Merging ALE into dev (#3590)

* Adds Ale into isis env (#3437)

* removed redundant scripts

* removed unused check from cmake lists

* removed debug prints

* removed v007 comment and boost debug flag

* added ale into ISIS

* removed debug prints

* remove load call

* reordered env.yml

* reordered env

* unpinned more stuff

* updated cmakelists

* Naif Keywords/SpicePosition/SpiceRotation now obtained from Ale label and not Spice kernels on Spiceinit (#3442)

* removed redundant scripts

* removed unused check from cmake lists

* removed debug prints

* removed v007 comment and boost debug flag

* added ale into ISIS

* removed debug prints

* working naif keywords from ale

* added PvlObject constructor from json

* reverted env file

* added loadcache(json)

* reverted spiceinit main

* Spice Rotation and Position now derived from ale

* added PvlObject from json null behavior

* type

* SpiceRotation no longer default to iden matrix

* Adding spiceinit classic as back up to Ale implementation.  (#3458)

* removed redundant scripts

* removed unused check from cmake lists

* removed debug prints

* removed v007 comment and boost debug flag

* added ale into ISIS

* removed debug prints

* working naif keywords from ale

* added PvlObject constructor from json

* reverted env file

* added loadcache(json)

* reverted spiceinit main

* Spice Rotation and Position now derived from ale

* added PvlObject from json null behavior

* type

* SpiceRotation no longer default to iden matrix

* added back ISIS spiceinit classic as a backup to ale

* added source keyword to Kernels group

* kernel group now added only in spiceinit

* updates as per comments

* Matrix p_cache (#3461)

* Converted quaternion into matrix when pushing onto the p_cache

* Removed extra print

* Tests docs (#3467)

* Reverted Blob change

* Added doc strings

* Moved usage into source files

* Added SpicePosition test

* changed thread inc to target

* Updated SpicePoition unitTest

* Added SpiceRotation unit test

* Updated SpiceRotation truth

* Merging Dev into ale_integration  (#3552)

* Fixed optimization flag for Linux and added -g for debug builds

* Bundleout Reformat  (#3447)

* Updated bundle text output to match expected output

* Further formatting for the bundle text output

* Added history comments

* Reformat of RMS output in bundleout.txt

* Updated BundleSolutionInfo unittest

* Updated version to 3.9.0_RC1 (#3448)

* Fixed compiler warnings. Fixes #3418, Fixes #3198 (#3459)

* Updated version to 3.9.0_RC1

* Removed compiler warnings with as few changes as possible

* Updated pvldiff to support PvlContainers with unequal keyword lengths (#3460)

* Updated pvldiff to support PvlContainers with unequal keyword lengths with IngoreKeys

* groups now remove keys as well

* Added Anaconda cloud badge (#3463)

* Ale integration into dev  (#3464)

* Adds Ale into isis env (#3437)

* removed redundant scripts

* removed unused check from cmake lists

* removed debug prints

* removed v007 comment and boost debug flag

* added ale into ISIS

* removed debug prints

* remove load call

* reordered env.yml

* reordered env

* unpinned more stuff

* updated cmakelists

* Naif Keywords/SpicePosition/SpiceRotation now obtained from Ale label and not Spice kernels on Spiceinit (#3442)

* removed redundant scripts

* removed unused check from cmake lists

* removed debug prints

* removed v007 comment and boost debug flag

* added ale into ISIS

* removed debug prints

* working naif keywords from ale

* added PvlObject constructor from json

* reverted env file

* added loadcache(json)

* reverted spiceinit main

* Spice Rotation and Position now derived from ale

* added PvlObject from json null behavior

* type

* SpiceRotation no longer default to iden matrix

* Adding spiceinit classic as back up to Ale implementation.  (#3458)

* removed redundant scripts

* removed unused check from cmake lists

* removed debug prints

* removed v007 comment and boost debug flag

* added ale into ISIS

* removed debug prints

* working naif keywords from ale

* added PvlObject constructor from json

* reverted env file

* added loadcache(json)

* reverted spiceinit main

* Spice Rotation and Position now derived from ale

* added PvlObject from json null behavior

* type

* SpiceRotation no longer default to iden matrix

* added back ISIS spiceinit classic as a backup to ale

* added source keyword to Kernels group

* kernel group now added only in spiceinit

* updates as per comments

* Matrix p_cache (#3461)

* Converted quaternion into matrix when pushing onto the p_cache

* Removed extra print

* Tests docs (#3467)

* Reverted Blob change

* Added doc strings

* Moved usage into source files

* Added SpicePosition test

* changed thread inc to target

* Updated SpicePoition unitTest

* Added SpiceRotation unit test

* Updated SpiceRotation truth

* Update README.md

fixes a white space formatting issue in step 7 which prevented a portion of the documentation being rendered correctly

* Correct documentation.

The file written to the path specified by CNETFILE will be in binary control network format, not plain-text PVL format.  

The incorrect description in this documentation has been incorrect for at least 7 years, based on the 'Blame' view of the relevant lines in hijitreg/main.cpp, ControlNet/ControlNet.h, and ControlNet/ControlNet.cpp.

* Revert "Ale integration into dev  (#3464)"

This reverts commit 48e4efd1.

* Converted PixelType unit test to gtest (#3478)

* converted Pixel type unit test to gtest

* removed old unit test and truth data

* converted Column unit test to gtest (#3480)

* converted Column unit test to gtest

* removed redundant tests

* Added Working BundleMeasure gtest File (#3470)

* Initial Stab at BundleMeasureTest with Fixtures.

* Added Working BundleMeasure gtest File

* Added a refernce to phocube to camdev docs

* Fixes Qmos grid to properly consider PositiveWest and PositiveEast (#3488)

* Fixes Qmos grid to properly consider PositiveWest and PositiveEast

* clean up

* update as per comments

* added comments on positive west angles as they come into the GridGraphicsItem constructor

* Bundleout Text file update (#3485)

* Initial changes to get the bundleout into a better place

* Added a few comments and updated how the spacing for the sprintfs is obtained

* Reverted unnecessary changes to BundleObservation

* Updated file path length checking as suggested

* Updates voy2isis to add an optional parameter to specify the instrument name (#3490)

* Update date and other metadata

* ckwriter_test_fix

* Fix unintentional cmakelists change

* Updated voy2isis to add instrument parameter which can be used to specify the instrument name wac or nac if it is not provided in the image label

* Added simple test

* Updates test and documentation for voy2isis adds instrument_name update

* Updated history documentation to add ticket number for voy2isis changes

* Warning for photomet added (#3486)

* added warning if anglesource option is used with mixed or topo normalization method; based on github tickets 3451 and 3452

* adding tests

* Addressing Stuarts comments

* Addressing Kristin's comment

* Updating Kaguya Distortion Model with Boresight (Finishing #3492) (#3498)

* added warning if anglesource option is used with mixed or topo normalization method; based on github tickets 3451 and 3452

* adding tests

* changes to KaguyaTC distortion map

* Fixed test on Aarons PR

* updated unit test

* reseting test data location

* Adding camera uptick

* Replaced code, removed earlier, that abandons work on a tile Fixes: #3466 (#3497)

* Replaced code, removed earlier, that abondons work on a tile when it is outside the output image

* Typo

* Cisscal Output Change (#3496)

* Updated cisscal output cub creation to after bitweight correction and dark subtraction

* Updated history in cisscal app xml

* Added issue number

* Added new test for cisscal

* Typo

* Removed cube when an exception is thrown rather than moving the instantiation point

* Austin Sander's "clemhirescal: Adds support for all MCP gain settings for filters A and D" (#3503)

* Added support for all MCP gain settings.

Closes #3190

* Revised comments to better reflect updated logic

* Added history comment.

* Added additional description and link to Robinson paper.

* added issue number

* Added dynamic creation of version file (#3502)

* Added dynamic creation of version file

* removed commented line

* Update README.md

* Updates marci2isis to add variable exposure times and associated frame sequences (#3501)

* Update date and other metadata

* ckwriter_test_fix

* Fix unintentional cmakelists change

* Updated voy2isis to add instrument parameter which can be used to specify the instrument name wac or nac if it is not provided in the image label

* Added simple test

* Updates test and documentation for voy2isis adds instrument_name update

* Updated history documentation to add ticket number for voy2isis changes

* Updated to reverse frameseq number appropriately with flip

* Remove commented-out code

* Added documentation for change and test

* Updated no exposure duration in varexp file condition

* Re-remove iTime.h

* Update warning message for assuming a single exposure time

* Modified to use the frame and exposure keywords added by marci2isis i… (#3505)

* Modified to use the frame and exposure keywords added by marci2isis instead of the varexp.tab file

* Added the issue that caused this to need to be fixed

* Update main.cpp

* Updated Readme with Contributing link

* Jenkins Build Script update (#3533)

* Updated pipeline to use TestPreferences where necessary

* Updated pipeline truth data

* Made preference parameter position consistant

* Updated pipeline truth data again

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

* Jenkins

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* Jenkins

* Changed testing avoid which failure

* Removed echo

* Pointed at install bin instead of build bin

* Added a forgotten /

* Added the actual install directory

* Changed isisroot to point to install directory

* More tweeks to the groovy script

* Removed conda prefix echo

* Moved path update to a single line

* new groove

* new groove

* new groove

* new groove

* new groove

* Updated spice rotation test with isis variable

* Testing with appjit

* Only testing app jit

* Changed app test to -R

* More messing with stuffs

* Added check for catlab

* Changed install directory location

* Changed paths again

* Echoed pwd in checkout

* Retry the print

* Pathing one more time

* Paths

* updated build.groovy

* Update Jenkinsfile (#3525)

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* Update Jenkinsfile

* fixed compiler warning. Fixes #3531

* Update kerneldbgen test to handle input file path edge case (#3536)

* Update date and other metadata

* ckwriter_test_fix

* Fix unintentional cmakelists change

* Updated kerneldbgen test to deal with specific filepath length edge case

* Updated groovy to use new Kakadu include (#3537)

* Updated groovy to use new Kakadu include

* Fixed typo in include path

* changed cisscal to no longer use absolute paths (#3541)

* excluded file group now prints original file

* Added preferences variable to shapemodel path.

* Update failing kerneldbgen ck test again (#3540)

* Update date and other metadata

* ckwriter_test_fix

* Fix unintentional cmakelists change

* Updated kerneldbgen test to deal with specific filepath length edge case

* Update kerneldbgen ck test to use IgnoreFilePaths

* Removed requirement of having to start a path with a slash, and added the dollar sign to the regex to allow the ignorepath feature to ignore file paths that start with an environment or isis variable

* Updating test and truth data to print relative file (#3545)

* Minor updates to "How to Write Documentation" documentation (#3510)

* Update date and other metadata

* ckwriter_test_fix

* Fix unintentional cmakelists change

* Minor updates to How to Write Documentation documentation to reflect build changes post-cmake

* remove additionally as per review comments

* Adding just the meta.yml, previous PR updated CMakeLists.txt (#3549)

* pinned boost (#3561)

* Merge Dev into Ale_integration (#3560)

* Updated version to 3.9.0_RC1 (#3448)

* Added dynamic creation of version file (#3502)

* Added dynamic creation of version file

* removed commented line

* Moved deactivates outside of the try block, also added an env clean up step (#3556)

* Jenkins Changes (#3557)

* Jenkins file update to make use of the web hook

* Added a groovy utilities file

* Changed the pipeline to load the right file

* Updated the name of the groovy file

* Removed unnecessary isis app -help commands

* Added ninja into environment.yml

* Add ALESPICEROOT to ENV (#3568)

* Updated variable initialization to include ALESPICEROOT

* Removed duplicate code from the isis3VarInit file

* Update isis3VarInit.py

* CkWriter Changes (#3571)

* Updated variable initialization to include ALESPICEROOT

* Removed couts and added CKs to the list of kernels to load

* Updated ckwriters lroc test

* Added AngularVelocities to the Ale load code in SpiceRotation

* Added history comment

* Removed unnecessary couts and variable

* Removed accidental duplicate argparse code

* Env update to support building with ALE (#3563)

* pinned boost

* updated envs for ale support

* trivial jenkinsfile change

* revert Jenkinsfile

* added excplicit ninja

* pcl now 1.8

* 1.8.1 -> 1.8 in cmake config

* experimenting with unpinned PCL

* removing versions from find PCL

* repinned some things

* unpinned some things

* moved order for gcc4

* more experiments with ale

* using env used on local prog24

* fit adjustment

* eeeeeeeehhhhhhh

* Moved usgs-astrogeology first in channel order

* Ticked ALE version up

* Forced Spice class to use ISIS when pointing is NADIR

* updated truth for SpiceRotation (#3577)

* Added flag to skip SSL verification in CI (#3572)

* Added flag to skip SSL verification on PR CI

* Added no SSL flag to nightly build script

* Update Jenkinsfile

* Update build.groovy

* Update build.groovy

* Update Jenkinsfile

* Added command to skip SSL verification in Anaconda

* Updated build.groovy with anaconda SSL flag

* Working on a working Linux env (#3578)

* Working on a working Linux env

* fixed ALE pin

* Removed FindFeatures filter test (#3582)

* updated truth for SpiceRotation

* removed findfeatures filter test

* Removed var_init call from jenkins nightly

* Changed to print out build environment

* cnet2dem tests updated with a tolerance  (#3586)

* updated truth for SpiceRotation

* removed findfeatures filter test

* updated cnet2dem tests to have a floating point tolerance

* fixed spacing

* Fixed test to account for numbers starting with plus signs (#3588)

* Restricted openssl version (#3589)

* Ticked ALE version

* Update Cube.cpp

No real change. Just removed spaces

* Removed NGINX cache for Jenkins tests (#3591)

* Changed to use c++ and