Merge branch 'latest' into fix-1423

.github/workflows/build-python-package.yml

@@ -78,17 +78,14 @@ jobs:
     # ubuntu 22 has a latest version of cmake, but setup-python 
     # does not seem to provide all necessary modules to find python
     # from cmake. works on my machine, test the wheels manually
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v4
-      # strategy:
-      #   matrix:
-      #     python: [3.12]
 
       - name: Install correct python version
         uses: actions/setup-python@v5
-        # with:
-        #   python-version: ${{ matrix.python }}
+        with:
+          python-version: '3.10'
 
       - name: Build wheel
         run: |

.github/workflows/build-wheels-push.yml

@@ -1,12 +1,12 @@
 name: build-wheels-push
 
-on: []
+# on: []
 # on: push
 
-# on:
-#  release:
-#    types:
-#      - published
+on:
+ release:
+   types:
+     - published
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -82,51 +82,22 @@ jobs:
           name: cibw-wheels-${{ matrix.python }}-${{ matrix.buildplat[1] }}
           path: wheelhouse/*.whl
 
-  upload_testpypi:
-    name: >-
-      Publish highspy to TestPyPI
-    runs-on: ubuntu-latest
-    needs: [build_wheels, build_sdist]
-    # needs: [build_sdist]
-
-    # upload to PyPI on every tag starting with 'v'
-    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
-
-    environment:
-      name: testpypi
-      url: https://test.pypi.org/p/highspy
-
-    permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
-    steps:
-      - uses: actions/download-artifact@v4
-        with:
-          pattern: cibw-*
-          path: dist
-          merge-multiple: true
-
-      - name: Download all
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          repository-url: https://test.pypi.org/legacy/
-          verbose: true
-
-  # upload_pypi:
+  # upload_testpypi:
   #   name: >-
-  #     Publish highspy to PyPI
+  #     Publish highspy to TestPyPI
   #   runs-on: ubuntu-latest
   #   needs: [build_wheels, build_sdist]
+  #   # needs: [build_sdist]
 
   #   # upload to PyPI on every tag starting with 'v'
   #   # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
 
   #   environment:
-  #     name: pypi
-  #     url: https://pypi.org/p/highspy
+  #     name: testpypi
+  #     url: https://test.pypi.org/p/highspy
 
   #   permissions:
   #     id-token: write  # IMPORTANT: mandatory for trusted publishing
-
   #   steps:
   #     - uses: actions/download-artifact@v4
   #       with:
@@ -136,3 +107,32 @@ jobs:
 
   #     - name: Download all
   #       uses: pypa/gh-action-pypi-publish@release/v1
+  #       with:
+  #         repository-url: https://test.pypi.org/legacy/
+  #         verbose: true
+
+  upload_pypi:
+    name: >-
+      Publish highspy to PyPI
+    runs-on: ubuntu-latest
+    needs: [build_wheels, build_sdist]
+
+    # upload to PyPI on every tag starting with 'v'
+    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/highspy
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: Download all
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/code-coverage.yml

@@ -0,0 +1,67 @@
+name: code-coverage
+
+on: [push, pull_request]
+
+jobs:
+  debug:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: install 
+        run: sudo apt-get update && sudo apt-get install lcov 
+
+      - name: Create Build Environment
+        run: cmake -E make_directory ${{runner.workspace}}/build
+
+      - name: Configure CMake
+        shell: bash
+        working-directory: ${{runner.workspace}}/build
+        run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Debug -DHIGHS_COVERAGE=ON -DALL_TESTS=ON -DBUILD_SHARED_LIBS=OFF -D CMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++
+
+      - name: Build
+        working-directory: ${{runner.workspace}}/build
+        shell: bash
+        run: |
+          cmake --build . --parallel --config Debug
+
+      - name: Test
+        working-directory: ${{runner.workspace}}/build
+        shell: bash
+        run: ctest --parallel --timeout 300 --output-on-failure 
+
+      - name: Generate Report
+        working-directory: ${{runner.workspace}}/build
+        shell: bash
+        run: |
+          lcov -d . -c -o cov.info --ignore-errors empty
+          lcov --remove cov.info "/usr/include/*" -o cov.info
+          lcov --remove cov.info "/usr/lib/*" -o cov.info
+          lcov --remove cov.info "extern/pdqsort/*" -o cov.info
+          lcov --remove cov.info "extern/zstr/*" -o cov.info
+          lcov --remove cov.info "extern/catch*" -o cov.info
+          lcov --remove cov.info "app/cxxopts*" -o cov.info
+          lcov --remove cov.info "src/test*" -o cov.info
+          lcov --list cov.info
+
+      - name: Genhtml Results Summary 
+        working-directory: ${{runner.workspace}}/build
+        shell: bash
+        run: |
+          genhtml -o coverage cov.info
+
+      # Made it past the first token issue. 
+      # May need some more time to porpagate on the codecov side. 
+      # - name: Upload coverage reports to Codecov
+      #   uses: codecov/codecov-action@v5
+      #   with:
+      #     token: ${{ secrets.CODECOV_TOKEN }}
+      #     slug: ERGO-Code/HiGHS
+      #     fail_ci_if_error: true # optional (default = false)
+      #     files: ${{runner.workspace}}/build/cov.info # optional
+      #     # name: codecov-umbrella # optional
+      #     verbose: true # optional (default = false)

.gitignore

@@ -230,6 +230,7 @@ pip-log.txt
 
 # Unit test / coverage reports
 .coverage
+cov.info
 .tox
 
 #Translations

CMakeLists.txt

@@ -103,6 +103,8 @@ if (PYTHON_BUILD_SETUP)
   set(ZLIB OFF)
 endif()
 
+option(HIGHS_COVERAGE "Activate the code coverage compilation" OFF)
+
 # Address | Thread | Leak 
 # Linux atm
 # Only Debug is theted atm 
@@ -328,16 +330,18 @@ if(NOT FAST_BUILD)
 endif()
 
 include(CheckCXXCompilerFlag)
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(ppc64|powerpc64)" AND NOT APPLE)
-    check_cxx_compiler_flag("-mpopcntd" COMPILER_SUPPORTS_POPCNTD)
-    if(COMPILER_SUPPORTS_POPCNTD)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcntd")
-    endif()
-else()
-    check_cxx_compiler_flag("-mpopcnt" COMPILER_SUPPORTS_POPCNT)
-    if(COMPILER_SUPPORTS_POPCNT)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt")
-    endif()
+if (NOT HIGHS_COVERAGE)
+  if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(ppc64|powerpc64)" AND NOT APPLE)
+      check_cxx_compiler_flag("-mpopcntd" COMPILER_SUPPORTS_POPCNTD)
+      if(COMPILER_SUPPORTS_POPCNTD)
+          set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcntd")
+      endif()
+  else()
+      check_cxx_compiler_flag("-mpopcnt" COMPILER_SUPPORTS_POPCNT)
+      if(COMPILER_SUPPORTS_POPCNT)
+          set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt")
+      endif()
+  endif()
 endif()
 
 option(DEBUGSOL "check the debug solution" OFF)
@@ -473,6 +477,58 @@ elseif (DEBUG_MEMORY STREQUAL "Leak")
       -fno-omit-frame-pointer ")
 endif()
 
+# HiGHS coverage update in progress
+if(FAST_BUILD AND HIGHS_COVERAGE)
+  if(WIN32)
+    message(FATAL_ERROR "Error: code coverage analysis is only available under Linux for now.")
+  endif()
+
+  if(NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
+    message(FATAL_ERROR "Warning: to enable coverage, you must compile in Debug mode")
+  endif()
+
+  # Disable IPO
+  set(CMAKE_INTERPROCEDURAL_OPTIMIZATION OFF)
+  message(STATUS "Building in coverage mode")
+
+  # Enable coverage flags
+  add_compile_options(-O0) 
+  add_compile_options(--coverage) 
+  add_compile_options(-fprofile-update=atomic) 
+
+  add_link_options(-O0) 
+  add_link_options(--coverage)    # Ensure coverage data is linked correctly
+
+  find_program(GCOV_PATH gcov)
+  find_program(LCOV_PATH lcov)
+  find_program(GENHTML_PATH genhtml)
+
+  if(NOT GCOV_PATH)
+    message(FATAL_ERROR "gcov not found! Please install lcov and gcov. Aborting...")
+  endif()
+
+  if(NOT LCOV_PATH)
+    message(FATAL_ERROR "lcov not found! Please install lcov and gcov. Aborting...")
+  endif()
+
+  if(NOT GENHTML_PATH)
+    message(FATAL_ERROR "genhtml not found! Please install lcov and gcov. Aborting...")
+  endif()
+
+  # add_custom_target(coverage
+  #   COMMAND ${LCOV_PATH} -d bin -c -o cov.info --ignore-errors empty
+  #   COMMAND ${LCOV_PATH} --remove "*/usr/include/*" -o ${CMAKE_BINARY_DIR}/cov.info.cleaned
+  # COMMAND ${LCOV_PATH} --remove "*/usr/lib/*" -o ${CMAKE_BINARY_DIR}/cov.info.cleaned
+  # COMMAND ${LCOV_PATH} --remove "extern/pdqsort/*" -o ${CMAKE_BINARY_DIR}/cov.info.cleaned
+  # COMMAND ${LCOV_PATH} --remove "extern/zstr/*" -o ${CMAKE_BINARY_DIR}/cov.info.cleaned
+  # COMMAND ${LCOV_PATH} --remove "app/cxxopts*" -o ${CMAKE_BINARY_DIR}/cov.info.cleaned
+  # COMMAND ${GENHTML_PATH} ${CMAKE_BINARY_DIR}/cov.info.cleaned -o ${CMAKE_BINARY_DIR}/cov_report
+  #   VERBATIM
+  #   WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+  # COMMENT "Generating code coverage report v2025.")
+
+endif()
+
 if(NOT FAST_BUILD)
   # For the moment keep above coverage part in case we are testing at CI.
   option(CI "CI extended tests" ON)
@@ -495,7 +551,7 @@ if(NOT FAST_BUILD)
   endif()
 
   if(HIGHS_COVERAGE)
-    if(NOT CMAKE_BUILD_TYPE STREQUAL "DEBUG")
+    if(NOT CMAKE_BUILD_TYPE STREQUAL "Debug" AND NOT CMAKE_BUILD_TYPE STREQUAL "DEBUG")
       message(FATAL_ERROR "Warning: to enable coverage, you must compile in DEBUG mode")
     endif()
   endif()

FEATURES.md

@@ -10,4 +10,12 @@ Added basis solve methods to highspy
 
 Added methods to get primal/dual ray and dual unboundedness direction to highspy
 
+When a presolved LP has model status kUnknown, rather than returning this to the user, it performs postsolve and then uses the basis to solve the original LP
 
+Fixed bug in presolve when pointers stored in HighsMatrixSlice get invalidated when the coefficient matrix is reallocated (e.g. when non-zeros are added in HPresolve::addToMatrix)
+
+Primal and dual residual tolerances - applied following IPM or PDLP solution - now documented as options
+
+Highs::getCols (Highs::getRows) now runs in linear time if the internal constraint matrix is stored column-wise (row-wise). Added ensureColwise/Rowwise to the Highs class, the C API and highspy so that users can set the internal constraint matrix storage orientation
+
+When columns and rows are deleted from the incumbent LP after a basic solution has been found, HiGHS no longer invalidates the basis. Now it maintains the basic and nonbasic status of the remaining variables and constraints. When the model is re-solved, this information is used to construct a starting basis.

app/CMakeLists.txt

@@ -54,10 +54,6 @@ else()
 
   target_link_libraries(highs libhighs)
 
-  if(EMSCRIPTEN AND EMSCRIPTEN_HTML)
-    set(CMAKE_EXECUTABLE_SUFFIX ".html")
-    set_target_properties(highs PROPERTIES LINK_DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/highs_webdemo_shell.html)
-  endif()
 
   target_include_directories(highs PRIVATE
     $<BUILD_INTERFACE:${HIGHS_SOURCE_DIR}/app>
@@ -66,4 +62,10 @@ else()
   # install the binary
   install(TARGETS highs EXPORT highs-targets
     RUNTIME)
+endif()
+
+# Add demo to FAST_BUILD as well.
+if(EMSCRIPTEN AND EMSCRIPTEN_HTML)
+  set(CMAKE_EXECUTABLE_SUFFIX ".html")
+  set_target_properties(highs PROPERTIES LINK_DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/highs_webdemo_shell.html)
 endif()

app/HighsRuntimeOptions.h

@@ -145,7 +145,7 @@ bool loadOptions(const HighsLogOptions& report_log_options, int argc,
         case HighsLoadOptionsStatus::kError:
           return false;
         case HighsLoadOptionsStatus::kEmpty:
-          writeOptionsToFile(stdout, options.records);
+          writeOptionsToFile(stdout, options.log_options, options.records);
           return false;
         default:
           break;

app/RunHighs.cpp

@@ -47,6 +47,7 @@ int main(int argc, char** argv) {
   // settings defined in any options file.
   highs.passOptions(loaded_options);
   //  highs.writeOptions("Options.md");
+  highs.writeOptions("", true);
 
   // Load the model from model_file
   HighsStatus read_status = highs.readModel(model_file);

app/cxxopts.hpp

@@ -2875,4 +2875,4 @@ Options::group_help(const std::string& group) const
 
 } // namespace cxxopts
 
-#endif //CXXOPTS_HPP_INCLUDED
+#endif //CXXOPTS_HPP_INCLUDED