Updates to PDS4 branch (DOI-USGS#4505)

* Initial isisimport application  (DOI-USGS#4470)

* Initial isisimport application modeled to work on importing tgocassis images

* Add template to toisis

* Draft cassis template file added to pds4 branch (DOI-USGS#4472)

* Initial isisimport application modeled to work on importing tgocassis images

* Add template to toisis

* actual cassis label template

* Reverted accidently modified template

* Add new locations of import and export templates and update cmake accordingly (DOI-USGS#4477)

* Update cmake to new locations of import and export templates

* Fix mixed tabs and spaces

* Removed topds4 directory from CMakeLists

* Updates XmlToJson parsing to be more inja-friendly (DOI-USGS#4478)

* Updates XmlToJson parsing to indicate XML attributes and text values in a way friendly to inja parsing of the json

* Update XmlToJson tests

* Tgocassis Template Completed for Instruments and Archive Groups (DOI-USGS#4481)

* Updates to cassis label template

* Further updates to cassis template

* Updates to accomodate PR 4478 changes

* Cassis template completed for Instrument and Archive Groups.

* Generalize PDS4 cube creation setup (DOI-USGS#4485)

* Updates XmlToJson parsing to indicate XML attributes and text values in a way friendly to inja parsing of the json

* Update XmlToJson tests

* Generalized line/sample/band setup

* PDS4PixelType as a callback, TEMPLATE default option, and working TGOCaSSIS.tpl (DOI-USGS#4479)

* Cassis Template Updated BandBin and AlphaCube Groups (DOI-USGS#4482)

* tgocassis Template Completed for AlphaCube and BandBin groups

* Additional template cleanup

* Updated Pixels Group

* Removed core object from template.

* protect template search and improve TGOCASSIS template (DOI-USGS#4486)

* Renamed topds4 to isisexport (DOI-USGS#4488)

* Updates to Cassis Template and XML and Minor corrections to isisimport (DOI-USGS#4490)

* Updates to cassis template. Corrections to isisimport to allow module tests to work properly.

* Added disclaimer to xml file.

* Added mapping group template file (DOI-USGS#4492)

* Added checks for existing keywords to be able to export an imported tgo image

* Added separate mapping group translation file

* Callbacks for YearDOY and ConvertUniqueIdtoObservationId (DOI-USGS#4491)

* isisimport can now default to correct template using a file template. Updated Cassis template name. Minor updates in isisimport. (DOI-USGS#4493)

* Updates mapping group in template. Added callback to handle added Z to StartTime. (DOI-USGS#4495)

* PDS4 - Fix template search and targetGroup template variable for tgocassis.tpl (DOI-USGS#4494)

* fix template search and targetGroup template variable for tgocassis.tpl

* remove accidental extra tag

* address feedback from amy

* Updated export template to produce parsable xml (DOI-USGS#4497)

* Updated export template to be functioning xml to be used in isisimport.

* Added back 3D_Array but left in comments.

* Adds tests with test data and fixes off-by-one error in isisimport (DOI-USGS#4502)

* Added intial working section of tests

* Update test with test data and fix off-by-one in isisimport

* Add test input image

* Clean up from old design of test

* Updated based on feedback

* Moved local function into ISIS namespace

* Ticked ISIS version to 6

* More tick to 6

* Updated CHANGELOG

We don't add the 6.0.0 heading until just before the actual release. I also added some missing periods.

Co-authored-by: Amy Stamile <74275278+amystamile-usgs@users.noreply.github.com>
Co-authored-by: Tim Giroux <62255438+tgiroux@users.noreply.github.com>
Co-authored-by: Stuart Sides <ssides@usgs.gov>
Co-authored-by: Kaitlyn Lee <kdl222@nau.edu>
Co-authored-by: Jesse Mapel <jmapel@usgs.gov>

CHANGELOG.md

@@ -38,6 +38,7 @@ release.
 ## [6.0.0] - 2021-08-27
 
 ### Added
+- Added a new application, isisimport. The application is designed to be a replacement for many of the mission/instrument specific import applications. It does not contain the templates for those applications at this time. It uses a templateing engine instead of the translation files.
 - Added a new dark current correction to hical that works with the higher temperatures recent images are captured at. Use the new config file, $ISISDATA/mro/calibration/hical.0023_darkrate.conf, to enable the new dark current correction over the old dark current correction. Runs of hical without the new dark current correction will also produce an extra line in the output log indicating that the ZeroDarkRate module is disabled. [#4324](https://github.com/USGS-Astrogeology/ISIS3/issues/4324)
 - Added the ability to bundle adjust CSM models in jigsaw. Use the new CSMSOLVESET, CSMSOLVETYPE, and CSMSOLVELIST arguments to specify what you solve for. [#4537](https://github.com/USGS-Astrogeology/ISIS3/pull/4537)
 
@@ -67,6 +68,11 @@ release.
 - Fixed Thm2isis to properly use output attributes [#4213](https://github.com/USGS-Astrogeology/ISIS3/issues/4213)
 - Fixed caminfo uselabel SegFault. [#4401](https://github.com/USGS-Astrogeology/ISIS3/issues/4401)
 
+### Changed
+- isisVarInit.py no longer writes a "cat" statement by default to the activate scripts which cause the ISIS version information to be written on conda activate.  This can be included in those scripts via a command line option to isisVarInit.py.  Also, a quiet option is provided to isisVarInit.py to suppress its own writing to standard out, if needed.
+- Changed the name of topds4 to isisexport. The application is designed to be a replacement for many of the mission/instrument specific export applications. It uses a templateing engine instead of the translation files.
+
+
 ## [5.0.0] - 2021-04-01
 
 ### Added

isis/CMakeLists.txt

@@ -33,7 +33,7 @@ set(PACKAGE            "ISIS")
 set(PACKAGE_NAME       "USGS ISIS")
 
 # Version number
-set(VERSION            "5.1.0")
+set(VERSION            "6.0.0")
 string(REPLACE "." ";" VERSION_LIST ${VERSION})
 list(GET VERSION_LIST 0 VERSION_MAJOR)
 list(GET VERSION_LIST 1 VERSION_MINOR)
@@ -422,24 +422,25 @@ install(DIRECTORY ${CMAKE_BINARY_DIR}/appdata DESTINATION ${CMAKE_INSTALL_PREFIX
 # Create the appdata directory with translations directory, images directory, templates directories
 file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/appdata/translations
                     ${CMAKE_BINARY_DIR}/appdata/templates/apollo
-		    ${CMAKE_BINARY_DIR}/appdata/templates/autoseed
-		    ${CMAKE_BINARY_DIR}/appdata/templates/autoreg
-		    ${CMAKE_BINARY_DIR}/appdata/templates/noproj
-		    ${CMAKE_BINARY_DIR}/appdata/templates/cnetref
-		    ${CMAKE_BINARY_DIR}/appdata/templates/cnetstats
-		    ${CMAKE_BINARY_DIR}/appdata/templates/cnet_validmeasure
-		    ${CMAKE_BINARY_DIR}/appdata/templates/controlnetworks
-	            ${CMAKE_BINARY_DIR}/appdata/templates/hidtmgen
-		    ${CMAKE_BINARY_DIR}/appdata/templates/findfeatures
-		    ${CMAKE_BINARY_DIR}/appdata/templates/fullcnetdiff
-		    ${CMAKE_BINARY_DIR}/appdata/templates/jigsaw
-		    ${CMAKE_BINARY_DIR}/appdata/templates/kernels
-	            ${CMAKE_BINARY_DIR}/appdata/templates/labels
-	            ${CMAKE_BINARY_DIR}/appdata/templates/topds4
-	            ${CMAKE_BINARY_DIR}/appdata/templates/maps
-		    ${CMAKE_BINARY_DIR}/appdata/templates/photometry
-	            ${CMAKE_BINARY_DIR}/appdata/images/icons
-	            ${CMAKE_BINARY_DIR}/appdata/images/targets)
+        ${CMAKE_BINARY_DIR}/appdata/templates/autoseed
+        ${CMAKE_BINARY_DIR}/appdata/templates/autoreg
+        ${CMAKE_BINARY_DIR}/appdata/templates/noproj
+        ${CMAKE_BINARY_DIR}/appdata/templates/cnetref
+        ${CMAKE_BINARY_DIR}/appdata/templates/cnetstats
+        ${CMAKE_BINARY_DIR}/appdata/templates/cnet_validmeasure
+        ${CMAKE_BINARY_DIR}/appdata/templates/controlnetworks
+        ${CMAKE_BINARY_DIR}/appdata/export
+        ${CMAKE_BINARY_DIR}/appdata/templates/hidtmgen
+        ${CMAKE_BINARY_DIR}/appdata/import
+        ${CMAKE_BINARY_DIR}/appdata/templates/findfeatures
+        ${CMAKE_BINARY_DIR}/appdata/templates/fullcnetdiff
+        ${CMAKE_BINARY_DIR}/appdata/templates/jigsaw
+        ${CMAKE_BINARY_DIR}/appdata/templates/kernels
+        ${CMAKE_BINARY_DIR}/appdata/templates/labels
+        ${CMAKE_BINARY_DIR}/appdata/templates/maps
+        ${CMAKE_BINARY_DIR}/appdata/templates/photometry
+        ${CMAKE_BINARY_DIR}/appdata/images/icons
+        ${CMAKE_BINARY_DIR}/appdata/images/targets)
 
 
 # Have CMake process all of the source code and tests.
@@ -554,9 +555,13 @@ add_custom_target(hidtmgen ALL COMMAND ${CMAKE_COMMAND} -E copy_if_different
   ${CMAKE_SOURCE_DIR}/appdata/templates/hidtmgen/* ${CMAKE_BINARY_DIR}/appdata/templates/hidtmgen/)
 add_dependencies(isis hidtmgen)
 
-add_custom_target(topds4 ALL COMMAND ${CMAKE_COMMAND} -E copy_if_different
-  ${CMAKE_SOURCE_DIR}/appdata/templates/topds4/* ${CMAKE_BINARY_DIR}/appdata/templates/topds4)
-add_dependencies(isis topds4)
+add_custom_target(import ALL COMMAND ${CMAKE_COMMAND} -E copy_if_different
+  ${CMAKE_SOURCE_DIR}/appdata/import/* ${CMAKE_BINARY_DIR}/appdata/import)
+add_dependencies(isis import)
+
+add_custom_target(export ALL COMMAND ${CMAKE_COMMAND} -E copy_if_different
+  ${CMAKE_SOURCE_DIR}/appdata/export/* ${CMAKE_BINARY_DIR}/appdata/export)
+add_dependencies(isis export)
 
 # Add a custom build target to clean out everything that gets added to the source
 #  directory during the build process.