Setup SQA documents for python

framework/doc/content/sqa/framework_srs.md

@@ -1,4 +1,4 @@
-!template load file=srs.md.template project=Framework
+!template load file=srs.md.template project=Framework category=framework
 
 !template! item key=system-purpose
 !include sqa/system_purpose.md
@@ -88,16 +88,16 @@ behaviors of each user-defined object.
 !template-end!
 
 !template item key=functional-requirements
-!sqa requirements link=False collections=FUNCTIONAL category=framework
+!sqa requirements link=False collections=FUNCTIONAL category={{category}}
 
 !template item key=usability-requirements
-!sqa requirements link=False collections=USABILITY category=framework
+!sqa requirements link=False collections=USABILITY category={{category}}
 
 !template item key=performance-requirements
-!sqa requirements link=False collections=PERFORMANCE category=framework
+!sqa requirements link=False collections=PERFORMANCE category={{category}}
 
 !template item key=system-interfaces-requirements
-!sqa requirements link=False collections=SYSTEM category=framework
+!sqa requirements link=False collections=SYSTEM category={{category}}
 
 !template! item key=human-system-integration
 !! human-system-integration-begin

framework/doc/content/syntax/Debug/index.md

@@ -4,11 +4,10 @@
 
 The `[Debug]` input file block is designed to contain options to enable debugging tools for a
 simulation. For example, the input file snippet below demonstrates how to enable the material
-property debugging tool. A complete list of the available options is provided in [#debug-params].
+property debugging tool. A complete list of the available options is provided below.
 
 !listing show_material_props_debug.i block=Debug
 
-
 !syntax parameters /Debug id=debug-params
 
 

framework/doc/content/syntax/Outputs/index.md

@@ -57,7 +57,7 @@ Note, the use of "file_base" anywhere in the `[Outputs]` block disables all defa
 
 [output-types] provides a list of the most common output types, including the short-cut syntax
 as well as the type to be used when creating a sub-block. A complete list of all available
-output objects is given is provided below in [#output-objects].
+output objects is provided below.
 
 !table id=output-types caption=List of common output objects included in core MOOSE framework
 !include output_types.md

modules/doc/config.yml

@@ -1,6 +1,7 @@
 Content:
-    - modules/doc/content
     - framework/doc/content
+    - python/doc/content
+    - modules/doc/content
     - modules/chemical_reactions/doc/content
     - modules/combined/doc/content
     - modules/contact/doc/content
@@ -155,6 +156,7 @@ Extensions:
         reports: !include modules/doc/sqa_reports.yml
         categories:
             framework: !include framework/doc/sqa_framework.yml
+            python: !include python/doc/sqa_python.yml
             contact: !include modules/contact/doc/sqa_contact.yml
             electromagnetics: !include modules/electromagnetics/doc/sqa_electromagnetics.yml
             fluid_properties: !include modules/fluid_properties/doc/sqa_fluid_properties.yml

modules/doc/content/application_usage/index.md

@@ -8,7 +8,7 @@ These documentation pages aid in running MOOSE-based applications.  For developm
 
 [Input File Syntax](input_syntax.md)
 
-[Peacock](peacock.md) - Graphical user interface and results visualization
+[Peacock](python/peacock.md) - Graphical user interface and results visualization
 
 [Tracked Apps](tracked_apps.md) - A list of applications being developed
 
@@ -17,4 +17,3 @@ These documentation pages aid in running MOOSE-based applications.  For developm
 [Restart and Recovery](restart_recover.md)
 
 [Hypre/BoomerAMG Preconditioning](hypre.md) - In-depth discussion of using Hypre's algebraic multigrid preconditioner: BoomerAMG
-

modules/doc/content/getting_started/examples_and_tutorials/tutorial01_app_development/step02_input_file.md

@@ -70,7 +70,7 @@ This will open the Peacock window and display the mesh used for the [simple diff
 Peacock is a python application. As such, during the initial execution binary files are cached, which often takes a few minutes. Subsequent executions of Peacock should be quicker.
 
 !alert note title=Bash alias for Peacock
-The command-line syntax for running Peacock can be simplified by creating a bash alias for it. Be sure to visit the [application_usage/peacock.md] page to learn how to do this.
+The command-line syntax for running Peacock can be simplified by creating a bash alias for it. Be sure to visit the [python/peacock.md] page to learn how to do this.
 
 ## Demonstration id=demo
 

modules/doc/content/getting_started/examples_and_tutorials/tutorial01_app_development/step06_input_params.md

@@ -116,7 +116,7 @@ Run the following commands to visualize the solution with PEACOCK:
          replace=['<d>', 'problems',
                   '<e>', 'pressure_diffusion_out']
 
-Since no numerical changes were made here, the results should be identical to the [previous step](tutorial01_app_development/step05_kernel_object.md#result-demo). Note that the above command uses the `peacock` alias so you'll need to set the `$PATH` environment variable in your bash profile (see the [application_usage/peacock.md] page). This syntax shall henceforth be used exclusively whenever executing PEACOCK.
+Since no numerical changes were made here, the results should be identical to the [previous step](tutorial01_app_development/step05_kernel_object.md#result-demo). Note that the above command uses the `peacock` alias so you'll need to set the `$PATH` environment variable in your bash profile (see the [python/peacock.md] page). This syntax shall henceforth be used exclusively whenever executing PEACOCK.
 
 ### Commit id=commit-demo
 

modules/doc/content/getting_started/examples_and_tutorials/tutorial03_verification/step03_analytical_solution.md

@@ -131,7 +131,7 @@ cd ~/projects/problems/verification
 ```
 
 When complete an output file will be produced with the name "1d_analytical_out.e", this file
-can be viewed using [Paraview](https://www.paraview.org/) or [application_usage/peacock.md].
+can be viewed using [Paraview](https://www.paraview.org/) or [python/peacock.md].
 
 
 ## Compute Error

modules/doc/content/getting_started/examples_and_tutorials/tutorial03_verification/step04_mms.md

@@ -127,7 +127,7 @@ cd ~/projects/problems/verification
 ```
 
 When complete an output file will be produced with the name "2d_main_out.e", this file
-can be viewed using [Paraview](https://www.paraview.org/) or [application_usage/peacock.md].
+can be viewed using [Paraview](https://www.paraview.org/) or [python/peacock.md].
 [tutorial03-snow-results] show the change in temperature across the domain with time. A key
 feature is that the surface remains cool as the heat source warms the snow internally, creating large
 temperature gradient at the surface.

modules/doc/content/getting_started/new_users.md

@@ -58,7 +58,7 @@ files and implement custom behavior in an application. The [first tutorial](tuto
 
 A text editor is necessary for creating application files. There are many options available, so please feel free to chose an editor that meets your needs. A popular option for application developers is [VSCode](https://code.visualstudio.com/), which has community developed add-ons specifically for MOOSE: [VSCode MOOSE](VSCode.md).
 
-A graphical post-processor, particularly one that can read [ExodusII](https://prod-ng.sandia.gov/techlib-noauth/access-control.cgi/1992/922137.pdf) files, is also necessary. [!ac](MOOSE) includes a [!ac](GUI): [PEACOCK](application_usage/peacock.md). Another popular tool is [ParaView](https://www.paraview.org/). Both of these applications are free and will allow you to visualize and process the results of your simulations.
+A graphical post-processor, particularly one that can read [ExodusII](https://prod-ng.sandia.gov/techlib-noauth/access-control.cgi/1992/922137.pdf) files, is also necessary. [!ac](MOOSE) includes a [!ac](GUI): [PEACOCK](python/peacock.md). Another popular tool is [ParaView](https://www.paraview.org/). Both of these applications are free and will allow you to visualize and process the results of your simulations.
 
 ## Join the Community id=join
 

modules/doc/content/index.md

@@ -50,4 +50,4 @@ Multiphysics Object-Oriented Simulation Environment
 
 !include upcoming_training.md
 
-!media media/inl_blue.png dark_src=media/inl_white.png style=width:30%;display:block;margin-top:3em;margin-left:auto;margin-right:auto;
+!media large_media/framework/inl_blue.png dark_src=large_media/framework/inl_white.png style=width:30%;display:block;margin-top:3em;margin-left:auto;margin-right:auto;

modules/doc/content/infrastructure/index.md

@@ -3,7 +3,7 @@
 The following pages describe some infrastructure that supports the development
 of MOOSE and MOOSE-based applications:
 
-- [Peacock](application_usage/peacock.md): The MOOSE graphical user interface
+- [Peacock](python/peacock.md): The MOOSE graphical user interface
 - [VSCode](help/development/VSCode.md)
 - [MooseDocs](MooseDocs/index.md): The MOOSE documentation system
 - [Python Tools](python/index.md)

modules/porous_flow/doc/content/modules/porous_flow/lava_lamp.md

@@ -19,7 +19,7 @@ and the temperature at 45$^{\circ}$C:
 !listing modules/porous_flow/examples/lava_lamp/2phase_convection.i start=[temperature] end=[brineco2]
 
 The porepressure is initialised to approximate hydrostatic conditions, and the total mass fraction of CO$_{2}$ is zero except towards the top of the model domain where it is 0.2.  This corresponds to a gas saturation of 0.29 (the gas is almost all CO$_{2}$ and only about 0.2% brine) and the mass-fraction of CO$_{2}$ in the liquid phase is 0.048.  The porosity is slightly randomised by sampling from a uniform distribution between the minimum and maximum values specified in the [RandomIC](RandomIC.md) initial condition, and this promotes initiation of the beautiful "fingers" of CO$_{2}$-rich brine seen in the results. The random field seed can be changed in the input file, or on the command line using [command line overriding](command_line_usage.md optional=True). The porosity field is output in the Exodus file that is created, so
-can be visualized in the MOOSE GUI [peacock](peacock.md optional=True) or in an external visualization package.
+can be visualized in the MOOSE GUI [peacock](python/peacock.md optional=True) or in an external visualization package.
 
 !listing modules/porous_flow/examples/lava_lamp/2phase_convection.i block=ICs
 

modules/scalar_transport/doc/config.yml

@@ -14,7 +14,6 @@ Content:
         root_dir: modules/doc/content
         content:
           - application_usage/command_line_usage.md
-          - media/inl_blue.png
 Renderer:
     type: MooseDocs.base.MaterializeRenderer
 Extensions:

modules/thermal_hydraulics/doc/config.yml

@@ -13,7 +13,6 @@ Content:
         root_dir: modules/doc/content
         content:
           - application_usage/command_line_usage.md
-          - media/inl_blue.png
 
 Renderer:
     type: MooseDocs.base.MaterializeRenderer

modules/thermal_hydraulics/doc/content/modules/thermal_hydraulics/index.md

@@ -91,4 +91,4 @@ Please use the [migration guide](howto/thm_ad_migration_guide.md) to update your
 
 ### Developed by class=center style=font-size:90%;margin-bottom:0.5em;font-weight:100
 
-!media media/inl_blue.png style=width:20%;display:block;margin-left:auto;margin-right:auto;
+!media large_media/framework/inl_blue.png style=width:20%;display:block;margin-left:auto;margin-right:auto;

python/MooseDocs/commands/build.py

@@ -55,7 +55,7 @@ def command_line_options(subparser, parent):
                         help="Create a local live server.")
     parser.add_argument('--dump', action='store_true',
                         help="Show page tree to the screen.")
-    parser.add_argument('--num-threads', '-j', type=int, choices=range(1,12),
+    parser.add_argument('--num-threads', '-j', type=int, choices=range(1,13),
                         default=int(min(multiprocessing.cpu_count() / 2, 12)),
                         help="The number of parallel threads to execute with. The max. is twelve.")
     parser.add_argument('--port', default='8000', type=str,

python/MooseDocs/extensions/sqa.py

@@ -18,6 +18,7 @@
 import uuid
 import json
 import time
+import itertools
 import pyhit
 
 import MooseDocs
@@ -183,14 +184,13 @@ def preExecute(self):
                 break
 
         # Setup the SQAMooseAppReports to use the syntax from the running app
-        for reports in self.__reports.values():
-            for app_report in reports[2]:
-                app_report.app_syntax = app_syntax
-                app_report.exe_directory = exe_dir
-                app_report.exe_name = exe_name.rsplit('-', maxsplit=1)[0] if exe_name else None
-                if app_syntax is None:
-                    msg = 'Attempting to inject application syntax into SQAMooseAppReport, but the syntax does not exist.'
-                    LOG.warning(msg)
+        for app_report in itertools.chain.from_iterable(reports[2] for reports in self.__reports.values() if reports[2] is not None):
+            app_report.app_syntax = app_syntax
+            app_report.exe_directory = exe_dir
+            app_report.exe_name = exe_name.rsplit('-', maxsplit=1)[0] if exe_name else None
+            if app_syntax is None:
+                msg = 'Attempting to inject application syntax into SQAMooseAppReport, but the syntax does not exist.'
+                LOG.warning(msg)
 
         # Set default collection and add RunException tests to FAILURE_ANALYSIS collection
         d_type = self['default_collection']
@@ -340,7 +340,7 @@ def _addRequirement(self, parent, info, page, req, requirements, category, setti
         # Skip add if ...
         if req.deprecated:
             return
-        if (collections is not None) and not any(c in collections for c in req.collections):
+        if (collections is not None) and (req.collections is not None) and not any(c in collections for c in req.collections):
             return
         if (types is not None) and not any(t in types for t in req.types or set()):
             return
@@ -1009,15 +1009,18 @@ def _getBadgeText(status):
 
 class RenderSQADocumentReport(RenderSQAReport):
     def createMaterialize(self, parent, token, page):
-        html.Tag(parent, 'h3', string='Necessary SQA Document Report(s)')
-        super().createMaterialize(parent, token, page)
+        if token['reports']:
+            html.Tag(parent, 'h3', string='Necessary SQA Document Report(s)')
+            super().createMaterialize(parent, token, page)
 
 class RenderSQARequirementReport(RenderSQAReport):
     def createMaterialize(self, parent, token, page):
-        html.Tag(parent, 'h3', string='Requirement Completion Report(s)')
-        super().createMaterialize(parent, token, page)
+        if token['reports']:
+            html.Tag(parent, 'h3', string='Requirement Completion Report(s)')
+            super().createMaterialize(parent, token, page)
 
 class RenderSQAMooseAppReport(RenderSQAReport):
     def createMaterialize(self, parent, token, page):
-        html.Tag(parent, 'h3', string='Application Design Page Report(s)')
-        super().createMaterialize(parent, token, page)
+        if token['reports']:
+            html.Tag(parent, 'h3', string='Application Design Page Report(s)')
+            super().createMaterialize(parent, token, page)

python/MooseDocs/test/subconfig/tests

@@ -1,6 +1,6 @@
 [Tests]
   issues = '#18137'
-  design = subsite/index.md
+  design = MooseDocs/index.md
 
   [build]
     type = RunCommand

python/doc/config.yml

@@ -0,0 +1,25 @@
+Content:
+    - framework/doc/content
+    - python/doc/content
+
+Renderer:
+    type: MooseDocs.base.MaterializeRenderer
+
+Extensions:
+    MooseDocs.extensions.appsyntax: disable
+    MooseDocs.extensions.navigation:
+        name: MOOSE Tools
+        repo: https://github.com/idaholab/moose
+        home: /python/index.md
+    MooseDocs.extensions.common:
+        shortcuts: !include framework/doc/globals.yml
+    MooseDocs.extensions.acronym:
+        acronyms: !include framework/doc/acronyms.yml
+    MooseDocs.extensions.template:
+        active: True
+    MooseDocs.extensions.sqa:
+        active: True
+        reports: !include python/doc/sqa_reports.yml
+        categories:
+            framework: !include framework/doc/sqa_framework.yml
+            python: !include python/doc/sqa_python.yml

modules/doc/content/python/MooseDocs/config.md → python/doc/content/python/MooseDocs/config.md

@@ -35,7 +35,7 @@ during translation allowing different pages to use different readers, renderers,
 extensions, which provides an extraordinary amount of flexibility about how your website is built.
 
 As a good example of how to resolve content conflicts, consider the main
-[MOOSE website](index.md exact=True) along with the [workshop/index.md alternative=missing_config.md].
+MOOSE website along with the [workshop/index.md alternative=missing_config.md].
 It is possible to build the [main site configuration](modules/doc/config.yml language=yaml) by
 itself by running the following commands:
 

modules/doc/content/python/MooseDocs/extensions/gallery.md → python/doc/content/python/MooseDocs/extensions/gallery.md

@@ -20,7 +20,7 @@ card command are listed in [card-settings].
                caption=Example use of the 'card' command.
 !card level_set/vortex_out.mp4 title=Vortex Benchmark style=width:50%;
 The level set equation is commonly used to for interface tracking, especially when the interface
-velocity is known. MOOSE contains a level set module, for more information see [level_set/index.md].
+velocity is known.
 !devel-end!
 
 !devel settings module=MooseDocs.extensions.gallery

modules/doc/content/python/MooseDocs/extensions/media.md → python/doc/content/python/MooseDocs/extensions/media.md

@@ -24,7 +24,7 @@ The "style" setting may be used, as in the example below, to control the placeme
 image.
 
 !devel! example id=example-media caption=Example of the media command with an image.
-!media media/inl_blue.png style=width:25%;float:right;margin-left:30px;
+!media large_media/framework/inl_blue.png style=width:25%;float:right;margin-left:30px;
 
 INL is part of the U.S. Department of Energy's complex of national laboratories. The laboratory
 performs work in each of the strategic goal areas of DOE: energy, national security, science and
@@ -70,7 +70,7 @@ possible to create numbered images that may be referenced, as shown in [example-
 The "id" and "caption" settings are available for both images and videos.
 
 !devel! example id=example-image-float caption=Example image with caption and numbered prefix.
-!media media/inl_blue.png
+!media large_media/framework/inl_blue.png
        id=inl-logo
        caption=The Idaho National Laboratory logo.
        style=width:50%;padding:20px;