IMPORTANT (for Python users): Python environment updated (34 software)

Summary: this is software update that involves Astropy and its
dependencies. In case you are using any of those, it is recommended to
reproduce the analysis of your project to make sure that the calls to the
various packages have not changed. If you are not using Astropy or its
dependencies, this commit will not affect your analysis.

Until this commit, Astropy and the whole Python environment of its
prerequisites were last updated more than 2 years go. So after the update
of the Basic and some high-level (Gnuastro dependencies) software, it was
necessary to update Astropy and its dependencies (for those who use it).

With this commit, the software listed in the last item below have been
updated as well as the following minor technical fixes:

  - Support bug 110738 (https://savannah.nongnu.org/support/?110738): when
    the build directory had the same base-name as the source directory (for
    exapmle '/PATH/proj' and /PATH/proj-build'), Maneage would complain and
    not continue.

  - The Python software are now built using the wheels system with
    'gpep517' (https://pypi.org/project/gpep517). Python packages that are
    not required by astropy/matplotlib/scipy have mostly not been updated,
    but updating their dependencies and adding the build method as
    'GPEP517' should be straightforward.

  - Updated software (dependencies of Astropy). Those with 'N/A' in their
    previous version string weren't in Maneage prior to this commit.

    High-level software (not written in Python):

       boost                   1.77.0          1.87.0
       ninja build system      n/a             1.12.1
       openblas                0.3.21          0.3.29

    Python packages:

       python                  3.10.6          3.13.2
       astropy                 5.1             7.0.1
       astropy-iers-data       n/a             0.2025.2.24.0.34.4
       contourpy               n/a             1.3.1
       cppy                    n/a             1.3.1
       cycler                  0.11.0          0.12.1
       cython                  0.29.24         3.0.12
       extension-helpers       0.1             1.2.0
       features                n/a             0.5.12
       flit-core               n/a             3.11.0
       fonttools               n/a             4.56.0
       gpep517                 n/a             16
       kiwisolver              1.0.1           1.4.8
       matplotlib              3.3.0           3.10.0
       meson                   n/a             1.7.0
       meson-python            n/a             0.17.1
       numpy                   1.21.3          2.2.3
       packaging               21.3            24.2
       pillow                  8.4.0           11.1.0
       pybind11                2.5.0           2.13.6
       pyerfa-version          2.0.0.1         2.0.1.5
       pyproject-metadata      n/a             0.9.0
       pyparsing               3.0.4           3.2.1
       python-dateutil         2.8.0           2.9.0.post0
       python-installer        n/a             0.7.0
       pyyaml                  5.1             6.0.2
       setuptools              58.3.0          75.8.0
       setuptools_scm          3.3.3           8.2.0
       scipy                   1.7.3           1.15.2
       six                     1.16.0          1.17.0
       wheel                   0.37.0          0.45.1

2 files changed, 32 insertions, 14 deletions

diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index dafd149..83bf4ed 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -884,14 +884,17 @@ The project's "source" (this directory) and "build" directories are treated
 separately. This greatly helps in managing the many intermediate files that
 are created during the build. The intermediate build files don't need to be
 archived or backed up: you can always re-build them with the contents of
-the source directory. The build directory also needs a relatively large
-amount of free space (atleast serveral Giga-bytes), while the source
-directory (all plain text) will usually be a mega-byte or less.
+the source directory. The build directory also needs a fairly large amount
+of free space (at least several gigabytes), while the source directory (all
+plain text, ignoring the .git directory if you have it) will usually be a
+megabyte or less.
 
-'.build' (a symbolic link to the build directory) will also be created
+The link '.build' (a symbolic link to the build directory) will be created
 during this configuration. It can help encourage you to set the actual
-build directory in a very different address from this one (one that can be
-deleted and has large volume), while having easy access to it from here.
+build directory to a very different path to that of the source (the build
+directory should be considered as a large volume directory of throwaway
+space that can be casually deleted), while making it easy to access from
+here without having to remember the particular path.
 
 --- CAUTION ---
 Do not choose any directory under the top source directory (this
@@ -905,12 +908,15 @@ EOF
     do
         # Ask the user (if not already set on the command-line).
         if [ x"$build_dir" = x ]; then
-            if read -p"Please enter the top build directory: " build_dir; then
+            if read -p"Please enter the top build directory: " build_dir;
+            then
                 just_a_place_holder_to_avoid_not_equal_test=1;
             else
-                echo "ERROR: shell is in non-interactive-mode and no build directory specified."
-                echo "The build directory (described above) is mandatory, configuration can't continue."
-                echo "Please use '--build-dir' to specify a build directory non-interactively."
+                printf "ERROR: shell is in non-interactive-mode and no "
+                printf "build directory specified. The build directory "
+                printf "(described above) is mandatory, configuration "
+                printf "can't continue. Please use '--build-dir' to "
+                printf "specify a build directory non-interactively"
                 exit 1
             fi
         fi
@@ -937,7 +943,7 @@ EOF
         # directory.
         if ! [ x"$bdir" = x ]; then
             if echo "$bdir/" \
-                    | grep '^'"$currentdir" 2> /dev/null > /dev/null; then
+                    | grep '^'"$currentdir/" 2> /dev/null > /dev/null; then
 
                 # If it was newly created, it will be empty, so delete it.
                 if ! [ "$(ls -A $bdir)" ]; then rm --dir "$bdir"; fi
diff --git a/reproduce/software/shell/tarball-prepare.sh b/reproduce/software/shell/tarball-prepare.sh
index 5b41aec..8e30931 100755
--- a/reproduce/software/shell/tarball-prepare.sh
+++ b/reproduce/software/shell/tarball-prepare.sh
@@ -176,6 +176,10 @@ for f in $allfiles; do
     name=$(echo $(basename $f) \
 	       | sed -e 's/.tar.*//' -e's/_/-/')
 
+    # Extract the software's name from the tarball name (needed later
+    # for software-specific checks).
+    sname=$(echo $name | sed -e's|-| |' | awk '{print $1}')
+
     # Lzip will not be available to unpack Lzip itself, so just use Tar.
     if [[ $name =~ ^lzip ]]; then
       outname=$name.tar
@@ -204,8 +208,9 @@ for f in $allfiles; do
     # Create a temporary directory name
     tmpdir=$odir/$name-tmpunpack
 
-    # If the temporary directory exists, mkdir will throw an error. The
-    # developer needs to intervene manually to fix the issue.
+    # If the temporary directory exists, delete it and build an empty
+    # directory to work on (to avoid potential conflicts).
+    if [ -d $tmpdir ]; then rm -rf $tmpdir; fi
     mkdir $tmpdir
 
 
@@ -235,8 +240,15 @@ for f in $allfiles; do
     # for large tarballs such as gcc's)
     find "$name"/ -type f -print0 | xargs -0 touch
 
+    # Some software source files (like Boost; https://www.boost.io)
+    # have names that are too long for the more robust 'ustar'
+    # format. So for we should use 'pax' for them.
+    if [ $sname = boost ]; then tarformat=pax
+    else                        tarformat=ustar
+    fi
+
     # Pack with recommended options
-    tar -c -Hustar --owner=root --group=root \
+    tar -c -H$tarformat --owner=root --group=root \
         -f $name.tar $name/
 
     # Lzip will not be available when unpacking Lzip, so we just use Tar.