7.0 (#4795)

* Add a list of browse records to the output rdr if they exist on the cube (#4774) * Converted TGO IngestReingest Category Test. (#4789) * Fixed disk trashing on input cube reads (#4793) * Prepwork for 7.0.0 RC1 * Cleaning up the Markdown a bit I saw that some sections had wrong section numbers as they were hardcoded instead of making use of Markdown's auto-numbering. I repaired the indents for auto-numbering to work in the first half of the document and didn't touch the 2nd half where things looked okay. * Fixed jigsaw observation mode (#4791) * Test modification * Added changelog * Revert "added custom target to copy over camera.plugin files on ninja install solves #3834 (#4769)" This reverts commit 2681ffe. * updates for conda build of 7.0 (#4783) * xalan is required for ISIS, see cmakelists.txt (#4785) * Mac OS 11.6 local build fixes (#4788) * xalan is required for ISIS, see cmakelists.txt * Fix conda build for Mac 11.6 Co-authored-by: acpaquette <[email protected]> Co-authored-by: Amy Stamile <[email protected]> Co-authored-by: Michael Aye <[email protected]> Co-authored-by: Jesse Mapel <[email protected]> Co-authored-by: Jesse Mapel <[email protected]>
DOI-USGS · Feb 11, 2022 · 8d4b96e · 8d4b96e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -67,6 +67,7 @@ Keywords when running CAMSTATS.  [#3605](https://github.com/USGS-Astrogeology/IS
 - Fixed Maptrim failures when mode=both for PositiveWest longitude direction. [#4646](https://github.com/USGS-Astrogeology/ISIS3/issues/4646)
 - Fixed the Vesta target name not being translated properly in dawnfc2isis. [#4638](https://github.com/USGS-Astrogeology/ISIS3/issues/4638)
 - Fixed a bug where the measure residuals reported in the bundleout.txt file were incorrect. [#4655](https://github.com/USGS-Astrogeology/ISIS3/issues/4655)
+- Fuxed a bug where jigsaw would raise an error when solving for framing camera pointing in observation mode. [#4686](https://github.com/USGS-Astrogeology/ISIS3/issues/4686)
 
 ## [6.0.0] - 2021-08-27
 

diff --git a/README.md b/README.md
@@ -40,64 +40,70 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+
 
 ### ISIS Installation With Conda
 
-1.  Download either the Anaconda or Miniconda installation script for your OS platform. Anaconda is a much larger distribtion of packages supporting scientific python, while Miniconda is a minimal installation and not as large: [Anaconda installer](https://www.anaconda.com/download), [Miniconda installer](https://conda.io/miniconda.html)
-2.  If you are running on some variant of Linux, open a terminal window in the directory where you downloaded the script, and run the following commands. In this example, we chose to do a full install of Anaconda, and our OS is Linux-based. Your file name may be different depending on your environment.
-
-        chmod +x Anaconda3-5.3.0-Linux-x86_64.sh
-        ./Anaconda3-5.3.0-Linux-x86_64.sh
-
-
+1. Download either the Anaconda or Miniconda installation script for your OS platform. Anaconda is a much larger distribtion of packages supporting scientific python, while Miniconda is a minimal installation and not as large: [Anaconda installer](https://www.anaconda.com/download), [Miniconda installer](https://conda.io/miniconda.html)
+1. If you are running on some variant of Linux, open a terminal window in the directory where you downloaded the script, and run the following commands. In this example, we chose to do a full install of Anaconda, and our OS is Linux-based. Your file name may be different depending on your environment.
+    
+    ```bash
+    chmod +x Anaconda3-5.3.0-Linux-x86_64.sh
+    ./Anaconda3-5.3.0-Linux-x86_64.sh
+    ```
     This will start the Anaconda installer which will guide you through the installation process.
 
-3.  If you are running Mac OS X, a pkg file (which looks similar to Anaconda3-5.3.0-MacOSX-x86\_64.pkg) will be downloaded. Double-click on the file to start the installation process.
-4.  After the installation has finished, open up a bash prompt in your terminal window.
-5.  Next setup your Anaconda environment for ISIS. In the bash prompt, run the following commands:
-
-        #Create a new conda environment to install ISIS in
-        conda create -n isis python=3.6
-
-        #Activate the environment
-        #Depending on your version of Anaconda use one of the following:
+1. If you are running Mac OS X, a pkg file (which looks similar to Anaconda3-5.3.0-MacOSX-x86\_64.pkg) will be downloaded. Double-click on the file to start the installation process.
+1. After the installation has finished, open up a bash prompt in your terminal window.
+1. Next setup your Anaconda environment for ISIS. In the bash prompt, run the following commands:
 
-        #Anaconda 3.4 and up:
-        conda activate isis
-
-        #Prior to Anaconda 3.4:
-        source activate isis
-
-        #Add the following channels to the environment
-        conda config --env --add channels conda-forge
-        conda config --env --add channels usgs-astrogeology
+    ```bash
+    #Create a new conda environment to install ISIS in
+    conda create -n isis python=3.6
 
-        #Verify you have the correct channels:
-        conda config --show channels
+    #Activate the environment
+    #Depending on your version of Anaconda use one of the following:
 
-        #You should see:
+    #Anaconda 3.4 and up:
+    conda activate isis
 
-        channels:
-            - usgs-astrogeology
-            - conda-forge
-            - defaults
+    #Prior to Anaconda 3.4:
+    source activate isis
 
-        #The order is important.  If conda-forge is before usgs-astrogeology, you will need to run:
+    #Add the following channels to the environment
+    conda config --env --add channels conda-forge
+    conda config --env --add channels usgs-astrogeology
 
-        conda config --env --add channels usgs-astrogeology
+    #Verify you have the correct channels:
+    conda config --show channels
 
-6.  Download [Mamba](https://github.com/mamba-org/mamba). The ISIS environment is quite large and the Conda solver can take hours to resolve it. Instead, we recommend you use the much faster [Mamba](https://github.com/mamba-org/mamba) solver:
+    #You should see:
 
-        conda install -n base -c conda-forge mamba
+    channels:
+        - usgs-astrogeology
+        - conda-forge
+        - defaults
 
-7.  The environment is now ready to download ISIS and its dependencies:
+    #The order is important.  If conda-forge is before usgs-astrogeology, you will need to run:
 
-        mamba install -c usgs-astrogeology isis
+    conda config --env --add channels usgs-astrogeology
+    ```
+
+1. Download [Mamba](https://github.com/mamba-org/mamba). The ISIS environment is quite large and the Conda solver can take hours to resolve it. Instead, we recommend you use the much faster [Mamba](https://github.com/mamba-org/mamba) solver:
+
+    ```bash
+    conda install -n base -c conda-forge mamba
+    ```
+1. The environment is now ready to download ISIS and its dependencies:
 
+    ```bash
+    mamba install -c usgs-astrogeology isis
+    ```
+
     If you would like to work with our latest ISIS version 3, rather than updating
     to ISIS 4, instead run:
 
-	    mamba install -c usgs-astrogeology isis=3.10.0
+    ```bash
+    mamba install -c usgs-astrogeology isis=3.10.0
+    ```
 
-
-8.  Finally, setup the environment variables:
+1. Finally, setup the environment variables:
 
     ISIS requires several environment variables to be set in order to run correctly.
     The variables include: ISISROOT and ISISDATA.
@@ -109,55 +115,54 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+
 
     There are two methods to configure the environment variables for ISIS:
 
-    7.1 Using `conda env config vars` *preferred*
-
-      Conda has a built in method for configuring environment variables that are specific to a conda environment since version 4.8.
-      This version number applies only to the conda package, not to the version of miniconda or anaconda that was installed.
+    1. Using `conda env config vars` *preferred*
 
-      To determine if your version of conda is recent enough run:
+       Conda has a built in method for configuring environment variables that are specific to a conda environment since version 4.8.
+       This version number applies only to the conda package, not to the version of miniconda or anaconda that was installed.
 
-          conda --version
+       To determine if your version of conda is recent enough run:
 
-      If the version number is less than 4.8, update conda to a newer version by running:
+           conda --version
 
-          conda update -n base conda
+       If the version number is less than 4.8, update conda to a newer version by running:
 
-      The version number should now be greater than 4.8.
+           conda update -n base conda
 
-      To use the built in environment variable configuration feature, first activate the environment by first running:
+       The version number should now be greater than 4.8.
 
-          conda activate isis
+       To use the built in environment variable configuration feature, first activate the environment by first running:
 
-      After activation, the environment variables can be set using the syntax: `conda config vars set KEY=VALUE`.
-      To set all the environment variables ISIS requires, run the following command, updating the path to `ISISDATA` as needed:
+           conda activate isis
 
-          conda env config vars set ISISROOT=$CONDA_PREFIX ISISDATA=[path to data directory]
+       After activation, the environment variables can be set using the syntax: `conda config vars set KEY=VALUE`.
+       To set all the environment variables ISIS requires, run the following command, updating the path to `ISISDATA` as needed:
 
-      To make these changes take effect, re-activate the isis environment by running:
+           conda env config vars set ISISROOT=$CONDA_PREFIX ISISDATA=[path to data directory]
 
-          conda activate isis
+       To make these changes take effect, re-activate the isis environment by running:
 
-      The environment variables are now set and ISIS is ready for use every time the isis environment is activated.
+           conda activate isis
 
-      **Note** This method will not enable tab completion for arguments in C-Shell.
+       The environment variables are now set and ISIS is ready for use every time the isis environment is activated.
 
+       **Note** This method will not enable tab completion for arguments in C-Shell.
 
-    7.2 Using the provided isisVarInit.py script:
 
-      To use the default values for: `$ISISROOT` and `$ISISDATA`, run the ISIS variable initialization script with default arguments:
+    1. Using the provided isisVarInit.py script:
 
-          python $CONDA_PREFIX/scripts/isisVarInit.py
+       To use the default values for: `$ISISROOT` and `$ISISDATA`, run the ISIS variable initialization script with default arguments:
 
-      Executing this script with no arguments will result in $ISISROOT=$CONDA\_PREFIX and $ISISDATA=$CONDA\_PREFIX/data. The user can specify different directories for `$ISISDATA` using the optional value:
+           python $CONDA_PREFIX/scripts/isisVarInit.py
 
-          python $CONDA_PREFIX/scripts/isisVarInit.py --data-dir=[path to data directory]
+       Executing this script with no arguments will result in $ISISROOT=$CONDA\_PREFIX and $ISISDATA=$CONDA\_PREFIX/data. The user can specify different directories for `$ISISDATA` using the optional value:
 
-      Now every time the isis environment is activated, $ISISROOT and $ISISDATA will be set to the values passed to isisVarInit.py.
-      This does not happen retroactively, so re-activate the isis environment with one of the following commands:
+           python $CONDA_PREFIX/scripts/isisVarInit.py --data-dir=[path to data directory]
 
-          for Anaconda 3.4 and up - conda activate isis
-          prior to Anaconda 3.4 - source activate isis
+       Now every time the isis environment is activated, $ISISROOT and $ISISDATA will be set to the values passed to isisVarInit.py.
+       This does not happen retroactively, so re-activate the isis environment with one of the following commands:
 
+           for Anaconda 3.4 and up - conda activate isis
+           prior to Anaconda 3.4 - source activate isis
 
 
 ### Installation with Docker

diff --git a/isis/CMakeLists.txt b/isis/CMakeLists.txt
@@ -574,13 +574,6 @@ 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)
 
-# Create the updateBuildPlugins.sh.in file
-configure_file(${CMAKE_SOURCE_DIR}/cmake/updateBuildPlugins.sh.in ${CMAKE_BINARY_DIR}/scripts/updateBuildPlugins.sh)
-
-# Add custom build target to copy modified Camera.plugin files to the build/lib/Camera.plugin file
-add_custom_target(cameraPlugins ALL COMMAND ${CMAKE_BINARY_DIR}/scripts/updateBuildPlugins.sh)
-add_dependencies(isis cameraPlugins)
-
 # Add a custom build target to clean out everything that gets added to the source
 #  directory during the build process.
 # - Only a few things are added in order to make the tests work properly so
@@ -600,7 +593,6 @@ install(FILES     ${CMAKE_SOURCE_DIR}/../AUTHORS.rst  DESTINATION  ${CMAKE_INSTA
 install(FILES     ${CMAKE_SOURCE_DIR}/../CHANGELOG.md DESTINATION  ${CMAKE_INSTALL_PREFIX})
 install(FILES     ${CMAKE_BINARY_DIR}/version         DESTINATION  ${CMAKE_INSTALL_PREFIX})
 install(DIRECTORY ${CMAKE_SOURCE_DIR}/scripts         DESTINATION  ${CMAKE_INSTALL_PREFIX})
-install(PROGRAMS ${CMAKE_BINARY_DIR}/lib/Camera.plugin DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/)
 
 # Trigger all post-install behavior.
 # - The only way to run commands post-install in CMake is to add a subdirectory at

diff --git a/isis/cmake/AddIsisModule.cmake b/isis/cmake/AddIsisModule.cmake
@@ -178,6 +178,9 @@ function(add_isis_obj folder reqLibs)
     # Append the plugin file to a single file in the build directory
     # where the .so files will be created.  During installation copy these
     # plugin files to the installation library folder.
+    set(pluginPath ${CMAKE_BINARY_DIR}/lib/${pluginName})
+    cat(${plugins} ${pluginPath})
+    install(PROGRAMS ${pluginPath} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/)
     # Record this library name for the caller
     set(newPluginLib ${libName}  PARENT_SCOPE)
   endif()

diff --git a/isis/cmake/updateBuildPlugins.sh.in b/isis/cmake/updateBuildPlugins.sh.in
diff --git a/isis/src/base/objs/ProcessMapMosaic/ProcessMapMosaic.cpp b/isis/src/base/objs/ProcessMapMosaic/ProcessMapMosaic.cpp
@@ -63,6 +63,7 @@ namespace Isis {
 
     CubeAttributeInput inAtt(inputFile);
     Cube *inCube = ProcessMosaic::SetInputCube(inputFile, inAtt);
+    inCube->addCachingAlgorithm(new UniqueIOCachingAlgorithm(2));
 
     Cube *mosaicCube = OutputCubes[0];
     Projection *iproj = inCube->projection();

diff --git a/isis/src/control/objs/BundleUtilities/BundleObservationVector.cpp b/isis/src/control/objs/BundleUtilities/BundleObservationVector.cpp
@@ -110,6 +110,8 @@ namespace Isis {
       addToExisting = true;
     }
 
+    bool isIsisObservation = bundleImage->camera()->GetCameraType() != Camera::Csm;
+
     if (addToExisting) {
       // if we have already added a BundleObservation with this number, we have to add the new
       // BundleImage to this observation
@@ -126,8 +128,6 @@ namespace Isis {
     else {
       // create new BundleObservation and append to this vector
 
-      bool isIsisObservation = bundleImage->camera()->GetCameraType() != Camera::Csm;
-
       if (isIsisObservation) {
         bundleObservation.reset(new IsisBundleObservation(bundleImage,
                                                       observationNumber,
@@ -167,14 +167,6 @@ namespace Isis {
 
       append(bundleObservation);
 
-      if (isIsisObservation) {
-        QSharedPointer<IsisBundleObservation> isisObs = qSharedPointerDynamicCast<IsisBundleObservation>(bundleObservation);
-        isisObs->initializeExteriorOrientation();
-        if (bundleSettings->solveTargetBody()) {
-          isisObs->initializeBodyRotation();
-        }
-      }
-
       // update observation number to observation ptr map
       m_observationNumberToObservationMap.insertMulti(observationNumber, bundleObservation);
 
@@ -191,6 +183,15 @@ namespace Isis {
       }
 
     }
+
+    // If it's an ISIS observation, setup the camera based on the solve settings
+    if (isIsisObservation) {
+      QSharedPointer<IsisBundleObservation> isisObs = qSharedPointerDynamicCast<IsisBundleObservation>(bundleObservation);
+      isisObs->initializeExteriorOrientation();
+      if (bundleSettings->solveTargetBody()) {
+        isisObs->initializeBodyRotation();
+      }
+    }
     return bundleObservation;
   }
 

diff --git a/isis/src/tgo/apps/tgocassisrdrgen/tgocassisrdrgen.cpp b/isis/src/tgo/apps/tgocassisrdrgen/tgocassisrdrgen.cpp
@@ -241,9 +241,33 @@ namespace Isis {
       footprintNode.parentNode().removeChild(footprintNode);
     }
 
+    if(label->findObject("IsisCube").hasGroup("Archive")) {
+      PvlGroup archiveGroup = label->findObject("IsisCube").findGroup("Archive");
+
+      if (archiveGroup.hasKeyword("Browse")) {
+        PvlKeyword browseKeyword = archiveGroup.findKeyword("Browse");
+
+        QDomElement referenceListNode = pdsLabelNext.documentElement().firstChildElement("Reference_List");
+        QDomElement browseNode = pdsLabel.createElement("Browse");
+
+        for (int i = 0; i < browseKeyword.size(); i++) {
+          QString browseFile = browseKeyword[i];
+          QStringList browseComponentList = browseFile.split(QLatin1Char('_'));
+
+          QDomElement browseItem = pdsLabel.createElement("browse_record");
+          browseItem.setAttribute("record_num", i);
+          browseItem.setAttribute("filterType", browseComponentList[4]);
+
+          QDomText browseText = pdsLabel.createTextNode(browseFile);
+          browseItem.appendChild(browseText);
+          browseNode.appendChild(browseItem);
+        }
+        referenceListNode.appendChild(browseNode);
+      }
+    }
+
     QString outFile = ui.GetFileName("TO");
 
     process.WritePds4(outFile);
   }
 }
-
diff --git a/isis/src/tgo/tsts/ingestReingest/Makefile b/isis/src/tgo/tsts/ingestReingest/Makefile