Fail on warnings in the documentation (Exawind#624)

* Fail on warnings in the documentation.

* Use https for HIP binaries.

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: AMR-Wind CI
+name: AMR-Wind-CI
 
 on:
   push:
@@ -10,8 +10,10 @@ jobs:
   Formatting:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: DoozyX/[email protected]
+    - name: Clone
+      uses: actions/checkout@v3
+    - name: Check formatting
+      uses: DoozyX/[email protected]
       with:
         source: './amr-wind ./unit_tests ./tools/utilities'
         exclude: '.'
@@ -45,7 +47,8 @@ jobs:
       uses: styfle/[email protected]
       with:
         access_token: ${{github.token}}
-    - uses: actions/checkout@v2
+    - name: Clone
+      uses: actions/checkout@v3
       with: 
         submodules: true
     - name: Dependencies
@@ -96,7 +99,8 @@ jobs:
         uses: styfle/[email protected]
         with:
           access_token: ${{github.token}}
-      - uses: actions/checkout@v2
+      - name: Clone
+        uses: actions/checkout@v3
         with:
           submodules: true
       - name: Prepare CUDA environment
@@ -128,13 +132,14 @@ jobs:
         uses: styfle/[email protected]
         with:
           access_token: ${{github.token}}
-      - uses: actions/checkout@v2
+      - name: Clone
+        uses: actions/checkout@v3
         with:
           submodules: true
       - name: Prepare HIP environment
         run: |
-          wget -q -O - http://repo.radeon.com/rocm/rocm.gpg.key | sudo apt-key add -
-          echo 'deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ ubuntu main' | sudo tee /etc/apt/sources.list.d/rocm.list
+          wget -q -O - https://repo.radeon.com/rocm/rocm.gpg.key | sudo apt-key add -
+          echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/debian/ ubuntu main' | sudo tee /etc/apt/sources.list.d/rocm.list
           echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' | sudo tee -a /etc/profile.d/rocm.sh
           sudo apt-get update
           sudo apt-get install -y --no-install-recommends ninja-build \
@@ -166,7 +171,8 @@ jobs:
         uses: styfle/[email protected]
         with:
           access_token: ${{github.token}}
-      - uses: actions/checkout@v2
+      - name: Clone
+        uses: actions/checkout@v3
         with:
           submodules: true
       - name: Prepare DPC++ environment
@@ -198,7 +204,8 @@ jobs:
         uses: styfle/[email protected]
         with:
           access_token: ${{github.token}}
-      - uses: actions/checkout@v2
+      - name: Clone
+        uses: actions/checkout@v3
         with:
           submodules: true
       - name: Dependencies
@@ -234,7 +241,8 @@ jobs:
         uses: styfle/[email protected]
         with:
           access_token: ${{github.token}}
-      - uses: actions/checkout@v2
+      - name: Clone
+        uses: actions/checkout@v3
         with:
           submodules: true
       - name: Dependencies
@@ -281,7 +289,8 @@ jobs:
 #        uses: styfle/[email protected]
 #        with:
 #          access_token: ${{github.token}}
-#      - uses: actions/checkout@v2
+#      - name: Clone
+#        uses: actions/checkout@v3
 #        with:
 #          submodules: true
 #      - name: Build and test

.github/workflows/docs.yml

@@ -1,4 +1,4 @@
-name: AMR-Wind Docs
+name: AMR-Wind-Docs
 
 on:
   push:
@@ -14,7 +14,8 @@ jobs:
         uses: styfle/[email protected]
         with:
           access_token: ${{github.token}}
-      - uses: actions/checkout@v2
+      - name: Clone
+        uses: actions/checkout@v3
       - name: Python
         uses: actions/setup-python@v2
         with:
@@ -31,7 +32,7 @@ jobs:
         # execute from top-level amr-wind directory
         run: |
           echo "::add-matcher::.github/problem-matchers/sphinx.json"
-          sphinx-build -M html ./docs/sphinx ./build_docs/manual 2>&1 | tee -a build-output.txt
+          sphinx-build -M html ./docs/sphinx ./build_docs/manual -W --keep-going -n 2>&1 | tee -a build-output.txt
           # Doxygen output gets parsed wrong by the sphinx problem matcher so unregister it
           echo "::remove-matcher owner=sphinx-problem-matcher-loose-no-severity::"
           echo "::remove-matcher owner=sphinx-problem-matcher-loose::"

docs/sphinx/developer/unit_testing.rst

@@ -175,11 +175,11 @@ a brief overview of the core classes and their purpose.
 ```````````````````````````````````
 
 Classes written in AMR-Wind often require user inputs that are generally read in
-from input files through :class:`amrex::ParmParse` (see `docs
+from input files through `amrex::ParmParse` (see `docs
 <https://amrex-codes.github.io/amrex/docs_html/Basics.html#parmparse>`_).
 ``pp_utils`` are a set of functions that create skeleton input data that are
 used by various classes during initialization. For example, it populates the
-problem domain, mesh sizes, etc. so that :class:`amrex::AmrMesh` can be
+problem domain, mesh sizes, etc. so that `amrex::AmrMesh` can be
 initialized properly.
 
 .. function:: default_mesh_inputs()
@@ -189,8 +189,7 @@ initialized properly.
 
 .. function:: default_time_inputs()
 
-   Populates ParmParse data structure with necessary inputs for
-   :class:`amr_wind::SimTime`.
+   Populates ParmParse data structure with necessary inputs for `amr_wind::SimTime`.
 
 .. class:: AmrexTestEnv
 
@@ -315,10 +314,10 @@ of this test fixture:
 
 .. class:: AmrTestMesh
 
-:class:`AmrTestMesh` is a concrete implementation of :class:`amrex::AmrCore`
+:class:`AmrTestMesh` is a concrete implementation of `amrex::AmrCore`
 that creates an AMR mesh that can be used with unit testing. In addition to
 implementing the basic level data creation methods and refinement routines
-``ErrorEst``, it also creates an :class:`amr_wind::FieldRepo` instance for
+``ErrorEst``, it also creates an `amr_wind::FieldRepo` instance for
 creating and manipulating fields from within unit tests. :class:`AmrTestMesh` is
 never directly created within unit tests, instead it is created on-demand
 through the test fixture :class:`MeshTest` described next.
@@ -328,7 +327,7 @@ through the test fixture :class:`MeshTest` described next.
 :class:`MeshTest` is the base test fixture for any test that requires a mesh and
 associated field data that will be used by the test. In addition to performing
 setup/teardown actions described in :class:`AmrexTest`, it also resets the
-default :class:`amrex::Geometry` static data so that different tests can run on
+default `amrex::Geometry` static data so that different tests can run on
 different problem domains perscribed by the test fixture.
 
 Almost all unit tests within AMR-Wind use :class:`MeshTest` as their base test
@@ -432,7 +431,7 @@ scratch. After a call to this function, the mesh is ready for use.
 .. function:: populate_parameters()
 
    Populate default parameters necessary for creating an AMRMesh and
-   :class:`amr_wind::SimTime` objects.
+   `amr_wind::SimTime` objects.
 
 
 .. function:: create_mesh_instance()
@@ -451,7 +450,7 @@ be used as starting points for users to write new tests:
 `test_simtime.cpp <https://github.com/Exawind/amr-wind/blob/development/unit_tests/core/test_simtime.cpp>`_
 
    Simple unit test example that tests the behavior of
-   :class:`amr_wind::SimTime`. This test only relies on :class:`AmrexTest` and
+   `amr_wind::SimTime`. This test only relies on :class:`AmrexTest` and
    does not require a mesh.
 
 `test_abl_init.cpp <https://github.com/Exawind/amr-wind/blob/development/unit_tests/wind_energy/test_abl_init.cpp>`_

docs/sphinx/user/inputs_MLMG.rst

@@ -40,7 +40,7 @@ temperature, to do that use "temperature_diffusion" as your prefix.
 
    **type:** Integer, optional, default = 200
 
-   Sets the max number of multigrid iterations. If :input_param:`do_fixed_iters`
+   Sets the max number of multigrid iterations. If :input_param:`diffusion.do_fixed_iters`
    is set to True, then AMReX will not abort if specified tolerance is not met
    after max iterations, otherwise it will abort.