Merge branch 'develop' into feature/rk_defaults

.github/workflows/build-ci-containers-e4s.yml

@@ -26,7 +26,7 @@ jobs:
         username: ${{ github.actor }}
         password: ${{ secrets.GITHUB_TOKEN }}
     - name: Build and push Docker images
-      uses: docker/build-push-action@v6.10.0
+      uses: docker/build-push-action@v6.12.0
       with:
           context: "./docker/sundials-ci/e4s-base"
           build-args: e4s_version=22.05
@@ -56,7 +56,7 @@ jobs:
         username: ${{ github.actor }}
         password: ${{ secrets.GITHUB_TOKEN }}
     - name: Build and push Docker images
-      uses: docker/build-push-action@v6.10.0
+      uses: docker/build-push-action@v6.12.0
       with:
           context: "./docker/sundials-ci/e4s-quarterly"
           build-args: spack_yaml=./int${{ matrix.indexsize }}-${{ matrix.precision }}/spack.yaml

.github/workflows/build-ci-containers-nightly.yml

@@ -32,7 +32,7 @@ jobs:
         username: ${{ github.actor }}
         password: ${{ secrets.GITHUB_TOKEN }}
     - name: Build and push Docker images
-      uses: docker/build-push-action@v6.10.0
+      uses: docker/build-push-action@v6.12.0
       with:
           context: "./docker/sundials-ci/spack-nightly"
           build-args: spack_yaml=./int${{ matrix.indexsize }}-${{ matrix.precision }}/spack.yaml

.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

CHANGELOG.md

@@ -27,6 +27,10 @@ Improved the efficiency of default ARKODE methods with the following changes:
 
 ### Bug Fixes
 
+Fixed the behavior of `SUNDIALS_ENABLE_ERROR_CHECKS` so additional runtime error
+checks are disabled by default with all release build types. Previously,
+`MinSizeRel` builds enabled additional error checking by default.
+
 Fixed bug in the ARKODE SPRKStep `SPRKStepReInit` function and `ARKodeReset` function
 with SPRKStep that could cause a segmentation fault when compensated summation is not
 used.

README.md

@@ -95,7 +95,7 @@ David J. Gardner, Alan C. Hindmarsh, Daniel R. Reynolds, Steven B. Roberts, and
 Carol S. Woodward. We thank Radu Serban for significant and critical past
 contributions.
 
-Other contributors to SUNDIALS include: James Almgren-Bell, Lawrence E. Banks,
+Other contributors to SUNDIALS include: Mustafa Aggul, James Almgren-Bell, Lawrence E. Banks,
 Peter N. Brown, George Byrne, Rujeko Chinomona, Scott D. Cohen, Aaron Collier,
 Keith E. Grant, Steven L. Lee, Shelby L. Lockhart, John Loffeld, Daniel McGreer,
 Yu Pan, Slaven Peles, Cosmin Petra, H. Hunter Schwartz, Jean M. Sexton,

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/SundialsBuildOptionsPre.cmake

@@ -76,10 +76,10 @@ endif()
 # Option to enable/disable error checking
 # ---------------------------------------------------------------
 
-if(CMAKE_BUILD_TYPE MATCHES "Release|RelWithDebInfo")
-  set(_default_err_checks OFF)
-else()
+if(CMAKE_BUILD_TYPE MATCHES "Debug")
   set(_default_err_checks ON)
+else()
+  set(_default_err_checks OFF)
 endif()
 
 set(DOCSTR

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/arkode/guide/source/Landing.rst

@@ -20,7 +20,7 @@
    Woodward. We thank Radu Serban for significant and critical past
    contributions.
 
-   Other contributors to SUNDIALS include: James Almgren-Bell,
+   Other contributors to SUNDIALS include: Mustafa Aggul, James Almgren-Bell,
    Lawrence E. Banks, Peter N. Brown, George Byrne, Rujeko Chinomona,
    Scott D. Cohen, Aaron Collier, Keith E. Grant, Steven L. Lee,
    Shelby L. Lockhart, John Loffeld, Daniel McGreer, Yu Pan, Slaven Peles,

doc/arkode/guide/source/conf.py

@@ -51,7 +51,7 @@
 
 # General information about the project.
 project = u'User Documentation for ARKODE'
-copyright = u"""2012-{year}, Daniel R. Reynolds, David J. Gardner, Carol S. Woodward, Rujeko Chinomona, and Cody J. Balos""".format(year = year)
+copyright = u"""2012-{year}, Daniel R. Reynolds, David J. Gardner, Carol S. Woodward, Cody J. Balos, Rujeko Chinomona, and Mustafa Aggul""".format(year = year)
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -217,8 +217,9 @@
     Daniel R. Reynolds$^1$,
     David J. Gardner$^2$,
     Carol S. Woodward$^2$,
+    Cody J. Balos$^2$
     Rujeko Chinomona$^3$, and
-    Cody J. Balos$^2$ \\
+    Mustafa Aggul$^1$ \\
     \\
     {\em $^1$Department of Mathematics, Southern Methodist University} \\
     {\em $^2$Center for Applied Scientific Computing, Lawrence Livermore National Laboratory} \\
@@ -275,7 +276,7 @@
 # (source start file, name, description, authors, manual section).
 man_pages = [
     ('index', 'ARKODE', u'ARKODE Documentation',
-     [u'Daniel R. Reynolds, David J. Gardner, Carol S. Woodward, Rujeko Chinomona, and Cody J. Balos'], 1)
+     [u'Daniel R. Reynolds, David J. Gardner, Carol S. Woodward, Cody J. Balos, Rujeko Chinomona, and Mustafa Aggul'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -289,7 +290,7 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
   ('index', 'ARKODE', u'ARKODE Documentation',
-   u'Daniel R. Reynolds, David J. Gardner, Carol S. Woodward, Rujeko Chinomona, and Cody J. Balos', 'ARKODE',
+   u'Daniel R. Reynolds, David J. Gardner, Carol S. Woodward, Cody J. Balos, Rujeko Chinomona, and Mustafa Aggul', 'ARKODE',
    'Time integration package for multi-rate systems of ordinary differential equations.',
    'Miscellaneous'),
 ]

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: