diff --git a/.gitignore b/.gitignore
index bce992dee063c10dd90b7cd4f4df94dcefd91750..d4bc1304e71214205655228aff9b534065c45d83 100644
--- a/.gitignore
+++ b/.gitignore
@@ -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
diff --git a/README.md b/README.md
index c51c3eb33f484d24f15ecb8c085b93a34ce10eef..f40ed0af64913fa298a20881bb3ecf6f3eb3a711 100644
--- a/README.md
+++ b/README.md
@@ -21,7 +21,7 @@ The ISIS project uses a Request for Comment (RFC) model whereby major potential
Current open RFCs:
* [Migration of ISIS Data to Git](https://github.com/USGS-Astrogeology/ISIS3/wiki/RFC4---Migration-of-ISIS-Data-to-Git)
* [Removal of LOLAGRAIL SPKs from the data area](https://github.com/USGS-Astrogeology/ISIS3/wiki/RFC5-Remove-old-LOLAGRAIL-SPKs)
-
+
We encourage all contributors and users to review open RFCs and comment as these proposed changes will impact use of the software.
## FAQ
@@ -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 $ISISTESTDATA will be set to the values passed to isis3VarInit.py. This does not happen retroactively, re-activate the isis envionment with one of the following commands:
for Anaconda 3.4 and up - conda activate isis
prior to Anaconda 3.4 - source activate isis
@@ -186,7 +186,7 @@ already done this.
that it starts with whatever you got from step 1, and ends in the
name of your isis environment, if you followed the installation
instructions above, you called that environment 'isis'.
-
+
You can do the same thing to find the path to your new 'working'
environment, but in this example, it will be at
`$HOME/anaconda3/envs/working`.
@@ -244,11 +244,11 @@ remove these elements to and from your path.
To update to our latest release candidate up to version 3.9.1, run `conda update -c usgs-astrogeology -c usgs-astrogeology/label/RC isis3`
- Note that for ISIS versions 3.10 and above, new versions and release candidates will only be
+ Note that for ISIS versions 3.10 and above, new versions and release candidates will only be
available under the package name `isis` and `conda update isis3` and
- `conda update -c usgs-astrogeology -c usgs-astrogeology/label/RC isis3`
+ `conda update -c usgs-astrogeology -c usgs-astrogeology/label/RC isis3`
will no longer work for additional updates. Instead, after installing an `isis` package,
- `conda update isis` should be used to update to a new version and
+ `conda update isis` should be used to update to a new version and
`conda update -c usgs-astrogeology/label/RC isis` to update to a new release candidate.
### Operating System Requirements
@@ -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
diff --git a/isis/src/docsys/build/Installation.xsl b/isis/src/docsys/build/Installation.xsl
index e1b67d8a94c1cdc3a82efc3f0a6ba1b267d1a21e..3679a8bc3ac07253ea3a6cb5363e1f5135b3f371 100644
--- a/isis/src/docsys/build/Installation.xsl
+++ b/isis/src/docsys/build/Installation.xsl
@@ -1,7 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
-<xsl:stylesheet version="1.0"
- xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
- xmlns:fo="http://www.w3.org/1999/XSL/Format"
+<xsl:stylesheet version="1.0"
+ xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+ xmlns:fo="http://www.w3.org/1999/XSL/Format"
exclude-result-prefixes="xmlns fo">
<!--
@@ -14,8 +14,8 @@ Deborah Lee Soltesz
-->
- <xsl:output
- media-type="text/html"
+ <xsl:output
+ media-type="text/html"
doctype-public="-//W3C//DTD HTML 4.01 Transitional//EN"
doctype-system="http://www.w3.org/TR/html4/loose.dtd"
indent="yes"
@@ -66,7 +66,7 @@ Deborah Lee Soltesz
var s = document.getElementsByTagName('script')[0];
s.parentNode.insertBefore(usgsAnalytics, s);
}
- })();
+ })();
]]></xsl:comment>
<xsl:text>
</xsl:text>
</script>
@@ -104,13 +104,13 @@ 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>
See the <a href="../documents/LegacyInstallGuide/index.html">Legacy ISIS 3 Installation Guide</a>
- for instructions on downloading and installing versions of ISIS3 3.5.2 and earlier.
+ for instructions on downloading and installing versions of ISIS3 3.5.2 and earlier.
</p>
<p>
@@ -297,4 +297,3 @@ Deborah Lee Soltesz
</xsl:template>
</xsl:stylesheet>
-
diff --git a/isis/src/docsys/build/homepage.xml b/isis/src/docsys/build/homepage.xml
index 725aed8532eadcf07fd2778d1917757f488e2976..1a41d138aa72ccf0a185a5f556a904600c709ebb 100644
--- a/isis/src/docsys/build/homepage.xml
+++ b/isis/src/docsys/build/homepage.xml
@@ -25,10 +25,10 @@
<td valign="top">
<h2>Welcome</h2>
<p>
- This is the home page for ISIS, a digital image processing software
- package. The focus of the software is to manipulate imagery collected
- by current and past NASA and International planetary missions sent
- throughout our Solar System.
+ This is the home page for ISIS, a digital image processing software
+ package. The focus of the software is to manipulate imagery collected
+ by current and past NASA and International planetary missions sent
+ throughout our Solar System.
</p>
<h2>Announcements</h2>
<div style="text-align:center;">
@@ -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>
diff --git a/isis/src/docsys/documents/InstallGuide/InstallGuide.xml b/isis/src/docsys/documents/InstallGuide/InstallGuide.xml
index 8c7047c6cb1600e852eacd8d7cd982ff2bd39138..c73152846eb8285b665106801891ef5b0dc50521 100644
--- a/isis/src/docsys/documents/InstallGuide/InstallGuide.xml
+++ b/isis/src/docsys/documents/InstallGuide/InstallGuide.xml
@@ -22,513 +22,20 @@ you must <em>not</em> upgrade the ISIS Data Files!!!
</p>
</div>
-->
- <h2>Overview</h2>
+ <p>
+ 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>
- This installation guide is for ISIS3 users interested in installing ISIS3 (3.6.0)+ through conda.
- If you are a developer, we refer you to our <a href="https://github.com/USGS-Astrogeology/ISIS3">GitHub repository.</a>
- </p>
+ <p>
+ See the <a href="../documents/LegacyInstallGuide/index.html">Legacy ISIS 3 Installation Guide</a>
+ for instructions on downloading and installing versions of ISIS 3.5.2 and earlier.
+ </p>
-
- <h3>ISIS3 Installation With Conda</h3>
- <ol>
- <li>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:
- <a href="https://www.anaconda.com/download">Anaconda installer</a>, <a href="https://conda.io/miniconda.html">Miniconda installer</a></li>
-
- <li>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.
- <pre>
- <strong>chmod +x Anaconda3-5.2.0-Linux-x86_64.sh</strong>
- <strong>./Anaconda3-5.2.0-Linux-x86_64.sh</strong>
- </pre>
-
- This will start the Anaconda installer which will guide you through the installation process.</li>
-
- <li>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.</li>
-
- <li>After the installation has finished, open up a bash prompt in your terminal window.</li>
-
- <li>Next setup your Anaconda environment for ISIS3. In the bash prompt, run the following commands:
- <pre>
- <em>#Create a new conda environment to install ISIS3 in</em>
- <strong>conda create -n isis3 python=3.6</strong>
-
- <em>#Activate the environment</em>
- <em>#Depending on your OS, you may need to use conda activate isis3 instead</em>
- <strong>source activate isis3</strong>
-
- <em>#Add the following channels to the environment</em>
- <strong>conda config --env --add channels conda-forge</strong>
- <strong>conda config --env --add channels usgs-astrogeology</strong>
-
- #Verify you have the correct channels:
- <strong>conda config --show channels</strong>
-
- <em>#You should see:</em>
-
- <strong>channels:</strong>
- <strong> - usgs-astrogeology</strong>
- <strong> - conda-forge</strong>
- <strong> - defaults</strong>
-
- <em>#The order is important. If conda-forge is before usgs-astrogeology, you will need to run:</em>
-
- <strong>conda config --env --add channels usgs-astrogeology</strong>
- </pre></li>
-
- <li>The environment is now ready to download ISIS3 and its dependencies:
- <pre>
- <strong>conda install -c usgs-astrogeology isis3</strong>
- </pre></li>
-
- <li>Finally, setup the environment variables:
- <pre>
- <em>#Execute the ISIS3 variable initialization script with default arguments.</em>
- <em>#This script prepares default values for: $ISISROOT/$ISISDATA/$ISISTESTDATA</em>
-
- <strong>python $CONDA_PREFIX/scripts/isis3VarInit.py</strong>
- </pre>
-
- 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:
- <pre>
- <strong>python $CONDA_PREFIX/scripts/isis3VarInit.py --data-dir=[path to data directory] --test-dir=[path to test data directory]</strong>
- </pre>
-
- More information about the ISISDATA environment variable and the ISIS3 Data Area
- can be found <a href="#ISIS3DataDownload">here.</a>
-
- Now everytime the isis3 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 isis3 envionment with the following command:
- <pre>
- <em>#Depending on your OS, you may need to use conda activate isis3 instead</em>
- <strong>source activate isis3</strong>
- </pre></li>
- </ol>
-
-
- <h3>Operating System Requirements</h3>
- <p>ISIS3 runs on many UNIX variants. ISIS does not run natively on MS Windows,
- although it has been successfully run on Windows 10 using the Windows
- Subsystem for Linux (WSL). Instructions for doing this can be found
- <a href="#RunningOnWindows">here.</a>
-
- The UNIX variants ISIS3 has been successfully built on are:</p>
- <ul>
- <li>Ubuntu 18.04 LTS</li>
- <li>Mac OS X 10.13.6 High Sierra</li>
- <li>Fedora 28</li>
- <li>CentOS 7.2</li>
- </ul>
-
-<p>
- ISIS3 may be run on other Linux or macOS operating systems then those listed above,
- but it has not been tested and is not supported.
-</p>
-
-
- <h3>Hardware Requirements</h3>
- <p>Here are the minimum hardware requirements</p>
- <ul>
- <li>64-bit (x86) processors</li>
- <li>2 GB RAM</li>
- <li>2.5 GB of disk space for ISIS3 binaries</li>
- <li>10 GB to 510 GB disk space for ISIS3 data</li>
- <li>10 GB to many TB disk space for processing images</li>
- <li>A quality graphics card</li>
- </ul>
-
- <p>To build and compile ISIS3 requires following the instructions listed below, which are given on
- the GitHub wiki page for the ISIS3 project:
- <ul>
- <li><a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#getting-started-with-github">Getting Started With GitHub</a></li>
- <li><a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#building-isis3">Building ISIS3 With cmake</a></li>
- <li><a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#new-environmental-variable-meanings">New ISIS3 environmental variables and their meanings</a></li>
- <li><a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#custom-data-and-test-data-directories">Custom data and test directories</a></li>
- <li><a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#cleaning-builds">Cleaning builds</a></li>
- <li><a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#building-individual-isis3-applicationsobjects">Building individual applications/objects</a></li>
- <li><a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#building-isis3-documentation">Building ISIS3 documentation</a></li>
- <li><a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#problems">What to do if you encounter any problems</a></li>
- </ul>
-</p>
-
-
-<A NAME="RunningOnWindows"> </A>
-<h3>Running ISIS3 on Windows 10</h3>
- <ul>
- <li><a href="https://docs.microsoft.com/en-us/windows/wsl/install-win10">Installing the Windows Subsystem for Linux</a></li>
- <li><a href="http://planetarygis.blogspot.com/2017/07/isis3-on-windows-10-bash.html">Instructions for using the Windows
- Subsystem for Linux (WSL) to run ISIS3</a></li>
- </ul>
- <p>
- While the ISIS3 development team has not examined these
- instructions for correctness or completeness, they appear to have
- successfully worked for a number of ISIS3 users within the USGS who run Windows.
- Thanks for these instructions are directed towards Trent Hare who maintains an
- excellent and thoughtful blog on <a href="http://planetarygis.blogspot.com/">Planetary GIS Science.</a>
- </p>
-
-<A NAME="RunningOnWindowsWithSSH"> </A>
-<h3>Setting Up X11 forwarding on Windows with Putty and Xming</h3>
-<p>
-Some ISIS3 users prefer to run ISIS3 in Windows, but SSH into a computer
-that is running ISIS3 and has enabled X11 forwarding. This requires the
-installation of an X server on Windows. Below are links to two popular choices
-in Astrogeology.
-</p>
- <ul>
- <li><a href="https://sourceforge.net/projects/xming/">Xming X server for Windows</a></li>
- <li><a href="https://sourceforge.net/projects/vcxsrv/">VcXsrv Windows X Server</a></li>
- </ul>
-<p>
-Additionally, a Windows SSH client is required to create an SSH connection. PuTTY
-is a popular choice and may be downloaded below.
-</p>
-<ul>
- <li><a href="https://www.putty.org/">PuTTY - an SSH and telnet client for the Windows platform.</a></li>
-</ul>
-
-<A NAME="ISIS3DataArea"></A>
-<h2>The ISIS3 Data Area</h2>
-
-<h3>Ancillary Data</h3>
- <p>Many ISIS3 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 ISIS3 Data Area. Any
- location can be used for the ISIS3 Data Area, the software simply requires that the ISISDATA
- environment variable is set to its location.
- </p>
-
-<h3>Structure of the ISIS3 Data Area</h3>
- <p>Under the root directory of the ISIS3 Data Area pointed to by the ISISDATA environment
- variable are a variety of sub-directories. Each mission supported by ISIS3 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.
- </p>
-
-<h3>Size of the ISIS3 Data Area</h3>
- <p>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
- <a href="#SPICEWebService">SPICE Web service</a> that can be used in lieu of downloading all of
- the SPICE files. This reduces the total download size to about 10 GB.
- </p>
-
-<A NAME="ISIS3DataDownload"></A>
-<h3>Full ISIS3 Data Area Download</h3>
-
- <p>The ISIS3 Data Area is hosted on rsync servers and not through conda channels like the
- ISIS3 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
- <a href="#MissionSpecific">click here</a>. To download all ISIS3 data files, continue reading.
- </p>
-
- <p>To download all ISIS3 data, enter the following commands in the location where you want
- to install the ISIS3 Data Area:
- </p>
-
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/ .
- </pre>
-
- <p><em>Note: The above command downloads all ISIS data including the required base data area
- and all of the optional missiondata areas.
- </em></p>
-
-
-<A NAME="MissionSpecific"> </A>
-<h3>Partial Download of ISIS3 Base Data (Required)</h3>
- <p>The base data area is separate from the source code. This data area is crucial to ISIS3 and
- must be downloaded.
- </p>
-
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/base .
- </pre>
-
-<h3>Partial Download of Mission Specific Data</h3>
-
-
- <p>There are many missions supported by ISIS. If you are only working with a few missions
- then you should download only those specific sub-directories of the ISIS3 Data Area. One way
- you can save time and space is to not download the SPICE data for the mission you need.
- If you choose to not download the SPICE data, read the next section about the SPICE Web Service
- that provides instructions for excluding the SPICE kernels. Otherwise
- <a href="#ApolloMission">jump</a> to the mission specific sections.
- </p>
-
-
-<A NAME="SPICEWebService"> </A>
-<h3>ISIS SPICE Web Service</h3>
-
- <p>ISIS can now use a service to retrieve the SPICE data for all instruments ISIS supports
- via the internet. To use this service instead of your local SPICE data, click the WEB check box
- in the spiceinit program GUI or type spiceinit web=yes at the command line. Using the ISIS SPICE
- Web Service will significantly reduce the size of the downloads from our data area.
-
- If you want to use this service, without having to download all the SPICE data, add the
- following argument to the mission-specific rsync command:
- </p>
-
- <pre>
- --exclude='kernels'
- </pre>
- <p>For example, the following command will download the Cassini mission data except for SPICE kernels:
- </p>
-
- <pre>
- cd $ISISDATA
- rsync -azv <strong>--exclude='kernels'</strong> --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/cassini .
- </pre>
-
- <span style="font-size:120%; color:red; font-weight:bold">
- WARNING: Some instruments require mission data to be present for calibration, which may
- not be supported by the SPICE Web Server exclusively, 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 callobration programs.
- </span>
-
-<A NAME="ApolloMission"> </A>
- <p>Apollo Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- 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 .
- </pre>
-
-<A NAME="CassiniMission"> </A>
- <p>Cassini Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/cassini .
- </pre>
-
-<A NAME="ChandrayaanMission"> </A>
- <p>Chandrayaan Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/chandrayaan1 .
- </pre>
-
-<A NAME="ClementineMission"> </A>
- <p>Clementine Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/clementine1 .
- </pre>
-
-<A NAME="DawnMission"> </A>
- <p>Dawn Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/dawn .
- </pre>
-
-<A NAME="TGOMission"> </A>
- <p>ExoMars Trace Gas Orbiter Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/tgo .
- </pre>
-
-<A NAME="GalileoMission"> </A>
- <p>Galileo Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/galileo .
- </pre>
-
-<A NAME="HayabusaMission"> </A>
- <p>Hayabusa Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/hayabusa .
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/hayabusa2 .
- </pre>
-
-<A NAME="JunoMission"> </A>
- <p>Juno Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/juno .
- </pre>
-
-<A NAME="KaguyaMission"> </A>
- <p>Kaguya Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/kaguya .
- </pre>
-
-<A NAME="LunarOrbiterMission"> </A>
- <p>Lunar Orbiter Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/lo .
- </pre>
-
-<A NAME="LunarReconnaissanceOrbiterMission"> </A>
- <p>Lunar Reconnaissance Orbiter Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/lro .
- </pre>
-
-<A NAME="MarsExplorationRoverMission"> </A>
- <p>Mars Exploration Rover Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/mer .
- </pre>
-
-<A NAME="Mariner10Mission"> </A>
- <p>Mariner10 Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/mariner10 .
- </pre>
-
-<A NAME="MessengerMission"> </A>
- <p>Messenger Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/messenger .
- </pre>
-
-<A NAME="MarsExpressMission"> </A>
- <p>Mars Express Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/mex .
- </pre>
-
-<A NAME="MarsGlobalSurveyorMission"> </A>
- <p>Mars Global Surveyor Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/mgs .
- </pre>
-
-<A NAME="MarsReconnaissanceOrbiterMission"> </A>
- <p>Mars Reconnaissance Orbiter Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/mro .
- </pre>
-
-<A NAME="MarsOdysseyMission"> </A>
- <p>Mars Odyssey Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/odyssey .
- </pre>
-
-<A NAME="NearMission"> </A>
- <p>Near Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/near .
- </pre>
-
-<A NAME="NewHorizonsMission"> </A>
- <p>New Horizons Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/newhorizons .
- </pre>
-
-<A NAME="OdysseyMission"> </A>
- <p>Odyssey Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/odyssey .
- </pre>
-
-<A NAME="RoloMission"> </A>
- <p>Rolo Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/rolo .
- </pre>
-
-<A NAME="RosettaMission"> </A>
- <p>Rosetta Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/rosetta .
- </pre>
-
-<A NAME="Smart1Mission"> </A>
- <p>Smart1 Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/smart1 .
- </pre>
-
-<A NAME="VikingMission"> </A>
- <p>Viking Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/viking1 .
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/viking2 .
- </pre>
-
-<A NAME="VoyagerMission"> </A>
- <p>Voyager Mission (kernels can be excluded):
- </p>
- <pre>
- cd $ISISDATA
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/voyager1 .
- rsync -azv --delete --partial isisdist.astrogeology.usgs.gov::isis3data/data/voyager2 .
- </pre>
-
-<h2>Installing older versions of ISIS</h2>
- <h3>How do I install ISIS2?</h3>
- <p>
- If you are looking for ISIS2, please
- <a href="http://isis.astrogeology.usgs.gov/Isis2/isis-bin/installation.cgi">refer to the ISIS 2 Installation
- Guide</a> for instructions on downloading and installing ISIS 2.
- </p>
-
-<h3>How do I install ISIS3.5.2 or earlier?</h3>
- <p>
- If you are looking for a version of ISIS3 prior to 3.6.0, please
- <a href="../../documents/LegacyInstallGuide/index.html">refer to the Legacy ISIS3 Installation
- Guide</a> for instructions on downloading and installing ISIS3, versions prior to 3.6.0.
- </p>
+ <p>
+ Refer to the <a href="http://isis.astrogeology.usgs.gov/Isis2/isis-bin/installation.cgi">ISIS 2 Installation Guide</a>
+ for instructions on downloading and installing ISIS 2.
+ </p>
</body>
@@ -548,6 +55,7 @@ is a popular choice and may be downloaded below.
<change name="Kristin Berry" date="2018-08-28">Original Version</change>
<change name ="Tyler Wilson along with the ASC Development Team" date="2018-09-26">Updated version to incorporate installation through Conda</change>
<change name="Tyler Wilson" date="2018-10-01">Updated version after feedback was received from outside users.</change>
+ <change name="Jesse Mapel" date="2020-02-12">Changed to point to Github and legacy install guide.</change>
</history>
@@ -555,8 +63,7 @@ is a popular choice and may be downloaded below.
<title>Installing ISIS</title>
<brief>Downloading and installing ISIS3</brief>
<description>
- This document describes how to download/compile and install a
- binary version of ISIS3 as well
+ This document describes how to download and install ISIS3
</description>
<author>ASC Development Team</author>
<date>2018-08-28</date>
diff --git a/isis/src/docsys/documents/LegacyInstallGuide/LegacyInstallGuide.xml b/isis/src/docsys/documents/LegacyInstallGuide/LegacyInstallGuide.xml
index 36950f49b0faf87e2f250e68ef6aa2a9a3dbd2ce..47084016d4f7104b3c9ce704165e498e426d1442 100644
--- a/isis/src/docsys/documents/LegacyInstallGuide/LegacyInstallGuide.xml
+++ b/isis/src/docsys/documents/LegacyInstallGuide/LegacyInstallGuide.xml
@@ -643,11 +643,12 @@ you must <em>not</em> upgrade the ISIS Data Files!!!
and how to tell what shell a user is using to the UNIX Enviroment Setup section. Fixes #5372.</change>
<change name="Ian Humphrey" date="2018-04-06">Updated for latest supported Fedora version (Fedora25).</change>
<change name="Kristin Berry and Adam Goins" date="2018-08-28">Removed references to deprecated Java-based installer and split off into a new Legacy ISIS3 installation instructions page. </change>
+ <change name="Jesse Mapel" date="2020-02-12">Fixed version spacing to be a little more consistant.</change>
</history>
<bibliography>
- <title>Installing Legacy Versions of ISIS3</title>
- <brief>Downloading and installing ISIS 3 versions 3.5.2.0 and earlier</brief>
+ <title>Installing Legacy Versions of ISIS3</title>
+ <brief>Downloading and installing ISIS versions 3.5.2.0 and earlier</brief>
<description>
This document describes how to download and install a
binary version of ISIS.