Revert "Implement and test LaTeX output for all MooseDocs extensions"

framework/doc/content/css/moose.css

@@ -3,12 +3,12 @@
     --inl-blue-light: rgba(0, 104, 179, 1.0);
     --dark-blue: rgba(0, 44, 78, 1.0);
     --gray: rgba(117, 117, 117);
-    --alert-error: rgba(153, 0, 0, 1);
-    --alert-error-content: rgba(153, 0, 0, 0.1);
-    --alert-note: rgba(0, 88, 151);
+    --alert-error: #ef5350;
+    --alert-error-content: #ffebee;
+    --alert-note: var(--inl-blue);
     --alert-note-content: rgba(0, 88, 151, 0.1);
-    --alert-warning: rgba(255, 255, 51, 1.0);
-    --alert-warning-content: rgba(255, 255, 51, 0.1);
+    --alert-warning: #fbc02d;
+    --alert-warning-content: #fffde7;
     --alert-construction: rgba(255, 114, 33, 1.0);
     --alert-construction-content: rgba(255, 114, 33, 0.1);
 }
@@ -45,20 +45,11 @@ main {
   -webkit-font-smoothing: antialiased;
 }
 
-.material-icons .moose-help{
+.moose-help .material-icons{
     color:white;
     margin-left:5px;
 }
 
-.moose-col-icon{
-    font-size: 32pt;
-    display:inline-block;
-    width:100%;
-    padding-top: 16pt;
-    color: var(--inl-blue);
-    text-align:center;
-}
-
 .moose-inline-icon{
     vertical-align:bottom;
 }
@@ -450,10 +441,6 @@ span.moose-sqa-error{
     color:red;
 }
 
-.moose-sqa-items a:not(:last-child):after{
-    content:"; "
-}
-
 /* Children/Input file lists */
 ul.moose-list-children,
 ul.moose-list-inputs{
@@ -844,7 +831,7 @@ li p {
 }
 
 .moose-alert-warning .moose-alert-title{
-  color: black;
+  color: white;
   background-color: var(--alert-warning);
 }
 

framework/doc/content/js/init.js

@@ -1,8 +1,7 @@
 (function($){
     $(function(){
-        $('.tooltipped').tooltip();
+
         $('.modal').modal();
-        $('.collapsible').collapsible();
         $('.slider').slider();
         $('.dropdown-trigger').dropdown({
             inDuration: 300,
@@ -13,7 +12,6 @@
             alignment: 'left' // Displays dropdown with edge aligned to the left of button
         });
 
-
    // $('.collapsible').collapsible({
    //   onOpen: function(el) {var icons = $(el).find('i'); $(icons[0]).text('keyboard_arrow_up');},
    //   onClose: function(el) {var icons = $(el).find('i'); $(icons[0]).text('keyboard_arrow_down');}

framework/doc/content/source/bcs/DiffusionFluxBC.md

@@ -16,7 +16,7 @@ The standard theory of elliptic operators requires the specification of boundary
 parts of the boundary, so "implicitly" computing a residual contribution in this manner (instead of
 replacing it with the correct "data") falls outside of this theory. That said, there are instances
 where such an approach gives reasonable results in practice, see, for example, the paper by
-[cite!griffiths1997noboundary].
+[cite:griffiths1997noboundary].
 
 As an example, consider the Poisson problem with mixed
 boundary conditions:

framework/doc/content/source/bcs/PenaltyDirichletBC.md

@@ -57,12 +57,12 @@ boundary condition
 \end{equation}
 
 replacing the original Dirichlet boundary condition. It has been shown
-[cite!juntunen2009nitsche] that in order for the solution to this perturbed
+[cite:juntunen2009nitsche] that in order for the solution to this perturbed
 problem to converge to the solution of the original problem in the
 limit as $\epsilon \rightarrow 0$, the penalty parameter must depend
 on the mesh size, and that as we refine the mesh, the problem becomes
 increasingly ill-conditioned.  A related method for imposing Dirichlet boundary
-conditions, known as Nitsche's method [cite!juntunen2009nitsche], does not
+conditions, known as Nitsche's method [cite:juntunen2009nitsche], does not
 suffer from the same ill-conditioning issues, and is slated for inclusion
 in MOOSE some time in the future.
 

framework/doc/content/source/kernels/ConservativeAdvection.md

@@ -33,7 +33,7 @@ Without numerical stabilization the corresponding Jacobian is given by
 Advective flow is notoriously prone to physically-incorrect overshoots
 and undershoots, so in many simulations some numerical stabilization
 is used to reduce or eliminate this spurious behaviour.
-Full-upwinding [cite!dalen1979,adhikary2011] is an example of
+Full-upwinding [cite:dalen1979,adhikary2011] is an example of
 numerical stabilization and this essentially adds numerical diffusion
 to completely eliminate overshoots and undershoots.  Full-upwinding is
 available in `ConservativeAdvection` by setting the `upwinding_type`
@@ -125,7 +125,7 @@ same time the `OutflowBC` is removing $\langle\psi_i, \vec{v} u \cdot
 `OutflowBC` is actually adding fluid at the same rate the
 `ConservativeAdvection` Kernel is removing it. The physical interpretation
 is that something external to the model is adding fluid at exactly the
-rate specified by the initial conditions at that boundary.
+rate specified by the initial conditions at that boundary. 
 
 Instead, for $\vec{v} \cdot \vec{n} < 0$ users typically want to specify a particular value for an
 injected flux.  This is achieved by using an `InflowBC`.  This adds $\langle\psi_i, \vec{v} u_{B} \cdot

framework/doc/content/source/meshgenerators/BreakMeshByBlockGenerator.md

@@ -2,7 +2,7 @@
 
 !syntax description /MeshGenerators/BreakMeshByBlockGenerator
 
-This class implement a MeshGenerator to split a monolithic mesh by blocks similar to what is proposed by VP Nguyen [cite!Nguyen2014].
+This class implement a MeshGenerator to split a monolithic mesh by blocks similar to what is proposed by VP Nguyen [cite:Nguyen2014].
 
 To split the mesh, nodes shared by multiple blocks are duplicated N-1 times (where N is the number of blocks sharing a particular node). Each duplicated nodes is assigned to one block and all the element sharing that node are updated. A new sideset identifying the new interface is added and it is always linked to elements belonging to blocks with the lower id.
 
@@ -16,3 +16,5 @@ If one block is not named, its name will default to `Block` plus the `blockID`.
 !syntax parameters /MeshGenerators/BreakMeshByBlockGenerator
 
 !syntax inputs /MeshGenerators/BreakMeshByBlockGenerator
+
+

framework/doc/content/source/meshmodifiers/BreakMeshByBlock.md

@@ -2,7 +2,7 @@
 
 !syntax description /MeshModifiers/BreakMeshByBlock
 
-This class implement a MeshModifiers to split a monolithic mesh by blocks similar to what is proposed by VP Nguyen [cite!Nguyen2014].
+This class implement a MeshModifiers to split a monolithic mesh by blocks similar to what is proposed by VP Nguyen [cite:Nguyen2014].
 
 To split the mesh, nodes shared by multiple blocks are duplicated N-1 times (where N is the number of blocks sharing a particular node). Each duplicated nodes is assigned to one block and all the element sharing that node are updated. A new sideset identifying the new interface is added and it is always linked to elements belonging to blocks with the lower id.
 

framework/doc/content/source/partitioner/PetscExternalPartitioner.md

@@ -51,19 +51,19 @@ regular users to upgrade PETSc on their own. We will officially upgrade PETSc so
 ### 4 subdomains
 
 !row!
-!col! small=12 medium=6 large=3
+!col! class=s12 m6 l3
 !media party_4parts.png caption=`Party`
 !col-end!
 
-!col! small=12 medium=6 large=3
+!col! class=s12 m6 l3
 !media chaco_4parts.png caption=`chaco`
 !col-end!
 
-!col! small=12 medium=6 large=3
+!col! class=s12 m6 l3
 !media parmetis_4parts.png caption=`parmetis`
 !col-end!
 
-!col! small=12 medium=6 large=3
+!col! class=s12 m6 l3
 !media ptscotch_4parts.png caption=`ptscotch`
 !col-end!
 !row-end!
@@ -72,19 +72,19 @@ regular users to upgrade PETSc on their own. We will officially upgrade PETSc so
 ### 8 subdomains
 
 !row!
-!col! small=12 medium=6 large=3
+!col! class=s12 m6 l3
 !media party_8parts.png caption=`Party`
 !col-end!
 
-!col! small=12 medium=6 large=3
+!col! class=s12 m6 l3
 !media chaco_8parts.png caption=`chaco`
 !col-end!
 
-!col! small=12 medium=6 large=3
+!col! class=s12 m6 l3
 !media parmetis_8parts.png caption=`parmetis`
 !col-end!
 
-!col! small=12 medium=6 large=3
+!col! class=s12 m6 l3
 !media ptscotch_8parts.png caption=`ptscotch`
 !col-end!
 !row-end!

framework/doc/content/source/timeintegrators/NewmarkBeta.md

@@ -4,7 +4,7 @@
 
 ## Description
 
-Newmark time integration [citep!newmark1959amethod] is one of the commonly used time integration methods in structural dynamics problems. In this method, the second ($\ddot{u}$) and first ($\dot{u}$) time derivatives of a variable $u$ at $t+\Delta t$ are written in terms of the $u$, $\dot{u}$ and $\ddot{u}$ at time $t$, and $u$ at $t+\Delta t$ as shown below:
+Newmark time integration [citep:newmark1959amethod] is one of the commonly used time integration methods in structural dynamics problems. In this method, the second ($\ddot{u}$) and first ($\dot{u}$) time derivatives of a variable $u$ at $t+\Delta t$ are written in terms of the $u$, $\dot{u}$ and $\ddot{u}$ at time $t$, and $u$ at $t+\Delta t$ as shown below:
 
 \begin{equation}
 \begin{aligned}
@@ -19,7 +19,7 @@ In the above equations, $\beta$ and $\gamma$ are Newmark time integration parame
 - $\beta = \frac{1}{6}$ and $\gamma = \frac{1}{2}$ results in the linear acceleration method where the acceleration is linearly varying between $t$ and $t+\Delta t$. This method is also implicit, unconditionally stable and second order accurate in time. However, there is a small numerical damping when the linear acceleration method is used.
 - For $\gamma = \frac{1}{2}$, the method is second order accurate and it is unconditionally stable for $\frac{1}{2} \le \gamma \le 2 \beta$.
 
-When using the constant average acceleration method that has no numerical damping, high frequency noise can sometimes be observed in the velocity and acceleration time histories for a problem with prescribed displacement  [citep!bathe2012insight]. Using other parameters for $\beta$ and $\gamma$ results in non-zero numerical damping that damps out part of the high frequency noise but not all of it. Hilber-Hughes-Taylor (HHT) time integration is a variation of the Newmark method that damps out high frequency noise especially in structural dynamics problems. More details about this Newmark and HHT time integration schemes can be found in these [lecture notes](http://people.duke.edu/~hpgavin/cee541/NumericalIntegration.pdf). HHT time integration requires modification to the equation of motion and is currently implemented only for structural dynamics problems in tensor mechanics module.
+When using the constant average acceleration method that has no numerical damping, high frequency noise can sometimes be observed in the velocity and acceleration time histories for a problem with prescribed displacement  [citep:bathe2012insight]. Using other parameters for $\beta$ and $\gamma$ results in non-zero numerical damping that damps out part of the high frequency noise but not all of it. Hilber-Hughes-Taylor (HHT) time integration is a variation of the Newmark method that damps out high frequency noise especially in structural dynamics problems. More details about this Newmark and HHT time integration schemes can be found in these [lecture notes](http://people.duke.edu/~hpgavin/cee541/NumericalIntegration.pdf). HHT time integration requires modification to the equation of motion and is currently implemented only for structural dynamics problems in tensor mechanics module.
 
 !syntax parameters /Executioner/TimeIntegrator/NewmarkBeta
 

framework/doc/templates/sqa/system_design_description.md.template

@@ -58,16 +58,16 @@ Add or revise spcific defintions.
 - +Baseline+: A specification or product (e.g., project plan, maintenance and operations (M&O) plan,
   requirements, or design) that has been formally reviewed and agreed upon, that thereafter serves as
   the basis for use and further development, and that can be changed only by using an approved change
-  control process [citep!ASME-NQA-1-2008].
+  control process [citep:ASME-NQA-1-2008].
 
 - +Validation+: Confirmation, through the provision of objective evidence (e.g., acceptance test),
   that the requirements for a specific intended use or application have been fulfilled
-  [citep!ISO-systems-software].
+  [citep:ISO-systems-software].
 
 - +Verification+: (1) The process of: evaluating a system or component to determine whether the
   products of a given development phase satisfy the conditions imposed at the start of that
   phase. (2) Formal proof of program correctness (e.g., requirements, design, implementation reviews,
-  system tests) [citep!ISO-systems-software].
+  system tests) [citep:ISO-systems-software].
 
 !sqa-end!
 

framework/doc/templates/sqa/system_requirement_specification.md.template

@@ -112,16 +112,16 @@ Add or revise spcific defintions.
 - +Baseline+: A specification or product (e.g., project plan, maintenance and operations (M&O) plan,
   requirements, or design) that has been formally reviewed and agreed upon, that thereafter serves as
   the basis for use and further development, and that can be changed only by using an approved change
-  control process [citep!ASME-NQA-1-2008].
+  control process [citep:ASME-NQA-1-2008].
 
 - +Validation+: Confirmation, through the provision of objective evidence (e.g., acceptance test),
   that the requirements for a specific intended use or application have been fulfilled
-  [citep!ISO-systems-software].
+  [citep:ISO-systems-software].
 
 - +Verification+: (1) The process of: evaluating a system or component to determine whether the
   products of a given development phase satisfy the conditions imposed at the start of that
   phase. (2) Formal proof of program correctness (e.g., requirements, design, implementation reviews,
-  system tests) [citep!ISO-systems-software].
+  system tests) [citep:ISO-systems-software].
 
 !sqa-end!
 

modules/chemical_reactions/doc/content/modules/chemical_reactions/index.md

@@ -2,7 +2,7 @@
 
 The chemical reactions module provides a set of tools for the calculation of multicomponent aqueous
 reactive transport in porous media, originally developed as the [MOOSE] application RAT
-[citep!guo2013].
+[citep:guo2013].
 
 ## Theory
 
@@ -11,7 +11,7 @@ species from which every other species (including minerals) can be expressed in
 chemical species that can be expressed as combinations of primary species are termed *secondary*
 species.
 
-Following [cite!lichtner1996], the mass conservation equation is formulated in terms of the total
+Following [citet:lichtner1996], the mass conservation equation is formulated in terms of the total
 concentration of a primary species $j$, $\Psi_j$, and has the form
 
 \begin{equation}
@@ -211,7 +211,7 @@ The syntax for solid kinetic reactions is similar, except that no equilibrium co
 the reactions block.
 
 To demonstrate the use of the reaction network parser, consider the geochemical model used in
-[cite!guo2013], which features aqueous equilibrium reactions as well as kinetic mineral dissolution
+[citet:guo2013], which features aqueous equilibrium reactions as well as kinetic mineral dissolution
 and precipitation.
 
 Equilibrium reactions:

modules/contact/doc/content/source/linesearches/ContactLineSearch.md

@@ -23,7 +23,7 @@ contact set is resolved late in the Newton solve, the linear tolerance will retu
 tolerance set through the traditional `l_tol` parameter.
 
 This line search helps significantly with the phenomenon in the contact
-literature known as jamming or zig-zagging [citep!wriggers2006computational]
+literature known as jamming or zig-zagging [citep:wriggers2006computational]
 where a Newton solve bounces back and forth between
 different contact sets. However, it is not a panacea. It will only partially
 assuage problems associated with "bad" linear solves which can arise during

modules/doc/config.yml

@@ -34,9 +34,6 @@ Extensions:
             Documentation: documentation.menu.md
             Help: help.menu.md
             News: newsletter/index.md
-    MooseDocs.extensions.bibtex:
-        duplicates:
-            - kim_phase-field_1999 # referenced in both Tensor Mechanics and Phase Field
     MooseDocs.extensions.appsyntax:
         executable: ${MOOSE_DIR}/modules/combined
         hide:

modules/doc/content/documentation.menu.md

@@ -1,5 +1,5 @@
 !row! class=row
-!col! small=12 medium=6 large=4
+!col! class=s12 m6 l4
 ## [Application Usage](application_usage/index.md)
 
 - [Examples](examples/index.md)
@@ -14,7 +14,7 @@
 - [Old Wiki(deprecated)](https://www.mooseframework.org/old/wiki)
 !col-end!
 
-!col! small=12 medium=6 large=4
+!col! class=s12 m6 l4
 ## [Application Development](application_development/index.md)
 
 - [Source Pages](source/index.md)
@@ -31,7 +31,7 @@
 - [libMesh Doxygen](http://mooseframework.org/docs/doxygen/libmesh/classes.html)
 !col-end!
 
-!col! small=12 medium=6 large=4
+!col! class=s12 m6 l4
 ## [MOOSEDocs](MooseDocs/index.md)
 
 - [MooseDocs/specification.md]

modules/doc/content/help.menu.md

@@ -1,5 +1,5 @@
 !row! class=row
-!col! small=12 medium=6 large=6
+!col! class=s12 m6 l6
 ## Questions
 
 - [MOOSE Users Mailing List](https://groups.google.com/forum/#!forum/moose-users)
@@ -8,7 +8,7 @@
 
 !col-end!
 
-!col! small=12 medium=6 large=6
+!col! class=s12 m6 l6
 ## Information and Tools
 
 - [A to Z Index](help/a-to-z.md)