Reorganizing documentation. Refs #3.

doc/config.yml

@@ -9,6 +9,7 @@ Content:
         root_dir: ${MOOSE_DIR}/modules/doc/content
         content:
             - getting_started/**
+            - application_usage/peacock.md
             - help/development/**
             - media/**
             - templates/**
@@ -24,19 +25,11 @@ Extensions:
         home: https://www.mooseframework.org/mastodon
         menu:
             Getting Started:
-                MacOS (Mojave): getting_started/macos_mojave.md
-                MacOS (Other): getting_started/macos_other.md
-                Ubuntu: getting_started/ubuntu.md
+                Installation: getting_started/installation.md
                 Running MASTODON: getting_started/running_mastodon.md
-            Examples: examples/index.md
-            Manuals:
-                Theory: manuals/theory/index.md
-                Software Quality: /sqa/index.md
-                User: manuals/user/index.md
-                Developer: manuals/developer/index.md
+            Documentation: documentation.menu.md
+            SQA: /sqa/index.md
             News: news/index.md
-            Docs:
-                Syntax: syntax/index.md
             Help:
                 FAQ: help/faq.md
                 Contact: help/contact_us.md

doc/content/bib/publications.md

@@ -0,0 +1,7 @@
+# MASTODON publications
+
+## Journal papers
+
+## Conference papers
+
+## Reports

doc/content/documentation.menu.md

@@ -0,0 +1,28 @@
+!row! class=row
+
+!col! small=12 medium=4 large=4
+## Usage
+
+- [Theory manual](manuals/theory/index.md)
+- [User manual](manuals/user/index.md)
+- [Syntax](syntax/index.md)
+- [Peacock](peacock.md)
+
+!col-end!
+
+!col! small=12 medium=4 large=4
+## Development
+
+- [Developers manual](manuals/developer/index.md)
+- [MOOSE Doxygen](https://mooseframework.org/docs/doxygen/moose/classes.html)
+
+!col-end!
+
+!col! small=12 medium=4 large=4
+## Demonstration
+
+- [Examples](examples/index.md)
+- [Publications](publications.md)
+
+!col-end!
+!row-end!

doc/content/examples/example9.md

@@ -0,0 +1,34 @@
+# Example 9: Fault tree analysis using the Python module in MASTODON
+
+This example demonstrates the use of the fault tree analysis and risk assessment
+in MASTODON using the FTA Python module.
+
+## Simple fault tree analysis with risk values
+Activated by `analysis='Risk'`
+Will assume that the distributions or the points estimates provided by the
+`basic_events` parameter are risk values. If distributions are provided it is
+assumed that they correspond to the risk distributions.
+
+
+## Fragility
+Activated by `analysis='Fragility'`
+Will assume that the distributions provided by the `basic_events` parameter
+correspond to the fragilities of the basic events.
+
+### Approach 1
+Basic event fragilities are first convolved with the hazard and the risk values
+for each basic event are calculated. The risk values are then propagated
+through the fault tree.
+
+### Approach 2
+Basic event fragilities are propagated through the fault tree first and the top
+event fragility is calculated. The top event fragility is convolved with the
+hazard curve to calculate the risk.
+
+### Lite
+Activated by `lite=True`
+Will only perform fragility analysis with approach 2 and the importance measures
+are not calculated. Results files are also not created. Good for situations in
+which, we only need the top risk with approach 2. 
+
+!bibtex bibliography

doc/content/getting_started/installation.md

@@ -0,0 +1,23 @@
+## Installation
+
+The MASTODON source code is available on [GitHub](https://github.com/idaholab/mastodon) and must be downloaded and compiled
+before using. Instructions for downloading and installing MASTODON are below.
+
+!alert warning title=No Mac OS 10.15 (Catalina) support at this time
+There are numerous changes with this operating system that we are working through including
+the removal of all 32-bit libraries, a new default shell, and changes to Python. Do NOT upgrade
+your system if you are developing or running MOOSE or MOOSE-based applications.
+
+- +MacOS+
+
+  - [Mojave](getting_started/macos_mojave.md)
+  - [High Sierra or older](getting_started/macos_other.md)
+
+- +Linux+
+
+  - [Ubuntu](getting_started/ubuntu.md)
+
+- +Windows 10+
+
+  - Windows 10 installation is possible, but is experimental and currently not supported. For
+    Windows 10 installation instructions, we recommend reaching out to the MASTODON team [here](help/contact_us.md).

doc/content/getting_started/macos_mojave.md

@@ -1,3 +1,3 @@
-!include installation/macos_mojave.md end=install_moose.md
+!include installation/macos_mojave.md end=install
 
 !include getting_started/mastodon.md

doc/content/manuals/developer/index.md

@@ -1,3 +1,10 @@
 # Developer Manual
 
+This manual provides the information needed for developers of MASTODON. This
+manual is actively being improved and more information is being added to make it
+more useful. Interested developers are therefore requested to reach out to the
+team as mentioned [here](contact_us.md).
+
+!include include/developer/development.md
+
 !include include/developer/documentation.md

doc/content/manuals/include/developer/development.md

@@ -0,0 +1,17 @@
+## Developing new objects
+
+MASTODON is built upon the [MOOSE Framework](https://mooseframework.inl.gov) and
+therefore uses the MOOSE architecture and protocols for development. Developers therefore are highly
+encouraged to look into the MOOSE Framework and also reach out to the MASTODON team [here](help/contact_us.md) when
+planning to develop new objects. Development and inclusion of a new object (material, boundary condition, etc.) in MASTODON (or MOOSE) involves the following steps:
+
+
+- Writing the code
+- Writing the documentation, which includes
+
+  - Syntax information
+  - Theory and references in the theory manual
+  - Usage instructions in the user manual
+
+- Examples, if any
+- Creating test problems that will be included in the list of tests

doc/content/manuals/include/developer/documentation.md

@@ -1,4 +1,4 @@
-## Instructions for documentation
+## Documenting new objects
 
 Prior to merging the code, MOOSE and MASTODON require adequate documentation
 describing the implemented feature, such as materials, post processors, etc.