Add chemfiles patches

0-chemfiles/.gitignore

@@ -0,0 +1,5 @@
+build/
+zlib/
+zlib.tar.gz
+
+!*.patch

0-chemfiles/0-apple-off64_t.patch

@@ -0,0 +1,16 @@
+diff --git a/zconf.h.cmakein b/zconf.h.cmakein
+index a7f24cce6..b8f2d4ad5 100644
+--- a/zconf.h.cmakein
++++ b/zconf.h.cmakein
+@@ -519,6 +519,11 @@ typedef uLong FAR uLongf;
+ #  define z_off_t long
+ #endif
+
++// Apple does not define off64_t, but off_t is 64-bit
++#ifdef __APPLE__
++#  define off64_t off_t
++#endif
++
+ #if !defined(_WIN32) && defined(Z_LARGE64)
+ #  define z_off64_t off64_t
+ #else

0-chemfiles/1-apple-lseek64.patch

@@ -0,0 +1,13 @@
+diff --git a/gzlib.c b/gzlib.c
+index 4105e6aff..50a9a9fd6 100644
+--- a/gzlib.c
++++ b/gzlib.c
+@@ -8,7 +8,7 @@
+ #if defined(_WIN32) && !defined(__BORLANDC__)
+ #  define LSEEK _lseeki64
+ #else
+-#if defined(_LARGEFILE64_SOURCE) && _LFS64_LARGEFILE-0
++#if !defined(__APPLE__) && defined(_LARGEFILE64_SOURCE) && _LFS64_LARGEFILE-0
+ #  define LSEEK lseek64
+ #else
+ #  define LSEEK lseek

0-chemfiles/2-win-gnu-z_off64_t.patch

@@ -0,0 +1,13 @@
+diff --git a/zconf.h.cmakein b/zconf.h.cmakein
+index 3a00233d9..95e4c90a2 100644
+--- a/zconf.h.cmakein
++++ b/zconf.h.cmakein
+@@ -527,7 +527,7 @@ typedef uLong FAR uLongf;
+ #if !defined(_WIN32) && defined(Z_LARGE64)
+ #  define z_off64_t off64_t
+ #else
+-#  if defined(_WIN32) && !defined(__GNUC__) && !defined(Z_SOLO)
++#  if defined(_WIN32) && !defined(Z_SOLO)
+ #    define z_off64_t __int64
+ #  else
+ #    define z_off64_t z_off_t

0-chemfiles/CMakeLists.txt

@@ -0,0 +1,86 @@
+cmake_minimum_required(VERSION 3.16)
+project(chemfiles-zlib C)
+
+if (POLICY CMP0063)
+    # Use of `<LANG>_VISIBILITY_PRESET` in OBJECT libraries
+    cmake_policy(SET CMP0063 NEW)
+endif()
+
+set(VERSION "1.2.13-chemfiles")
+
+include(CheckTypeSize)
+include(CheckFunctionExists)
+include(CheckIncludeFile)
+
+check_include_file(sys/types.h HAVE_SYS_TYPES_H)
+check_include_file(stdint.h    HAVE_STDINT_H)
+check_include_file(stddef.h    HAVE_STDDEF_H)
+
+# Check for fseeko
+check_function_exists(fseeko HAVE_FSEEKO)
+# Check for unistd.h
+check_include_file(unistd.h Z_HAVE_UNISTD_H)
+
+# parse the full version number from zlib.h and include in ZLIB_FULL_VERSION
+file(READ ${CMAKE_CURRENT_SOURCE_DIR}/zlib.h _zlib_h_contents)
+string(REGEX REPLACE ".*#define[ \t]+ZLIB_VERSION[ \t]+\"([-0-9A-Za-z.]+)\".*"
+    "\\1" ZLIB_FULL_VERSION ${_zlib_h_contents})
+
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.cmakein
+	${CMAKE_CURRENT_BINARY_DIR}/zconf.h @ONLY
+)
+
+set(ZLIB_PUBLIC_HDRS
+    ${CMAKE_CURRENT_BINARY_DIR}/zconf.h
+    zlib.h
+)
+set(ZLIB_PRIVATE_HDRS
+    crc32.h
+    deflate.h
+    gzguts.h
+    inffast.h
+    inffixed.h
+    inflate.h
+    inftrees.h
+    trees.h
+    zutil.h
+)
+set(ZLIB_SRCS
+    adler32.c
+    compress.c
+    crc32.c
+    deflate.c
+    gzclose.c
+    gzlib.c
+    gzread.c
+    gzwrite.c
+    inflate.c
+    infback.c
+    inftrees.c
+    inffast.c
+    trees.c
+    uncompr.c
+    zutil.c
+)
+
+add_library(chemfiles_zlib OBJECT ${ZLIB_SRCS} ${ZLIB_PUBLIC_HDRS} ${ZLIB_PRIVATE_HDRS})
+
+set_target_properties(chemfiles_zlib PROPERTIES C_VISIBILITY_PRESET hidden)
+
+target_include_directories(chemfiles_zlib PUBLIC
+    ${CMAKE_CURRENT_BINARY_DIR}
+    ${CMAKE_CURRENT_SOURCE_DIR}
+)
+
+if(NOT HAVE_FSEEKO)
+    target_compile_options(chemfiles_zlib PUBLIC -DNO_FSEEKO)
+endif()
+
+# Require support for large (64-bit) files
+target_compile_options(chemfiles_zlib PUBLIC -D_LARGEFILE64_SOURCE=1 -D_LFS64_LARGEFILE=1)
+
+if(MSVC)
+    target_compile_options(chemfiles_zlib PUBLIC -D_CRT_SECURE_NO_DEPRECATE)
+    target_compile_options(chemfiles_zlib PUBLIC -D_CRT_NONSTDC_NO_DEPRECATE)
+endif()

0-chemfiles/create-archive.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+set -eu
+
+SCRIPT_DIR=$(cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd)
+
+cd "$SCRIPT_DIR"
+
+# Create archive with only required files
+rm -rf zlib.tar.gz zlib
+mkdir zlib
+cp ../{*.c,*.h,zconf.h.cmakein,Changelog,README,LICENSE} zlib
+cp CMakeLists.txt zlib
+rm -f zlib/zconf.h
+
+# apply custom patches
+cd zlib
+patch -p1 < ../0-apple-off64_t.patch
+patch -p1 < ../1-apple-lseek64.patch
+patch -p1 < ../2-win-gnu-z_off64_t.patch
+
+cd ..
+
+tar cf zlib.tar zlib/
+gzip -9 -f zlib.tar
+
+echo "created 0-chemfiles/zlib.tar.gz"