Build matrix based on cmake

.github/workflows/build.yml

@@ -0,0 +1,69 @@
+
+name: InChI build matrix
+
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  define-matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.define-matrix.outputs.matrix }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Define build matrix
+        id: define-matrix
+        run: |
+          echo "matrix=$(cat .github/workflows/matrix.json| jq -c .)" >> $GITHUB_OUTPUT
+
+  build-inchi:
+    needs: define-matrix
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          ${{ fromJson(needs.define-matrix.outputs.matrix) }}
+
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    container: 
+      image: ${{ matrix.image || '' }} 
+
+    steps:
+      - name: Install build dependencies
+        run: ${{ matrix.prebuild }}
+
+      - uses: actions/checkout@v4
+
+      - name: Set up Visual Studio shell
+        if: runner.os == 'Windows'
+        uses: egor-tensin/vs-shell@v2
+        with:
+          arch: x64
+
+      - name: Build InChI
+        run: |
+          cmake -B builddir -G Ninja
+          cmake --build builddir
+
+      - name: save artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: inchi-${{ matrix.slug }}-${{ github.sha }}
+          path: builddir
+
+      - uses: actions/setup-python@v5
+        if: matrix.slug != 'alpine'
+        with:
+          python-version: '3.12'
+
+      - name: Install test dependencies
+        if: matrix.slug != 'alpine'
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e INCHI-1-TEST[invariance-tests]
+
+      - name: Run executable tests
+        if: matrix.slug != 'alpine'
+        run: cmake --build builddir --target run-tests

.github/workflows/matrix.json

@@ -0,0 +1,34 @@
+[
+    {
+        "os": "ubuntu-22.04",
+        "slug": "ubuntu",
+        "name": "Ubuntu 22.04",
+        "prebuild": "sudo apt update && sudo apt install -y cmake ninja-build"
+    },
+    {
+        "os": "windows-2019",
+        "slug": "windows",
+        "name": "Windows Server 2019",
+        "prebuild": "choco install ninja"
+    },
+    {
+        "os": "macos-14",
+        "slug": "macos",
+        "name": "MacOS 14",
+        "prebuild": "brew install ninja"
+    },
+    {
+        "os": "ubuntu-22.04",
+        "slug": "alpine",
+        "name": "Alpine Linux",
+        "prebuild": "apk add bash git musl-dev gcc g++ make python3 py-pip cmake ninja",
+        "image": "python:3.12-alpine"
+    },
+    {
+        "os": "ubuntu-22.04",
+        "slug": "gcc_latest",
+        "name": "GCC latest",
+        "prebuild": "apt update && apt install -y cmake ninja-build",
+        "image": "gcc:latest"
+    }
+]

.gitignore

@@ -11,3 +11,7 @@ __pycache__
 *.egg-info/
 # Ignore core dump files
 core.*[0-9]
+gcc_crash_report.txt
+
+# default vscode/cmake build directory
+build/

CMakeLists.txt

@@ -0,0 +1,26 @@
+cmake_minimum_required(VERSION 3.18)
+
+project( 
+    inchi 
+    VERSION 1.07
+)
+
+option(BUILD_SHARED_LIBS "Build using shared libraries" ON)
+
+set( CMAKE_C_STANDARD 11 )
+
+# this works but maybe it's preferable to only export 
+# the symbols that are needed to consume the library
+set( CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON )
+
+add_subdirectory( INCHI-1-SRC/INCHI_BASE/src )
+add_subdirectory( INCHI-1-SRC/INCHI_API/libinchi/src )
+add_subdirectory( INCHI-1-SRC/INCHI_API/demos/inchi_main/src )
+add_subdirectory( INCHI-1-SRC/INCHI_API/demos/mol2inchi/src )
+add_subdirectory( INCHI-1-SRC/INCHI_API/demos/test_ixa/src )
+add_subdirectory( INCHI-1-SRC/INCHI_EXE/inchi-1/src )
+
+add_custom_target( run-tests 
+    COMMAND pytest INCHI-1-TEST/tests/test_executable --exe-path $<TARGET_FILE:inchi-1> -vv
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+)

INCHI-1-SRC/INCHI_API/demos/inchi_main/src/CMakeLists.txt

@@ -0,0 +1,29 @@
+add_executable(
+    inchi_main
+
+    e_0dstereo.c
+    e_ichimain.c
+    e_ichi_io.c
+    e_ichi_parms.c
+    e_inchi_atom.c
+    e_mol2atom.c
+    e_readinch.c
+    e_readmol.c
+    e_readstru.c
+    e_util.c
+    e_ichimain_a.c
+
+)
+
+target_compile_definitions(
+    inchi_main
+PRIVATE
+    BUILD_LINK_AS_DLL 
+    TARGET_EXE_USING_API
+)
+
+target_link_libraries(
+    inchi_main
+    PRIVATE
+    inchi
+)

INCHI-1-SRC/INCHI_API/demos/mol2inchi/src/CMakeLists.txt

@@ -0,0 +1,19 @@
+add_executable(
+    mol2inchi
+
+    mol2inchi.c	
+    moreutil.c
+)
+
+target_compile_definitions(
+    mol2inchi    
+PRIVATE
+    BUILD_LINK_AS_DLL 
+    TARGET_EXE_USING_API
+    )
+
+target_link_libraries(
+    mol2inchi
+PRIVATE
+    inchi
+)

INCHI-1-SRC/INCHI_API/demos/mol2inchi/src/mol2inchi.h

@@ -244,8 +244,7 @@ int  m2i_WorkPool_wait_and_print_all( m2i_WorkPool *pool, THREAD_PTR *Thread );
 
 #ifdef _WIN32
 #define M2I_THREADFUNC unsigned __stdcall
-#endif
-#if ( !defined(_WIN32) && defined(__linux__) )
+#else
 #define M2I_THREADFUNC void *
 #endif
 

INCHI-1-SRC/INCHI_API/demos/mol2inchi/src/moreutil.c

@@ -51,6 +51,7 @@
 #ifdef _WIN32
 #include <windows.h>
 #else
+#include <sys/time.h>
 #endif
 
 #include "moreutil.h"
@@ -764,8 +765,7 @@ unsigned int get_msec_timer( void )
 
 #if ( defined(_WIN32) && defined(_MSC_VER) )
     t = GetTickCount( );
-#endif
-#if ( !defined(_WIN32) && defined(__linux__) )
+#else
     /* NB: not reboot/date-change safe */
     struct timeval tv;
     gettimeofday( &tv, NULL );

INCHI-1-SRC/INCHI_API/demos/test_ixa/src/CMakeLists.txt

@@ -0,0 +1,18 @@
+add_executable(
+    test_ixa
+
+    moreutil.c	
+    test_ixa.c
+)
+target_compile_definitions(
+    test_ixa
+PRIVATE
+    BUILD_LINK_AS_DLL 
+    TARGET_EXE_USING_API
+)
+
+target_link_libraries(
+    test_ixa
+PRIVATE
+    inchi
+)

INCHI-1-SRC/INCHI_API/libinchi/src/CMakeLists.txt

@@ -0,0 +1,17 @@
+target_sources(
+    inchi
+PRIVATE
+    ixa/ixa_inchikey_builder.c
+    ixa/ixa_read_mol.c
+    ixa/ixa_status.c
+    ixa/ixa_builder.c
+    ixa/ixa_mol.c
+    ixa/ixa_read_inchi.c
+
+    ichilnct.c
+    inchi_dll.c
+    inchi_dll_main.c
+    inchi_dll_a.c
+    inchi_dll_a2.c
+    inchi_dll_b.c
+)

INCHI-1-SRC/INCHI_BASE/src/CMakeLists.txt

@@ -0,0 +1,77 @@
+add_library( 
+    inchi
+
+    ichican2.c
+    ichicano.c
+    ichi_io.c
+    ichierr.c
+    ichicans.c
+    ichiisot.c
+    ichimak2.c
+    ichimake.c
+    ichimap1.c
+    ichimap2.c
+    ichimap4.c
+    ichinorm.c
+    ichiparm.c
+    ichiprt1.c
+    ichiprt2.c
+    ichiprt3.c
+    ichiqueu.c
+    ichiring.c
+    ichisort.c
+    ichister.c
+    ichitaut.c
+    ichi_bns.c
+    ichiread.c
+    ichirvr1.c
+    ichirvr2.c
+    ichirvr3.c
+    ichirvr4.c
+    ichirvr5.c
+    ichirvr6.c
+    ichirvr7.c
+    ikey_dll.c
+    ikey_base26.c
+    mol_fmt1.c
+    mol_fmt2.c
+    mol_fmt3.c
+    mol2atom.c
+    mol_fmt4.c
+    readinch.c
+    runichi.c
+    runichi2.c
+    runichi3.c
+    runichi4.c
+    sha2.c
+    strutil.c
+    util.c
+    bcf_s.c
+)
+
+target_link_libraries(
+    inchi
+PUBLIC
+    # link libm in linux
+    $<$<BOOL:${LINUX}>:m>
+)
+
+# not sure this can stay PRIVATE
+target_compile_definitions(
+    inchi
+PRIVATE
+    TARGET_API_LIB
+    COMPILE_ANSI_ONLY # why would one want to compile without this?
+)
+
+set_target_properties(
+    inchi
+    PROPERTIES
+    VERSION ${inchi_VERSION}
+    SOVERSION 1
+)
+
+# makefile in INCHI-1-INCHI_API/libinchi/gcc
+# applies a libinchi.map file to the linker (line 52 and bejond)
+# is that necessary? can we do that with cmake? 
+# maybe we can acvhieve the same effect with another method

INCHI-1-SRC/INCHI_BASE/src/ichimain.h

@@ -586,8 +586,6 @@ void EditINCHI_HidePolymerZz( INCHI_IOSTREAM *out, int n_pzz, int n_zy );
 
 /* MISCELLANEOUS */
 
-
-void SplitTime( unsigned long ulTotalTime, int *hours, int *minutes, int *seconds, int *mseconds );
 void set_line_separators( int bINChIOutputOptions, char **pLF, char **pTAB );
 void save_command_line( int argc, char *argv[], INCHI_IOSTREAM *plog );
 void emit_empty_inchi( INPUT_PARMS *ip, long num_inp,