[cfitsio] Update to 3.49 and fix dependency zlib (#14064)

* [cfitsio] Update to 3.49 and fix dependency zlib

* export unofficial cmake targets

* [cfitsio] Fix file paths, export cmake targets

* [cfitsio] Required cmake_policy CMP0012

* [ccfits] Fix dependency cfitsio

* [cfitsio] Fixup pkgconfig

* [healpix] Fix dependency cfitsio

* [cfitsio] fix homepage and patches

Co-authored-by: Nicole Mazzuca <mazzucan@outlook.com>

12 files changed, 206 insertions, 65 deletions

diff --git a/ports/ccfits/CONTROL b/ports/ccfits/CONTROL
index 02234c94e..4fbc3ad80 100644
--- a/ports/ccfits/CONTROL
+++ b/ports/ccfits/CONTROL
@@ -1,5 +1,6 @@
 Source: ccfits
-Version: 2.5-5
+Version: 2.5
+Port-Version: 6
 Homepage: https://heasarc.gsfc.nasa.gov/fitsio/ccfits
 Description: CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++.
 Build-Depends: cfitsio
diff --git a/ports/ccfits/fix-dependency.patch b/ports/ccfits/fix-dependency.patch
new file mode 100644
index 000000000..15cffeb4e
--- /dev/null
+++ b/ports/ccfits/fix-dependency.patch
@@ -0,0 +1,15 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index d72ae85..405d96b 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -22,8 +22,8 @@ ENDIF()
+ 
+ #add_subdirectory (src)
+ 
+-find_package(CFITSIO REQUIRED)
+-INCLUDE_DIRECTORIES(${CFITSIO_INCLUDE_DIR})
++find_package(unofficial-cfitsio CONFIG REQUIRED)
++set(CFITSIO_LIBRARY cfitsio)
+ 
+ SET (LIB_TYPE STATIC)
+ IF (BUILD_SHARED_LIBS)
diff --git a/ports/ccfits/portfile.cmake b/ports/ccfits/portfile.cmake
index 6c33b383b..2071e4af8 100644
--- a/ports/ccfits/portfile.cmake
+++ b/ports/ccfits/portfile.cmake
@@ -7,7 +7,9 @@ vcpkg_download_distfile(ARCHIVE
 vcpkg_extract_source_archive_ex(
     ARCHIVE ${ARCHIVE}
     OUT_SOURCE_PATH SOURCE_PATH
-    PATCHES dll_exports.patch
+    PATCHES
+        dll_exports.patch
+        fix-dependency.patch
 )
 
 vcpkg_configure_cmake(
diff --git a/ports/cfitsio/0001-correct-headers-for-getcwd.patch b/ports/cfitsio/0001-correct-headers-for-getcwd.patch
deleted file mode 100644
index afd63b61a..000000000
--- a/ports/cfitsio/0001-correct-headers-for-getcwd.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-From 67400fcbd3ab2f7e68a8e7a60139b1b615debae2 Mon Sep 17 00:00:00 2001
-From: Nicole Mazzuca <mazzucan@outlook.com>
-Date: Wed, 23 Sep 2020 10:27:43 -0700
-Subject: [PATCH] correct headers for getcwd
-
----
- fitsio.h | 3 +++
- group.c  | 2 +-
- 2 files changed, 4 insertions(+), 1 deletion(-)
-
-diff --git a/fitsio.h b/fitsio.h
-index ec26d9d..792bb95 100644
---- a/fitsio.h
-+++ b/fitsio.h
-@@ -39,6 +39,9 @@ SERVICES PROVIDED HEREUNDER."
- #define CFITSIO_MAJOR 3
- #define CFITSIO_SONAME 5
- 
-+/* Required for getcwd() */
-+#define _POSIX_C_SOURCE 200112L
-+
- /* the SONAME is incremented in a new release if the binary shared */
- /* library (on linux and Mac systems) is not backward compatible */
- /* with the previous release of CFITSIO */
-diff --git a/group.c b/group.c
-index 9326c57..cec0f6a 100644
---- a/group.c
-+++ b/group.c
-@@ -24,7 +24,7 @@
- #include <direct.h>   /* defines the getcwd function on Windows PCs */
- #endif
- 
--#if defined(unix) || defined(__unix__)  || defined(__unix) || defined(HAVE_UNISTD_H)
-+#if defined(unix) || defined(__unix__)  || defined(__unix) || defined(__APPLE__) || defined(HAVE_UNISTD_H)
- #include <unistd.h>  /* needed for getcwd prototype on unix machines */
- #endif
- 
--- 
-2.24.3 (Apple Git-128)
-
diff --git a/ports/cfitsio/0001-fix-dependencies.patch b/ports/cfitsio/0001-fix-dependencies.patch
new file mode 100644
index 000000000..d8df38548
--- /dev/null
+++ b/ports/cfitsio/0001-fix-dependencies.patch
@@ -0,0 +1,39 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 6d6af49..9e7d2ee 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -94,9 +94,8 @@ IF (NOT MSVC)
+ 
+     # Find curl library, for HTTPS support:
+     IF (UseCurl)
+-        FIND_PACKAGE(CURL)
++        FIND_PACKAGE(CURL CONFIG REQUIRED)
+         IF (CURL_FOUND)
+-            INCLUDE_DIRECTORIES(${CURL_INCLUDE_DIR})
+             ADD_DEFINITIONS(-DCFITSIO_HAVE_CURL)
+         ENDIF()
+     ENDIF()
+@@ -128,18 +127,20 @@ SET(SRC_FILES
+ 
+ # Only include zlib source files if we are building a shared library.
+ # Users will need to link their executable with zlib independently.
+-IF (BUILD_SHARED_LIBS)
++IF (0)
+     set(SRC_FILES ${SRC_FILES}
+         zlib/adler32.c zlib/crc32.c zlib/deflate.c zlib/infback.c
+         zlib/inffast.c zlib/inflate.c zlib/inftrees.c zlib/trees.c
+         zlib/uncompr.c zlib/zutil.c
+         )
++ELSE()
++    FIND_PACKAGE(ZLIB REQUIRED)
+ ENDIF()
+ 
+ ADD_LIBRARY(${LIB_NAME} ${LIB_TYPE} ${H_FILES} ${SRC_FILES})
+-TARGET_LINK_LIBRARIES(${LIB_NAME} ${PTHREADS_LIBRARY} ${M_LIB})
++TARGET_LINK_LIBRARIES(${LIB_NAME} ${PTHREADS_LIBRARY} ${M_LIB} ZLIB::ZLIB)
+ IF (CURL_FOUND)
+-    TARGET_LINK_LIBRARIES(${LIB_NAME} ${CURL_LIBRARIES})
++    TARGET_LINK_LIBRARIES(${LIB_NAME} CURL::libcurl)
+ ENDIF(CURL_FOUND)
+ 
+ SET_TARGET_PROPERTIES(${LIB_NAME} PROPERTIES VERSION ${${PROJECT_NAME}_VERSION} SOVERSION ${${PROJECT_NAME}_MAJOR_VERSION})
diff --git a/ports/cfitsio/0002-export-cmake-targets.patch b/ports/cfitsio/0002-export-cmake-targets.patch
new file mode 100644
index 000000000..ab3a46cfe
--- /dev/null
+++ b/ports/cfitsio/0002-export-cmake-targets.patch
@@ -0,0 +1,48 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 9e7d2ee..5b37adc 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -24,7 +24,7 @@ OPTION(UseCurl "UseCurl" ON)
+ 
+ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
+ set (LIB_DESTINATION "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}")
+-set (INCLUDE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/include/")
++set (INCLUDE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/include/cfitsio")
+ 
+ # Define project version
+ SET(${PROJECT_NAME}_MAJOR_VERSION 3)
+@@ -138,19 +138,31 @@ ELSE()
+ ENDIF()
+ 
+ ADD_LIBRARY(${LIB_NAME} ${LIB_TYPE} ${H_FILES} ${SRC_FILES})
+-TARGET_LINK_LIBRARIES(${LIB_NAME} ${PTHREADS_LIBRARY} ${M_LIB} ZLIB::ZLIB)
++TARGET_INCLUDE_DIRECTORIES(${LIB_NAME} PUBLIC $<INSTALL_INTERFACE:include/cfitsio>)
++TARGET_LINK_LIBRARIES(${LIB_NAME} PUBLIC ${PTHREADS_LIBRARY} ${M_LIB} ZLIB::ZLIB)
+ IF (CURL_FOUND)
+-    TARGET_LINK_LIBRARIES(${LIB_NAME} CURL::libcurl)
++    TARGET_LINK_LIBRARIES(${LIB_NAME} PUBLIC CURL::libcurl)
+ ENDIF(CURL_FOUND)
+ 
+ SET_TARGET_PROPERTIES(${LIB_NAME} PROPERTIES VERSION ${${PROJECT_NAME}_VERSION} SOVERSION ${${PROJECT_NAME}_MAJOR_VERSION})
+-install(TARGETS ${LIB_NAME} DESTINATION ${LIB_DESTINATION})
+ install(TARGETS ${LIB_NAME}
++                            EXPORT unofficial-${LIB_NAME}-config
+                             RUNTIME DESTINATION bin
+                             LIBRARY DESTINATION lib
+                             ARCHIVE DESTINATION lib)
+ install(FILES ${H_FILES} DESTINATION ${INCLUDE_INSTALL_DIR} COMPONENT Devel)
+ 
++set(CFITSIO_VERSION 3.49)
++include(CMakePackageConfigHelpers)
++write_basic_package_version_file(unofficial-${LIB_NAME}-version.cmake VERSION ${CFITSIO_VERSION} COMPATIBILITY ExactVersion)
++
++install(FILES ${CMAKE_BINARY_DIR}/unofficial-${LIB_NAME}-version.cmake DESTINATION share/unofficial-${LIB_NAME})
++
++install(
++    EXPORT unofficial-${LIB_NAME}-config
++    DESTINATION share/unofficial-${LIB_NAME}
++)
++
+ # Only build test code and executables if building a shared library:
+ IF (BUILD_SHARED_LIBS)
+ 
diff --git a/ports/cfitsio/0003-add-Wno-error-implicit-funciton-declaration-to-cmake.patch b/ports/cfitsio/0003-add-Wno-error-implicit-funciton-declaration-to-cmake.patch
new file mode 100644
index 000000000..288a1d263
--- /dev/null
+++ b/ports/cfitsio/0003-add-Wno-error-implicit-funciton-declaration-to-cmake.patch
@@ -0,0 +1,27 @@
+From af09ca45ad71a540aafc4989676e9a0b88bf2948 Mon Sep 17 00:00:00 2001
+From: Nicole Mazzuca <mazzucan@outlook.com>
+Date: Fri, 16 Oct 2020 12:28:37 -0700
+Subject: [PATCH] add `-Wno-error=implicit-funciton-declaration` to cmake
+
+---
+ CMakeLists.txt | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 5b37adc..fead70c 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -6,6 +6,10 @@ SET(CMAKE_LEGACY_CYGWIN_WIN32 0)
+ PROJECT(CFITSIO)
+ CMAKE_MINIMUM_REQUIRED(VERSION 2.8.0)
+ 
++if (NOT MSVC)
++  add_compile_options(-Wno-error=implicit-function-declaration)
++endif()
++
+ # Allow @rpath token in target install name on Macs.
+ # See "cmake --help-policy CMP0042" for more information.
+ IF(POLICY CMP0042)
+-- 
+2.28.0.windows.1
+
diff --git a/ports/cfitsio/CONTROL b/ports/cfitsio/CONTROL
index e7a638303..85ff87432 100644
--- a/ports/cfitsio/CONTROL
+++ b/ports/cfitsio/CONTROL
@@ -1,5 +1,13 @@
 Source: cfitsio
-Version: 3.410
-Port-Version: 4
-Homepage: https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c
+Version: 3.49
+Homepage: https://heasarc.gsfc.nasa.gov/fitsio/
 Description: Library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format
+Build-Depends: zlib
+
+Feature: curl
+Description: UseCurl
+Build-Depends: curl
+
+Feature: pthreads
+Description: Thread-safe build (using pthreads)
+Build-Depends: pthreads (windows)
diff --git a/ports/cfitsio/portfile.cmake b/ports/cfitsio/portfile.cmake
index 12e3e2d4a..095a9e62e 100644
--- a/ports/cfitsio/portfile.cmake
+++ b/ports/cfitsio/portfile.cmake
@@ -1,38 +1,65 @@
 vcpkg_download_distfile(ARCHIVE
-    URLS "http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio3410.tar.gz"
-    FILENAME "cfitsio3410.tar.gz"
-    SHA512 b2ac31ab17e19eeeb4f1601f42f348402c0a4ab03725dbf74fe75eaabbee2f44f64f0c0ee7f0b2688bd93a9cc0dccf29f07e73b9148fff97fc78bebdbb5f6f0f
+    URLS "http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio-3.49.tar.gz"
+    FILENAME "cfitsio-3.49.tar.gz"
+    SHA512 9836a4af3bbbfed1ea1b4c70b9d500ac485d7c3d8131eb8a25ee6ef6662f46ba52b5161c45c709ed9a601ff0e9ec36daa5650eaaf4f2cc7d6f4bb5640f10da15
 )
 
 vcpkg_extract_source_archive_ex(
     OUT_SOURCE_PATH SOURCE_PATH
     ARCHIVE ${ARCHIVE}
     PATCHES
-        0001-correct-headers-for-getcwd.patch
+        0001-fix-dependencies.patch
+        0002-export-cmake-targets.patch
+        0003-add-Wno-error-implicit-funciton-declaration-to-cmake.patch
 )
 
+vcpkg_check_features(OUT_FEATURE_OPTIONS FEATURE_OPTIONS
+    curl        UseCurl
+)
+
+if ("curl" IN_LIST FEATURES)
+    set(FIND_CURL_DEPENDENCY "find_dependency(CURL CONFIG)")
+endif()
+
+if ("pthreads" IN_LIST FEATURES)
+    if (VCPKG_TARGET_IS_WINDOWS)
+        set(WITH_PTHREADS ON)
+        set(FIND_PTHREADS_DEPENDENCY "find_dependency(pthreads)")
+    else()
+        message(WARNING "Feature pthreads only support Windows, disable it now.")
+        set(WITH_PTHREADS OFF)
+    endif()
+endif()
+
 vcpkg_configure_cmake(
     SOURCE_PATH ${SOURCE_PATH}
     PREFER_NINJA
+    OPTIONS ${FEATURE_OPTIONS}
+        -DUSE_PTHREADS=${WITH_PTHREADS}
 )
 
 vcpkg_install_cmake()
+vcpkg_fixup_pkgconfig(SYSTEM_LIBRARIES m)
+vcpkg_fixup_cmake_targets(CONFIG_PATH share/unofficial-cfitsio TARGET_PATH share/unofficial-cfitsio)
+
+file(READ ${CURRENT_PACKAGES_DIR}/share/unofficial-cfitsio/unofficial-cfitsio-config.cmake ASSIMP_CONFIG)
+file(WRITE ${CURRENT_PACKAGES_DIR}/share/unofficial-cfitsio/unofficial-cfitsio-config.cmake "
+include(CMakeFindDependencyMacro)
+${FIND_CURL_DEPENDENCY}
+${FIND_PTHREADS_DEPENDENCY}
+find_dependency(ZLIB)
+${ASSIMP_CONFIG}
+")
 
-# Remove duplicate include files
-file(REMOVE_RECURSE ${CURRENT_PACKAGES_DIR}/debug/include ${CURRENT_PACKAGES_DIR}/include/unistd.h)
+vcpkg_replace_string(${CURRENT_PACKAGES_DIR}/share/unofficial-cfitsio/unofficial-cfitsio-config.cmake
+    "cmake_policy(VERSION 2.6)"
+    "cmake_policy(VERSION 2.6)\r\n\
+# Required for the evaluation of \"if(@BUILD_SHARED_LIBS@)\" below to function\r\n\
+cmake_policy(SET CMP0012 NEW)\r\n"
+)
 
-# cfitsio uses very common names for its headers, so they must be moved to a subdirectory
-file(RENAME ${CURRENT_PACKAGES_DIR}/include ${CURRENT_PACKAGES_DIR}/cfitsio)
-file(MAKE_DIRECTORY ${CURRENT_PACKAGES_DIR}/include)
-file(RENAME ${CURRENT_PACKAGES_DIR}/cfitsio ${CURRENT_PACKAGES_DIR}/include/cfitsio)
+file(REMOVE_RECURSE ${CURRENT_PACKAGES_DIR}/debug/include ${CURRENT_PACKAGES_DIR}/include/unistd.h ${CURRENT_PACKAGES_DIR}/debug/share)
 
-if(VCPKG_LIBRARY_LINKAGE STREQUAL dynamic)
-    # move DLLs to bin directories for dynamic builds
-    file(MAKE_DIRECTORY ${CURRENT_PACKAGES_DIR}/bin)
-    file(RENAME  ${CURRENT_PACKAGES_DIR}/lib/cfitsio.dll ${CURRENT_PACKAGES_DIR}/bin/cfitsio.dll)
-    file(MAKE_DIRECTORY ${CURRENT_PACKAGES_DIR}/debug/bin)
-    file(RENAME  ${CURRENT_PACKAGES_DIR}/debug/lib/cfitsio.dll ${CURRENT_PACKAGES_DIR}/debug/bin/cfitsio.dll)
-endif()
+file(INSTALL ${SOURCE_PATH}/FindPthreads.cmake DESTINATION ${CURRENT_PACKAGES_DIR}/share/unofficial-cfitsio)
 
-# Handle copyright
-file(INSTALL ${SOURCE_PATH}/License.txt DESTINATION ${CURRENT_PACKAGES_DIR}/share/cfitsio RENAME copyright)
+file(INSTALL ${SOURCE_PATH}/License.txt DESTINATION ${CURRENT_PACKAGES_DIR}/share/${PORT} RENAME copyright)
diff --git a/ports/healpix/CONTROL b/ports/healpix/CONTROL
index 8b1e856e2..554f8fb1f 100644
--- a/ports/healpix/CONTROL
+++ b/ports/healpix/CONTROL
@@ -1,6 +1,6 @@
 Source: healpix
 Version: 1.12.10
-Port-Version: 6
+Port-Version: 7
 Homepage: http://healpix.sourceforge.net/
 Description: HEALPix is an acronym for Hierarchical Equal Area isoLatitude Pixelation of a sphere.
 Build-Depends: cfitsio
diff --git a/ports/healpix/fix-dependency.patch b/ports/healpix/fix-dependency.patch
new file mode 100644
index 000000000..87d7336f5
--- /dev/null
+++ b/ports/healpix/fix-dependency.patch
@@ -0,0 +1,13 @@
+diff --git a/src/cxx/configure.ac b/src/cxx/configure.ac
+index 63f05d7..e284f0d 100644
+--- a/src/cxx/configure.ac
++++ b/src/cxx/configure.ac
+@@ -175,7 +175,7 @@ CXXCFLAGS_NO_C="$CXXCFLAGS $CPPFLAGS"
+ LDCCFLAGS="$LDFLAGS $CCFLAGS"
+ LDCXXFLAGS="$LDFLAGS $CXXCFLAGS"
+ 
+-AC_CHECK_LIB([cfitsio],[ffgnrwll],,AC_MSG_ERROR([could not find the cfitsio library]),[-lm])
++AC_CHECK_LIB([cfitsio -lz],[ffgnrwll],,AC_MSG_ERROR([could not find the cfitsio library]),[-lm -lz])
+ AC_CHECK_HEADERS([fitsio.h],,AC_MSG_ERROR([could not find the cfitsio header file]),)
+ 
+ AC_SUBST(SILENT_RULE)
diff --git a/ports/healpix/portfile.cmake b/ports/healpix/portfile.cmake
index c1fa90f36..dde1ac3c1 100644
--- a/ports/healpix/portfile.cmake
+++ b/ports/healpix/portfile.cmake
@@ -7,6 +7,7 @@ vcpkg_from_sourceforge(
     REF Healpix_${HEALPIX_VER}
     FILENAME "Healpix_${HEALPIX_PACK_NAME}.tar.gz"
     SHA512 29fe680d757bd94651bf029654257cb67286643aad510df4c2f0b06245174411376ec1beca64feebfac14a6fc0194525170635842916d79dcaddeddd9ac6f6c7
+    PATCHES fix-dependency.patch
 )
 
 vcpkg_configure_make(