Unverified Commit eb5eb4cd authored by Jesse Mapel's avatar Jesse Mapel Committed by GitHub
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Updated user documentation content (#4856)

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        </table>


<!-- API Reference​ -->
<!-- Documentation Guides​ -->
    <hr/>
    <h2>ISIS API Reference</h2>
    <h2>Documentation Guides</h2>
      <p>
        The ISIS API reference is particularly useful if you are working on an application
        or interested in using the ISIS library as a dependency.
        If you're not familiar with working on the ISIS documentation,
        these guides can help get you started.
      </p>
      <table class="tableTOC">

        <!-- hardcoded links -->
        <tr valign="top">
          <th style="width:25%">
            <a href="https://astrodiscuss.usgs.gov/">
            astrodiscuss</a>
          </th>
          <td>
          Ask or answer questions on out community discussion board.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/issues">
            GitHub Issues</a>
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Contributing-Application-Documentation">
            Contributing ISIS Application Documentation</a>
          </th>
          <td>
          Comment on bug reports or feature requests from other users.
          This how-to guide will take you through the steps required to write and modify the ISIS
          application documentation.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/discussions?discussions_q=label%3ARFC">
            Requests for Comment</a>
            <a href="../documents/HowToApplicationExamples/index.html">
            ISIS Application Examples Guide</a>
          </th>
          <td>
          Provide feedback on major changes proposed for ISIS.
          This how-to guide covers writing examples for ISIS application documentation.
          Application examples are a specialized section of the ISIS application
          documentation and require additional steps besides editing the application XML.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS_TC">
            ISIS Technical Committee</a>
            <a href="../documents/HowToGeneralDocumentation/index.html">
            General ISIS Documentation Guide</a>
          </th>
          <td>
          Get involved in project governance.
          This how-to guide covers writing documentation for this website.
          </td>
        </tr>
      </table>


<!-- XML Schemas -->
<!-- Testing Guides -->
    <hr/>
      <h2>XML Schemas</h2>
    <h2>Testing Guides</h2>
      <p>
        The interface for ISIS applications and much of the ISIS documentation (including this
        very page) are generated from XML files. These schemas are a helpful reference if you
        are creating a new application, modifying application arguments, or writing documentation.
        Testing is a crucial component of creating sustainable software and a requirement for all
        code contributions to ISIS. These guides will help you run and modify the ISIS test suite.
      </p>
      <table class="tableTOC">

        <!-- hardcoded links -->
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#getting-started-with-github">
            Downloading the Source Code</a>
          </th>
          <td>
          How to pull the source code from GitHub.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#anaconda-and-isis3-dependencies">
            Dependency Management</a>
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Writing-ISIS3-Tests-Using-Gtest-and-Ctest">
            Writing Tests Using GTest and CTest</a>
          </th>
          <td>
          How to download the dependencies required to build ISIS.
          As of version 3.6, ISIS uses googletest and CTest for testing. This how-to guide will
          walk you through the steps required to write tests using the new frameworks. It also
          covers the steps needed to convert ISIS applications to the new callable format.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#building-isis3">
            Building</a>
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Test-Data-Obtaining,-Maintaining,-and-Submitting">
            ISIS Test Data</a>
          </th>
          <td>
          How to build ISIS once you have the source code and dependencies downloaded.
          Legacy Makefile based tests in ISIS use a input and truth data to confirm that the
          aplications produce the proper output. This page explains how to download these
          files required to run the ISIS test suite.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#running-tests">
            Running the Test Suite</a>
            <a href="../documents/HowToApplicationCategoryTest/index.html">
            Legacy Makefile Tests Guide</a>
          </th>
          <td>
          How to run the ISIS test suite once ISIS is built.
          This documents describes how legacy Makefile tests work. Contributors are required
          to use the new googletest system for new tests, but there are rare situations where
          existing legacy Makefile tests need to be updated and cannot be converted.
          </td>
        </tr>
      </table>


<!-- Documentation Guides​ -->
<!-- Maintainer Guides​ -->
    <hr/>
    <h2>Documentation Guides</h2>
    <h2>Maintainer Guides</h2>
      <p>
        If you're not familiar with working on the ISIS documentation,
        these guides can help get you started.
        These resources are useful for maintainers and outline the processes that
        support the broader user and contributor community.
      </p>
      <table class="tableTOC">

        <!-- hardcoded links -->
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Exercises_1">
            Basic ISIS3 Programming</a>
          </th>
          <td>
          hese exercises will walk you through the basics of ISIS applications.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Exercises_2">
            Advanced ISIS Programming Exercises</a>
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Public-Release-Process">
            Release Process</a>
          </th>
          <td>
          These exercises give you the chance to explore more yourself and interact with more
          complex components of the ISIS API.
          This guide goes through all the steps required to create both release candidates
          and full releases.
          </td>
        </tr>
      </table>


<!-- Testing Guides -->
<!-- API Reference​ -->
    <hr/>
    <h2>Testing Guides</h2>
    <h2>ISIS API Reference</h2>
      <p>
        Testing is a crucial component of creating sustainable software and a requirement for all
        code contributions to ISIS. These guides will help you run and modify the ISIS test suite.
        The <a href="../Object/Developer/index.html">ISIS API reference</a> is particularly
        useful if you are working on an application or interested in using the ISIS library
        as a dependency.
      </p>
      <table class="tableTOC">

        <!-- hardcoded links -->
        <tr valign="top">
          <th style="width:25%">
            <a href="">
            Adding a New Feature</a>
          </th>
          <td>
          This document will walk you through what's needed when adding a new feature to ISIS.
          If there is something you think is missing in ISIS this will walk you through the
          steps needed to add it.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="">
            Modifying an Existing Feature</a>
          </th>
          <td>
          Modifying an existing feature is slightly more complex than adding a new feature to ISIS.
          This document will walk you through what is different when you are building from an
          existing feature instead of something new.
          </td>
        </tr>
      </table>


<!-- Maintainer Guides​ -->
<!-- XML Schemas -->
      <hr/>
    <h2>Maintainer Guides</h2>
      <h2>XML Schemas</h2>
      <p>
        These resources are useful for maintainers and outline the processes that
        support the broader user and contributor community.
        The interface for ISIS applications and much of the ISIS documentation (including this
        very page) are generated from XML files. These schemas are a helpful reference if you
        are creating a new application, modifying application arguments, or writing documentation.
      </p>
      <table class="tableTOC">

        <!-- hardcoded links -->
        <tr valign="top">
          <th style="width:25%">
            <a href="">
            Adding a New Feature</a>
            <a href="../Schemas/Application/documentation/index.html">
            ISIS Application XML Schema</a>
          </th>
          <td>
          This document will walk you through what's needed when adding a new feature to ISIS.
          If there is something you think is missing in ISIS this will walk you through the
          steps needed to add it.
          This schema defines the ISIS application XML format. This includes the applications
          documentation and all of the application arguments.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="">
            Modifying an Existing Feature</a>
            <a href="../Schemas/Documentation/documentation/index.html">
            ISIS Web Documentation XML Schema</a>
          </th>
          <td>
          Modifying an existing feature is slightly more complex than adding a new feature to ISIS.
          This document will walk you through what is different when you are building from an
          existing feature instead of something new.
          This schema defines the XML documentation format used to generate this documentation.
          If you want to make a change to the ISIS website documentation, then you will need to
          reference this schema for your changes.
          </td>
        </tr>
      </table>
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@@ -121,49 +121,30 @@ Deborah Lee Soltesz
    <hr/>
    <h2>GitHub Issues</h2>
      <p>
        The first step for all code contributions to ISIS is a GitHub issue. Look at the open
        enhancement requests to see what other members of the community have asked for and maybe
        there will be something you are interested in too. It you just want to get started with
        contributing code; issues labeled with Good First Issue are an excellent place for
        newcomers to start.
        The first step for all code contributions to ISIS is a GitHub issue. If you want to get started with
        contributing code, then start with the currently open issues.
      </p>
      <table class="tableTOC">

        <!-- hardcoded links -->
        <tr valign="top">
          <th style="width:25%">
            <a href="https://astrodiscuss.usgs.gov/">
            astrodiscuss</a>
            <a href="https://github.com/USGS-Astrogeology/ISIS3/issues?q=is%3Aopen+is%3Aissue+label%3Aenhancement">
            Enhancement Requests</a>
          </th>
          <td>
          Ask or answer questions on out community discussion board.
          Look at the open enhancement requests to see what other members of the community have
          asked for and maybe there will be something you are interested in too.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/issues">
            GitHub Issues</a>
            <a href="https://github.com/USGS-Astrogeology/ISIS3/issues?q=is%3Aopen+is%3Aissue+label%3A%22good+first+issue%22">
            Good First Issues</a>
          </th>
          <td>
          Comment on bug reports or feature requests from other users.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/discussions?discussions_q=label%3ARFC">
            Requests for Comment</a>
          </th>
          <td>
          Provide feedback on major changes proposed for ISIS.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS_TC">
            ISIS Technical Committee</a>
          </th>
          <td>
          Get involved in project governance.
          Issues labeled with Good First Issue have been idenditifed by other contributors as
          places where newcomers can get started.
          </td>
        </tr>
      </table>
@@ -173,50 +154,11 @@ Deborah Lee Soltesz
      <hr/>
      <h2>GitHub Pull Requests</h2>
      <p>
        If you are interested in what other contributors are working on, look at the GitHub
        pull requests that are currently open. Even if you do not have write permissions to the
        If you are interested in what other contributors are working on, look at the
        <a href="https://github.com/USGS-Astrogeology/ISIS3/pulls">GitHub pull requests</a>
        that are currently open. Even if you do not have write permissions to the
        repository, input and testing on pull requests are always appreciated.
      </p>
      <table class="tableTOC">

        <!-- hardcoded links -->
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#getting-started-with-github">
            Downloading the Source Code</a>
          </th>
          <td>
          How to pull the source code from GitHub.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#anaconda-and-isis3-dependencies">
            Dependency Management</a>
          </th>
          <td>
          How to download the dependencies required to build ISIS.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#building-isis3">
            Building</a>
          </th>
          <td>
          How to build ISIS once you have the source code and dependencies downloaded.
          </td>
        </tr>
        <tr valign="top">
          <th style="width:25%">
            <a href="https://github.com/USGS-Astrogeology/ISIS3/wiki/Developing-ISIS3-with-cmake#running-tests">
            Running the Test Suite</a>
          </th>
          <td>
          How to run the ISIS test suite once ISIS is built.
          </td>
        </tr>
      </table>


<!-- FOOTER -->
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@@ -97,16 +97,13 @@ Deborah Lee Soltesz
          <tr valign="top">
            <td align="left">
              <h1>
                User Explore in Detail 
                Explore Using ISIS in Detail 
              </h1>
              <p>
                Now that you have some experience running applications and working with data, you may have some questions 
                about how exactly ISIS works.
              </p>
              <p>
                On this page you will find a wide variety of resources explaining the specific details of how ISIS works. Many 
                components of ISIS were created in response to the needs of specific data sets. So, there are a wide variety of 
                processing paths and customizations that you can leverage when creating a workflow.
                Now that you have some experience running applications and working with data, understanding the finer details
                about how ISIS works can make you a more efficient and powerful ISIS user.
                On this page you will find resources explaining individual components of ISIS.
                
              </p>
            </td>
            <td align="right" class="caption">
@@ -121,7 +118,7 @@ Deborah Lee Soltesz
      <hr/>
      <h2>General Purpose</h2>
      <p>
        These resources are useful regardless of what you are using ISIS for. They provide details about fundamental components of ISIS that 
        These resources provide details about fundamental components of ISIS that 
        are used across applications.
      </p>
      <table class="tableTOCmulticol">
@@ -206,8 +203,9 @@ Deborah Lee Soltesz
    <hr/>
    <h2>Task Specific Guides</h2>
      <p>
        These resources apply to specific applications or specialized processing methods. They provide particulars about how to work with individual 
        applications or how specialized data is formatted.
        These resources apply to specific applications or specialized processing methods.
        Over the years, ISIS has evolved in response to the needs of new datasets; so, there are a wide variety of 
        processing paths and customizations that you can leverage when creating your workflow.
      </p>
      <table class="tableTOCmulticol">

@@ -271,7 +269,7 @@ Deborah Lee Soltesz
            Release Schedule</a>
          </th>
          <td>
          Description of Astrogeology Science Center's ISIS release cadence and expected dates of future releases.
          A description of ISIS's release cadence and expected dates of future releases.
          </td>
        </tr>

@@ -281,7 +279,7 @@ Deborah Lee Soltesz
            Backward Compatibility Policy</a>
          </th>
          <td>
          Policy for ISIS backward compatibility for users.
          What users can expect to still work after updating to a new version of ISIS.
          </td>
        </tr>

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@@ -97,12 +97,16 @@ Deborah Lee Soltesz
          <tr valign="top">
            <td align="left">
              <h1>
                User Get Inspired
                Get Inspired by Other ISIS Users
              </h1>
              <p>
                Let's zoom out and look at what community members have used ISIS to do in the past. These papers, talks and 
                These papers, talks and 
                demonstrations are examples that you can draw inspiration from and model your own workflows after.
              </p>
              <p>
                If you have examples you would like to add to this page, submit a pull request on
                <a href="https://github.com/USGS-Astrogeology/ISIS3">GitHub</a>!
              </p>
            </td>
            <td align="right" class="caption">
            <a href="../index.html">Home</a>
@@ -135,8 +139,8 @@ Deborah Lee Soltesz
            Using the Community Sensor Model with Planetary Data</a>
          </th>
          <td>
            A talk given by Jesse Mapel at the OpenPlanetary Lunch covering the Community Sensor Model API and the USGS ASC's implementation of it and 
            supported cameras as of October 2021.
            A talk given by Jesse Mapel at an OpenPlanetary Lunch covering the Community Sensor Model API, the USGS ASC's implementation of it, 
            supported cameras as of October 2021, and how to use them in ISIS.
          </td>
        </tr>
      </table>
@@ -180,7 +184,7 @@ Deborah Lee Soltesz

<!-- Papers and Posters -->
    <hr/>
    <h2>Papers and Posters</h2>
    <h2>Papers, Posters, and Abstracts</h2>
      <table class="tableTOC">

        <!-- hardcoded links -->
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