For ISIS 4.2.0 and earlier, use: 
+    For ISIS 4.2.0 and earlier, use:
 
         python $CONDA_PREFIX/scripts/isis3VarInit.py --data-dir=[path to data directory]  --test-dir=[path to test data directory]
 
-    For versions of ISIS after 4.2.0, use: 
+    For versions of ISIS after 4.2.0, use:
 
         python $CONDA_PREFIX/scripts/isisVarInit.py --data-dir=[path to data directory]  --test-dir=[path to test data directory]
 
@@ -285,12 +285,12 @@ Here are the minimum hardware requirements
 To build and compile ISIS requires following the instructions listed below, which are given on the GitHub wiki page for the ISIS project:
 
 -   [Getting Started With GitHub](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#getting-started-with-github)
--   [Building ISIS3 With cmake](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#building-isis3)
--   [New ISIS3 environmental variables and their meanings](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#new-environmental-variable-meanings)
+-   [Building ISIS With cmake](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#building-isis3)
+-   [New ISIS environmental variables and their meanings](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#new-environmental-variable-meanings)
 -   [Custom data and test directories](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#custom-data-and-test-data-directories)
 -   [Cleaning builds](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#cleaning-builds)
 -   [Building individual applications/objects](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#building-individual-isis3-applicationsobjects)
--   [Building ISIS3 documentation](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#building-isis3-documentation)
+-   [Building ISIS documentation](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#building-isis3-documentation)
 -   [What to do if you encounter any problems](https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#problems)
 
 ## Citing ISIS
@@ -308,7 +308,7 @@ Under the root directory of the ISIS Data Area pointed to by the ISISDATA/ISIS3D
 
 ### Versions of the ISIS Data Area
 
-In ISIS version 4.1.0, several files previously stored in the data area closely associated with ISIS applications were moved into version control with the ISIS source code. Additionally, the environment variables used for the ISIS Data Area and the rsync location for the ISIS Data Area were also updated. 
+In ISIS version 4.1.0, several files previously stored in the data area closely associated with ISIS applications were moved into version control with the ISIS source code. Additionally, the environment variables used for the ISIS Data Area and the rsync location for the ISIS Data Area were also updated.
 
 The correct environment variable names and rsync modules to use for the ISIS Data Area for each version of ISIS are summarized in the table below:
 
@@ -326,7 +326,7 @@ The ISIS Data rsync module specifies where to rsync the data from and is the nam
 
 If you plan to work with data from all missions, then the download will require about 520 GB for all the ancillary data. However, most of this volume is taken up by SPICE files. We have a [Web service](#isis-spice-web-service) that can be used in lieu of downloading all of the SPICE files. This reduces the total download size to about 10 GB.
 
-### Full ISIS3 Data Download
+### Full ISIS Data Download
 
 The ISIS Data Area is hosted on rsync servers and not through conda channels like the ISIS binaries. This requires using the rsync command from within a terminal window within your Unix distribution, or from within WSL if running Windows 10.  Downloading all mission data requires over 520 GB of disk space. If you want to acquire only certain mission data [click here](#Mission-Specific-Data-Downloads). To download all ISIS data files, continue reading.
 
@@ -335,7 +335,7 @@ To download all ISIS data, enter the following commands in the location where yo
     cd $ISISDATA
     rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/ .
 
-For earlier versions, use: 
+For earlier versions, use:
 
     cd $ISIS3DATA
     rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/ .

isis/IsisPreferences

@@ -1,6 +1,6 @@
 #######################################################
 # This file allows the user to customize their Isis
-# configuration.  See the Isis Preference Dictionary
+# configuration.  See the ISIS Preference Dictionary
 # on our website isis.astrogeology.usgs.gov for a
 # full description of each group.
 ########################################################
@@ -10,7 +10,7 @@
 #
 # ProgressBarPercent = 1 | 2 | 5 | 10
 # ProgressBar = On | Off
-# GuiStyle = windows | motif | cde | motifplus | 
+# GuiStyle = windows | motif | cde | motifplus |
 #            platinum | sgi | kde | aqua
 # GuiHelpBrowser = { your preferred browser, may need path }
 # GuiFontName = helvetica | times | charter | any legal font
@@ -52,16 +52,16 @@ EndGroup
 ########################################################
 # Specify which ray-tracing engine to use for shape
 # models.
-# 
+#
 # Leave the ShapeModel Group commented-out to continue
-# using the ISIS3 default. 
+# using the ISIS default.
 #
 # RayTraceEngine = Bullet | Embree
 # OnError = Continue | Fail
 # Tolerance = { numerical value that will be set as the
 #           tolerance for the Bullet or Embree shape
-#           model } 
-# 
+#           model }
+#
 ########################################################
 
 #Group = ShapeModel
@@ -88,7 +88,7 @@ EndGroup
 #                           window displaying the error.
 #    Off - in command-line mode - only the results are
 #                           reported to the terminal, or
-#                           in the case of an error, 
+#                           in the case of an error,
 #                           the error is reported in Pvl
 #                           to the terminal.
 #        - in interactive mode - same as command-line mode,
@@ -119,7 +119,7 @@ Group = CubeCustomization
   Overwrite  = Allow
   Format     = Attached
   History    = On
-  MaximumSize = 12 
+  MaximumSize = 12
 EndGroup
 
 ########################################################
@@ -136,16 +136,16 @@ Group = FileCustomization
 EndGroup
 
 ########################################################
-# Customize how Isis uses your computer's resources.
+# Customize how ISIS uses your computer's resources.
 #
 # CubeWriteThread = Always | Optimized | Never
-#   Always - Override Isis program defaults and always
+#   Always - Override ISIS program defaults and always
 #     use a separate thread for writing out cubes. This
 #     will probably improve performance for some
 #     programs, will probably negatively impact programs
 #     that read/write the same file. This option should
 #     be used with caution.
-#   Optimized - Let the Isis program decide based on
+#   Optimized - Let the ISIS program decide based on
 #     it's own internal knowledge.
 #   Never - Revert to the original method of writing
 #     cubes always.
@@ -186,7 +186,7 @@ EndGroup
 ########################################################
 # Customize the location of mission specific data
 # files (calibration and spice kernels).  Usually this
-# should be left to the Isis administrator
+# should be left to the ISIS administrator
 ########################################################
 
 Group = DataDirectory

isis/Makefile

@@ -19,18 +19,18 @@ include $(ISISROOT)/make/isismake.os
 # Let the user know how to use the system
 #----------------------------------------------------------------------------
 help:
-	echo "Isis Make System Commands"
+	echo "ISIS Make System Commands"
 	echo "------------------------ "
 	echo "make all        : Build and install the entire system (incs,api,apps,docs)"
 	echo "make thirdParty : Copy required 3rdParty libraries into distribution"
 	echo "make incs       : Install API include files"
-	echo "make api        : Build and install the Isis API"
-	echo "make apps       : Build and install Isis Applications"
-	echo "make docs       : Build Isis Web Documentation"
+	echo "make api        : Build and install the ISIS API"
+	echo "make apps       : Build and install ISIS Applications"
+	echo "make docs       : Build ISIS Web Documentation"
 	echo "make quickclean : Clean binaries from source tree but not app test areas"
 	echo "make cleansrc   : Clean binaries from source tree"
 	echo "make clean      : Clean source tree and install area"
-	echo "make unitTest   : Build and execute unit tests for Isis API"
+	echo "make unitTest   : Build and execute unit tests for ISIS API"
 	echo "make appTest    : Build and execute application tests"
 	echo "make catTest    : Build and execute category tests"
 	echo "make coverage   : Build a test coverage report from generated coverage info"
@@ -65,7 +65,7 @@ incs:
 # Target = api
 # Dependencies = objects
 #
-# The Isis API is essentially libisis.a which will be created in the
+# The ISIS API is essentially libisis.a which will be created in the
 # directory $(ISISROOT)/lib.  Make api traverses the objs directories
 # (src/base/objs/*) and archives the ".o" files into libisis.a.  Therefore
 # the ".o" files must exist.
@@ -83,10 +83,10 @@ incs:
 #----------------------------------------------------------------------------
 
 api:
-	echo $(CURTIMESTAMP) "Building Isis API"
+	echo $(CURTIMESTAMP) "Building ISIS API"
 	mkdir -p lib
 	$(MAKE) --directory=src objects
-	echo $(CURTIMESTAMP) "Finished building Isis API"
+	echo $(CURTIMESTAMP) "Finished building ISIS API"
 	echo $(CURTIMESTAMP) ""
 	echo $(CURTIMESTAMP) "Adding API objects"
 	if [ "$(HOST_ARCH)" == "Linux" ]; then            \
@@ -113,27 +113,27 @@ osx_static:
 		$(MAKE) --directory=$$i plugin install; 	  \
 	done
 
-#	echo "Building Isis API with debugging"
+#	echo "Building ISIS API with debugging"
 #	cd src; $(MAKE) objects MODE=DEBUG
 #	cd src; $(MAKE) api MODE=DEBUG
-#	echo "Finished building Isis API with debugging"
+#	echo "Finished building ISIS API with debugging"
 #	echo " "
 
 #----------------------------------------------------------------------------
 # Target = apps
 # Dependencies = none
 #
-# This will build and install all the Isis application in the directory
+# This will build and install all the ISIS application in the directory
 # $(ISISROOT)/bin.  It also installs the application Xml file in
 # $(ISISROOT/bin/xml.  Again the make system traverse the apps directories
 # (src/base/apps) and builds/installs each application.  Of course the
 # API must be built for this to work properly
 #----------------------------------------------------------------------------
 apps:
-	echo $(CURTIMESTAMP) "Building Isis Applications"
+	echo $(CURTIMESTAMP) "Building ISIS Applications"
 	mkdir -p bin/xml
 	$(MAKE) --directory=src applications
-	echo $(CURTIMESTAMP) "Finished building Isis Applications"
+	echo $(CURTIMESTAMP) "Finished building ISIS Applications"
 	echo $(CURTIMESTAMP) " "
 
 #----------------------------------------------------------------------------
@@ -143,28 +143,28 @@ apps:
 # This target traverse both the objs and apps directories and moves the
 # Xml and assets directories into specific sub-directories under
 # $(ISISROOT)/src/docsys.  Then it builds the entire docsys tree which
-# generates the Isis Documentation under $(ISISROOT)/doc
+# generates the ISIS Documentation under $(ISISROOT)/doc
 #----------------------------------------------------------------------------
 docs:
-	echo $(CURTIMESTAMP) "Building Isis Documentation"
+	echo $(CURTIMESTAMP) "Building ISIS Documentation"
 	mkdir -p doc
 	$(MAKE) --directory=src documentation
 	$(MAKE) --directory=src/docsys docs
-	echo $(CURTIMESTAMP) "Finished building Isis Documentation"
+	echo $(CURTIMESTAMP) "Finished building ISIS Documentation"
 
 
 #----------------------------------------------------------------------------
 # Target = coverage
 # Dependencies = none
 #
-# This target builds a report on how much of Isis is tested in the automated
+# This target builds a report on how much of ISIS is tested in the automated
 # tests. This is currently excluding applications that run other applications
 # because of the amount of time it takes to generate the report (and that's
 # not how we want to test our applications ideally).
 #----------------------------------------------------------------------------
 coverage:
 	if [ "$(CODE_COVERAGE_BIN_DIR)" == "" ]; then                         \
-	  echo "Make sure you use MODE=TC when building Isis for a coverage"  \
+	  echo "Make sure you use MODE=TC when building ISIS for a coverage"  \
 	       "report.";                                                     \
 	  exit 1;                                                             \
 	fi;                                                                   \
@@ -174,7 +174,7 @@ coverage:
 	CSEXEFILES=(`find src/ -name "*.csexe"` `find bin/ -name "*.csexe"`); \
 	if [ "$${#CSMESFILES[@]}" == "0" ] ||                                 \
 	   [ "$${#CSEXEFILES[@]}" == "0" ]; then                              \
-	  echo "Please build Isis and run the tests with MODE=TC before "     \
+	  echo "Please build ISIS and run the tests with MODE=TC before "     \
 	       "trying to build a coverage report.";                          \
 	  exit 1;                                                             \
 	fi;                                                                   \
@@ -198,21 +198,21 @@ coverage:
 	done;                                                                     \
 	$(ECHO) -ne $(CURTIMESTAMP) "Scope Coverage:      ";                      \
 	$(CODE_COVERAGE_BIN_DIR)/cmreport                                         \
-	    --title="Isis System-Wide Test Scope Coverage"                        \
+	    --title="ISIS System-Wide Test Scope Coverage"                        \
 	    -m "`basename $$PWD`.csmes" --select=".*" --bargraph --toc --stat     \
 	    --global=all --method=all --source=all --execution=all                \
 	    --method-sort=coverage --execution-sort=coverage                      \
 	    --source-sort=coverage -h scopecoverage;                              \
 	$(ECHO) -ne $(CURTIMESTAMP) "Line Coverage:       ";                      \
 	$(CODE_COVERAGE_BIN_DIR)/cmreport                                         \
-	    --title="Isis System-Wide Test Line Coverage"                         \
+	    --title="ISIS System-Wide Test Line Coverage"                         \
 	    -m "`basename $$PWD`.csmes" --select=".*" --bargraph --toc --stat     \
 	    --global=all --method=all --source=all --execution=all                \
 	    --method-sort=coverage --execution-sort=coverage                      \
 	    --source-sort=coverage --line-coverage -h linecoverage;               \
 	$(ECHO) -ne $(CURTIMESTAMP) "Function Coverage:   ";                      \
 	$(CODE_COVERAGE_BIN_DIR)/cmreport                                         \
-	    --title="Isis System-Wide Test Function Coverage"                     \
+	    --title="ISIS System-Wide Test Function Coverage"                     \
 	    -m "`basename $$PWD`.csmes" --select=".*" --bargraph --toc --stat     \
 	    --global=all --method=all --source=all --execution=all                \
 	    --method-sort=coverage --execution-sort=coverage                      \
@@ -222,7 +222,7 @@ coverage:
 #----------------------------------------------------------------------------
 # Target = quickclean
 #
-# This target cleans the entire Isis system enough for a recompile.  It cleans ".o" files and
+# This target cleans the entire ISIS system enough for a recompile.  It cleans ".o" files and
 # binary executables from the source tree.  It also, clears the running
 # areas under $ISISROOT (inc, doc, bin, bin/xml, and lib)
 #
@@ -232,7 +232,7 @@ coverage:
 # This walks the src tree and removes ".o" files and binary files
 #----------------------------------------------------------------------------
 quickclean:
-	echo $(CURTIMESTAMP) "Cleaning Isis (quick)"; \
+	echo $(CURTIMESTAMP) "Cleaning ISIS (quick)"; \
 	$(MAKE) --directory=src quickclean;   \
 	rm -rf inc;                           \
 	rm -rf doc;                           \
@@ -248,7 +248,7 @@ quickclean:
 # Target = clean
 # Dependencies = cleansrc
 #
-# This target cleans the entire Isis system.  It cleans ".o" files and
+# This target cleans the entire ISIS system.  It cleans ".o" files and
 # binary executables from the source tree.  It also clears the running
 # areas under $ISISROOT (inc, doc, bini, bin/xml, and lib)
 #
@@ -277,7 +277,7 @@ tabcomplete:
 	if [ ! -d bin ]; then                                                    \
 	  echo $(CURTIMESTAMP) "You must build the applications first";          \
 	elif [ ! -f bin/isiscomplete ]; then                                     \
-	  echo $(CURTIMESTAMP) "Isis application 'isiscomplete' is missing";     \
+	  echo $(CURTIMESTAMP) "ISIS application 'isiscomplete' is missing";     \
 	else                                                                     \
 	  echo "#!/bin/csh" > $$ISISROOT/scripts/tabcomplete.csh;                \
 	  isiscomplete `ls $$ISISROOT/bin | grep -v xml` | sed 's/; /;~/g' |     \
@@ -295,19 +295,19 @@ tabcomplete:
 # output data (whether it be a cube, text file, postscript file, etc)
 #----------------------------------------------------------------------------
 unitTest:
-	echo $(CURTIMESTAMP) "Testing Isis API"
+	echo $(CURTIMESTAMP) "Testing ISIS API"
 	$(MAKE) --directory=src unitTest
-	echo $(CURTIMESTAMP) "Finished testing Isis API"
+	echo $(CURTIMESTAMP) "Finished testing ISIS API"
 
 appTest:
-	echo $(CURTIMESTAMP) "Testing Isis Applications version 2"
+	echo $(CURTIMESTAMP) "Testing ISIS Applications version 2"
 	$(MAKE) --directory=src appTest
-	echo $(CURTIMESTAMP) "Finished testing Isis Applications version 2"
+	echo $(CURTIMESTAMP) "Finished testing ISIS Applications version 2"
 
 catTest:
-	echo $(CURTIMESTAMP) "Testing Isis Category"
+	echo $(CURTIMESTAMP) "Testing ISIS Category"
 	$(MAKE) --directory=src catTest
-	echo $(CURTIMESTAMP) "Finished testing Isis Category"
+	echo $(CURTIMESTAMP) "Finished testing ISIS Category"
 
 #----------------------------------------------------------------------------
 # Target = thirdParty