Merge branch 'feature/sunadjoint-core-modules' into feature/sunadjoin…

…t-arkode

.github/workflows/check-format.yml

@@ -82,6 +82,8 @@ jobs:
     if: ${{ always() && contains(join(needs.*.result, ','), 'failure') && (github.event_name == 'issue_comment' && startsWith(github.event.comment.body, '/autofix')) }}
     needs: format_check
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     steps:
       # Checkout the GitHub created reference for the PR.
       # The only way to do this is by using the "issue" number

.github/workflows/check-spelling.yml

@@ -62,6 +62,8 @@ jobs:
     if: ${{ always() && contains(join(needs.*.result, ','), 'failure') && (github.event_name == 'issue_comment' && startsWith(github.event.comment.body, '/autofix')) }}
     needs: spelling_check
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     steps:
       # Checkout the GitHub created reference for the PR.
       # The only way to do this is by using the "issue" number

.github/workflows/check-swig.yml

@@ -70,6 +70,8 @@ jobs:
     if: ${{ always() && contains(join(needs.*.result, ','), 'failure') && (github.event_name == 'issue_comment' && startsWith(github.event.comment.body, '/autofix')) }}
     needs: swig_check
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     steps:
       # Checkout the GitHub created reference for the PR.
       # The only way to do this is by using the "issue" number

.github/workflows/docs-pdfs.yml

@@ -0,0 +1,211 @@
+name: Docs - PDFs
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+  merge_group:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref_name }}
+  cancel-in-progress: true
+
+jobs:
+  docs_install_guide_pdf:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Install latex
+        run: |
+          sudo apt update
+          sudo apt install -y --no-install-recommends \
+            fonts-texgyre \
+            latexmk \
+            tex-gyre \
+            texlive-latex-extra \
+            texlive-fonts-recommended \
+            texlive-plain-generic
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Install sphinx
+        run: |
+          pip install -r doc/requirements.txt
+
+      - name: Build docs
+        run: cd doc/install_guide && make latexpdf
+
+      - name: Archive files from failed build
+        uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: latex_build_files
+          path: |
+            ${{github.workspace}}/doc/install_guide/build/latex
+
+      - name: Archive PDF from successful build
+        uses: actions/upload-artifact@v4
+        if: success()
+        with:
+          name: install_guide
+          path: |
+            ${{github.workspace}}/doc/install_guide/build/latex/INSTALL_GUIDE.pdf
+
+  docs_package_pdf:
+    runs-on: ubuntu-latest
+
+    strategy:
+      max-parallel: 2
+      matrix:
+        package: [arkode, cvode, cvodes, ida, idas, kinsol]
+        # TODO(DJG): when all user guides and example docs use sphinx remove
+        # the example documentation jobs below and use the alternative lines
+        # commented out in this job
+        # type: [guide, examples]
+
+    steps:
+      - name: Install latex
+        run: |
+          sudo apt update
+          sudo apt install -y --no-install-recommends \
+            fonts-texgyre \
+            latexmk \
+            tex-gyre \
+            texlive-latex-extra \
+            texlive-fonts-recommended \
+            texlive-plain-generic
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Install sphinx
+        run: |
+          pip install -r doc/requirements.txt
+
+      - name: Build docs
+        run: cd doc/${{matrix.package}}/guide && make latexpdf
+        # run: cd doc/${{matrix.package}}/${{matrix.type}} && make latexpdf
+
+      - name: Archive files from failed build
+        uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: latex_build_files
+          path: |
+            ${{github.workspace}}/doc/${{matrix.package}}/guide/build/latex
+          # path: |
+          # ${{github.workspace}}/doc/${{matrix.package}}/${{matrix.type}}/build/latex
+
+      - name: Archive PDFs from successful build
+        uses: actions/upload-artifact@v4
+        if: success()
+        with:
+          name: ${{matrix.package}}_user_guide
+          path: |
+            ${{github.workspace}}/doc/${{matrix.package}}/guide/build/latex/*_guide.pdf
+          # name: ${{matrix.package}}_${{matrix.type}}
+          # path: |
+          #   ${{github.workspace}}/doc/${{matrix.package}}/${{matrix.type}}/build/latex/*_${{matrix.type}}.pdf
+
+  # Sphinx examples documentation PDFs
+  docs_examples_sphinx_pdf:
+    runs-on: ubuntu-latest
+
+    strategy:
+      max-parallel: 2
+      matrix:
+        package: [arkode]
+
+    steps:
+      - name: Install latex
+        run: |
+          sudo apt update
+          sudo apt install -y --no-install-recommends \
+            fonts-texgyre \
+            latexmk \
+            tex-gyre \
+            texlive-latex-extra \
+            texlive-fonts-recommended \
+            texlive-plain-generic
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Install sphinx
+        run: |
+          pip install -r doc/requirements.txt
+
+      - name: Build docs
+        run: cd doc/${{matrix.package}}/examples && make latexpdf
+
+      - name: Archive files from failed build
+        uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: latex_build_files
+          path: |
+            ${{github.workspace}}/doc/${{matrix.package}}/examples/build/latex
+
+      - name: Archive PDFs from successful build
+        uses: actions/upload-artifact@v4
+        if: success()
+        with:
+          name: ${{matrix.package}}_examples_docs
+          path: |
+            ${{github.workspace}}/doc/${{matrix.package}}/examples/build/latex/*_examples.pdf
+
+  # Latex examples documentation PDFs
+  docs_examples_latex_pdf:
+    runs-on: ubuntu-latest
+
+    strategy:
+      max-parallel: 2
+      matrix:
+        package: [cvode, cvodes, ida, idas, kinsol]
+
+    steps:
+      - name: Install latex
+        run: |
+          sudo apt update
+          sudo apt install -y --no-install-recommends \
+            fonts-texgyre \
+            latexmk \
+            tex-gyre \
+            texlive-latex-extra \
+            texlive-fonts-recommended \
+            texlive-plain-generic
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Build docs
+        run: cd doc/${{matrix.package}} && make ex
+
+      - name: Archive files from failed build
+        uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: latex_build_files
+          path: |
+            ${{github.workspace}}/doc/${{matrix.package}}
+            !${{github.workspace}}/doc/${{matrix.package}}/guide
+
+      - name: Archive PDFs from successful build
+        uses: actions/upload-artifact@v4
+        if: success()
+        with:
+          name: ${{matrix.package}}_examples_docs
+          path: |
+            ${{github.workspace}}/doc/${{matrix.package}}/*_examples.pdf

benchmarks/diffusion_2D/diffusion_2D.hpp

@@ -48,11 +48,10 @@
 #endif
 
 // Macros for problem constants
-#define PI    SUN_RCONST(3.141592653589793238462643383279502884197169)
-#define ZERO  SUN_RCONST(0.0)
-#define ONE   SUN_RCONST(1.0)
-#define TWO   SUN_RCONST(2.0)
-#define EIGHT SUN_RCONST(8.0)
+#define PI   SUN_RCONST(3.141592653589793238462643383279502884197169)
+#define ZERO SUN_RCONST(0.0)
+#define ONE  SUN_RCONST(1.0)
+#define TWO  SUN_RCONST(2.0)
 
 // Macro to access (x,y) location in 1D NVector array
 #define IDX(x, y, n) ((n) * (y) + (x))

cmake/SundialsSetupCompilers.cmake

@@ -85,7 +85,8 @@ if(ENABLE_ALL_WARNINGS)
   set(WARNING_FLAGS
       "-Wno-unknown-warning-option -Wall -Wpedantic -Wextra -Wshadow \
 -Wwrite-strings -Wcast-align -Wdisabled-optimization -Wvla -Walloca \
--Wduplicated-cond -Wduplicated-branches")
+-Wduplicated-cond -Wduplicated-branches -Wunused-macros \
+-Wunused-local-typedefs")
   # TODO(SBR): Try to add -Wredundant-decls once SuperLU version is updated in
   # CI tests
 

doc/cvode/guide/source/Usage/index.rst

@@ -1140,7 +1140,7 @@ Main solver optional input functions
 
    **Notes:**
     SUNDIALS must be compiled appropriately for specialized kernels to be available. The CMake option ``SUNDIALS_BUILD_PACKAGE_FUSED_KERNELS`` must be set to
-    ``ON`` when SUNDIALS is compiled. See the entry for this option in :numref:`Installation.CMake.options` for more information.
+    ``ON`` when SUNDIALS is compiled. See the entry for this option in :numref:`Installation.Options` for more information.
     Currently, the fused kernels are only supported when using CVODE with the :ref:`NVECTOR_CUDA <NVectors.CUDA>` and :ref:`NVECTOR_HIP <NVectors.Hip>` implementations of the ``N_Vector``.
 
 .. _CVODE.Usage.CC.optional_input.optin_ls:

doc/shared/FAQ.rst

@@ -46,16 +46,18 @@ Installation
 
 .. collapse:: How do I install SUNDIALS on Windows systems?
 
-   One way of obtaining Windows libraries for the SUNDIALS solvers is to use cygwin
-   `cygwin <www.cygwin.com>`_, in which case the installation procedure is the same
-   as for any other Linux system.
+   One way of obtaining Windows libraries for the SUNDIALS solvers is to use
+   `cygwin <https://www.cygwin.com/>`__, in which case the installation
+   procedure is the same as for any other Linux/Unix system (see the
+   :ref:`Installation.CMake.Unix` installation section).
 
-   Otherwise, refer to :ref:`Installation.CMake.Windows`.
+   Otherwise, refer to the :ref:`Installation.CMake.Windows` installation
+   section.
 
 
 .. collapse:: Everything installed fine! How do I link the SUNDIALS libraries to my own application?
 
-   Refer to :ref:`Installation.Results`.
+   Refer to :ref:`Installation.UsingSUNDIALS`.
 
 
 CVODE(S) / IDA(S) / ARKODE

doc/shared/nvectors/NVector_Kokkos.rst

@@ -24,7 +24,7 @@ variety of backends including serial, OpenMP, CUDA, HIP, and SYCL. Since Kokkos
 a modern C++ library, the module is also written in modern C++ (it requires
 C++14) as a header only library. To utilize this ``N_Vector`` users will need to
 include ``nvector/nvector_kokkos.hpp``. More instructions on building SUNDIALS
-with Kokkos enabled are given in :numref:`Installation.CMake.ExternalLibraries`.
+with Kokkos enabled are given in :numref:`Installation.Options.Kokkos`.
 For instructions on building and using Kokkos, refer to the `Kokkos
 <https://kokkos.github.io/kokkos-core-wiki/index.html>`_ documentation.