Huge PR to get closer to 1.0

.github/workflows/run-unit-tests.yml

@@ -0,0 +1,58 @@
+name: MOOSE Tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Install Apptainer
+        uses: eWaterCycle/setup-apptainer@v2
+        with:
+         apptainer-version: 1.3.6
+
+      - name: Restore Apptainer library
+        run: |
+          apptainer remote add --no-login SylabsCloud cloud.sycloud.io
+          apptainer remote use SylabsCloud
+
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          path:  Fizzy 
+
+      - name: Pull Apptainer image
+        run: |
+          apptainer pull library://billellis.07/fizzy/fizzy_cont_202112
+
+      - name: Build application
+        run: |
+          apptainer cache clean --force
+          df -h
+          apptainer overlay create --size 1024 overlay.img
+          apptainer exec \
+            --bind ${{ github.workspace }}:/workspace \
+            --overlay overlay.img \
+            fizzy_cont_202112_latest.sif \
+            bash -c "
+              . /opt/intel/oneapi/setvars.sh &&
+              cd /workspace/Fizzy/unit &&
+              make -j$(nproc)
+            "
+
+      - name: Run tests
+        run: |
+          apptainer exec \
+            --bind ${{ github.workspace }}:/workspace \
+            fizzy_cont_202112_latest.sif \
+            bash -c "
+              cd /workspace/Fizzy/unit &&
+              ./fizzy-unit-opt -j$(nproc)
+            "

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "FizzyCompiledSource"]
+	path = FizzyCompiledSource
+	url = https://github.com/TheBEllis/FizzyCompiledSource

Makefile

@@ -86,18 +86,23 @@ export LDFLAGS := $(libmesh_LDFLAGS)
 export LIBS := $(libmesh_LIBS)
 
 FISPACT_DIR ?= ${MOOSE_DIR}/../FISPACT/ubuntu/20.10
+FISPACT_DIR ?= ${MOOSE_DIR}
 FISPACT_INCLUDES ?= -I ${FISPACT_DIR}/include/c -I ${FISPACT_DIR}/include/cpp
-FISPACT_LIB_DIR ?= ${FISPACT_DIR}/lib/
-# FISPACT_LIB ?= 
+FISPACT_LIB_DIR ?= ${FISPACT_DIR}/lib/linux
 
 PUGIXML_DIR ?= $(MOOSE_DIR)/../pugixml/
 PUGIXML_INCLUDES ?= -I $(PUGIXML_DIR)/src/
 PUGIXML_LIB_DIR ?= ${PUGIXML_DIR}/build/
 
 HDF5_DIR ?= /usr/lib/x86_64-linux-gnu/hdf5/openmpi/lib/
 
-ADDITIONAL_LIBS := -L$(FISPACT_LIB_DIR) -ljsonfortran -lmonitor -lfispact -lfispactapi -lfmt -L$(PUGIXML_LIB_DIR) -lpugixml -L$(HDF5_DIR) -lhdf5 -lhdf5_cpp
-ADDITIONAL_LIBS += $(CC_LINKER_SLFLAG)$(FISPACT_LIB_DIR)
+ADDITIONAL_LIBS := -L$(FISPACT_LIB_DIR) -ljsonfortran -lmonitor -lfispact -lfispactapi -L$(PUGIXML_LIB_DIR) -lpugixml -L$(HDF5_DIR) -lhdf5 -lspdlog
+# ADDITIONAL_LIBS += $(CC_LINKER_SLFLAG)$(FISPACT_LIB_DIR)
 
 ADDITIONAL_CPPFLAGS += $(FISPACT_INCLUDES) ${PUGIXML_INCLUDES}
 
+FIZZY_EXTERNAL_FLAGS = ${ADDITIONAL_LIBS} ${ADDITIONAL_CPPFLAGS}
+
+$(app_LIB): EXTERNAL_FLAGS := $(FIZZY_EXTERNAL_FLAGS)
+$(app_test_LIB): EXTERNAL_FLAGS := $(FIZZY_EXTERNAL_FLAGS)
+$(app_EXEC): EXTERNAL_FLAGS := $(FIZZY_EXTERNAL_FLAGS)

README.md

@@ -1,6 +1,69 @@
-Fizzy
-=====
+# Fizzy
+
+Fizzy is a MOOSE application wrapping the nuclear inventory, source term and multi-physics code, FISPACT-II.
+
+## Dependencies
+- [FISPACT-II](https://www.ukaea.org/service/fispact/)(5.0+) binaries.
+- A working [MOOSE](https://mooseframework.inl.gov/) build.
+    - Being a MOOSE based application, Fizzy also has the same [minimum requirements](https://mooseframework.inl.gov/sqa/minimum_requirements.html) as MOOSE.
+- PugiXML
+    - PugiXML can be installed easily from most package managers
+    - `sudo apt install libpugixml`
+
+## Obtaining Fizzy
+
+To obtain Fizzy, simply clone this repository.
+
+```language=bash
+git clone https://github.com/TheBEllis/Fizzy.git
+cd Fizzy
+```
+
+## Install
+
+> [!WARNING]
+> Fizzy has only been tested on Ubuntu 24.04 (so far). Other Linux distros, MacOS and Windows have not been tested. If users trying to run Fizzy on these platforms
+experience issues with installation and/or running, please report the issue on Fizzy's [github issues](https://github.com/TheBEllis/Fizzy/issues) page.
+
+To install Fizzy, users must specify the directory containg their FISPACT-II binaries. This can be done using the environment variable `FISPACT_DIR`. The exact directory will differe depending on the version of FISPACT-II being used. 
+
+Users must also make sure that the relevent FISPACT-II libraries are present in their `LD_LIBRARY_PATH`.
+
+#### For FISPACT-II V5.1
+
+```language=bash
+export FISPACT_DIR=/path/to/FISPACT/api/
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path/to/FISPACT/api/lib/linux
+```
+
+#### For FISPACT-II V5.0
+
+```language=bash
+export FISPACT_DIR=/path/to/FISPACT/ubuntu/20.10
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path/to/FISPACT/ubuntu/20.10/lib
+```
+
+> [!IMPORTANT]
+> The exact directories that need to be set may differ depending on users directory structure. By setting `FISPACT_DIR`, Fizzy will automatically look for FISPACT libraries and includes at `${FISPACT_DIR}/lib/linux` and `${FISPACT_DIR}/includes/cpp`. Users can manually set the locations of libraries and includes by settings the environment variables `FISPACT_LIB_DIR` and `FISPACT_INCLUDE_DIR`.
+
+The final step is to run `make` in the Fizzy root directory. After a successful install, an executable called `Fizzy-opt` should be found in the application root directory. 
+
+```language=bash
+cd /path/to/Fizzy
+make -j 4
+```
+
+## Building docs
+Due to Fizzy currently being private, the only way to access documentation is by building it locally. Users can do this by running.
+
+```
+cd /path/to/Fizzy/doc
+./moosedocs.py build --destination ./build_folder
+```
+
+This will populate the specified `build_folder` with html files. To access the documentation after building, `cd` into the build folder and open `index.html` from your chosen web browser.
+
+## References
+
 
-Fork "Fizzy" to create a new MOOSE-based application.
 
-For more information see: [https://mooseframework.inl.gov/getting_started/new_users.html#create-an-app](https://mooseframework.inl.gov/getting_started/new_users.html#create-an-app)

doc/config.yml

@@ -3,18 +3,80 @@ Content:
         root_dir: ${ROOT_DIR}/doc/content
     moose:
         root_dir: ${MOOSE_DIR}/framework/doc/content
+    fluid_properties:
+        root_dir: ${MOOSE_DIR}/modules/fluid_properties/doc/content
+    heat_transfer:
+        root_dir: ${MOOSE_DIR}/modules/heat_transfer/doc/content
+    navier_stokes:
+        root_dir: ${MOOSE_DIR}/modules/navier_stokes/doc/content
+    ray_tracing:
+        root_dir: ${MOOSE_DIR}/modules/ray_tracing/doc/content
+    reactor:
+        root_dir: ${MOOSE_DIR}/modules/reactor/doc/content
+    solid_mechanics:
+        root_dir: ${MOOSE_DIR}/modules/solid_mechanics/doc/content
+    solid_properties:
+        root_dir: ${MOOSE_DIR}/modules/solid_properties/doc/content
+    stochastic_tools:
+        root_dir: ${MOOSE_DIR}/modules/stochastic_tools/doc/content
+    subchannel:
+        root_dir: ${MOOSE_DIR}/modules/subchannel/doc/content
+    thermal_hydraulics:
+        root_dir: ${MOOSE_DIR}/modules/thermal_hydraulics/doc/content
+    modules:
+        root_dir: ${MOOSE_DIR}/modules/doc/content
         content:
-            - js/*
-            - css/*
-            - contrib/**
-            - media/**
+            - help/development/VSCode.md
+            - help/development/analyze_jacobian.md
+            - help/finite_element_concepts/nodal_patch_recovery.md
+            - application_development/performance_benchmarking.md
+            - application_usage/restart_recover.md
+            - application_usage/command_line_usage.md
+    python:
+        root_dir: ${MOOSE_DIR}/python/doc/content
+        content:
+            - python/mms.md
+            - python/MooseDocs/**
+            - python/moosesqa/index.md
+            - python/source/moosetree/Node.md
+            - python/testers/**
+            - python/CSVDiff.md
+            - python/TestHarness.md
+
 Renderer:
     type: MooseDocs.base.MaterializeRenderer
+
 Extensions:
     MooseDocs.extensions.navigation:
         name: Fizzy
+        repo: https://github.com/TheBEllis/Fizzy
+        menu:
+          Getting Started:
+            Installation: start.md
+          Documentation:
+            Tutorials: /tutorials/index.md
+            Input Syntax: /source/index.md
+
+    MooseDocs.extensions.common:
+      shortcuts: 
+        !include ${MOOSE_DIR}/framework/doc/globals.yml
+
     MooseDocs.extensions.appsyntax:
         executable: ${ROOT_DIR}
-        remove: !include ${MOOSE_DIR}/framework/doc/remove.yml
-        includes:
-            - include
+        app_name: Fizzy
+        # remove:
+        #     framework: !include ${MOOSE_DIR}/framework/doc/remove.yml
+        # unregister:
+        #     framework: !include ${MOOSE_DIR}/framework/doc/unregister.yml
+
+    MooseDocs.extensions.acronym:
+        acronyms: !include ${MOOSE_DIR}/framework/doc/acronyms.yml
+
+    MooseDocs.extensions.template:
+        active: True
+
+globals:
+    type: MooseDocs.extensions.common
+    shortcuts:
+
+

doc/content/index.md

@@ -1,3 +1,11 @@
 !config navigation breadcrumbs=False scrollspy=False
 
-# FizzyApp
+# Fizzy class=center style=font-weight:200;font-size:400%
+
+!style halign=center fontsize=120%
+Enabling FISPACT-II solves on unstructured meshes
+
+Fizzy utilises [FISPACT-II](https://www.ukaea.org/service/fispact/) APIs to enable easier usage of the nuclear inventory and source term code on unstructured meshes. 
+
+It is primarily designed for use when the user has tallied neutron transport results on an unstructured mesh.
+

doc/content/media/FizzyDocsFlow.drawio

@@ -0,0 +1,47 @@
+<mxfile host="app.diagrams.net">
+  <diagram name="Page-1" id="nuHiYNkpX3rEI0BLqaq0">
+    <mxGraphModel dx="808" dy="458" grid="0" gridSize="16" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="1100" pageHeight="850" math="0" shadow="0">
+      <root>
+        <mxCell id="0" />
+        <mxCell id="1" parent="0" />
+        <mxCell id="fN4mFnTmdzPNVWRfBsAc-1" edge="1" parent="1" source="ZBh9AiTcaC5hWOgsyVWg-1" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;entryX=0;entryY=0.5;entryDx=0;entryDy=0;strokeColor=light-dark(#000000,#FFFFFF);" target="ZBh9AiTcaC5hWOgsyVWg-2">
+          <mxGeometry relative="1" as="geometry" />
+        </mxCell>
+        <mxCell id="ZBh9AiTcaC5hWOgsyVWg-1" parent="1" style="rounded=1;whiteSpace=wrap;html=1;fillColor=#1ba1e2;fontColor=#ffffff;strokeColor=#006EAF;" value="for(elem_id in local_elements)" vertex="1">
+          <mxGeometry height="68" width="112" x="32" y="80" as="geometry" />
+        </mxCell>
+        <mxCell id="fN4mFnTmdzPNVWRfBsAc-2" edge="1" parent="1" source="ZBh9AiTcaC5hWOgsyVWg-2" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;entryX=0;entryY=0.5;entryDx=0;entryDy=0;strokeColor=light-dark(#000000,#FFFFFF);" target="ZBh9AiTcaC5hWOgsyVWg-3">
+          <mxGeometry relative="1" as="geometry" />
+        </mxCell>
+        <mxCell id="ZBh9AiTcaC5hWOgsyVWg-2" parent="1" style="rounded=1;whiteSpace=wrap;html=1;fillColor=#1ba1e2;fontColor=#ffffff;strokeColor=#006EAF;" value="flux_spectra = read_flux(elem_id)" vertex="1">
+          <mxGeometry height="68" width="112" x="192" y="80" as="geometry" />
+        </mxCell>
+        <mxCell id="fN4mFnTmdzPNVWRfBsAc-6" edge="1" parent="1" source="ZBh9AiTcaC5hWOgsyVWg-3" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;entryX=0;entryY=0.5;entryDx=0;entryDy=0;strokeColor=light-dark(#000000,#FFFFFF);" target="ZBh9AiTcaC5hWOgsyVWg-4">
+          <mxGeometry relative="1" as="geometry" />
+        </mxCell>
+        <mxCell id="ZBh9AiTcaC5hWOgsyVWg-3" parent="1" style="rounded=1;whiteSpace=wrap;html=1;fillColor=#1ba1e2;fontColor=#ffffff;strokeColor=#006EAF;" value="input_data = set_input(elem_id, flux, material_props, irradiation_schedule)" vertex="1">
+          <mxGeometry height="68" width="128" x="352" y="80" as="geometry" />
+        </mxCell>
+        <mxCell id="fN4mFnTmdzPNVWRfBsAc-5" edge="1" parent="1" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;entryX=0.47;entryY=1.005;entryDx=0;entryDy=0;entryPerimeter=0;strokeColor=light-dark(#000000,#FFFFFF);" target="ZBh9AiTcaC5hWOgsyVWg-2">
+          <mxGeometry relative="1" as="geometry">
+            <Array as="points">
+              <mxPoint x="756" y="208" />
+              <mxPoint x="245" y="208" />
+            </Array>
+            <mxPoint x="755.63" y="148.00000000000003" as="sourcePoint" />
+            <mxPoint x="239.99800000000005" y="148.68000000000004" as="targetPoint" />
+          </mxGeometry>
+        </mxCell>
+        <mxCell id="fN4mFnTmdzPNVWRfBsAc-8" edge="1" parent="1" source="ZBh9AiTcaC5hWOgsyVWg-4" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;entryX=0;entryY=0.5;entryDx=0;entryDy=0;strokeColor=light-dark(#000000,#FFFFFF);" target="fN4mFnTmdzPNVWRfBsAc-7">
+          <mxGeometry relative="1" as="geometry" />
+        </mxCell>
+        <mxCell id="ZBh9AiTcaC5hWOgsyVWg-4" parent="1" style="rounded=1;whiteSpace=wrap;html=1;fillColor=#1ba1e2;fontColor=#ffffff;strokeColor=#006EAF;" value="fispact_run(&lt;div&gt;input_data, output_data)&lt;/div&gt;" vertex="1">
+          <mxGeometry height="68" width="112" x="528" y="80" as="geometry" />
+        </mxCell>
+        <mxCell id="fN4mFnTmdzPNVWRfBsAc-7" parent="1" style="rounded=1;whiteSpace=wrap;html=1;fillColor=#1ba1e2;fontColor=#ffffff;strokeColor=#006EAF;" value="extract_inventory_data&lt;div&gt;(output_data)&lt;/div&gt;" vertex="1">
+          <mxGeometry height="68" width="136" x="688" y="80" as="geometry" />
+        </mxCell>
+      </root>
+    </mxGraphModel>
+  </diagram>
+</mxfile>

doc/content/source/actions/AddPhotonSpectraVectorPPAllBlocks.md

@@ -0,0 +1,21 @@
+# AddPhotonSpectraVectorPPAllBlocks
+
+!alert construction title=Undocumented Action Class
+The AddPhotonSpectraVectorPPAllBlocks has not been documented. The content listed below should be used as a starting point for
+documenting the class, which includes the typical automatic documentation associated with an Action;
+however, what is contained is ultimately determined by what is necessary to make the documentation
+clear for users.
+
+!syntax description /VectorPostprocessors/PhotonEmissionAllBlocks/AddPhotonSpectraVectorPPAllBlocks
+
+## Overview
+
+!! Replace these lines with information regarding the AddPhotonSpectraVectorPPAllBlocks action.
+
+## Example Input File Syntax
+
+!! Describe and include an example of how to use the AddPhotonSpectraVectorPPAllBlocks action.
+
+!syntax description /VectorPostprocessors/PhotonEmissionAllBlocks/AddPhotonSpectraVectorPPAllBlocks
+
+!syntax parameters /VectorPostprocessors/PhotonEmissionAllBlocks/AddPhotonSpectraVectorPPAllBlocks

doc/content/source/auxkernels/FispactElementKernel.md

@@ -0,0 +1,23 @@
+# FispactElementKernel
+
+!alert construction title=Undocumented Class
+The FispactElementKernel has not been documented. The content listed below should be used as a starting point for
+documenting the class, which includes the typical automatic documentation associated with a
+MooseObject; however, what is contained is ultimately determined by what is necessary to make the
+documentation clear for users.
+
+!syntax description /AuxVariables/AuxKernel/FispactElementKernel
+
+## Overview
+
+!! Replace these lines with information regarding the FispactElementKernel object.
+
+## Example Input File Syntax
+
+!! Describe and include an example of how to use the FispactElementKernel object.
+
+!syntax parameters /AuxVariables/AuxKernel/FispactElementKernel
+
+!syntax inputs /AuxVariables/AuxKernel/FispactElementKernel
+
+!syntax children /AuxVariables/AuxKernel/FispactElementKernel

doc/content/source/auxkernels/FispactNuclideKernel.md

@@ -0,0 +1,23 @@
+# FispactNuclideKernel
+
+!alert construction title=Undocumented Class
+The FispactNuclideKernel has not been documented. The content listed below should be used as a starting point for
+documenting the class, which includes the typical automatic documentation associated with a
+MooseObject; however, what is contained is ultimately determined by what is necessary to make the
+documentation clear for users.
+
+!syntax description /AuxVariables/AuxKernel/FispactNuclideKernel
+
+## Overview
+
+!! Replace these lines with information regarding the FispactNuclideKernel object.
+
+## Example Input File Syntax
+
+!! Describe and include an example of how to use the FispactNuclideKernel object.
+
+!syntax parameters /AuxVariables/AuxKernel/FispactNuclideKernel
+
+!syntax inputs /AuxVariables/AuxKernel/FispactNuclideKernel
+
+!syntax children /AuxVariables/AuxKernel/FispactNuclideKernel

doc/content/source/index.md

@@ -0,0 +1,4 @@
+!config navigation collapsible-sections=[None, 'open', 'open', 'open', 'open', 'open']
+
+!content location=source
+