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

1 files changed, 36 insertions, 25 deletions

diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 861b5c5..97548b8 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -109,7 +109,7 @@ astrometrynet-version = 0.91
 atlas-version = 3.10.3
 autoconf-version = 2.72
 automake-version = 1.17
-boost-version = 1.77.0
+boost-version = 1.87.0
 cairo-version = 1.16.0
 cdsclient-version = 3.84
 cfitsio-version = 4.5.0
@@ -142,7 +142,8 @@ libtiff-version = 4.7.0
 libtirpc-version = 1.2.6
 metastore-version = 1.1.2-23-fa9170b
 missfits-version = 2.8.0
-openblas-version = 0.3.21
+ninjabuild-version = 1.12.1
+openblas-version = 0.3.29
 openmpi-version = 4.1.1
 openssh-version = 8.0p1
 patch-version = 2.7.6
@@ -187,7 +188,7 @@ libgit2-version = 1.9.0
 
 # Python should only be updated by the maintainer for Python packages; see
 # https://savannah.nongnu.org/task/?16622.
-python-version = 3.10.6
+python-version = 3.13.2
 
 # Netpbm's questions in the configure steps maybe change with different or
 # new versions.
@@ -197,7 +198,6 @@ netpbm-version = 10.73.39
 # version.
 minizip-version = $(zlib-version)
 
-
 # Be careful with updateing hdf5 because h5py 2.10.0 doesn't work with
 # version 1.12.0.
 hdf5-version = 1.13.1
@@ -218,67 +218,78 @@ hdf5-version = 1.13.1
 # CLASS:PYTHON-START (important identifier for 'awk'; don't modify this line)
 asn1crypto-version = 0.24.0
 asteval-version = 0.9.16
-astropy-version = 5.1
+astropy-version = 7.0.1
+astropy-iers-data-version = 0.2025.2.24.0.34.4
 beautifulsoup4-version = 4.10.0
 beniget-version = 0.4.1
 certifi-version = 2018.11.29
 cffi-version = 1.15.0
 chardet-version = 3.0.4
+contourpy-version = 1.3.1
 corner-version = 2.0.1
-cycler-version = 0.11.0
-cython-version = 0.29.24
+cppy-version = 1.3.1
+cycler-version = 0.12.1
+cython-version = 3.0.12
 eigency-version = 1.77
 emcee-version = 3.0.1
 entrypoints-version = 0.3
 esutil-version = 0.6.9
-extension-helpers-version = 0.1
+extension-helpers-version = 1.2.0
+features-version = 0.5.12
 flake8-version = 3.7.8
+flit-core-version = 3.11.0
+fonttools-version = 4.56.0
 future-version = 0.18.1
 galsim-version = 2.3.5
 gast-version = 0.5.3
+gpep517-version = 16
 h5py-version = 2.10.0
 html5lib-version = 1.0.1
 idna-version = 2.8
 jeepney-version = 0.4
 jinja2-version = 3.0.3
-kiwisolver-version = 1.0.1
+kiwisolver-version = 1.4.8
 lmfit-version = 0.9.14
 lsstdesccoord-version = 1.2.0
 markupsafe-version = 2.0.1
+meson-version = 1.7.0
+meson-python-version = 0.17.1
 mpi4py-version = 3.1.3
 mpmath-version = 1.1.0
-numpy-version = 1.21.3
-packaging-version = 21.3
+numpy-version = 2.2.3
+packaging-version = 24.2
 pexpect-version = 4.7.0
-pillow-version = 8.4.0
+pillow-version = 11.1.0
 pip-version = 19.0.2
 ply-version = 3.11
-pybind11-version = 2.5.0
+pybind11-version = 2.13.6
 pycodestyle-version = 2.5.0
 pycparser-version = 2.19
-pyerfa-version = 2.0.0.1
+pyerfa-version = 2.0.1.5
 pyflakes-version = 2.1.1
-pyparsing-version = 3.0.4
+pyproject-metadata-version = 0.9.0
+pyparsing-version = 3.2.1
 pypkgconfig-version = 1.5.1
-python-dateutil-version = 2.8.0
+python-dateutil-version = 2.9.0.post0
+python-installer-version = 0.7.0
 pythran-version = 0.11.0
-pyyaml-version = 5.1
+pyyaml-version = 6.0.2
 requests-version = 2.21.0
-setuptools-version = 58.3.0
-setuptools_scm-version = 3.3.3
+setuptools-version = 75.8.0
+setuptools-scm-version = 8.2.0
 sip_tpv-version = 1.1
-six-version = 1.16.0
+six-version = 1.17.0
 soupsieve-version = 1.8
 sympy-version = 1.4
 uncertainties-version = 3.1.6
 urllib3-version = 1.24.1
 webencodings-version = 0.5.1
-wheel-version = 0.37.0
+wheel-version = 0.45.1
 
-# More recent versions of Matplotlib and Scipy have issues with finding
-# dependencies in our Python build system.
-scipy-version = 1.7.3
-matplotlib-version = 3.3.0
+# Matplotlib and Scipy are big packages that may have difficulty resolving
+# their dependency hell:
+matplotlib-version = 3.10.0
+scipy-version = 1.15.2
 
 # CLASS:PYTHON-END (important identifier for 'awk'; don't modify this line)