Merge branch 'main' into release

Author: boulderdaze

.devcontainer/Dockerfile.codespace

@@ -1,4 +1,4 @@
-FROM fedora:37
+FROM fedora:latest
 
 RUN dnf -y update \
     && dnf -y install \

.github/ISSUE_TEMPLATE/release.md

@@ -0,0 +1,32 @@
+---
+name: Version Release
+about: Create an issue to make a new release
+title: 'Release X.X.X'
+labels: ''
+assignees: ''
+
+---
+
+## Testing
+
+- [ ] GitHub Actions are passing on `main`
+- [ ] Update the version number in the include path in the README example
+- [ ] Verify the README example compiles and runs successfully
+- [ ] Confirm the README example output matches what is shown in the README
+
+## Deployment
+
+- [ ] Create a new branch (do **not** name it `release`)
+- [ ] Update the version number in `CMakeLists.txt`
+- [ ] Run the CMake configure step from the MICM source directory:
+  ```
+  cmake -B build -S .
+  ```
+  This forces CMake to write the correct version file into the include directory.
+- [ ] Open `docs/sources/_static/switcher.json`
+  - The first object points to the stable version — update its `name` to the new version number
+- [ ] Update the version number in `CITATION.cff`
+- [ ] On GitHub, merge `main` into `release` — **do NOT squash and merge**
+  - Alternatively, merge locally and push: `git checkout release && git merge main && git push`
+- [ ] Create a tag and add release notes on GitHub
+  - Be sure to select the `release` branch as the target

.github/workflows/docker_and_coverage.yml

@@ -18,11 +18,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
         dockerfile:
           - Dockerfile
           - Dockerfile.coverage
-          - Dockerfile.llvm
           - Dockerfile.memcheck
           - Dockerfile.nvhpc
           - Dockerfile.openmp
@@ -34,33 +32,28 @@ jobs:
         with:
           submodules: recursive
 
-      - name: Delete huge unnecessary tools folder
+      - name: Free disk space
         run: rm -rf /opt/hostedtoolcache
 
       - name: Build Docker image
         run: docker build -t micm -f docker/${{ matrix.dockerfile }} .
 
       - name: Run tests in container
         # only run this if we are not running coverage tests or have built the cuda files
-        if: matrix.dockerfile != 'Dockerfile.coverage' && matrix.dockerfile != 'Dockerfile.nvhpc' && matrix.dockerfile != 'Dockerfile.llvm'
+        if: matrix.dockerfile != 'Dockerfile.coverage' && matrix.dockerfile != 'Dockerfile.nvhpc'
         run: docker run --name test-container -t micm bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
 
-      - name: Run tests using LLVM in container
-        # excludes some very expensive memcheck tests
-        if: matrix.dockerfile == 'Dockerfile.llvm'
-        run: docker run --name test-container -t micm bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8 -E \"memcheck_jit_linear_solver|memcheck_analytical_rosenbrock_integration\""'
-
       - name: Run coverage tests in container
         if: matrix.dockerfile == 'Dockerfile.coverage'
-        run: docker run --name test-container -t micm bash -c 'make coverage ARGS="--rerun-failed --output-on-failure -j8"'
+        run: docker run --name test-container -t micm bash -c 'make coverage'
 
       - name: Copy coverage from container
         if: matrix.dockerfile == 'Dockerfile.coverage'
         run: docker cp test-container:build/coverage.info .
 
       - name: Upload coverage report
         if: matrix.dockerfile == 'Dockerfile.coverage'
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: coverage.info

.github/workflows/gh_pages.yml

@@ -13,7 +13,7 @@ concurrency:
 
 jobs:
   gcc:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         build_type: [Release]
@@ -36,7 +36,7 @@ jobs:
           ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
 
   clang:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         build_type: [Release]

.github/workflows/ubuntu.yml

@@ -7,3 +7,4 @@ doc/latex/
 .vscode
 xcode/
 __pycache__
+.claude

.gitignore

@@ -0,0 +1,19 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+---
+# Required
+version: 2
+
+conda:
+  environment: environment.yml
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "mambaforge-22.9"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+

.readthedocs.yaml

@@ -1,7 +1,7 @@
 cff-version: 1.2.0
 message: If you use this software, please cite it as below.
 title: Model Independent Chemistry Module (MICM)
-version: v3.11.0
+version: v3.12.0
 doi: "10.5281/zenodo.10472189"
 authors:
   - family-names: Dawson

CITATION.cff

@@ -1,9 +1,9 @@
 ################################################################################
 # Preamble
-cmake_minimum_required(VERSION 3.21)
+cmake_minimum_required(VERSION 3.24)
 
 # project and version must be on the same line so that the docs can extract it
-project(micm VERSION 3.11.0 LANGUAGES CXX)
+project(micm VERSION 3.12.0 LANGUAGES CXX)
 
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "Release" CACHE STRING
@@ -30,18 +30,12 @@ option(MICM_ENABLE_OPENMP "Enable OpenMP support" OFF)
 option(MICM_ENABLE_COVERAGE "Enable code coverage output" OFF)
 option(MICM_ENABLE_MEMCHECK "Enable memory checking in tests" OFF)
 option(MICM_BUILD_DOCS "Build the documentation" OFF)
-option(MICM_ENABLE_LLVM "Build with LLVM support for JIT-compiling" OFF)
 option(MICM_ENABLE_TESTS "Build the tests" ON)
 option(MICM_ENABLE_PROFILE "Profile MICM Solver" OFF)
+option(MICM_BUILD_SHARED_LIBS "Build micm_cuda as shared libraries" OFF)
 set(MICM_DEFAULT_VECTOR_SIZE "4" CACHE STRING "Default size for vectorizable matrix types")
 set(MICM_GPU_TYPE "None" CACHE STRING "The GPU type being targeted")
 
-# on ubuntu with clang, an incorrect version of the c++ standard library was being linked
-if (${CMAKE_HOST_SYSTEM_NAME} MATCHES "Linux" AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
-    # If the compiler is Clang, use libc++
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-endif()
-
 # on Windows with MSVC, add the /bigobj flag to allow for large object files
 if (${CMAKE_HOST_SYSTEM_NAME} MATCHES "Windows" AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
   # If the compiler is MSVC or Clang on Windows, use /bigobj
@@ -74,8 +68,8 @@ if(PROJECT_IS_TOP_LEVEL AND MICM_ENABLE_TESTS)
         NAME coverage
         EXECUTABLE "ctest"
         EXCLUDE "${PROJECT_SOURCE_DIR}/test/*"
-        BASE_DIRECTORY "${PROJECT_SOURCE_DIR}/src")
-
+        BASE_DIRECTORY "${PROJECT_SOURCE_DIR}/src"
+        LCOV_ARGS "--ignore-errors" "mismatch")
   endif()
 
   enable_testing()
@@ -88,12 +82,4 @@ endif()
 # only include packaging if we are the top level project being built
 if(PROJECT_IS_TOP_LEVEL)
   add_subdirectory(packaging)
-endif()
-
-################################################################################
-
-# on ubuntu with clang, an incorrect version of the c++ standard library was being linked
-if (${CMAKE_HOST_SYSTEM_NAME} MATCHES "Linux" AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
-    # If the compiler is Clang, use libc++
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
-endif()
+endif()