<pre style='margin:0'>
Herby Gillot (herbygillot) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/e52b0344d544627056e4ec9b0a0faa42599d277a">https://github.com/macports/macports-ports/commit/e52b0344d544627056e4ec9b0a0faa42599d277a</a></p>
<pre style="white-space: pre; background: #F8F8F8">The following commit(s) were added to refs/heads/master by this push:
<span style='display:block; white-space:pre;color:#404040;'> new e52b0344d54 minc, libminc: replace minc with libminc
</span>e52b0344d54 is described below
<span style='display:block; white-space:pre;color:#808000;'>commit e52b0344d544627056e4ec9b0a0faa42599d277a
</span>Author: nilason <n_larsson@yahoo.com>
AuthorDate: Wed Sep 6 09:41:08 2023 +0200
<span style='display:block; white-space:pre;color:#404040;'> minc, libminc: replace minc with libminc
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> Upstreams, minc was split into libminc and minc-tools. This makes the
</span><span style='display:block; white-space:pre;color:#404040;'> broken port 'minc' obsolete with the new port 'libminc' (version 2.4.05)
</span><span style='display:block; white-space:pre;color:#404040;'> as a replacement.
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> The upstreams tool package minc-tools, apparently unmaintained with its
</span><span style='display:block; white-space:pre;color:#404040;'> last modification dated in 2015, doesn't build because of missing header
</span><span style='display:block; white-space:pre;color:#404040;'> files (among other reasons) and is therefore omitted from this change.
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> Closes: https://trac.macports.org/ticket/28749
</span><span style='display:block; white-space:pre;color:#404040;'> Closes: https://trac.macports.org/ticket/60321
</span>---
science/libminc/Portfile | 73 +++++++++++++++++++++++++++++++
science/libminc/files/patch-cmake.diff | 11 +++++
science/minc/Portfile | 26 ++++-------
science/minc/files/patch-MAX_NC_OPEN.diff | 51 ---------------------
4 files changed, 92 insertions(+), 69 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/libminc/Portfile b/science/libminc/Portfile
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..0fc5ac61d29
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/libminc/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,73 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortSystem 1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup cmake 1.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup github 1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup active_variants 1.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup BIC-MNI libminc 2.4.05 release-
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories science
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+maintainers nomaintainer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# The MINC package itself and most of the associated tools are licensed under a modified BSD license.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license BSD
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description Library handling the MINC file format
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description {*}${description}, which is a highly flexible medical image \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ file format built on the HDF5 generalized data format. \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ The format is simple, self-describing, extensible, \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ portable and N-dimensional, with programming interfaces \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ for both low-level data access and high-level volume \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ manipulation. On top of the libraries is a suite of generic \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ image-file manipulation tools. The format, libraries and \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ tools are designed for use in a medical-imaging research \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ environment: they are simple and powerful and make no \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ attempt to provide a pretty interface to users.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage https://www.bic.mni.mcgill.ca/ServicesSoftware/MINC
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 65e13eaa8b11a191592256f43b4179da757528be \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 bfb4d2755a4794a75c5c47a737c5cbfac41d131d70d92f366e46113875e5be54 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 811951
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_build-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:bison \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:flex
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append port:hdf5 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:libaec \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:netcdf \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:nifticlib \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:zlib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+pre-configure {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # Figure out HDF5's mpi include directory
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ set mpl_include_dir ""
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if {![catch {set result [active_variants hdf5 openmpi]}]} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if {$result} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ set mpl_include_dir "-I${prefix}/include/openmpi-mp"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if {![catch {set result [active_variants hdf5 mpich]}]} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if {$result} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ set mpl_include_dir "-I${prefix}/include/mpich-mp"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if {$mpl_include_dir ne ""} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ configure.cflags-append ${mpl_include_dir}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles patch-cmake.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.args-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DLIBMINC_BUILD_SHARED_LIBS=ON \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DLIBMINC_MINC1_SUPPORT=ON \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -DLIBMINC_USE_SYSTEM_NIFTI=ON
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+post-destroot {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ file mkdir ${destroot}${prefix}/lib/cmake/LIBMINC
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ move {*}[glob ${destroot}${prefix}/lib/cmake/*.cmake] ${destroot}${prefix}/lib/cmake/LIBMINC
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/libminc/files/patch-cmake.diff b/science/libminc/files/patch-cmake.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..c58c85677be
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/libminc/files/patch-cmake.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,11 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- CMakeLists.txt.orig
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ CMakeLists.txt
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -524,7 +524,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # config for install dir
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-SET(LIBMINC_USE_FILE_CONFIG "\${LIBMINC_INSTALL_PREFIX}/lib/cmake/Use${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINC.cmake" )
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++SET(LIBMINC_USE_FILE_CONFIG "\${LIBMINC_INSTALL_PREFIX}/lib/cmake/LIBMINC/Use${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINC.cmake" )
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SET(LIBMINC_INCLUDE_DIRS_CONFIG "\${LIBMINC_INSTALL_PREFIX}/include" )
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SET(LIBMINC_LIBRARY_DIRS_CONFIG "\${LIBMINC_INSTALL_PREFIX}/lib" )
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SET(LIBMINC_STATIC_LIBRARIES_CONFIG "" )
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/minc/Portfile b/science/minc/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index f356b5580ec..ae30249728e 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/minc/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/minc/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,21 +1,11 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-PortSystem 1.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-name minc
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version 1.5.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision 6
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories science
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-platforms darwin
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-maintainers nomaintainer
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-description This package contains tools to manipulate MINC files.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-long_description The Minc file format is a highly flexible medical image file format built on top of the NetCDF generalized data format. The format is simple, self-describing, extensible, portable and N-dimensional, with programming interfaces for both low-level data access and high-level volume manipulation. On top of the libraries is a suite of generic image-file manipulation tools. The format, libraries and tools are designed for use in a medical-imaging research environment: they ar [...]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-master_sites http://packages.bic.mni.mcgill.ca/tgz/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortSystem 1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup obsolete 1.0
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums sha1 ee2a2930754e6248f3decc12579d689ae29c8bdb \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- rmd160 a5b1cafbeb52a6b0d5a55e6bca95953fdec7e01a
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+name minc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+version 1.5.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 7
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories science
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_lib port:netcdf
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-patchfiles patch-MAX_NC_OPEN.diff
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.args --with-build-path=${prefix}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+replaced_by libminc
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/minc/files/patch-MAX_NC_OPEN.diff b/science/minc/files/patch-MAX_NC_OPEN.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 503844fef01..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/minc/files/patch-MAX_NC_OPEN.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,51 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- libsrc/minc.h.orig 2004-09-28 15:23:40.000000000 -0500
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ libsrc/minc.h 2011-03-12 01:44:21.000000000 -0600
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -358,7 +358,9 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- /* Constants for image conversion variable (icv) properties */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- /* Maximum number of icv's allowed */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--#define MI_MAX_NUM_ICV MAX_NC_OPEN
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+/* changed to 32 as netcdf 4.x no longer defines MAX_NC_OPEN */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+/* #define MI_MAX_NUM_ICV MAX_NC_OPEN */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#define MI_MAX_NUM_ICV 32
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- /* Default max and min for normalization */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #define MI_DEFAULT_MAX 1.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #define MI_DEFAULT_MIN 0.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- libsrc/voxel_loop.c.orig 2004-09-28 15:23:40.000000000 -0500
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ libsrc/voxel_loop.c 2011-03-12 01:44:57.000000000 -0600
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1946,7 +1946,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- /* Keep track of number of files that we can open */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- num_free_files = loop_options->max_open_files;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- if (num_free_files > MAX_NC_OPEN) num_free_files = MAX_NC_OPEN;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ if (num_free_files > MI_MAX_NUM_ICV) num_free_files = MI_MAX_NUM_ICV;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- /* Check to see if we can open output files (we must leave room for one
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- input file) */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2661,7 +2661,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- loop_options->is_signed = TRUE;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- loop_options->valid_range[0] = 0.0;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- loop_options->valid_range[1] = 0.0;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- loop_options->max_open_files = MAX_NC_OPEN - 2;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ loop_options->max_open_files = MI_MAX_NUM_ICV - 2;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- loop_options->check_all_input_dim_info = TRUE;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- loop_options->convert_input_to_scalar = FALSE;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- loop_options->output_vector_size = 0;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2776,7 +2776,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- @NAME : set_loop_max_open_files
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- @INPUT : loop_options - user options for looping
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- max_open_files - maximum number of open files allowed (between
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- 1 and MAX_NC_OPEN)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ 1 and MI_MAX_NUM_ICV)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- @OUTPUT : (none)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- @RETURNS : (nothing)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- @DESCRIPTION: Routine to set the maximum number of open minc files.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2789,7 +2789,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- MNCAPI void set_loop_max_open_files(Loop_Options *loop_options,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int max_open_files)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- if ((max_open_files <= 0) || (max_open_files > MAX_NC_OPEN)) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ if ((max_open_files <= 0) || (max_open_files > MI_MAX_NUM_ICV)) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- (void) fprintf(stderr,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- "Bad number of files %d in set_loop_max_open_files\n",
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- max_open_files);
</span></pre><pre style='margin:0'>
</pre>