Final version of 1.07.2

.gitattributes

@@ -1,10 +1,20 @@
 # This file configures how Git treats line endings.
 # This is important because we're working on both Windows and Unix machines.
-# For details see https://adaptivepatchwork.com/2012/03/01/mind-the-end-of-your-line/.
+# For details see https://adaptivepatchwork.com/2012/03/01/mind-the-end-of-your-line/
+# and https://www.aleksandrhovhannisyan.com/blog/crlf-vs-lf-normalizing-line-endings-in-git/.
 
 # Git runs CRLF to LF replacement on files marked as `text`
 # every time they are written to the object database
 # and the reverse replacement when writing to the working directory.
+
+# When spurious diffs due to EOL changes occur (e.g., after pulling remote), do the following:
+# * Inspect EOL with `git ls-files --eol`.
+# * Stage the diffs.
+# * Run `git rm --cached -r . && git reset --hard`.
+# * Run `git add --renormalize .`.
+# * Inspect EOL with `git lf-files --eol` again to verify that conversion worked.
+# * Commit the change containing the EOL conversions.
+
 *.c         text
 *.h         text
 *.py        text
@@ -16,6 +26,15 @@
 *.yml       text
 *.yaml      text
 *.sdf       text
+*.props     text
+*.ruleset   text
+*.sln       text
+*.vcxproj   text
+*.def       text
+*.map       text
+*.user      text
+makefile    text
+makefile32  text
 
 *.sqlite    binary
 *.png       binary
@@ -24,4 +43,6 @@
 *.zip       binary
 *.dll       binary
 *.docx      binary
-*.pdf       binary
+*.pdf       binary
+*.jpg       binary
+*.lib       binary

.github/workflows/ci.yml

@@ -9,20 +9,14 @@ on:
 
 jobs:
   test_glibc_gcc:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     container: gcc:14
 
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-
       - name: Install test dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install -e INCHI-1-TEST[invariance-tests]
+        run: cd INCHI-1-TEST && ./install.sh
 
       - uses: ./.github/actions/compile_inchi_exe
         id: compile_exe
@@ -51,12 +45,8 @@ jobs:
 
 
   test_musl_gcc:
-    runs-on: ubuntu-latest
-    # We need Python 3.12. That's why we're using alpine:edge.
-    # Currently (May 2024) edge is the only Alpine version with Python 3.12.
-    # Once edge advances, the Alpine Python version will be bumped and `python -m pip install -e INCHI-1-TEST` will break.
-    # TODO: Find more sustainable solution.
-    container: alpine:edge
+    runs-on: ubuntu-24.04
+    container: alpine:latest
 
     steps:
       - name: Install build and test environment

INCHI-1-SRC/INCHI_API/demos/inchi_main/gcc/makefile

@@ -41,11 +41,15 @@ endif
 ifndef C_COMPILER
 ifeq ($(CCN),2)
 C_COMPILER = clang
-$(info Both GCC and Clang/LLVM detected. Compiling with Clang -- please edit makefile to compile with GCC.)
+$(info Both GCC and Clang/LLVM detected. Compiling with Clang(++) -- please edit makefile to compile with GCC.)
 $(info )
 else
+ifeq ($(OS_ID),0)
+C_COMPILER = gcc -static
+else
 C_COMPILER = gcc
-$(info Both GCC and Clang/LLVM detected. Compiling with GCC (default) -- please edit makefile to compile with Clang/LLVM.)
+endif
+$(info Both GCC and Clang/LLVM detected. Compiling with GCC/G++ (default) -- please edit makefile to compile with Clang/LLVM.)
 $(info )
 endif
 endif
@@ -116,9 +120,9 @@ endif
 # === C Compiler Options =======
 ifndef C_OPTIONS
 	ifndef CALLER_IS_MOL2INCHI
-	C_OPTIONS = -std=c11 -ansi -O2 -c -fno-strict-aliasing
+	C_OPTIONS = -std=c11 -ansi -O1 -c -fno-strict-aliasing
 	else
-	C_OPTIONS = -std=c11 -O2 -c -fno-strict-aliasing
+	C_OPTIONS = -std=c11 -O1 -c -fno-strict-aliasing
 	endif
 	ifneq ($(OS_ID),0)
 	ifndef C_SO_OPTIONS
@@ -176,7 +180,7 @@ else ifeq ($(OS_ID),2)
 # jwm: linking to .dylib on OS X
 $(API_CALLER_PATHNAME) : $(API_CALLER_OBJS) $(INCHI_LIB_PATHNAME).so$(VERSION)
 	$(LINKER) -o $(API_CALLER_PATHNAME) $(API_CALLER_OBJS) \
-$(INCHI_LIB_PATHNAME).dylib$(VERSION) -lm
+$(INCHI_LIB_PATHNAME)$(VERSION).dylib -lm
 else
 # djb-rwth: linking to .so on Linux
 $(API_CALLER_PATHNAME) : $(API_CALLER_OBJS) $(INCHI_LIB_PATHNAME).so$(VERSION)
@@ -255,9 +259,9 @@ $(INCHI_LIB_PATHNAME).dll$(VERSION): $(INCHI_LIB_OBJS)
 $(INCHI_LIB_OBJS) -Wl$(LINUX_MAP),-soname,$(INCHI_LIB_NAME).dll$(VERSION) -Wl,--subsystem,windows -lm
 else ifeq ($(OS_ID), 2)
 # jwm: creating .dylib on OS X
-$(INCHI_LIB_PATHNAME).dylib$(VERSION): $(INCHI_LIB_OBJS)
-	$(SHARED_LINK) $(SHARED_LINK_PARM) -o $(INCHI_LIB_PATHNAME).dylib$(VERSION)	\
-$(INCHI_LIB_OBJS) -Wl$(LINUX_MAP)$(LINUX_Z_RELRO) -install_name $(INCHI_LIB_NAME).dylib$(VERSION) -lm
+$(INCHI_LIB_PATHNAME)$(VERSION).dylib: $(INCHI_LIB_OBJS)
+	$(SHARED_LINK) $(SHARED_LINK_PARM) -o $(INCHI_LIB_PATHNAME)$(VERSION).dylib	\
+$(INCHI_LIB_OBJS) -Wl$(LINUX_MAP)$(LINUX_Z_RELRO) -install_name $(INCHI_LIB_NAME)$(VERSION).dylib -lm
 else
 # djb-rwth: creating .so on Linux
 $(INCHI_LIB_PATHNAME).so$(VERSION): $(INCHI_LIB_OBJS)

INCHI-1-SRC/INCHI_API/demos/inchi_main/gcc/makefile32

@@ -37,18 +37,26 @@ ifeq ($(CCN),$(filter $(CCN),1 2))
 ifeq ($(GCC_DETECTED),1)
 ifeq ($(CLANG_DETECTED),1)
 # djb-rwth: Choose C compiler if both GCC and Clang are detected -- CCN = 1 for GCC, CCN = 2 for Clang/LLVM
-CCN = 1
+CCN = 2
 endif
 endif
 # === C Compiler ===============
 ifndef C_COMPILER
 ifeq ($(CCN),2)
+ifeq ($(OS_ID),0)
+C_COMPILER = clang -static
+else
 C_COMPILER = clang
-$(info Both GCC and Clang/LLVM detected. Compiling with Clang -- please edit makefile to compile with GCC.)
+endif
+$(info Both GCC and Clang/LLVM detected. Compiling with Clang(++) -- please edit makefile to compile with GCC.)
 $(info )
 else
+ifeq ($(OS_ID),0)
+C_COMPILER = gcc -static
+else
 C_COMPILER = gcc
-$(info Both GCC and Clang/LLVM detected. Compiling with GCC (default) -- please edit makefile to compile with Clang/LLVM.)
+endif
+$(info Both GCC and Clang/LLVM detected. Compiling with GCC/G++ (default) -- please edit makefile to compile with Clang/LLVM.)
 $(info )
 endif
 endif
@@ -116,9 +124,9 @@ endif
 # === C Compiler Options =======
 ifndef C_OPTIONS
 	ifndef CALLER_IS_MOL2INCHI
-	C_OPTIONS = -std=c11 -m32 -ansi -O2 -c -fno-strict-aliasing
+	C_OPTIONS = -std=c11 -m32 -ansi -O1 -c -fno-strict-aliasing
 	else
-	C_OPTIONS = -std=c11 -m32 -O2 -c -fno-strict-aliasing
+	C_OPTIONS = -std=c11 -m32 -O1 -c -fno-strict-aliasing
 	endif
 	ifneq ($(OS_ID),0)
 	ifndef C_SO_OPTIONS

INCHI-1-SRC/INCHI_API/demos/inchi_main/src/e_0dstereo.c

@@ -48,7 +48,6 @@
 #include <math.h>
 #include <string.h>
 #include <ctype.h>
-#include <stdbool.h>
 
 
 #include "e_mode.h"
@@ -329,11 +328,17 @@ int e_GetElType( inchi_Atom *at, int cur_atom )
     S_CHAR num_bonds[MAX_BOND_TYPE];
     int  i;
     int  nRadicalValence = 0;
-    bool cndt1, cndt2;
+    int cndt1 = 0, cndt2 = 0;
 
     /* djb-rwth: avoiding non-zero constant warning */
-    cndt1 = sizeof(at->num_iso_H) != sizeof(num_iso_H);
-    cndt2 = sizeof(at->num_iso_H[0]) != sizeof(num_iso_H[0]);
+    if (sizeof(at->num_iso_H) != sizeof(num_iso_H))
+    {
+        cndt1 = 1;
+    }
+    if (sizeof(at->num_iso_H[0]) != sizeof(num_iso_H[0]))
+    {
+        cndt2 = 1;
+    }
 
     if ( cndt1 || cndt2 )
     {

INCHI-1-SRC/INCHI_API/demos/inchi_main/src/e_ichi_parms.c

@@ -2724,15 +2724,15 @@ void HelpCommandLineParms(INCHI_IOSTREAM* f)
     inchi_ios_print_nodisplay(f, "  SLUUD       Make labels for unknown and undefined stereo different\n");
     inchi_ios_print_nodisplay(f, "  RecMet      Include reconnected metals results\n");
     inchi_ios_print_nodisplay(f, "  FixedH      Include Fixed H layer\n");
-    inchi_ios_print_nodisplay(f, "  KET         Account for keto-enol tautomerism (experimental)\n");
-    inchi_ios_print_nodisplay(f, "  15T         Account for 1,5-tautomerism (experimental)\n");
-
-    inchi_ios_print_nodisplay(f, "  PT_22_00    Account for PT_22_00 tautomerism (experimental)\n");
-    inchi_ios_print_nodisplay(f, "  PT_16_00    Account for PT_16_00 tautomerism (experimental)\n");
-    inchi_ios_print_nodisplay(f, "  PT_06_00    Account for PT_06_00 tautomerism (experimental)\n");
-    inchi_ios_print_nodisplay(f, "  PT_39_00    Account for PT_39_00 tautomerism (experimental)\n");
-    inchi_ios_print_nodisplay(f, "  PT_13_00    Account for PT_13_00 tautomerism (experimental)\n");
-    inchi_ios_print_nodisplay(f, "  PT_18_00    Account for PT_18_00 tautomerism (experimental)\n");
+
+    inchi_ios_print_nodisplay(f, "  KET         Consider keto-enol tautomerism (experimental)\n");
+    inchi_ios_print_nodisplay(f, "  15T         Consider 1,5-tautomerism (experimental)\n");
+    inchi_ios_print_nodisplay(f, "  PT_06_00    Consider 1,3 heteroatom shift (experimental)\n");
+    inchi_ios_print_nodisplay(f, "  PT_13_00    Consider keten-ynol exchange (experimental)\n");
+    inchi_ios_print_nodisplay(f, "  PT_16_00    Consider nitroso-oxime tautomerism (experimental)\n");
+    inchi_ios_print_nodisplay(f, "  PT_18_00    Consider cyanic/iso-cyanic acids (experimental)\n");
+    inchi_ios_print_nodisplay(f, "  PT_22_00    Consider imine/imine tautomerism (experimental)\n");
+    inchi_ios_print_nodisplay(f, "  PT_39_00    Consider nitrone/azoxy or Behrend rearrangement (experimental)\n");
 
 
     inchi_ios_print_nodisplay(f, "Generation\n");

INCHI-1-SRC/INCHI_API/demos/inchi_main/src/e_mode.h

@@ -43,6 +43,7 @@
 #define __MODE_H__
 
 #include <stdio.h>
+#include "../../../../INCHI_BASE/src/bcf_s.h"
 
 
 
@@ -189,9 +190,10 @@ MS VC compiler pragmas
 #undef APP_DESCRIPTION
 #endif
 #ifndef CREATE_INCHI_STEP_BY_STEP
-#define APP_DESCRIPTION "InChI version 1, Software v. 1.07 (Library call example, classic API)"
+/* djb-rwth: adding full version number in the output -- GH issue #61 */
+#define APP_DESCRIPTION "InChI version 1, Software " CURRENT_VER " (Library call example, classic API)"
 #else
-#define APP_DESCRIPTION "InChI version 1, Software v. 1.07 (Library call example, modularized API)"
+#define APP_DESCRIPTION "InChI version 1, Software " CURRENT_VER " (Library call example, modularized API)"
 #endif