KPP 3.3.1 release

.ci-pipelines/ci-cleanup-script.sh

@@ -17,8 +17,8 @@ cwd=$(pwd -P)
 for this_test in ${GENERAL_TESTS}; do
     clean_ci_test_folder "${this_test}" "${this_test}" "${cwd}"
 done
-clean_ci_test_folder "${MCM_1}" "${MCM_1}" "${cwd}"
-clean_ci_test_folder "${MCM_2}" "mcm"      "${cwd}"
+clean_ci_test_folder "${MCM_1}" mcm "${cwd}"
+clean_ci_test_folder "${MCM_2}" mcm "${cwd}"
 
 # Remove any log files used to store C-I test results
 cd $cwd

.ci-pipelines/ci-common-defs.sh

@@ -16,6 +16,7 @@ F90_feuler
 F90_lsode
 F90_radau
 F90_rk
+F90_rkadj
 F90_rktlm
 F90_ros
 F90_rosadj
@@ -27,7 +28,9 @@ F90_rostlm
 F90_ros_upcase
 F90_saprc_2006
 F90_sd
+F90_sd4
 F90_sdadj
+F90_sdtlm
 F90_seulex
 F90_small_strato
 "

.github/workflows/lint-ci-workflows.yml

@@ -0,0 +1,58 @@
+# Workflow to run linting checks on source
+name: Lint
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on pushes to the "main" branch, i.e., PR merges
+  push:
+    branches: [ "main" ]
+
+  # Triggers the workflow on pushes to open pull requests with code changes
+  pull_request:
+    paths:
+      - '.github/workflows/*.yml'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Cancel jobs running if new commits are pushed
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+# Workflow run - one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "lint"
+  lint:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: Checkout code
+        with:
+          persist-credentials: false
+        uses: actions/checkout@v6
+
+      - name: Install Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m venv ci_venv
+          . ci_venv/bin/activate
+          pip install zizmor==0.9.2
+
+      # Apply GitHub Actions linter, zizmor
+      - name: zizmor
+        if: always()
+        run: |
+          cd ${{ github.workspace }}
+          . ci_venv/bin/activate
+          zizmor .github/workflows/*.yml

.github/workflows/run-ci-tests.yml

@@ -0,0 +1,68 @@
+---
+#
+# GitHub Action to run C-I tests with GCC compilers
+#
+name: Run C-I tests
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      KPP_HOME: ${{ github.workspace }}
+      KPP_FLEX_LIB_DIR: /usr/lib/x86_64-linux-gnu
+    strategy:
+      matrix:
+        gcc-version: [9, 10, 11, 12, 13]
+
+
+    name: Run C-I tests with GCC ${{ matrix.gcc-version }}
+    steps:
+      - name: Checkout KPP
+        uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+
+
+      - name: Install libraries
+        run: |
+          sudo apt update -y
+          sudo apt install -y flex bison libfl-dev
+          sudo apt install -y gcc-${{ matrix.gcc-version }} g++-${{ matrix.gcc-version }} gfortran-${{ matrix.gcc-version }}
+          sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${{ matrix.gcc-version }} 100 \
+             --slave /usr/bin/g++ g++ /usr/bin/g++-${{ matrix.gcc-version }} \
+             --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${{ matrix.gcc-version }}
+
+
+      - name: Verify environment
+        run: |
+          echo '%%% COMPILERS %%%'
+          gcc --version
+          echo ''
+          g++ --version
+          echo ''
+          gfortran --version
+          echo ''
+          echo '%%% ENVIRONMENT %%%'
+          echo "flex             = $(which flex)"
+          echo "bison            = $(which bison)"
+          echo "KPP_HOME         = $KPP_HOME"
+          echo "KPP_FLEX_LIB_DIR = $KPP_FLEX_LIB_DIR"
+
+      - name: Compile with Make
+        run: |
+          cd $KPP_HOME/src
+          make all
+
+
+      - name: Run C-I tests
+        run: |
+          cd $KPP_HOME/.ci-pipelines
+          ./ci-testing-script.sh

.gitignore

@@ -1,73 +1,72 @@
+# KPP .gitignore file
+#
+# For info on how .gitignore rules work, see:
 # https://www.atlassian.com/git/tutorials/saving-changes/gitignore
 # https://linuxize.com/post/gitignore-ignoring-files-in-git
 
-# temporary files:
-*.~*
-*~
-.\#*
-\#*
+# Keep empty directory for executables, but ignore its contents
+/bin/*
+
+# Ignore temporary files everywhere
+**/*.~*
+**/*~
+**/.\#*
+**/\#*
 
-# files generated by bison:
+# Ignore files generated by bison (in src/)
 /src/lex.yy.c
 /src/y.tab.c
 /src/y.tab.h
 
-# from compiler:
-*.mod
-*.o
-*.exe
+# Ignore files generated by the compiler (everywhere)
+**/*.mod
+**/*.o
+**/*.exe
 
-# results from ci-tests:
+# Ignore files generated by C-I tests (in ci-tests/*)
+/ci-tests/**/*.dat
+/ci-tests/**/*.h
 /ci-tests/**/*.m
+/ci-tests/**/Makefile_*
 /ci-tests/**/*results*
-/ci-tests/**/*.exe
-/ci-tests/**/*.h
-/ci-tests/**/*.log
-/ci-tests/**/*.dat
 
-# keep empty directory for executables, but not its contents:
-/bin/*
-!/bin/.gitkeep
-
-# KPP-generated files:
-*_Function*
-*_Global*
-*_Hessian*
-*_HessianSP*
-*_Initialize*
-*_Integrator*
-*_Jacobian*
-*_JacobianSP*
-*_LinearAlgebra*
-*.log
-*_Main*
-*_mex_Fun*
-*_mex_Hessian*
-*_mex_Jac_SP*
-*_Model*
-*_Monitor*
-*_Parameters*
-*_Precision*
-*_Rates*
-*_Stoichiom*
-*_StoichiomSP*
-*_Util*
-Makefile_*
+# Ignore files generated by KPP (everywhere)
+**/*_Function*
+**/*_Global*
+**/*_Hessian*
+**/*_HessianSP*
+**/*_Initialize*
+**/*_Integrator*
+**/*_Jacobian*
+**/*_JacobianSP*
+**/*_LinearAlgebra*
+**/*.log
+**/*_Main*
+**/*_*ex_Fun*
+**/*_*ex_Hessian*
+**/*_*ex_Jac_SP*
+**/*_Model*
+**/*_Monitor*
+**/*_Parameters*
+**/*_Precision*
+**/*_Rates*
+**/*_Stoichiom*
+**/*_StoichiomSP*
+**/*_Util*
 
-# LaTeX and BibTeX files:
-/manual/*.aux
-/manual/*.bbl
-/manual/*.blg
-/manual/*.log
-/manual/*.toc
-
-# ReadTheDocs files
+# Ignore files generated by ReadTheDocs (in docs/build)
 docs/build/*
 
-# are there any *.dat files to exclude?
-*.dat
-
-# Other files/dirs to exclude
+# Ignore other files & folders
 *.pdf
-/examples/mcm*/__pycache__
+**/__pycache__
 
+# IMPORTANT: Do not ignore these files!
+!/bin/.gitkeep
+!/docs/figures/*.pdf
+!/util/*.c
+!/util/*.f
+!/util/*.h
+!/util/*.f90
+!/util/*.m
+!/util/Makefile*

CHANGELOG.md

@@ -11,6 +11,30 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.3.1] - 2026-03-27
+### Added
+- Added GitHub Action to run C-I tests with GCC compilers v9, v10, v11, v12, and v13
+- Added "Lint" GitHub Action to check other actions for security issues
+- Added new example files: `rkadj.kpp`, `sd4.kpp`, `sdtlm.kpp`
+- Added new C-I tests: `F90_rkadj`, `F90_sd4`, `F90_sdtlm`
+- Added `docs/read_the_docs_environment.yml`
+
+### Changed
+- Updated ReadTheDocs documentation to reflect that C-I tests are now done as a GitHub Action
+- Updated the `docs/source/reference/editing_these_docs.rst` instructions for clarity
+- Updated GitHub Actions to the latest versions
+
+## Fixed
+- Moved the `which kpp` instruction to the end of the "Build the KPP executable" section in the installation guide on ReadTheDocs
+- Updated rules to ignore files in `.gitignore` and updated comments accordingly
+- Fixed a bug that prevented `.ci-pipelines/ci-cleanup-script.sh` from removing KPP-generated files for MCM mechanisms
+- Fixed typo in error message in `int/rosenbrock_autoreduce.f90`
+- Fixed a bug in Makefile template that caused `KPP_ROOT_Stoichiom.f90` not compiled if `#STOICMAT ON` and `#HESSIAN OFF`
+
+### Removed
+- Removed C-I tests on Microsoft Azure Dev Pipelines
+- Replaced BLAS functions (`WAXPY`, `WCOPY`, `WSCAL`, `WADD`, `WLAMCH`, `WDOT`) with pure F90 code from `int/*.f90` integrators (thanks to AI for the help)
+
 ## [3.3.0] - 2025-07-17
 ### Added
 - New integrator: `rosenbrock_h211b_qssa.f90`

ci-tests/F90_rkadj/F90_rkadj.kpp

@@ -0,0 +1 @@
+../../examples/rkadj.kpp

ci-tests/F90_sd4/F90_sd4.kpp

@@ -0,0 +1 @@
+../../examples/sd4.kpp

ci-tests/F90_sdtlm/F90_sdtlm.kpp

@@ -0,0 +1 @@
+../../examples/sdtlm.kpp