Unverified Commit ceaf6b0b authored by Jesse Mapel's avatar Jesse Mapel Committed by GitHub
Browse files

Cleaned up installation instructions (#3916) 



* Cleaned up installation instructions

* Update README.md

Just a couple changes

Co-authored-by: default avatarStuart Sides <ssides@usgs.gov>
parent e3d95712

.gitignore

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@@ -49,6 +49,9 @@ print.prt 
build/

install/



# Unignore the documentation build

!isis/src/docsys/build



# Created by https://www.gitignore.io/api/macos

# Edit at https://www.gitignore.io/?templates=macos

README.md

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@@ -90,17 +90,17 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+ 
7.  Finally, setup the environment variables:



        #Execute the ISIS variable initialization script with default arguments.

        #This script prepares default values for:  $ISISROOT, $ISIS3DATA, $ISIS3TESTDATA

        #This script prepares default values for:  $ISISROOT, $ISISDATA, $ISISTESTDATA



        python $CONDA_PREFIX/scripts/isis3VarInit.py





    Executing this script with no arguments will result in $ISIS3DATA=$CONDA\_PREFIX/data, and $ISIS3TESTDATA=$CONDA\_PREFIX/testdata. The user can specify different directories for both of these optional values:

    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:



        python $CONDA_PREFIX/scripts/isis3VarInit.py --data-dir=[path to data directory]  --test-dir=[path to test data directory]





    More information about the ISIS3DATA environment variable and the ISIS Data Area can be found [here]("#The-ISIS-Data-Area"). Now everytime the isis environment is activated, $ISISROOT, $ISIS3DATA, and $ISIS3TESTDATA will be set to the values passed to isis3VarInit.py. This does not happen retroactively, re-activate the isis envionment with one of the following commands:

    More information about the ISISDATA environment variable and the ISIS Data Area can be found [here]("#The-ISIS-Data-Area"). Now everytime the isis environment is activated, $ISISROOT, $ISISDATA, and $ISISTESTDATA will be set to the values passed to isis3VarInit.py. This does not happen retroactively, re-activate the isis envionment with one of the following commands:



        for Anaconda 3.4 and up - conda activate isis

        prior to Anaconda 3.4 - source activate isis
@@ -288,11 +288,11 @@ To build and compile ISIS requires following the instructions listed below, whic 


### Ancillary Data



Many ISIS applications require ancillary data. For example, ingestion applications require translation tables to convert labels, calibration applications require flat files to do flat field correct, and map projection applications require DTMs to accurately compute intersections. Due to its size, this data is stored in a separate directory called the ISIS Data Area. Any location can be used for the ISIS Data Area, the software simply requires that the ISIS3DATA environment variable is set to its location.

Many ISIS applications require ancillary data. For example, calibration applications require flat files to do flat field corrections, and map projection applications require DTMs to accurately compute intersections. Due to its size, this data is stored in a separate directory called the ISIS Data Area. Any location can be used for the ISIS Data Area, the software simply requires that the ISISDATA environment variable is set to its location.



### Structure of the ISIS3 Data Area



Under the root directory of the ISIS Data Area pointed to by the ISIS3DATA environment variable are a variety of sub-directories. Each mission supported by ISIS has a sub-directory that contains mission specific processing data such as flat files and mission specific SPICE. There are also data areas used by more generic applications. These sub-directories contain everything from templates to test data.

Under the root directory of the ISIS Data Area pointed to by the ISISDATA environment variable are a variety of sub-directories. Each mission supported by ISIS has a sub-directory that contains mission specific processing data such as flat files and mission specific SPICE. There are also data areas used by more generic applications. These sub-directories contain everything from templates to test data.



### Size of the ISIS3 Data Area
@@ -304,19 +304,19 @@ The ISIS Data Area is hosted on rsync servers and not through conda channels lik 


To download all ISIS data, enter the following commands in the location where you want to install the ISIS Data Area:



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/ .





> Note: The above command downloads all ISIS data including the required base data area and all of the optional mission data areas.





### Partial Download of ISIS Base Data (Required)

### Partial Download of ISIS Base Data



The base data area is separate from the source code. This data area is crucial to ISIS and must be downloaded. To do that run the following commands:

This data area contains data that is common between multiple missions such as DEMS and leap second kernels. As of ISIS 4.1, the base data area is no longer required to run many applications as data such as icons and templates has been moved into the binary distribution. If you plan to work with any applications that use camera models (e.g., cam2map, campt, qview), it is still recommended you download the base data area. To download the base data area run the following commands:



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/base .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/base .



### Partial Download of Mission Specific Data
@@ -331,8 +331,8 @@ ISIS can now use a service to retrieve the SPICE data for all instruments ISIS s 
For example:



<pre>

cd $ISIS3DATA

rsync -azv <b>--exclude='kernels'</b> --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/cassini .

cd $ISISDATA

rsync -azv <b>--exclude='kernels'</b> --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/cassini .

</pre>



**WARNING:** Some instruments require mission data to be present for radiometric calibration, which is not supported by the SPICE Web Server, and some programs that are designed to run an image from ingestion through the mapping phase do not have an option to use the SPICE Web Service. For information specific to an instrument, see the documentation for radiometric calibration programs.
@@ -341,163 +341,163 @@ rsync -azv <b>--exclude='kernels'</b> --delete --partial isisdist.astrogeology.u 


**Apollo Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/apollo15 .

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/apollo16 .

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/apollo17 .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/apollo15 .

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/apollo16 .

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/apollo17 .





**Cassini Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/cassini .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/cassini .





**Chandrayaan Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/chandrayaan1 .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/chandrayaan1 .





**Clementine Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/clementine1 .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/clementine1 .





**Dawn Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/dawn .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/dawn .





**ExoMars Trace Gas Orbiter Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/tgo .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/tgo .





**Galileo Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/galileo .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/galileo .





**Hayabusa Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/hayabusa .

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/hayabusa2 .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/hayabusa .

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/hayabusa2 .





**Juno Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/juno .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/juno .





**Kaguya Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/kaguya .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/kaguya .





**Lunar Orbiter Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/lo .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/lo .





**Lunar Reconnaissance Orbiter Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/lro .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/lro .





**Mars Exploration Rover Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/mer .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/mer .





**Mariner10 Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/mariner10 .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/mariner10 .





**Messenger Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/messenger .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/messenger .





**Mars Express Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/mex .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/mex .





**Mars Global Surveyor Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/mgs .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/mgs .





**Mars Reconnaissance Orbiter Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/mro .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/mro .





**Mars Odyssey Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/odyssey .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/odyssey .





**Near Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/near .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/near .





**New Horizons Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/newhorizons .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/newhorizons .





**Rolo Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/rolo .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/rolo .





**Rosetta Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/rosetta .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/rosetta .





**Smart1 Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/smart1 .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/smart1 .





**Viking Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/viking1 .

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/viking2 .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/viking1 .

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/viking2 .





**Voyager Mission:**



    cd $ISIS3DATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/voyager1 .

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/voyager2 .

    cd $ISISDATA

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/voyager1 .

    rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isisdata/data/voyager2 .





## Installing older versions of ISIS

isis/src/docsys/build/Installation.xsl

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@@ -104,8 +104,8 @@ Deborah Lee Soltesz 
        </table>



      <p>

      See the <a href="https://github.com/USGS-Astrogeology/ISIS3#installation">ISIS 3 Installation Guide</a>

      for instructions on downloading and installing ISIS 3.

      See the <a href="https://github.com/USGS-Astrogeology/ISIS3#installation">ISIS Installation Guide</a>

      for instructions on downloading and installing ISIS 3.6 and later.

      </p>



      <p>
@@ -297,4 +297,3 @@ Deborah Lee Soltesz 


  </xsl:template>

</xsl:stylesheet>

isis/src/docsys/build/homepage.xml

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@@ -38,6 +38,14 @@ 
            </script>

          </div>

        </div>

        <h2>Request for comments</h2>

        <p>

          Major changes to how ISIS works are now handled through Requests for Comment (RFCs).

          These are a venue for the user community to voice their opinions on how they would

          like the software to work.

          Currently open RFCs can be found on the

          <a href="https://github.com/USGS-Astrogeology/ISIS3#requests-for-comment" target="top">ISIS Github</a>.

        </p>

        <h2>Popular Destinations</h2>

        <ul>

          <li>
@@ -46,7 +54,7 @@ 
            </a>

          </li>

          <li>

            <a href="Application/index.html">ISIS 3 Application Table of Contents</a>

            <a href="Application/index.html">ISIS Application Table of Contents</a>

          </li>

        </ul>

isis/src/docsys/documents/InstallGuide/InstallGuide.xml

+14 −507

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