GNU bug report logs - #76480
[PATCH 00/51] Astro update 2025/02

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Package: guix-patches;

Reported by: Sharlatan Hellseher <sharlatanus <at> gmail.com>

Date: Fri, 21 Feb 2025 21:49:02 UTC

Severity: normal

Tags: patch

Done: Sharlatan Hellseher <sharlatanus <at> gmail.com>

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Report forwarded to andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:
bug#76480; Package guix-patches. (Fri, 21 Feb 2025 21:49:03 GMT) Full text and rfc822 format available.

Acknowledgement sent to Sharlatan Hellseher <sharlatanus <at> gmail.com>:
New bug report received and forwarded. Copy sent to andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org. (Fri, 21 Feb 2025 21:49:03 GMT) Full text and rfc822 format available.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 00/51] Astro update 2025/02
Date: Fri, 21 Feb 2025 21:48:16 +0000

Hi Guix!

Few days after FOSDEM 2025, few days before python-team will be merged with
Python 3.11, and right now all packages in Astro collection have 100% build
success!

The main highlights:
* Guix provides 172 verity of Astro* packages for scientific calculation or
  just for fun. Talking about fun, astronomy, terminal and beyond take a look
  at recently included astroterm (#76071) - providing observatory in a
  terminal!
* Long, not resolved failures and update pendings: Casacore updated to the
  latest version, python-stcal <at> 1.11.1 solved the build issue for python-jwst.
* I'm glad to mention 100%, the entire collection can be successfully built
  with the majority tests enabled on x86_64-linux! 32 packages have their
  tests disabled due to not provided by upstream, requiring networking or
  introducing cycles, which may insure functionality sort of guarantee for the
  collection.

The log:
- added [9/9]
  - [X] python-astrocut :: Cutout tools for astronomical images
  - [X] python-casacore :: Python wrapper for Casacore
  - [X] python-cmocean :: Colormap setup for standardizing commonly-plotting
    oceanographic variables
  - [X] python-esutil :: Numerical, scientific, and astrophysical computing
    utilities
  - [X] python-lofar-h5plot :: GUI for plotting H5Parms produced during LOFAR
    calibration
  - [X] python-losoto :: LOFAR Solution Tool
  - [X] python-mpsplines :: Mean preserving interpolation with splines
  - [X] python-s3path :: Pathlib extension for AWS S3 Service
  - [X] python-sndata :: Interface for data published by various supernova
    surveys
- updated [32/32]
  - [X] casacore :: 3.4.0->3.6.1
  - [X] indi :: 2.1.1->2.1.2.1
  - [X] libsep, python-sep :: 1.2.1->1.4.0
  - [X] libxisf :: 0.2.12->0.2.13
  - [X] python-asdf :: 4.0.0->4.1.0
  - [X] python-asdf-astropy :: 0.7.0->0.7.1
  - [X] python-astropy-healpix :: 1.0.3->1.1.2
  - [X] python-astropy-iers-data :: 0.2025.1.20.0.32.27->0.2025.2.17.0.34.13
  - [X] python-astroquery :: 0.4.8->0.4.9.post1
  - [X] python-cmyt :: 2.0.1->2.0.2
  - [X] python-jwst :: 1.16.1->1.17.1
  - [X] python-czml3 :: 2.3.0->2.3.4
  - [X] python-drizzle :: 2.0.0->2.0.1
  - [X] python-drms :: 0.8.0->0.9.0
  - [X] python-ephem :: 4.1.6->4.2
  - [X] python-fitsio :: 1.2.4->1.2.5
  - [X] python-glue-core :: 1.21.1->1.22.0
  - [X] python-gwcs :: 0.22.1->0.24.0
  - [X] python-halotools :: 0.9.2->0.9.3
  - [X] python-mpl-scatter-density :: 0.7->0.8
  - [X] python-ndcube :: 2.3.0->2.3.1
  - [X] python-pyvo :: 1.6->1.6.1
  - [X] python-rad :: 0.23.0->0.23.1
  - [X] python-roman-datamodels :: 0.23.0->0.23.1
  - [X] python-sep-pjw :: 1.3.7->1.3.8
  - [X] python-sgp4 :: 2.23->2.24
  - [X] python-sncosmo :: 2.11.2->2.12.0
  - [X] python-soxs :: 4.8.5->5.0.0
  - [X] python-stcal :: 1.10.0->1.11.1
  - [X] python-stsci-stimage :: 0.2.9->0.2.10
  - [X] python-sunkit-image :: 0.5.1->0.6.0
  - [X] python-viresclient :: 0.12.1->0.12.2
  - [X] scamp :: 2.10.0->2.13.1
- issues [0/8][0%]
  - Help needed for enabling tests for NumPy 2+ which already on master
    branch.
  - python-naima :: would be upgraded from 0.10.0 to 0.10.2; blocked by NumPy
    2+
  - python-photutils :: would be upgraded from 1.10.0 to 1.11.0; requires
    numpy>=1.25 and resolve new build issues. release which has a lot of
    fixes.
  - python-pynbody :: would be upgraded from 1.6.0.post0 to 2.0.0; majore
    update, depends on NumPy 2+
  - python-spherical-geometry :: would be upgraded from 1.3.2 to 1.3.3; NumPy 2+
  - imppg :: would be upgraded from 1.9.2-beta to 2.0.0; tests hangs
  - python-webbpsf :: would be upgraded from 1.5.0 to 2.0.0; project in
    migration to https://github.com/spacetelescope/stpsf

The build stats for x8664-linux:

--8<---------------cut here---------------start------------->8---
> ./pre-inst-env guix build casacore indi libsep libxisf python-asdf
  python-asdf-astropy python-astrocut python-astropy python-astropy-healpix
  python-astropy-iers-data python-astroquery python-casacore python-cmocean
  python-cmyt python-czml3 python-drizzle python-drms python-ephem python-esutil
  python-extinction python-fitsio python-glfw python-glue-core python-gwcs
  python-halotools python-jwst python-jwst-reffiles python-lofar-h5plot
  python-losoto python-mpl-scatter-density python-mpsplines python-ndcube
  python-poliastro python-pyvo python-rad python-roman-datamodels python-s3path
  python-sep-pjw python-sep-pjw python-sgp4 python-sncosmo python-sndata
  python-soxs python-specreduce python-spherical-geometry python-stcal
  python-stsci-stimage python-sunkit-image python-tweakwcs python-viresclient
  scamp

/gnu/store/ipc89bdspiwchfgjvb2g9mypmwv33z4f-casacore-3.6.1
/gnu/store/lfklx4mav5y82zxmmak0i7v1a3zlkqvk-indi-2.1.2.1
/gnu/store/bw0zjmajsbjf8c57fn7mdrajnwfi711z-libsep-1.4.0
/gnu/store/dmwzwyag5kf46v0524jl39ilm58d74br-libxisf-0.2.13
/gnu/store/vcyx95a6apy8ckn43b6grr8gma6p3ivy-python-asdf-4.1.0
/gnu/store/6rrsxqdp7zj20zrmvs4q83dmjbcq383h-python-asdf-astropy-0.7.1
/gnu/store/m4y4w3ia68w0w7wln8zcalml8qbq51fr-python-astrocut-0.12.0
/gnu/store/jpq28y5mbblavg1mys67xq46cc8mc81f-python-astropy-6.1.7
/gnu/store/b8zqznwank5hicp1g0d2wm37jrdrf0dn-python-astropy-healpix-1.1.2
/gnu/store/5fi14qp38zb2rxbziapknq57mqklq0g5-python-astropy-iers-data-0.2025.2.17.0.34.13
/gnu/store/bfms20spsgbvpf23hsh1vrhfn5imvkj7-python-astroquery-0.4.9.post1
/gnu/store/4h5jidadikl45kbkpw4np8fnf3hl5444-python-casacore-3.6.1
/gnu/store/xpw69rdmsa58awbji5f42drsdkab9yby-python-cmocean-4.0.3
/gnu/store/jj28zpjg8hrw8yhk0rgg655wk00k0ncy-python-cmyt-2.0.2
/gnu/store/41dn583hpbvqvd876sw2bq7hwlv60sl6-python-czml3-2.3.4
/gnu/store/9d5m09c71rkq7xh7zkva6l658rpj7348-python-drizzle-2.0.1
/gnu/store/7ciadvykbd2y31h6n14ldljl391fjgsi-python-drms-0.9.0
/gnu/store/3p5404d9ns3jgh0ihqqc5z1wqidp7kxc-python-ephem-4.2
/gnu/store/pz18m350q0slfh6f8r867j4j6w4l0bg9-python-esutil-0.6.16
/gnu/store/0jrwb7rmgfq2z9y75zxgyqa67siinw3a-python-extinction-0.4.7
/gnu/store/n4lcs1gvqil3c9aa81297k29gsqcg1rw-python-fitsio-1.2.5
/gnu/store/pi4dxya23s7l36w8zkhxs0kyb9gf6gjs-python-glfw-2.8.0
/gnu/store/0wkw33s0yj2q6ly8k5bfdxrbmwb0xmg8-python-glue-core-1.22.0
/gnu/store/brzcqflailsb08yds32586ajgl8vd4i9-python-gwcs-0.24.0
/gnu/store/5w65x618z2bnyqwi9nk2r034px5ds41p-python-halotools-0.9.3
/gnu/store/sc2xalhvxzk3gqx9nxc3k5llljb1nii4-python-jwst-1.17.1
/gnu/store/frc320hk3sgsk6vdsgmlc9g6w4wcynd7-python-jwst-reffiles-1.0.1
/gnu/store/x54jlgzi3xnm27zs58aa1qz1g8fmwlhx-python-lofar-h5plot-2.9.1
/gnu/store/n0465nlp8jka7199f04mll17ph2772w0-python-losoto-2.4.4
/gnu/store/5wn86mxkl35hxx9j6c74ra2qsk9vxbwq-python-mpl-scatter-density-0.8
/gnu/store/0sl73d3vydhbxasrgwaqwjpa44m2k8nq-python-mpsplines-0.0.0-0.4967655
/gnu/store/hi5m60jsr92dvdgk129w6lz2ijarlhdp-python-ndcube-2.3.1
/gnu/store/wnzsicgrcgff0iqvx8nlf20qlsmpn39f-python-poliastro-0.17.0
/gnu/store/scglbfic6zqifnfmamf1bwa5zvvf8fi3-python-pyvo-1.6.1
/gnu/store/0nnzkhg0v0hhmafgqzckdnkqw2nzw0fp-python-rad-0.23.1
/gnu/store/d0cy5sjqbr18s66r49d3dqdwy8w6lp0a-python-roman-datamodels-0.23.1
/gnu/store/9njpvq6niwr7jcd7sbp0c24rxvcs2ayf-python-s3path-0.6.0
/gnu/store/n4m2rbd5px94s5f82bl87yww90llpnrw-python-sep-pjw-1.3.8
/gnu/store/n4m2rbd5px94s5f82bl87yww90llpnrw-python-sep-pjw-1.3.8
/gnu/store/wbwvb3p7h4wlgzfib8xbmanwiawlhy1i-python-sgp4-2.24
/gnu/store/xkxacr3i1r2zih1dwsxzh6jpn4rjv6w9-python-sncosmo-2.12.0
/gnu/store/j32khr176shhfnxzbc5ddx8lwycij75g-python-sndata-1.3.0
/gnu/store/d2a4k4gbmv2w2vqasamfgxlcb946x24p-python-soxs-5.0.0
/gnu/store/yr5pdi0xqgv0mwb3wiabfydhv2wq9qzw-python-specreduce-1.4.1
/gnu/store/ybsh1smmqm13q2g79rhl5yi77v0fy1zc-python-spherical-geometry-1.3.2
/gnu/store/6m5xb4j35y2qr0iayhf2p3hnz01rhzgs-python-stcal-1.11.1
/gnu/store/d973d6lk1mi9hgcnvqhjv8yhigkbw9gl-python-stsci-stimage-0.2.10
/gnu/store/d26wgzw3qggfnv66hfk068302m9pfjbi-python-sunkit-image-0.6.0
/gnu/store/hlzmg0swxvrviibdab5kxsfg3xxvzlzg-python-tweakwcs-0.8.9
/gnu/store/fy79pwy96pxlig9j15fm348264vqp2hk-python-viresclient-0.12.2
/gnu/store/zfn3a0fa313gm4y21ankfqkfbhzjgxm5-scamp-2.13.1

> ./pre-inst-env guix refresh --list-dependent casacore indi libsep libxisf
  python-asdf python-asdf-astropy python-astrocut python-astropy
  python-astropy-healpix python-astropy-iers-data python-astroquery
  python-casacore python-cmocean python-cmyt python-czml3 python-drizzle
  python-drms python-ephem python-esutil python-extinction python-fitsio
  python-glfw python-glue-core python-gwcs python-halotools python-jwst
  python-jwst-reffiles python-lofar-h5plot python-losoto
  python-mpl-scatter-density python-mpsplines python-ndcube python-poliastro
  python-pyvo python-rad python-roman-datamodels python-s3path python-sep-pjw
  python-sep-pjw python-sgp4 python-sncosmo python-sndata python-soxs
  python-specreduce python-spherical-geometry python-stcal python-stsci-stimage
  python-sunkit-image python-tweakwcs python-viresclient scamp

Building the following 35 packages would ensure 102 dependent packages are
rebuilt: aoflagger <at> 3.4.0 stellarium <at> 24.4-0.60b6bec siril <at> 1.3.3
python-asdf-compression <at> 0.0.1-1.7cfd07c python-asdf-zarr <at> 0.0.4
python-viresclient <at> 0.12.2 python-lofar-h5plot <at> 2.9.1 python-zodipy <at> 1.1.0
python-regularizepsf <at> 1.0.2 python-naima <at> 0.10.0 python-cesium <at> 0.12.1
python-coolest <at> 0.1.9 python-spisea <at> 2.1.13 python-statmorph <at> 0.6.1
python-holodeck <at> 1.5.2 python-mapsims <at> 2.6.0 python-kanon <at> 0.6.6
python-halotools <at> 0.9.3 scamp <at> 2.13.1 ginga-qt5 <at> 5.2.0 python-poliastro <at> 0.17.0
python-astroalign <at> 2.6.1 python-astroplan <at> 0.10.1 python-radiospectra <at> 0.6.0
python-sunkit-image <at> 0.6.0 python-yt-astro-analysis <at> 1.1.3 python-glue-qt <at> 0.3.2
python-sbpy <at> 0.5.0 python-acstools <at> 3.7.2 python-webbpsf <at> 1.5.0 python-sndata <at> 1.3.0
python-pyxsim <at> 4.4.2 python-glue-astronomy <at> 0.10.0 python-astrocut <at> 0.12.0
python-jwst-reffiles <at> 1.0.1

/gnu/store/pwninw4dkhy9n5aw5adp1x496zyxp3hh-aoflagger-3.4.0
/gnu/store/67y9p81rfjbsmg05zw0ygja2k7an3b55-stellarium-24.4-0.60b6bec
/gnu/store/j3qiz04km9xjlk7ipjv4rsghji533cxw-siril-1.3.3
/gnu/store/f2rsy04jckyza744ksavhq5jlc544chl-python-asdf-compression-0.0.1-1.7cfd07c
/gnu/store/7hvm8yyy4r73dxfc7fx04f5rp0bw73dm-python-asdf-zarr-0.0.4
/gnu/store/fy79pwy96pxlig9j15fm348264vqp2hk-python-viresclient-0.12.2
/gnu/store/x54jlgzi3xnm27zs58aa1qz1g8fmwlhx-python-lofar-h5plot-2.9.1
/gnu/store/1zy1v6m9wjgxvipg5q2qc07c3n8m5j1p-python-zodipy-1.1.0
/gnu/store/9an1lmc8c8na5vw53alvnzhqv7l42xlc-python-regularizepsf-1.0.2
/gnu/store/scfyj5r03j5ws9awhl3mbvjfsqmxh7kk-python-naima-0.10.0
/gnu/store/x5561w9zdn8p3bdncy2i170h2z29zg9d-python-cesium-0.12.1
/gnu/store/4n3phd9p77rvlylpicwa37p7v4p7acxs-python-coolest-0.1.9
/gnu/store/il0sgb3d427f82jhzddx91ksqlygdn3v-python-spisea-2.1.13
/gnu/store/by9zlycklyd3nfbyp2xsxjrhwm0d9ii3-python-statmorph-0.6.1
/gnu/store/nk32pm8bqfjlkpfn6nxwhci8yb7lgzqs-python-holodeck-1.5.2
/gnu/store/zzrs0my2qk6wvwxnrnpx066bh23xs3hs-python-mapsims-2.6.0
/gnu/store/dqk8k03fivcghsysw4l194i0w80mq5nv-python-kanon-0.6.6
/gnu/store/5w65x618z2bnyqwi9nk2r034px5ds41p-python-halotools-0.9.3
/gnu/store/zfn3a0fa313gm4y21ankfqkfbhzjgxm5-scamp-2.13.1
/gnu/store/4q7m61lrdp883vsh9kidnmhm6ygigibm-ginga-qt5-5.2.0
/gnu/store/wnzsicgrcgff0iqvx8nlf20qlsmpn39f-python-poliastro-0.17.0
/gnu/store/nrcrhzmj0zir71z1g1ff2a27sc8gnnwz-python-astroalign-2.6.1
/gnu/store/07r13b2rxp9yhjg8rifmrkxq9xwnarhi-python-astroplan-0.10.1
/gnu/store/2xh3yi7ayfba20izyd24r42m1x92cw5c-python-radiospectra-0.6.0
/gnu/store/d26wgzw3qggfnv66hfk068302m9pfjbi-python-sunkit-image-0.6.0
/gnu/store/krmw7qdlp03s7wnsbpfhny0w4zmrzqig-python-yt-astro-analysis-1.1.3
/gnu/store/liirr51a4r3x4mvvk5c57db7jd4h421z-python-glue-qt-0.3.2
/gnu/store/bikwp1csdk70d8w4kn2yi60ch2gbjlh2-python-sbpy-0.5.0
/gnu/store/232rs047129knqppwsqxp66wzwp37j40-python-acstools-3.7.2
/gnu/store/a07q177nfn8kd9r2d3hsydmqf1976vm9-python-webbpsf-1.5.0
/gnu/store/j32khr176shhfnxzbc5ddx8lwycij75g-python-sndata-1.3.0
/gnu/store/kdmnq5s3mwpznd2sj0b1g8s45ii8xdgv-python-pyxsim-4.4.2
/gnu/store/4cn8jsaa2lzv0yvi9ir5kpcyiiypgdyn-python-glue-astronomy-0.10.0
/gnu/store/m4y4w3ia68w0w7wln8zcalml8qbq51fr-python-astrocut-0.12.0
/gnu/store/frc320hk3sgsk6vdsgmlc9g6w4wcynd7-python-jwst-reffiles-1.0.1
--8<---------------cut here---------------end--------------->8---

Sharlatan Hellseher (51):
  gnu: casacore: Update to 3.6.1.
  gnu: Add python-casacore.
  gnu: indi-2.0: Update to 2.1.2.1.
  gnu: libsep: Update to 1.4.0.
  gnu: libxisf: Update to 0.2.13.
  gnu: scamp: Update to 2.13.1.
  gnu: python-asdf: Update to 4.1.0.
  gnu: python-asdf-astropy: Update to 0.7.1.
  gnu: python-astropy: Simplify check phase.
  gnu: python-astropy-healpix: Update to 1.1.2.
  gnu: python-astropy-iers-data: Update to 0.2025.2.17.0.34.13.
  gnu: python-astroquery: Update to 0.4.9.post1.
  gnu: python-cmyt: Update to 2.0.2.
  gnu: python-czml3: Update to 2.3.4.
  gnu: python-drizzle: Update to 2.0.1.
  gnu: python-drms: Update to 0.9.0.
  gnu: python-extinction: Fix source and home-page URL.
  gnu: python-ephem: Update to 4.2.
  gnu: python-fitsio: Update to 1.2.5.
  gnu: python-mpl-scatter-density: Update to 0.8.
  gnu: python-glue-core: Update to 1.22.0.
  gnu: python-gwcs: Update to 0.24.0.
  gnu: python-tweakwcs: Skip 2 tests.
  gnu: python-halotools: Update to 0.9.3.
  gnu: python-ndcube: Update to 2.3.1.
  gnu: python-pyvo: Update to 1.6.1.
  gnu: python-rad: Update to 0.23.1.
  gnu: python-roman-datamodels: Update to 0.23.1.
  gnu: python-sep-pjw: Simplify.
  gnu: python-sep-pjw: Update to 1.3.8.
  gnu: python-sgp4: Update to 2.24.
  gnu: python-sncosmo: Update to 2.12.0.
  gnu: python-specreduce: Simplify.
  gnu: python-spherical-geometry: Remove bundled libqd source.
  gnu: python-soxs: Update to 5.0.0.
  gnu: python-stsci-stimage: Update to 0.2.10.
  gnu: python-sunkit-image: Update to 0.6.0.
  gnu: python-viresclient: Update to 0.12.2.
  gnu: Add python-cmocean.
  gnu: Add python-esutil.
  gnu: Add python-glfw.
  gnu: Add python-losoto.
  gnu: Add python-lofar-h5plot.
  gnu: Add python-mpsplines.
  gnu: Add python-sndata.
  gnu: Add python-s3path.
  gnu: Add python-astrocut.
  gnu: python-poliastro: Disable more failing tests.
  gnu: python-stcal: Update to 1.11.1.
  gnu: python-jwst: Update to 1.17.1.
  gnu: python-jwst-reffiles: Enable tests and sanity-check.

 gnu/packages/astronomy.scm       | 749 +++++++++++++++++++++----------
 gnu/packages/python-graphics.scm |  35 ++
 gnu/packages/python-science.scm  |  66 ++-
 gnu/packages/python-web.scm      |  28 ++
 4 files changed, 636 insertions(+), 242 deletions(-)


base-commit: dfabaa8a6faa58612a069eb47ee3f35a94b146fb
-- 
2.47.1

Information forwarded to andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:
bug#76480; Package guix-patches. (Fri, 21 Feb 2025 21:51:04 GMT) Full text and rfc822 format available.

Message #8 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 01/51] gnu: casacore: Update to 3.6.1.
Date: Fri, 21 Feb 2025 21:48:55 +0000

* gnu/packages/astronomy.scm (casacore): Update to 3.6.1.
[argument] <phases>: Add 'hide-gfortran.
[inputs]: Add gsl.

Change-Id: I702427857cf001d583b775189f9d8f5d35fc7183
---
 gnu/packages/astronomy.scm | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 52c295d98ad..1cd4d743597 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -401,7 +401,7 @@ (define-public calcmysky-qt5
 (define-public casacore
   (package
     (name "casacore")
-    (version "3.4.0")
+    (version "3.6.1")
     (source
      (origin
        (method git-fetch)
@@ -410,7 +410,7 @@ (define-public casacore
              (commit (string-append "v" version))))
        (sha256
         (base32
-         "05ar5gykgh4dm826xplj5ri5rw7znhxrvin2l67a3mjwfys7r2a0"))
+         "0ja0ss1cjfx9j2pnmqzr51ipxrfij7i2c4bq4nqkgaxfk5q447i5"))
        (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (arguments
@@ -458,7 +458,18 @@ (define-public casacore
             (lambda _
               (substitute* "build-tools/casacore_assay"
                 (("QSUBP=.*$") "QSUBP=\n")
-                (("YODP=.*$") "YODP=\n")))))))
+                (("YODP=.*$") "YODP=\n"))))
+          ;; XXX: It fails to find the stdlib types when the gfortran header
+          ;; is used.  Remove gfortran from CPLUS_INCLUDE_PATH as a
+          ;; workaround.  Taken from <https://issues.guix.gnu.org/73439#45>.
+          (add-after 'set-paths 'hide-gfortran
+            (lambda _
+              (let ((gfortran #$(this-package-input "gfortran")))
+                (setenv "CPLUS_INCLUDE_PATH"
+                        (string-join
+                         (delete (string-append gfortran "/include/c++")
+                                 (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
+                         ":"))))))))
     (native-inputs
      (list bison
            boost
@@ -469,6 +480,7 @@ (define-public casacore
            fftw
            fftwf
            gfortran
+           gsl
            hdf5
            ncurses
            openblas
-- 
2.47.1

Message #11 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 05/51] gnu: libxisf: Update to 0.2.13.
Date: Fri, 21 Feb 2025 21:48:59 +0000

* gnu/packages/astronomy.scm (libxisf): Update to 0.2.13.

Change-Id: I7c8c8350bf4903bc4937df606e7bfe066cf62567
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 25826c22703..15a4c5b7ec9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1364,7 +1364,7 @@ (define-public libskry
 (define-public libxisf
   (package
     (name "libxisf")
-    (version "0.2.12")
+    (version "0.2.13")
     (source
      (origin
        (method git-fetch)
@@ -1373,7 +1373,7 @@ (define-public libxisf
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1bvf3x0xdipkg28c75j6jav3b2llbqvfa6lkwiacxxlzmj0226s2"))))
+        (base32 "0zhj4xijr374c9raddxw8ibawx0n66lqvypgpccb81g41qkkdkmx"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags #~(list "-DUSE_BUNDLED_LIBS=OFF")))
-- 
2.47.1

Message #14 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 06/51] gnu: scamp: Update to 2.13.1.
Date: Fri, 21 Feb 2025 21:49:00 +0000

* gnu/packages/astronomy.scm (scamp): Update to 2.13.1.

Change-Id: I37d49a55c42b71ea69e0048433103be563a16c1f
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 15a4c5b7ec9..9af0bad5edc 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -7103,7 +7103,7 @@ (define-public qfits
 (define-public scamp
   (package
     (name "scamp")
-    (version "2.10.0")
+    (version "2.13.1")
     (source
      (origin
        (method git-fetch)
@@ -7112,7 +7112,7 @@ (define-public scamp
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0qic52mzw9avf1a1fsr85mlh63b7hq6d4wj2d00zgdllmclj5l9q"))))
+        (base32 "05ka5a7llzlg8r9il8flbpz42sd9nbjma6imp09rfv81qyh6c5mj"))))
     (build-system gnu-build-system)
     (arguments
      (list
-- 
2.47.1

Message #17 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 02/51] gnu: Add python-casacore.
Date: Fri, 21 Feb 2025 21:48:56 +0000

* gnu/packages/astronomy.scm (python-casacore): New variable.

Change-Id: I25182daf664c00945f560cb5b7e66c796e165d3f
---
 gnu/packages/astronomy.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 1cd4d743597..54e974c5a6b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2053,6 +2053,38 @@ (define-public python-casa-formats-io
 is independent of and does not use @code{casacore}.")
     (license license:lgpl2.0)))
 
+(define-public python-casacore
+  (package
+    (name "python-casacore")
+    (version "3.6.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "python_casacore" version))
+       (sha256
+        (base32 "10dva4b3mz0n885d1n91dyzmwj1gwn6mcwd2qrm678kfdccarhfx"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list boost
+           cmake-minimal
+           python-pytest
+           python-scikit-build-core
+           python-setuptools-scm))
+    (inputs
+     (list casacore
+           cfitsio
+           hdf5
+           openblas
+           wcslib))
+    (propagated-inputs
+     (list python-numpy))
+    (home-page "https://casacore.github.io/python-casacore")
+    (synopsis "Python wrapper for Casacore")
+    (description
+     "This package provides a wrapper around @code{casacore}, the radio
+astronomy library.")
+    (license license:gpl3+)))
+
 (define-public python-ccdproc
   (package
     (name "python-ccdproc")
-- 
2.47.1

Message #20 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 09/51] gnu: python-astropy: Simplify check phase.
Date: Fri, 21 Feb 2025 21:49:03 +0000

* gnu/packages/astronomy.scm (python-astropy) [phases] {check}: Remove
make file writable and build extension steps.  Run tests from output,
which provides access to built library.

Change-Id: I87168de8197bed0c47274bca5fb3a92a02f5b845
---
 gnu/packages/astronomy.scm | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 230eb7f76c9..d75c20f0d1e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3729,14 +3729,10 @@ (define-public python-astropy
             (lambda* (#:key tests? test-flags #:allow-other-keys)
               (when tests?
                 (setenv "HOME" "/tmp")
-                (make-file-writable "astropy/_compiler.c")
-                ;; Extensions have to be rebuilt before running the tests.
-                (invoke "python" "setup.py" "build_ext" "--inplace"
-                        "-j" (number->string (parallel-job-count)))
                 ;; Step out of the source directory to avoid interference; we
                 ;; want to run the installed code with extensions etc.
-                (with-directory-excursion "/tmp"
-                  (apply invoke "pytest" "-v" test-flags))))))))
+                (with-directory-excursion #$output
+                  (apply invoke "pytest" "-vv" test-flags))))))))
     (native-inputs
      (list nss-certs-for-test
            pkg-config
-- 
2.47.1

Message #23 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 08/51] gnu: python-asdf-astropy: Update to 0.7.1.
Date: Fri, 21 Feb 2025 21:49:02 +0000

* gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.7.1.
[propagated-inputs]: Add python-asdf-standard.
[native-inputs]: Remove python-coverage.

Change-Id: I18c99197d7fe4f9af4ee00c65ef2236c6b8f6517
---
 gnu/packages/astronomy.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a91bc5e523c..230eb7f76c9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1717,13 +1717,13 @@ (define-public python-asdf-3
 (define-public python-asdf-astropy
   (package
     (name "python-asdf-astropy")
-    (version "0.7.0")
+    (version "0.7.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf_astropy" version))
        (sha256
-        (base32 "0985bhmhnjzlf8n78r1i1dfhbvq167xqz0667kg3jm0l2177b0f9"))))
+        (base32 "1ir4c2mp6hbkkcry2q22sa2rxcs3ry3gpa4v9a1vsi89xr4a99as"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1734,8 +1734,7 @@ (define-public python-asdf-astropy
           (add-before 'check 'set-home-env
             (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-coverage
-           python-h5py
+     (list python-h5py
            python-pandas
            python-pytest
            python-pytest-astropy
@@ -1746,6 +1745,7 @@ (define-public python-asdf-astropy
     (propagated-inputs
      (list python-asdf
            python-asdf-coordinates-schemas
+           python-asdf-standard
            python-asdf-transform-schemas
            python-astropy
            python-numpy
-- 
2.47.1

Message #26 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 03/51] gnu: indi-2.0: Update to 2.1.2.1.
Date: Fri, 21 Feb 2025 21:48:57 +0000

* gnu/packages/astronomy.scm (indi-2.0): Update to 2.1.2.1.

Change-Id: I8a9bb361dfbde52ceb8e4cf878b1f54607cf8ee9
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 54e974c5a6b..e82a9274dfe 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1005,7 +1005,7 @@ (define-public imppg
 (define-public indi-2.0
   (package
     (name "indi")
-    (version "2.1.1")
+    (version "2.1.2.1")
     (source
      (origin
        (method git-fetch)
@@ -1014,7 +1014,7 @@ (define-public indi-2.0
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1mkcql7hsc6qirpmwmfsz9j0bl9msi11d8p87hc840w1ximmglab"))))
+        (base32 "0c0fi6n9243l3xfk84qjpk7n83w6q6k6yjj4a59zfhd8zk0fd8hi"))))
     (build-system cmake-build-system)
     (arguments
      (list
-- 
2.47.1

Message #29 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 04/51] gnu: libsep: Update to 1.4.0.
Date: Fri, 21 Feb 2025 21:48:58 +0000

* gnu/packages/astronomy.scm (libsep): Update to 1.4.0.
[arguments] <test-target>: Set to "test".
<phases>: Add 'pre-check and use default 'check.

(python-sep) [arguments] <phases>: Add 'set-version.
[native-inputs]: Add python-setuptools-scm-next.

Change-Id: I04ee0704fb52c1fb02d6efa0a2bc6b7e07a516de
---
 gnu/packages/astronomy.scm | 42 ++++++++++++++++++++++++--------------
 1 file changed, 27 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e82a9274dfe..25826c22703 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1245,7 +1245,7 @@ (define-public libpasastro
 (define-public libsep
   (package
     (name "libsep")
-    (version "1.2.1")
+    (version "1.4.0")
     (source
      (origin
        (method git-fetch)
@@ -1254,20 +1254,21 @@ (define-public libsep
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0sag96am6r1ffh9860yq40js874362v3132ahlm6sq7padczkicf"))))
+        (base32 "03a9v3g8bq5sqq0ckxzkk63vij2y6ljpmymdvvvvb72q175pzpkd"))))
     (build-system cmake-build-system)
     (arguments
      (list
-      #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
-                           (string-append "PREFIX=" #$output))
-      #:phases #~(modify-phases %standard-phases
-                   (replace 'check
-                     (lambda* (#:key tests? #:allow-other-keys)
-                       (when tests?
-                         (chdir "../source")
-                         (invoke "make"
-                                 (string-append "CC=" #$(cc-for-target))
-                                 "test")))))))
+      #:make-flags
+      #~(list (string-append "CC=" #$(cc-for-target))
+              (string-append "PREFIX=" #$output))
+      #:test-target "test"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'pre-check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (chdir "../source")
+                (setenv "CC" #$(cc-for-target))))))))
     (native-inputs
      (list python-wrapper))
     (home-page "https://github.com/kbarbary/sep")
@@ -6137,11 +6138,22 @@ (define-public python-sep
     (name "python-sep")
     (build-system pyproject-build-system)
     (arguments
-     (list #:test-flags #~(list "test.py")))
+     (list
+      #:test-flags #~(list "test.py")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-version
+            (lambda _
+              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
+                      #$(package-version this-package)))))))
     (native-inputs
-     (list python-cython python-pytest python-setuptools python-wheel))
+     (list python-cython
+           python-pytest
+           python-setuptools
+           python-setuptools-scm-next
+           python-wheel))
     (propagated-inputs
-     (list  python-numpy))
+     (list python-numpy))
     (synopsis "Python library for Source Extraction and Photometry")))
 
 (define-public python-sep-pjw
-- 
2.47.1

Message #32 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 07/51] gnu: python-asdf: Update to 4.1.0.
Date: Fri, 21 Feb 2025 21:49:01 +0000

* gnu/packages/astronomy.scm (python-asdf): Update to 4.1.0.
[arguments] <phases>: Remove 'patch-pyproject-toml.
[native-inputs]: Remove python-setuptools-scm; add
python-setuptools-scm-next.

Change-Id: Ice7068e715146c5cd49eca402d3f3434ab26ede7
---
 gnu/packages/astronomy.scm | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9af0bad5edc..a91bc5e523c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1663,26 +1663,18 @@ (define-public python-aplpy
 (define-public python-asdf
   (package
     (name "python-asdf")
-    (version "4.0.0")
+    (version "4.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf" version))
        (sha256
-        (base32 "1nzrgsyidcynhgiqxy7pwny07prza1g6b7hs17ybg6fh9zas6kc6"))))
+        (base32 "189d282d8c3yyv5fk473rvfm5yra05zsn4lmkaynimszr294kx0g"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
-      #~(list "--numprocesses" (number->string (parallel-job-count)))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'patch-pypojrect-toml
-            (lambda _
-              (substitute* "pyproject.toml"
-                ;; TypeError: Configuration.__init__() got an unexpected
-                ;; keyword argument 'version_file'
-                (("version_file = \"asdf/_version.py\"") "")))))))
+      #~(list "--numprocesses" (number->string (parallel-job-count)))))
     (native-inputs
      (list python-fsspec
            python-psutil
@@ -1690,7 +1682,7 @@ (define-public python-asdf
            python-pytest-doctestplus
            python-pytest-remotedata
            python-pytest-xdist
-           python-setuptools-scm
+           python-setuptools-scm-next
            python-wheel))
     (propagated-inputs
      (list python-asdf-standard
-- 
2.47.1

Message #35 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 11/51] gnu: python-astropy-iers-data: Update to
 0.2025.2.17.0.34.13.
Date: Fri, 21 Feb 2025 21:49:05 +0000

* gnu/packages/astronomy.scm (python-astropy-iers-data): Update to 0.2025.2.17.0.34.13.
[synopsis]: Fix lint warning, shorten it.

Change-Id: I689e20b12f59392c85b609d128aa0e9e2c149c4d
---
 gnu/packages/astronomy.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index db3500c2910..cc7da2e021a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3840,13 +3840,13 @@ (define-public python-astropy-healpix
 (define-public python-astropy-iers-data
   (package
     (name "python-astropy-iers-data")
-    (version "0.2025.1.20.0.32.27")
+    (version "0.2025.2.17.0.34.13")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy_iers_data" version))
        (sha256
-        (base32 "1r4vdg90kk4d84vd0gjhnqlwazccsa1w53lj0d1dlkfnbhlkdfmi"))))
+        (base32 "0q390s0by2szq82lligwgpbmvmdwi0jyxp0sh51kzrijg928bdil"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f)) ; no tests
@@ -3855,7 +3855,7 @@ (define-public python-astropy-iers-data
            python-setuptools-scm
            python-wheel))
     (home-page "https://docs.astropy.org/en/latest/utils/iers.html")
-    (synopsis "IERS Earth Rotation and Leap Second tables for the astropy core package")
+    (synopsis "IERS Earth Rotation and Leap Second tables for Astropy core")
     (description
      "The @code{iers} package provides access to the tables provided by the
 @acronym{International Earth Rotation and Reference Systems, IERS} service, in
-- 
2.47.1

Message #38 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 10/51] gnu: python-astropy-healpix: Update to 1.1.2.
Date: Fri, 21 Feb 2025 21:49:04 +0000

* gnu/packages/astronomy.scm (python-astropy-healpix): Update to 1.1.2.
[arguments] <phases>: Remove 'writable-compiler
'prepare-test-environment and use custom 'check; add
'relax-requirements.
[native-inputs]: Add python-setuptools.

Change-Id: If8705cb47dc1f2f15b11e31b1c08688c9b991ebe
---
 gnu/packages/astronomy.scm | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d75c20f0d1e..db3500c2910 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3801,30 +3801,33 @@ (define-public python-astropy-minimal
 (define-public python-astropy-healpix
   (package
     (name "python-astropy-healpix")
-    (version "1.0.3")
+    (version "1.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy_healpix" version))
        (sha256
-        (base32 "0ilpwwvdnd4nchivwnbiy1hl07hd2mdg4wb90r2p05kvr5z2lpfy"))))
+        (base32 "1r362081aj5jqxshcxw0bpzn4qvqnra52k94ghskpv1n5bqisrq3"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:phases
       #~(modify-phases %standard-phases
-          ;; This file is opened in both install and check phases.
-          (add-before 'install 'writable-compiler
-            (lambda _ (make-file-writable "astropy_healpix/_compiler.c")))
-          (add-before 'check 'prepare-test-environment
+          (add-after 'unpack 'relax-requirements
             (lambda _
-              ;; Extensions have to be rebuilt before running the tests.
-              (invoke "python" "setup.py" "build_ext" "--inplace")
-              (make-file-writable "astropy_healpix/_compiler.c"))))))
+              (substitute* "setup.cfg"
+                ;; numpy>=1.25
+                ((">=1.25") ">=1.24"))))
+          (replace 'check
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
+              (when tests?
+                (with-directory-excursion #$output
+                  (apply invoke "pytest" "-vv" test-flags))))))))
     (native-inputs
      (list python-extension-helpers
            python-hypothesis
            python-pytest-astropy
+           python-setuptools
            python-setuptools-scm
            python-wheel))
     (propagated-inputs
-- 
2.47.1

Message #41 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 12/51] gnu: python-astroquery: Update to 0.4.9.post1.
Date: Fri, 21 Feb 2025 21:49:06 +0000

* gnu/packages/astronomy.scm (python-astroquery): Update to 0.4.9.post1.

Change-Id: I747b055ba53b20f4fc1732aafa57e54b871fb02b
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index cc7da2e021a..bb9436a2732 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3953,13 +3953,13 @@ (define-public python-astroplan
 (define-public python-astroquery
   (package
     (name "python-astroquery")
-    (version "0.4.8")
+    (version "0.4.9.post1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astroquery" version))
        (sha256
-        (base32 "1dgc792xp6bpb63kqhwqpmc7ck9ifr6wlcqqgl091mfrjy40h4aw"))))
+        (base32 "15viynwq96gyb12q894fi2j4jlzmba3lk86l469ixmrnj3qnn4aw"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.47.1

Message #44 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 13/51] gnu: python-cmyt: Update to 2.0.2.
Date: Fri, 21 Feb 2025 21:49:07 +0000

* gnu/packages/astronomy.scm (python-cmyt): Update to 2.0.2.

Change-Id: I7829b96d3cf0802f06237a2981f155f00fbae60c
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index bb9436a2732..33264de56c6 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4091,7 +4091,7 @@ (define-public python-ci-watson
 (define-public python-cmyt
   (package
     (name "python-cmyt")
-    (version "2.0.1")
+    (version "2.0.2")
     (source
      (origin
        (method git-fetch) ; no tests in the PyPI tarball
@@ -4100,7 +4100,7 @@ (define-public python-cmyt
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0d1szsgjd09ya53vx7g5ryz2jdxl19p9rvrm4xz8v53vbqrp18cv"))))
+        (base32 "1d257xlgxc06x47k07xn5ml2kjqzc7dgjal4bl9x2w6b90xn0pm1"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.47.1

Message #47 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 14/51] gnu: python-czml3: Update to 2.3.4.
Date: Fri, 21 Feb 2025 21:49:08 +0000

* gnu/packages/astronomy.scm (python-czml3): Update to 2.3.4.

Change-Id: I924e8f0e6e5414ce75b2edd829aaf1a2366c22bf
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 33264de56c6..32ddad9b1ca 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2276,7 +2276,7 @@ (define-public python-crds
 (define-public python-czml3
   (package
     (name "python-czml3")
-    (version "2.3.0")
+    (version "2.3.4")
     (source
      (origin
        (method git-fetch)
@@ -2287,7 +2287,7 @@ (define-public python-czml3
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1125239knl4w2njnrqvdc5qzjvq80zlf247z72za7qz6k0rnv3rw"))))
+        (base32 "1ws26kx975c48s6zzj57fyi1d0aiv0arxcrb4hg7jdvhrcyh3nlk"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-- 
2.47.1

Message #50 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 17/51] gnu: python-extinction: Fix source and home-page URL.
Date: Fri, 21 Feb 2025 21:49:11 +0000

* gnu/packages/astronomy.scm (python-extinction) [source] <url>: It
permanent redirects to <https://github.com/sncosmo/extinction>, adjust
accordingly.
[home-page]: Likewise.

Change-Id: I96da111424481f15576612cd46217f43f6f7cb24
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 36d022f8ae3..7aa708ab1c4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2441,7 +2441,7 @@ (define-public python-extinction
      (origin
        (method git-fetch) ; No tests in PyPI
        (uri (git-reference
-             (url "https://github.com/kbarbary/extinction")
+             (url "https://github.com/sncosmo/extinction")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
@@ -2457,7 +2457,7 @@ (define-public python-extinction
            python-wheel))
     (propagated-inputs
      (list python-numpy))
-    (home-page "http://github.com/kbarbary/extinction")
+    (home-page "https://github.com/sncosmo/extinction")
     (synopsis "Fast interstellar dust extinction laws")
     (description
      "This package provides a cython-optimized implementations of empirical dust
-- 
2.47.1

Message #53 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 15/51] gnu: python-drizzle: Update to 2.0.1.
Date: Fri, 21 Feb 2025 21:49:09 +0000

* gnu/packages/astronomy.scm (python-drizzle): Update to 2.0.1.
[propagated-inputs]: Remove python-astropy.
[native-inputs]: Add python-astropy-minimal and python-gwcs.

Change-Id: I27f910d31a96b1578b876696cb11edf1bbcff0e2
---
 gnu/packages/astronomy.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 32ddad9b1ca..6e1d8d4e8bb 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2311,7 +2311,7 @@ (define-public python-czml3
 (define-public python-drizzle
   (package
     (name "python-drizzle")
-    (version "2.0.0")
+    (version "2.0.1")
     (source
      (origin
        (method git-fetch) ;PyPi doesn't have the test data sets
@@ -2320,7 +2320,7 @@ (define-public python-drizzle
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1psa98n81wphin15j7k0392rh94dkhnwrjp32lr40gb9ldp52mcm"))))
+        (base32 "113fqr87glqkvh4szqvbv0b6brr3bwp4d65qy1r1q4b90318p2zf"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2334,16 +2334,16 @@ (define-public python-drizzle
               ;; Cython extensions have to be built before running the tests.
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
-     (list python-pytest
+     (list python-astropy-minimal
+           python-gwcs
+           python-pytest
            python-setuptools
            python-setuptools-scm
            python-wheel))
     (propagated-inputs
-     (list python-astropy
-           python-numpy))
+     (list python-numpy))
     (home-page "https://github.com/spacetelescope/drizzle")
-    (synopsis
-     "Astronomical tool for combining dithered images into a single image")
+    (synopsis "Combining dithered images into a single image")
     (description
      "The drizzle library is a Python package for combining dithered images
 into a single image.  This library is derived from code used in DrizzlePac.
-- 
2.47.1

Message #56 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 16/51] gnu: python-drms: Update to 0.9.0.
Date: Fri, 21 Feb 2025 21:49:10 +0000

* gnu/packages/astronomy.scm (python-drms): Update to 0.9.0.
[propagated-inputs]: Add python-packaging.
[native-inputs]: Remove python-astropy and python-setuptools-scm; add
python-astropy-minimal and python-setuptools-scm-next.

Change-Id: I160e85a89985f194d1701800c56301c3a70599d9
---
 gnu/packages/astronomy.scm | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6e1d8d4e8bb..36d022f8ae3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2357,22 +2357,24 @@ (define-public python-drizzle
 (define-public python-drms
   (package
     (name "python-drms")
-    (version "0.8.0")
+    (version "0.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "drms" version))
        (sha256
-        (base32 "19lqy510d7iyxfz445h2rn4d0rvmd4d3lnjmvbkvv270ckpfw09f"))))
+        (base32 "0nnyqzy9dblis3q1xhx77z8ys1k969fh9qqdvmapn46v91299gml"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-astropy
+     (list python-astropy-minimal
            python-pytest-astropy
            python-setuptools
-           python-setuptools-scm
+           python-setuptools-scm-next
            python-wheel))
     (propagated-inputs
-     (list python-numpy python-pandas))
+     (list python-numpy
+           python-packaging
+           python-pandas))
     (home-page "https://sunpy.org")
     (synopsis "Access astronomical HMI, AIA and MDI data with Python")
     (description
-- 
2.47.1

Message #59 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 18/51] gnu: python-ephem: Update to 4.2.
Date: Fri, 21 Feb 2025 21:49:12 +0000

* gnu/packages/astronomy.scm (python-ephem): Update to 4.2.

Change-Id: I9f6a486b9f22527f0ad444e4bc86c755a8f330b9
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 7aa708ab1c4..c6324d44a63 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2410,13 +2410,13 @@ (define-public python-dust-extinction
 (define-public python-ephem
   (package
     (name "python-ephem")
-    (version "4.1.6")
+    (version "4.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ephem" version))
        (sha256
-        (base32 "0ps2lr6aa477262yw13w3hh0h5rzmywdlji0wbnkxnzrfvmf9lhf"))))
+        (base32 "0rb0vc3kgmw5rzhfhxffg94bcwasm46sf814hv7l13ry8m7xckrw"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools
-- 
2.47.1

Message #62 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 19/51] gnu: python-fitsio: Update to 1.2.5.
Date: Fri, 21 Feb 2025 21:49:13 +0000

* gnu/packages/astronomy.scm (python-fitsio): Update to 1.2.5.

Change-Id: Ide5b5ae6843775bee0f4aa46d6a42f420a66c70a
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c6324d44a63..df0ae5cc118 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2467,13 +2467,13 @@ (define-public python-extinction
 (define-public python-fitsio
   (package
     (name "python-fitsio")
-    (version "1.2.4")
+    (version "1.2.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "fitsio" version))
        (sha256
-        (base32 "0y7n7wh73ha6439djrhwmqbvgpagrdgaasbrikvw2zb5qx3y6zym"))
+        (base32 "1mnhzljaqjvslqxp4wblram7g9zbn6a29ri0phcrw8l2ry4qc7h0"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove the bundled cfitsio. When update the package check the
-- 
2.47.1

Information forwarded to

lars <at> 6xq.net, marius <at> gnu.org, me <at> bonfacemunyoki.com, sharlatanus <at> gmail.com, tanguy <at> bioneland.org, jgart <at> dismail.de, guix-patches <at> gnu.org

:
bug#76480; Package guix-patches. (Fri, 21 Feb 2025 21:52:15 GMT) Full text and rfc822 format available.

Message #65 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 20/51] gnu: python-mpl-scatter-density: Update to 0.8.
Date: Fri, 21 Feb 2025 21:49:14 +0000

* gnu/packages/python-science.scm (python-mpl-scatter-density): Update to 0.8.
[source] <uri>: Adjust it as PyPI archive name has been changed upstream.

Change-Id: Ic049ea153503cfa92c5d19b272afb00e64f7a28e
---
 gnu/packages/python-science.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index beff4353ce6..489ab461539 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1049,13 +1049,13 @@ (define-public python-meshzoo
 (define-public python-mpl-scatter-density
   (package
     (name "python-mpl-scatter-density")
-    (version "0.7")
+    (version "0.8")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "mpl-scatter-density" version))
+       (uri (pypi-uri "mpl_scatter_density" version))
        (sha256
-        (base32 "083n4xkwjmxvij9i1xhfnxz8vk39ay0baam4nf0khvcihw47bkna"))))
+        (base32 "0cynk1rk6k2xklgv69difphrz6id77x3xb58kbs4mc4q7z6bvfid"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.47.1

Message #68 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 21/51] gnu: python-glue-core: Update to 1.22.0.
Date: Fri, 21 Feb 2025 21:49:15 +0000

* gnu/packages/astronomy.scm (python-glue-core): Update to 1.22.0.

Change-Id: I01b61ac8c4046044cd734d53ce5b033c3bd238a5
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index df0ae5cc118..1ebc6a9d46a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2689,13 +2689,13 @@ (define-public python-glue-astronomy
 (define-public python-glue-core
   (package
     (name "python-glue-core")
-    (version "1.21.1")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "glue_core" version))
        (sha256
-        (base32 "1xms896ds70sbym1cr5lrbjl4i8vixy3mcc6qsg1b3ppvky76vmn"))))
+        (base32 "0cx97zbi58fjl9j6wg8clygdiv6a95wgc2azw7ffg16y3qlqwkzs"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      (list python-astrodendro
-- 
2.47.1

Message #71 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 22/51] gnu: python-gwcs: Update to 0.24.0.
Date: Fri, 21 Feb 2025 21:49:16 +0000

* gnu/packages/astronomy.scm (python-gwcs): Update to 0.24.0.

Change-Id: I83e762ab80b9dac07f4e6879c9c4e5b1d7e50175
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 1ebc6a9d46a..4f06cc28791 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2785,13 +2785,13 @@ (define-public python-glue-qt
 (define-public python-gwcs
   (package
     (name "python-gwcs")
-    (version "0.22.1")
+    (version "0.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "gwcs" version))
        (sha256
-        (base32 "0lvab51ryfb4sjsnckmap7idh29as2mjngkyin4ngfy7hdzknvg9"))))
+        (base32 "0q3f2rnl4d1p98kypr1jfkajwih22sbx3smn492yf9dbj92bv1v3"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.47.1

Message #74 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 23/51] gnu: python-tweakwcs: Skip 2 tests.
Date: Fri, 21 Feb 2025 21:49:17 +0000

* gnu/packages/astronomy.scm (python-tweakwcs) [arguments] <test-flags>:
Skip 2 not compatible with GWCS <at> 0.24 tests.
[native-inputs]: Remove python-codecov and python-pytest-cov.

Change-Id: I1e0c1be92970613f4b3c04e6e9821884db6bcb8d
---
 gnu/packages/astronomy.scm | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 4f06cc28791..516969fb3a8 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6743,6 +6743,15 @@ (define-public python-tweakwcs
        (sha256
         (base32 "0a1ygsar9l6jybji9qibz6ja3picv9aiw2jmdcsqdfqhrppknqp7"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; 2 tests are not compatible with gwcs>=0.24, skip them for now
+      ;; and enable in the next release, see
+      ;; <https://github.com/spacetelescope/tweakwcs/pull/220>.
+      #~(list "-k" (string-append
+                    "not test_jwstgwcs_bad_pipelines_no_vacorr"
+                    " and not test_jwstgwcs_bad_pipelines_with_vacorr"))))
     (propagated-inputs
      (list python-astropy
            python-gwcs
@@ -6752,9 +6761,7 @@ (define-public python-tweakwcs
            python-stsci-imagestats
            python-stsci-stimage))
     (native-inputs
-     (list python-codecov
-           python-pytest
-           python-pytest-cov
+     (list python-pytest
            python-scipy
            python-setuptools
            python-setuptools-scm
-- 
2.47.1

Message #77 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 24/51] gnu: python-halotools: Update to 0.9.3.
Date: Fri, 21 Feb 2025 21:49:18 +0000

* gnu/packages/astronomy.scm (python-halotools): Update to 0.9.3.
[arguments] <phases>: Remove 'build-extensions and use custom 'check.

Change-Id: Ia6ce0c7de0544c0a9ad071aa0ef5dd63ff57c544
---
 gnu/packages/astronomy.scm | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 516969fb3a8..3147674ae89 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2830,23 +2830,25 @@ (define-public python-gwcs
 (define-public python-halotools
   (package
     (name "python-halotools")
-    (version "0.9.2")
+    (version "0.9.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "halotools" version))
        (sha256
-        (base32 "1fa4w8dabr0zx6xwnrdwdipf4s6sg7q25jmq42n9q8n64kjx60vb"))))
+        (base32 "004nqlyiv6gyzmjk840a1hl3j4sgi5xwbfibankwi7281gq4hx3d"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; Tests are shaky in parallel.
       #:phases
       #~(modify-phases %standard-phases
-          (add-before 'check 'build-extensions
-            (lambda _
-              (setenv "HOME" "/tmp")
-              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+          ;; Use built library for tests.
+          (replace 'check
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
+              (when tests?
+                (with-directory-excursion #$output
+                  (setenv "HOME" "/tmp")
+                  (apply invoke "pytest" "-vv" test-flags))))))))
     (native-inputs
      (list python-cython-3
            python-extension-helpers
-- 
2.47.1

Message #80 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 27/51] gnu: python-rad: Update to 0.23.1.
Date: Fri, 21 Feb 2025 21:49:21 +0000

* gnu/packages/astronomy.scm (python-rad): Update to 0.23.1.

Change-Id: If7ceee351ac61c2c7e9004835517b54a408ca698
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 04e7bf7925b..23d0c42039b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6528,13 +6528,13 @@ (define python-asdf-wcs-schemas
 (define-public python-rad
   (package
     (name "python-rad")
-    (version "0.23.0")
+    (version "0.23.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "rad" version))
        (sha256
-        (base32 "1c771lxj45iakj4ynjmfg332cm10yllmwniigs9zzjnb02kmaks5"))))
+        (base32 "14zl3nsqbzm28yrghf7n66qmhf369dyw5bqymmgcq515llm42428"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.47.1

Message #83 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 26/51] gnu: python-pyvo: Update to 1.6.1.
Date: Fri, 21 Feb 2025 21:49:20 +0000

* gnu/packages/astronomy.scm (python-pyvo): Update to 1.6.1.
[propagated-inputs]: Add python-defusedxml.

Change-Id: I9aedd6c2f6f9459739ae65505035bee61531afa7
---
 gnu/packages/astronomy.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 1d252cc6f45..04e7bf7925b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4783,13 +4783,13 @@ (define-public python-pyavm
 (define-public python-pyvo
   (package
     (name "python-pyvo")
-    (version "1.6")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyvo" version))
        (sha256
-        (base32 "1ahcazgxhmxscjgz58mxw75k9g0xm7iffnc4lqfbm3h0wqiz8vnv"))))
+        (base32 "0hfdsb6yqda6g987b96jqaw4kqj4qh9qz3am6inx0nl2m5y735pq"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -4802,7 +4802,8 @@ (define-public python-pyvo
            python-wheel))
     (propagated-inputs
      (list python-astropy
-           python-pillow
+           python-defusedxml ; extra requirements
+           python-pillow     ; extra requirements
            python-requests))
     (home-page "https://github.com/astropy/pyvo")
     (synopsis "Access Virtual Observatory data and services")
-- 
2.47.1

Message #86 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 38/51] gnu: python-viresclient: Update to 0.12.2.
Date: Fri, 21 Feb 2025 21:49:32 +0000

* gnu/packages/astronomy.scm (python-viresclient): Update to 0.12.2.

Change-Id: I06f24963aa1432182f27e1e3d6ff484616c6cd66
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index eb5baef06e9..b0a572ca993 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6742,13 +6742,13 @@ (define-public python-tweakwcs
 (define-public python-viresclient
   (package
     (name "python-viresclient")
-    (version "0.12.1")
+    (version "0.12.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "viresclient" version))
        (sha256
-        (base32 "04micg72jag8zyvszc9hhi5p0zr8j3k93chhd5gkl20bvk69l3fp"))))
+        (base32 "1x1xgs6fs7rmhqs6f32x173gsz1mlrcpji0rf307x232lyav7wds"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-flit-core
-- 
2.47.1

Information forwarded to

lars <at> 6xq.net, marius <at> gnu.org, me <at> bonfacemunyoki.com, sharlatanus <at> gmail.com, tanguy <at> bioneland.org, jgart <at> dismail.de, guix-patches <at> gnu.org

:
bug#76480; Package guix-patches. (Fri, 21 Feb 2025 21:54:03 GMT) Full text and rfc822 format available.

Message #89 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 39/51] gnu: Add python-cmocean.
Date: Fri, 21 Feb 2025 21:49:33 +0000

* gnu/packages/python-science.scm (python-cmocean): New variable.

Change-Id: I8b304c0280832f202714df278960493cbd3b12df
---
 gnu/packages/python-science.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 489ab461539..5a473b391b9 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -174,6 +174,33 @@ (define-public pyre
 maintainability.")
     (license license:bsd-3)))
 
+(define-public python-cmocean
+  (package
+    (name "python-cmocean")
+    (version "4.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cmocean" version))
+       (sha256
+        (base32 "0z0d4ma6i228gwpgnkai8scs9bmzz41rirlnqpmb8hazzfcq71ip"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-matplotlib
+           python-numpy
+           python-packaging))
+    (home-page "https://github.com/matplotlib/cmocean")
+    (synopsis "Colormaps for Oceanography")
+    (description
+     "This package contains colormaps for commonly-used oceanographic
+variables.  Most of the colormaps started from @code{matplotlib} colormaps,
+but have now been adjusted using the viscm tool to be perceptually uniform.")
+    (license license:expat)))
+
 (define-public python-cvxpy
   (package
     (name "python-cvxpy")
-- 
2.47.1

Message #92 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 37/51] gnu: python-sunkit-image: Update to 0.6.0.
Date: Fri, 21 Feb 2025 21:49:31 +0000

* gnu/packages/astronomy.scm (python-sunkit-image): Update to 0.6.0.
[arguments] <tests?>: Upstream resolved the issue, enable them.
<test-flags>: Skip just one failing test, add "--numprocesses" option,
upstream support parallel tests.
[native-inputs]: Remove python-astroscrappy, python-beautifulsoup4,
python-drms, python-importlib-resources, python-setuptools-scm, and
python-zeep; add python-pytest, python-pytest-xdist, python-setuptools,
python-setuptools-scm-next, and python-wheel.

Change-Id: Ib95857c434946dd6633874b20113f931aa7bc3b0
---
 gnu/packages/astronomy.scm | 40 +++++++++++++++-----------------------
 1 file changed, 16 insertions(+), 24 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a13a4c232d3..eb5baef06e9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3596,35 +3596,37 @@ (define-public python-specreduce
 (define-public python-sunkit-image
   (package
     (name "python-sunkit-image")
-    (version "0.5.1")
+    (version "0.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sunkit_image" version))
        (sha256
-        (base32 "1wzii7dy0yb2lx0k8m3iak5vxc0wbybj5cdkvrk93sr14k9crqds"))))
+        (base32 "0gdbg3g8jxcgkwd34ls6342zj90m6ncas4f655q9dh79lqy7hhm8"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; XXX: Disable as not compatible with Pytest 8+, check with upstream.
-      ;;
-      ;; pytest.PytestRemovedIn9Warning: Marks applied to fixtures have no
-      ;; effect
-      ;;
-      ;; See docs: <https://docs.pytest.org/en/stable/deprecations.html>.
-      #:tests? #f
-      ;; XXX: Check with upstram: assert False.
       #:test-flags
-      #~(list "-k" (string-append
-                    "not test_fnrgf"
-                    " and not test_calculate_solar_rotate_shift"
-                    " and not test_mapsequence_solar_derotate"))
+      #~(list "--numprocesses" (number->string (parallel-job-count))
+              ;; One test fails with assertion, probably in NumPy array
+              ;; precision calculation: np.allclose and
+              ;; sunpy.map.mapbase.GenericMap are not matched.
+              "--deselect=sunkit_image/tests/test_radial.py::test_fnrgf")
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'set-home
             (lambda _
               ;; For tests: Permission denied: '/homeless-shelter'
               (setenv "HOME" "/tmp"))))))
+    (native-inputs
+     (list python-dask
+           python-pytest
+           python-pytest-astropy
+           python-pytest-mpl
+           python-pytest-xdist
+           python-setuptools
+           python-setuptools-scm-next
+           python-wheel))
     (propagated-inputs
      (list python-astropy
            python-matplotlib
@@ -3632,16 +3634,6 @@ (define-public python-sunkit-image
            python-scikit-image
            python-scipy
            python-sunpy))
-    (native-inputs
-     (list python-astroscrappy
-           python-beautifulsoup4
-           python-dask
-           python-drms
-           python-importlib-resources
-           python-pytest-astropy
-           python-pytest-mpl
-           python-setuptools-scm
-           python-zeep))
     (home-page "https://github.com/sunpy/sunkit-image/")
     (synopsis "Solar Physics image processing toolbox")
     (description
-- 
2.47.1

Message #95 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 40/51] gnu: Add python-esutil.
Date: Fri, 21 Feb 2025 21:49:34 +0000

* gnu/packages/astronomy.scm (python-esutil): New variable.

Change-Id: I0a2a5351639e18d5d5c95df3eebabb9650d17e1d
---
 gnu/packages/astronomy.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b0a572ca993..1cc549c214f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2433,6 +2433,36 @@ (define-public python-ephem
 of dates.")
     (license license:expat)))
 
+(define-public python-esutil
+  (package
+    (name "python-esutil")
+    (version "0.6.16")
+    (source
+     (origin
+       (method git-fetch) ; no tests in the PyPI tarball
+       (uri (git-reference
+             (url "https://github.com/esheldon/esutil")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "05csk5asq3si7gdq8mpfh288z10rs45ylpcrrcjx0009q52l95xq"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-numpy
+           python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-numpy
+           python-scipy))
+    (home-page "https://github.com/esheldon/esutil")
+    (synopsis "Numerical, scientific, and astrophysical computing utilities")
+    (description
+     "This package provides a wide variety of utilities, focused primarily on
+numerical python, statistics, and file input/output.  Includes specialized
+tools for astronomers.")
+    (license license:gpl2+)))
+
 (define-public python-extinction
   (package
     (name "python-extinction")
-- 
2.47.1

Information forwarded to

lars <at> 6xq.net, marius <at> gnu.org, me <at> bonfacemunyoki.com, sharlatanus <at> gmail.com, tanguy <at> bioneland.org, jgart <at> dismail.de, guix-patches <at> gnu.org

:
bug#76480; Package guix-patches. (Fri, 21 Feb 2025 21:54:05 GMT) Full text and rfc822 format available.

Message #98 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 41/51] gnu: Add python-glfw.
Date: Fri, 21 Feb 2025 21:49:35 +0000

* gnu/packages/python-graphics.scm (python-glfw): New variable.

Change-Id: Icfc1413fbec367c2b9efc9f9461c9cf24e05fa12
---
 gnu/packages/python-graphics.scm | 35 ++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/python-graphics.scm b/gnu/packages/python-graphics.scm
index da8ef2d4df1..4539a3398d2 100644
--- a/gnu/packages/python-graphics.scm
+++ b/gnu/packages/python-graphics.scm
@@ -100,6 +100,41 @@ (define-public python-glcontext
 ModernGL on multiple platforms.")
       (license license:expat))))
 
+(define-public python-glfw
+  (package
+    (name "python-glfw")
+    (version "2.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "glfw" version))
+       (sha256
+        (base32 "1w36jvn6fx8p7irhwj6bbl67m2id3s0227b3w7bgw9hbicr0vsch"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #f ; no tests provided
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-lib-paths
+            (lambda _
+              (substitute* "glfw/library.py"
+                (("_get_library_search_paths\\(\\), ")
+                 (format #f "[ '~a/lib' ],"
+                         #$(this-package-input "glfw")))))))))
+    (native-inputs
+     (list python-pytest
+           python-setuptools
+           python-wheel))
+    (inputs
+     (list glfw))
+    (home-page "https://github.com/FlorianRhiem/pyGLFW")
+    (synopsis "Python bindings for GLFW")
+    (description
+     "This package provides Python bindings for @url{http://www.glfw.org/,
+GLFW} OpenGL application development library.")
+    (license license:expat)))
+
 (define-public python-pyglet
   (package
     (name "python-pyglet")
-- 
2.47.1

Message #101 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 25/51] gnu: python-ndcube: Update to 2.3.1.
Date: Fri, 21 Feb 2025 21:49:19 +0000

* gnu/packages/astronomy.scm (python-ndcube): Update to 2.3.1.
[native-inputs]: Remove python-setuptools-scm; add python-setuptools-scm-next.

Change-Id: Ib8472b7ce9a7d52554304078ad7e397ff8c68d96
---
 gnu/packages/astronomy.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 3147674ae89..1d252cc6f45 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4478,13 +4478,13 @@ (define-public python-naima
 (define-public python-ndcube
   (package
     (name "python-ndcube")
-    (version "2.3.0")
+    (version "2.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ndcube" version))
        (sha256
-        (base32 "1pza5g38gn941dwy8yahkd37lb7z80czs1yj38xhn2cf0s69779h"))))
+        (base32 "0hf261l36jxmd0r8sh2vyxaapv8gcdmnnv82k0hqvq6wh1qp5ksv"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -4526,7 +4526,7 @@ (define-public python-ndcube
            python-pytest-xdist
            python-scipy
            python-setuptools
-           python-setuptools-scm
+           python-setuptools-scm-next
            python-sunpy
            python-wheel))
     (home-page "https://docs.sunpy.org/projects/ndcube/")
-- 
2.47.1

Message #104 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 28/51] gnu: python-roman-datamodels: Update to 0.23.1.
Date: Fri, 21 Feb 2025 21:49:22 +0000

* gnu/packages/astronomy.scm (python-roman-datamodels): Update to 0.23.1.

Change-Id: Icdddb67902dc469cef8676158a2fa40c05758a61
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 23d0c42039b..8376ea4ae46 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6645,13 +6645,13 @@ (define-public python-radiospectra
 (define-public python-roman-datamodels
   (package
     (name "python-roman-datamodels")
-    (version "0.23.0")
+    (version "0.23.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "roman_datamodels" version))
        (sha256
-        (base32 "1r7l93z89d93kkpfcxcy12g1ijy2q942j4g4s1d62rzdcz11gann"))))
+        (base32 "14awdf4ndx9rhdz70s3mayp5j8cfmn9bb37yf3cp3s4w62ydmwfi"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.47.1

Message #107 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 29/51] gnu: python-sep-pjw: Simplify.
Date: Fri, 21 Feb 2025 21:49:23 +0000

* gnu/packages/astronomy.scm (python-sep-pjw) [arguments] <phases>:
Remove 'relax-requirements.
[native-inputs]: Remove python-setuptools-scm; add
python-setuptools-scm-next.

Change-Id: Ibe66f67a638649967d1e1c9dfa1b5dd6d0843ca1
---
 gnu/packages/astronomy.scm | 14 ++------------
 1 file changed, 2 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 8376ea4ae46..8664d073a7f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6165,22 +6165,12 @@ (define-public python-sep-pjw
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags #~(list "test.py")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'relax-requirements
-            (lambda _
-              (substitute* "pyproject.toml"
-                ;; numpy>=1.23.5
-                (("1.23.5") "1.23.2")
-                ;; TypeError: Configuration.__init__() got an unexpected
-                ;; keyword argument 'version_file'
-                (("version_file = .*") "")))))))
+      #:test-flags #~(list "test.py")))
     (native-inputs
      (list python-cython
            python-pytest
            python-setuptools
-           python-setuptools-scm
+           python-setuptools-scm-next
            python-wheel))
     (propagated-inputs
      (list python-numpy))
-- 
2.47.1

Message #110 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 31/51] gnu: python-sgp4: Update to 2.24.
Date: Fri, 21 Feb 2025 21:49:25 +0000

* gnu/packages/astronomy.scm (python-sgp4): Update to 2.24.

Change-Id: I6c2e839353d4c6f27821a91631910dd02c36dfcc
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 48df06b008e..0765ad96a15 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4965,13 +4965,13 @@ (define-public python-reproject
 (define-public python-sgp4
   (package
     (name "python-sgp4")
-    (version "2.23")
+    (version "2.24")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sgp4" version))
        (sha256
-        (base32 "0aalbmldks6ykgkcxwkvnp04q0avhv903m5zwvg8i7zvl99xrbfq"))))
+        (base32 "0ll3gxjf697llh6nvisxnj2h4hl23nq1m24ymsykz8kf4ygj8man"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-setuptools
-- 
2.47.1

Message #113 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 30/51] gnu: python-sep-pjw: Update to 1.3.8.
Date: Fri, 21 Feb 2025 21:49:24 +0000

* gnu/packages/astronomy.scm (python-sep-pjw): Update to 1.3.8.
[propagated-inputs]: Add python-sep.

Change-Id: I3a98f356224fbd7bde28dd4a1bee61557c9d1cfd
---
 gnu/packages/astronomy.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 8664d073a7f..48df06b008e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6155,13 +6155,13 @@ (define-public python-sep
 (define-public python-sep-pjw
   (package
     (name "python-sep-pjw")
-    (version "1.3.7")
+    (version "1.3.8")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sep_pjw" version))
        (sha256
-        (base32 "1z8m2l3ccxj1izdazv7a0hg6zd1495bvby8w114s5ji7fd91vdv7"))))
+        (base32 "0lhxfq1acc6qc8nszfdrpwq6dizaypz3b6frknfv5qm59mb488r0"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -6173,7 +6173,8 @@ (define-public python-sep-pjw
            python-setuptools-scm-next
            python-wheel))
     (propagated-inputs
-     (list python-numpy))
+     (list python-numpy
+           python-sep))
     (home-page "https://github.com/PJ-Watson/sep-pjw")
     (synopsis "Alternative fork of SEP library")
     (description
-- 
2.47.1

Message #116 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 32/51] gnu: python-sncosmo: Update to 2.12.0.
Date: Fri, 21 Feb 2025 21:49:26 +0000

* gnu/packages/astronomy.scm (python-sncosmo): Update to 2.12.0.
[arguments] <test-flags>: Ignore the whole file with tests requiring
network access; skip more tests requiring networking.
[phases] {relax-requirements}: Remove relaxation for pyyaml; add for
h5py.
[propagated-inputs]: Add python-h5py.
[native-inputs]: Remove python-cython and python-pytest-cov; add
python-cython-3.

Change-Id: I592cf6cdde0186e4db24db4359b5d6875b69c394
---
 gnu/packages/astronomy.scm | 48 ++++++++++++++------------------------
 1 file changed, 17 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 0765ad96a15..d406bab2717 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3396,58 +3396,44 @@ (define-public python-sirilic
 (define-public python-sncosmo
   (package
     (name "python-sncosmo")
-    (version "2.11.2")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sncosmo" version))
        (sha256
-        (base32 "1n7kh2qinp04ilf8d26hgjs6c3bdy5vbmppc6ps9jy1q0ll8gi69"))))
+        (base32 "0n5ygpq888hgdy7d4b8zz3hbfdi4vn4lsdp9m9ii0a6ghh61f803"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
-      ;; Disable tests requireing remote access to download test data.
       #~(list
+         ;; 23/27 tests fail requiring network access, ignore the whole file.
+         "--ignore=sncosmo/tests/test_builtins.py"
          "-k" (string-join
-               (list "not test_megacampsf_bandpass"
-                     "test_builtins_remote_aa"
-                     "test_builtins_remote_nm"
-                     "test_builtins_remote_um"
-                     "test_builtins_remote_wfc3"
-                     "test_builtins_megacampsf"
-                     "test_builtins_timeseries_ascii"
-                     "test_builtins_timeseries_fits"
-                     "test_builtins_salt2model"
-                     "test_builtins_salt3model"
-                     "test_builtins_2011fe"
-                     "test_builtins_mlcs2k2"
-                     "test_builtins_snemo"
-                     "test_builtins_sugar"
-                     "test_builtins_magsys_fits"
-                     "test_builtins_magsys_csp"
-                     "test_builtins_magsys_ab_b12"
-                     "test_builtins_magsys_jla"
-                     "test_csp_magsystem"
-                     "test_compositemagsystem_band_error"
+               ;; Tests require network access.
+               (list "not test_C11"
                      "test_G10"
-                     "test_C11"
-                     "test_salt2source_timeseries_vs_snfit"
-                     "test_salt2source_rcov_vs_snfit"
                      "test_bandflux"
                      "test_bandflux_multi"
                      "test_bandflux_zpsys"
                      "test_bandfluxcov"
                      "test_bandmag"
-                     "test_sugarsource")
+                     "test_compositemagsystem_band_error"
+                     "test_csp_magsystem"
+                     "test_megacampsf_bandpass"
+                     "test_salt2source_rcov_vs_snfit"
+                     "test_salt2source_timeseries_vs_snfit"
+                     "test_sugarsource"
+                     "test_ztf_bandpass")
                " and not "))
       #:phases
       #~(modify-phases %standard-phases
          (add-after 'unpack 'relax-requirements
            (lambda _
              (substitute* "setup.cfg"
-               ;; pyyaml>=6.0.1
-               (("6.0.1") "6.0"))))
+               ;; h5py>=3.11
+               (("3.11") "3.8.0"))))
           (add-before 'check 'prepare-test-environment
             (lambda _
               (setenv "HOME" "/tmp")
@@ -3455,16 +3441,16 @@ (define-public python-sncosmo
     (propagated-inputs
      (list python-astropy
            python-extinction
+           python-h5py
            python-looseversion
            python-numpy
            python-pyyaml
            python-scipy))
     (native-inputs
      (list ;; python-iminuit ; not packed, optional
-           python-cython
+           python-cython-3
            python-pytest
            python-pytest-astropy
-           python-pytest-cov
            python-setuptools
            python-wheel))
     (home-page "https://sncosmo.readthedocs.org")
-- 
2.47.1

Message #119 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 33/51] gnu: python-specreduce: Simplify.
Date: Fri, 21 Feb 2025 21:49:27 +0000

* gnu/packages/astronomy.scm (python-specreduce) [arguments] <phases>:
Remove 'patch-pyproject-toml.
[native-inputs]: Remove python-setuptools-scm; add
python-setuptools-scm-next.

Change-Id: Ia582574b00bfb5a08a39c8ac8bac591fd661706e
---
 gnu/packages/astronomy.scm | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d406bab2717..9df3e2f828f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3566,12 +3566,6 @@ (define-public python-specreduce
                     " and not specreduce.calibration_data.get_reference_file_path"))
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'patch-pypojrect-toml
-            (lambda _
-              (substitute* "pyproject.toml"
-                ;; TypeError: Configuration.__init__() got an unexpected
-                ;; keyword argument 'version_file'
-                (("version_file = .*") ""))))
          (add-before 'check 'set-home
            (lambda _
              ;; Relax matplotlib warning: ... because the default path
@@ -3581,7 +3575,7 @@ (define-public python-specreduce
     (native-inputs
      (list python-photutils
            python-pytest-astropy
-           python-setuptools-scm
+           python-setuptools-scm-next
            python-wheel))
     (propagated-inputs
      (list python-astropy
-- 
2.47.1

Message #122 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 34/51] gnu: python-spherical-geometry: Remove bundled libqd
 source.
Date: Fri, 21 Feb 2025 21:49:28 +0000

* gnu/packages/astronomy.scm (python-spherical-geometry) [source]
<snippet>: Delete bundled "libqd" source.
[arguments] <tests-flags>: Run all tests; add "--pyargs" options.
<phases>: Remove 'prepare-test-environment.

Change-Id: Id162e455b9369204ed8cb0545435c548cfbd2fad
---
 gnu/packages/astronomy.scm | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9df3e2f828f..636bcb8717e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5247,27 +5247,24 @@ (define-public python-spherical-geometry
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0znzfy3bmnsncvahf8qdav0c9403fn99d1gp25lainhv7kxfk44c"))))
+        (base32 "0znzfy3bmnsncvahf8qdav0c9403fn99d1gp25lainhv7kxfk44c"))
+       (modules '((guix build utils)))
+       (snippet
+        #~(begin
+            ;; Remove bundled library.
+            (delete-file-recursively "libqd")))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; XXX: Disable one failing test
-      ;; See https://github.com/spacetelescope/spherical_geometry/issues/252
-      #:test-flags #~(list "-k" "not test_overlap")
+      #:test-flags
+      #~(list "--pyargs" "spherical_geometry")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'preparations
             (lambda _
               (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
               ;; Use our own libraries in place of bundles.
-              (setenv "USE_SYSTEM_QD" "1")))
-          (add-before 'check 'prepare-test-environment
-            (lambda _
-              (invoke "python" "setup.py" "build_ext" "--inplace")
-              (call-with-output-file "pytest.ini"
-                (lambda (port)
-                  (format port "[pytest]
-python_files = test_*.py"))))))))
+              (setenv "USE_SYSTEM_QD" "1"))))))
     (native-inputs
      (list python-pytest
            python-pytest-astropy-header
-- 
2.47.1

Message #125 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 35/51] gnu: python-soxs: Update to 5.0.0.
Date: Fri, 21 Feb 2025 21:49:29 +0000

* gnu/packages/astronomy.scm (python-soxs): Update to 5.0.0.

Change-Id: I9640fb9f0ef181d787b4e7c817660c9d4c271da1
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 636bcb8717e..82b4aecf1a9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3496,13 +3496,13 @@ (define-public python-so-noise-models
 (define-public python-soxs
   (package
     (name "python-soxs")
-    (version "4.8.5")
+    (version "5.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "soxs" version))
        (sha256
-        (base32 "1m5q3i7hk7jqdpd46h13c4a16b74p0k4mqkxhs43b4vi95h70qrj"))))
+        (base32 "1pckpyg8b34ql79zr0bzxrl41nynd522skdjmk2cs23k7ps32nwm"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.47.1

Message #128 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 36/51] gnu: python-stsci-stimage: Update to 0.2.10.
Date: Fri, 21 Feb 2025 21:49:30 +0000

* gnu/packages/astronomy.scm (python-stsci-stimage): Update to 0.2.10.

Change-Id: I917c3ed9456fd2d7a5595c33ddb6da8645aacd2c
---
 gnu/packages/astronomy.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 82b4aecf1a9..a13a4c232d3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5467,13 +5467,13 @@ (define-public python-stsci-imagestats
 (define-public python-stsci-stimage
   (package
     (name "python-stsci-stimage")
-    (version "0.2.9")
+    (version "0.2.10")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "stsci_stimage" version))
               (sha256
                (base32
-                "18sqmjiyn76hzkmv3g8549vfygi136gnar6pb0s7wb44j7cvc0in"))))
+                "02qzblw11kfdw9rp2m26zbzlzl3w0dnrhncn383a3sw3dwjn9lpf"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.47.1

Message #131 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 42/51] gnu: Add python-losoto.
Date: Fri, 21 Feb 2025 21:49:36 +0000

* gnu/packages/astronomy.scm (python-losoto): New variable.

Change-Id: I402823c3c2cd01b709f17d1c863975b5d73c2091
---
 gnu/packages/astronomy.scm | 42 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 1cc549c214f..ae1030b922a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3051,6 +3051,48 @@ (define-public python-holodeck
 observationally-derived galaxy merger catalogs.")
     (license license:expat)))
 
+(define-public python-losoto
+  (package
+    (name "python-losoto")
+    (version "2.4.4")
+    (source
+     (origin
+       (method git-fetch) ; no tests data in the PyPI tarball
+       (uri (git-reference
+             (url "https://github.com/revoltek/losoto")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0sdg30fi3dl4w5k4a4ry8b4rgx8ydf18s0yrka1ba1sin34jkwnk"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                ;; Test steps are taken from GitHub Actions
+                ;; <.github/workflows/python.yml>.
+                (invoke "python" "tools/losoto_test.py")))))))
+    (native-inputs
+     (list python-cython-3
+           python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-configparser
+           python-matplotlib
+           python-numpy
+           python-casacore
+           python-scipy
+           python-tables))
+    (home-page "https://github.com/revoltek/losoto")
+    (synopsis "LOFAR Solution Tool")
+    (description
+     "This package provides a @acronym{Low-Frequency Array,
+@url{http://www.lofar.org/, LOFAR}} a large radio telescope Solution Tool.")
+    (license license:gpl3)))
+
 (define-public python-mapsims
   (package
     (name "python-mapsims")
-- 
2.47.1

Message #134 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 43/51] gnu: Add python-lofar-h5plot.
Date: Fri, 21 Feb 2025 21:49:37 +0000

* gnu/packages/astronomy.scm (python-lofar-h5plot): New variable.

Change-Id: I4d780726b242cf4055fb82ef26ad97abf3419ce9
---
 gnu/packages/astronomy.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ae1030b922a..ce8a1291c4c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3051,6 +3051,37 @@ (define-public python-holodeck
 observationally-derived galaxy merger catalogs.")
     (license license:expat)))
 
+(define-public python-lofar-h5plot
+  (package
+    (name "python-lofar-h5plot")
+    (version "2.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "lofar_h5plot" version))
+       (sha256
+        (base32 "0gxri18iqsw1l5zxn40475zj34h5nn1bscfrhkc739vpqjmj60hz"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f)) ; no tests provided
+    (native-inputs
+     (list python-cython-3
+           python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-losoto
+           python-matplotlib
+           python-numpy
+           python-pyqt
+           python-pyqt5-sip))
+    (home-page "https://github.com/tikk3r/lofar-h5plot")
+    (synopsis "GUI for plotting H5Parms produced during LOFAR calibration")
+    (description
+     "H5plot is a small GUI to view the solutions in an H5parm interactively.
+It is a spiritual successor to @code{ParmDBplot} for quickly reviewing gain
+solutions generated by NDPPP.")
+    (license license:gpl3)))
+
 (define-public python-losoto
   (package
     (name "python-losoto")
-- 
2.47.1

Information forwarded to

lars <at> 6xq.net, marius <at> gnu.org, me <at> bonfacemunyoki.com, sharlatanus <at> gmail.com, tanguy <at> bioneland.org, jgart <at> dismail.de, guix-patches <at> gnu.org

:
bug#76480; Package guix-patches. (Fri, 21 Feb 2025 21:54:14 GMT) Full text and rfc822 format available.

Message #137 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 44/51] gnu: Add python-mpsplines.
Date: Fri, 21 Feb 2025 21:49:38 +0000

* gnu/packages/python-science.scm (python-mpsplines): New variable.

Change-Id: I1ae05c5bff783f7716e578bfc01699a10d13c337
---
 gnu/packages/python-science.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 5a473b391b9..444081d2fa2 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1106,6 +1106,39 @@ (define-public python-mpl-scatter-density
 density maps, both for interactive and non-interactive use.")
     (license license:bsd-2)))
 
+(define-public python-mpsplines
+  ;; No release on PyPI no git tag, use the latest commit.
+  (let ((commit "4967655fca8f4d0fc0685486c8ec2f1fe2f199d2")
+        (revision "0"))
+    (package
+      (name "python-mpsplines")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/jararias/mpsplines")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1wqfvjp1d6xzb07qnq72h76f0mx7za9pasgw3qp3ciaycmlkvdr3"))))
+      (build-system pyproject-build-system)
+      (arguments
+       (list #:tests? #f)) ; no tests provided
+      (native-inputs
+       (list python-setuptools
+             python-wheel))
+      (propagated-inputs
+       (list python-scipy
+             python-numpy
+             python-loguru))
+      (home-page "https://github.com/jararias/mpsplines")
+      (synopsis "Mean preserving interpolation with splines")
+      (description
+       "Thi package implements a functionality for mean-preserving
+interpolation of 1D data (for example, time series) with splines.")
+      (license license:bsd-3))))
+
 (define-public python-pyamg
   (package
     (name "python-pyamg")
-- 
2.47.1

Information forwarded to

lars <at> 6xq.net, marius <at> gnu.org, me <at> bonfacemunyoki.com, sharlatanus <at> gmail.com, tanguy <at> bioneland.org, jgart <at> dismail.de, guix-patches <at> gnu.org

:
bug#76480; Package guix-patches. (Fri, 21 Feb 2025 21:54:15 GMT) Full text and rfc822 format available.

Message #140 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 46/51] gnu: Add python-s3path.
Date: Fri, 21 Feb 2025 21:49:40 +0000

* gnu/packages/python-web.scm (python-s3path): New variable.

Change-Id: I04c3fe63b9bf4b37d76a78c1df35617495955414
---
 gnu/packages/python-web.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 3430997abcb..840855805ae 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1805,6 +1805,34 @@ (define-public python-requests-cache
 files.")
     (license license:bsd-2)))
 
+(define-public python-s3path
+  (package
+    (name "python-s3path")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "s3path" version))
+       (sha256
+        (base32 "0gbvyr60mkpm7jbjiya0pmx26q6cfp27p5czw08jwn3k5cp77krk"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX: All tests fail with error: fixture 's3_mock' not found.
+      #:tests? #f))
+    (native-inputs
+     (list python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-boto3
+           python-smart-open))
+    (home-page "https://github.com/liormizr/s3path")
+    (synopsis "Pathlib extension for AWS S3 Service")
+    (description
+     "S3Path provide a Python convenient File-System/Path like interface for
+AWS S3 Service using boto3 S3 resource as a driver.")
+    (license license:asl2.0)))
+
 (define-public python-sarif-om
   (package
     (name "python-sarif-om")
-- 
2.47.1

Message #143 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 45/51] gnu: Add python-sndata.
Date: Fri, 21 Feb 2025 21:49:39 +0000

* gnu/packages/astronomy.scm (python-sndata): New variable.

Change-Id: Ie56d1617a7c4f331ccf277bd71d50cd941b97921
---
 gnu/packages/astronomy.scm | 65 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ce8a1291c4c..f2d21ab3404 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3563,6 +3563,71 @@ (define-public python-sncosmo
 to make such analysis both as flexible and clear as possible.")
     (license license:bsd-3)))
 
+(define-public python-sndata
+  (package
+    (name "python-sndata")
+    (version "1.3.0")
+    (source
+     (origin
+       (method git-fetch) ; no tests data in the PyPI tarball
+       (uri (git-reference
+             (url "https://github.com/sncosmo/SNData")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1jci6ry2b8jylda4v7zhl857pifslpnslrbj2207nz4hw43nz3mp"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-k" (string-join
+                    ;; Network access is required for these tests.
+                    (list "not test_duplicate_obj_id_strings"
+                          "test_obj_id_as_str"
+                          "test_coordinates_0_0"
+                          "test_bad_table_id_err"
+                          "test_cache_not_mutated"
+                          "test_comments_not_in_metadata"
+                          "test_get_zp"
+                          "test_id_joining"
+                          "test_ids_are_sorted"
+                          "test_jd_time_format"
+                          "test_join_id_string_error"
+                          "test_minimal_metadata_keys"
+                          "test_no_duplicate_aliases"
+                          "test_no_empty_data_tables"
+                          "test_no_empty_ids"
+                          "test_paper_tables_are_parsed"
+                          "test_sncosmo_registered_band_names"
+                          "test_standard_column_names"
+                          "test_unique_ids")
+                    " and not "))))
+    (native-inputs
+     (list nss-certs-for-test
+           python-cython-3
+           python-poetry-core
+           python-pytest))
+    (propagated-inputs
+     (list python-astropy
+           python-beautifulsoup4
+           python-numpy
+           python-pandas
+           python-pytz
+           python-pyyaml
+           python-requests
+           python-sncosmo
+           python-tqdm))
+    (home-page "https://sndata.readthedocs.io/en/latest/")
+    (synopsis "Interface for data published by various supernova surveys")
+    (description
+     "SNData provides an access to data releases published by a variety of
+supernova (SN) surveys.  It is designed to support the development of scalable
+analysis pipelines that translate with minimal effort between and across data
+sets.  A summary of accessible data is provided below.  Access to additional
+surveys is added upon request or as needed for individual research projects
+undertaken by the developers.")
+    (license license:gpl3+)))
+
 (define-public python-so-noise-models
   (let ((commit "fac881eb5ee012673d8994443caa3c6ad7fac2b6")
         (revision "0"))
-- 
2.47.1

Message #146 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 48/51] gnu: python-poliastro: Disable more failing tests.
Date: Fri, 21 Feb 2025 21:49:42 +0000

* gnu/packages/astronomy.scm (python-poliastro) [arguments]
<test-flags>: Ignore all tests from "test_czml.py" as all failed, skip
one more test.

Change-Id: Ie10688a0dbdeb25a0fe89417bc60839d44e6057c
---
 gnu/packages/astronomy.scm | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 2b7e0e8b5d7..683e9b90bc4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4852,14 +4852,12 @@ (define-public python-poliastro
               ;; TODO: Review failing tests later when any upstream
               ;; suggestions are provided:
               ;; https://github.com/poliastro/poliastro/issues/1618
-              "-k" (string-append "not test_czml_add_trajectory"
-                                  " and not test_czml_custom_packet"
-                                  " and not test_czml_ground_station"
-                                  " and not test_czml_groundtrack"
-                                  " and not test_czml_preamble"
-                                  ;; This fails with "ufunc 'isfinite' not
-                                  ;; supported for the input types"
-                                  " and not test_porkchop_plotting"))
+              "--ignore=tests/test_czml.py"
+              "-k" (string-append
+                    ;; This fails with "ufunc 'isfinite' not
+                    ;; supported for the input types"
+                    "not test_porkchop_plotting"
+                    " and not test_maneuver_constructor_raises_error_if_invalid_delta_v"))
       #:phases
       #~(modify-phases %standard-phases
          (add-after 'unpack 'relax-requirements
-- 
2.47.1

Message #149 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 49/51] gnu: python-stcal: Update to 1.11.1.
Date: Fri, 21 Feb 2025 21:49:43 +0000

* gnu/packages/astronomy.scm (python-stcal): Update to 1.11.1. Fix build.
[argumens] <test-flags>: Run tests in parallel.
<phases>: Remove 'silent-check-for-opencv, add 'relax-requirements.
[native-inputs]: Add python-pytest-xdist.

Change-Id: I175d4fc3e52efdcad4eac0d8e05f7637245f8e92
---
 gnu/packages/astronomy.scm | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 683e9b90bc4..928fe882c0c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5740,18 +5740,19 @@ (define-public python-stsci-stimage
 (define-public python-stcal
   (package
     (name "python-stcal")
-    (version "1.10.0")
+    (version "1.11.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stcal" version))
        (sha256
-        (base32 "1h0vkc3nd77qm2ph1nihpd1n7dzr3d4rw2wga6j7siqjiwmphj3g"))))
+        (base32 "0xafli4b3wyimpaxmvb0h5bha5g5kg76s4hykk63wkxrjrd2m2vf"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
-      #~(list "-k" (string-join
+      #~(list "--numprocesses" (number->string (parallel-job-count))
+              "-k" (string-join
                     ;; Tests requiring network access.
                     (list "not test_absolute_align"
                           "test_relative_align[True]"
@@ -5770,11 +5771,16 @@ (define-public python-stcal
                 ;; contain the variable: error: ‘NPY_NTYPES_LEGACY’ undeclared
                 ;; (first use in this function)
                 ((".*NPY_NTYPES_LEGACY.*") ""))))
-          (add-before 'build 'silent-check-for-opencv
+          (add-before 'build 'relax-requirements
             (lambda _
-              ;; XXX: Can't detect opencv-python version. The input opencv
-              ;; might not set the version correctly.
               (substitute* "pyproject.toml"
+                ;; Relax some requirements as all tests passed successfully.
+                ;; numpy>=1.25.0
+                (("1.25.0") "1.24.4")
+                ;; scipy>=1.14.1
+                (("1.14.1") "1.12.0")
+                ;; XXX: Can't detect opencv-python version. The input opencv
+                ;; might not set the version correctly.
                 ((".*opencv-python-headless.*") ""))))
           (add-before 'check 'build-extensions
             (lambda _
@@ -5784,6 +5790,7 @@ (define-public python-stcal
      (list python-cython-3
            python-psutil
            python-pytest
+           python-pytest-xdist
            python-pytest-doctestplus
            python-setuptools
            python-setuptools-scm
-- 
2.47.1

Message #152 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 47/51] gnu: Add python-astrocut.
Date: Fri, 21 Feb 2025 21:49:41 +0000

* gnu/packages/astronomy.scm (python-astrocut): New variable.

Change-Id: I507a512bd65742869aadc7e423cc3e2d1574a3ff
---
 gnu/packages/astronomy.scm | 75 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index f2d21ab3404..2b7e0e8b5d7 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1882,6 +1882,81 @@ (define-public python-astroalign
 astronomical images, especially when there is no WCS information available.")
     (license license:expat)))
 
+(define-public python-astrocut
+  (package
+    (name "python-astrocut")
+    (version "0.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "astrocut" version))
+       (sha256
+        (base32 "19smfpb3qbw9s065wx8n0xwg5x8pgj99641hr3lj71dnrfxfwa40"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-k" (string-join
+                    ;; Tests requiring network access.
+                    (list "not test_cube_cut_from_footprint[SPOC]"
+                          "test_cube_cut_from_footprint[TICA]"
+                          "test_cube_cut_from_footprint_all_sequences"
+                          "test_cube_cut_from_footprint_invalid_sequence"
+                          "test_cube_cut_from_footprint_multi_sequence"
+                          "test_cube_cut_from_footprint_outside_coords"
+                          "test_fits_cut[SPOC]"
+                          "test_fits_cut[TICA]"
+                          "test_get_cutout_limits"
+                          "test_get_cutout_wcs"
+                          "test_multithreading"
+                          "test_s3_cube_cut")
+                    " and not "))
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; TODO: Report upstream: ModuleNotFoundError: No module named
+          ;; 'packagename'.
+         (add-after 'unpack 'fix-setup.cfg
+           (lambda _
+             (substitute* "setup.cfg"
+               (("console_scripts =") "")
+               (("astropy-package-template-example.*") "")))))))
+    (native-inputs
+     (list nss-certs-for-test
+           python-pytest
+           python-astroquery
+           python-pytest-astropy
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
+    (propagated-inputs
+     (list python-asdf
+           python-astropy
+           python-cachetools
+           python-fsspec
+           python-pillow
+           python-requests-next
+           python-roman-datamodels
+           python-s3fs
+           python-s3path
+           python-scipy
+           python-spherical-geometry))
+    (home-page "https://astrocut.readthedocs.io")
+    (synopsis "Cutout tools for astronomical images")
+    (description
+     "Astrocut provides tools for making cutouts from sets of astronomical
+images with shared footprints.  It is under active development.
+
+Three main areas of functionality are included:
+@itemize
+@item solving the specific problem of creating image cutouts from sectors of
+@acronym{Transiting Exoplanet Survey Satellite, TESS} full-frame images
+@item general fits file cutouts including from single images and sets of
+images with the shared WCS/pixel scale
+@item cutout post-processing functionality, including centering cutouts along
+a path (for moving targets) and combining cutouts
+@end itemize")
+    (license license:bsd-3)))
+
 (define-public python-astrodendro
   (package
     (name "python-astrodendro")
-- 
2.47.1

Message #155 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 50/51] gnu: python-jwst: Update to 1.17.1.
Date: Fri, 21 Feb 2025 21:49:44 +0000

* gnu/packages/astronomy.scm (python-jwst): Update to 1.17.1.
[arguments] <phases>: Enable 'sanity-check; add 'relax-requirements.
[propagated-inputs]: Remove python-stsci-image.

Change-Id: I58d6080c880e2e2358145971b2b84703b44392d5
---
 gnu/packages/astronomy.scm | 30 +++++++++++++++++++++---------
 1 file changed, 21 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 928fe882c0c..9ce7ca50f8e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4413,13 +4413,13 @@ (define-public python-jplephem
 (define-public python-jwst
   (package
     (name "python-jwst")
-    (version "1.16.1")
+    (version "1.17.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "jwst" version))
               (sha256
                (base32
-                "1bqfgqp4gdm1ky5dvzhzpgygwr710h4mbykp5sb9aw3cw9jg1bk7"))
+                "0brlj2w0jjg9p4zwna05bk9l8nb7xkcss7p5rjdjaj3hxlskzfkq"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -4435,12 +4435,25 @@ (define-public python-jwst
       ;; XXX: Tests require access to https://jwst-crds-pub.stsci.edu server for
       ;; getting data sets.
       #:tests? #f
-      #:phases #~(modify-phases %standard-phases
-                   ;; NOTE: (Sharlatan-20230529T113448+0100): opencv-python's
-                   ;; version can't be detected, it could the way it's packed in
-                   ;; Guix. Review failing sanity check with more efforts,
-                   ;; disable for now to make package buildable.
-                   (delete 'sanity-check))))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'relax-requirements
+            (lambda _
+              (substitute* "pyproject.toml"
+                ;; gwcs>=0.22.0,<0.23.0
+                ((">=0.22.0,<0.23.0") ">=0.22.0")
+                ;; numpy<2.0,>=1.25
+                ((">=1.25,<2.0") ">=1.24,<2.0")
+                ;; scipy>=1.14.1
+                (("1.14.1") "1.12.0")
+                ;; XXX: Can't detect opencv-python version. The input opencv
+                ;; might not set the version correctly.
+                ((".*opencv-python-headless.*") "")
+                ;; jwst.csv_tools was removed.
+                (("csvconvert = .*") "")
+                ;; ImportError: module 'jwst.scripts.asn_gather' has no
+                ;; attribute 'main'
+                (("asn_gather = .*") "")))))))
     ;; opencv provides OpenCV-Python which is Listed as install requirement.
     (propagated-inputs (list opencv
                              python-asdf
@@ -4467,7 +4480,6 @@ (define-public python-jwst
                              python-stcal
                              python-stdatamodels
                              python-stpipe
-                             python-stsci-image
                              python-stsci-imagestats
                              python-synphot
                              python-tweakwcs
-- 
2.47.1

Message #158 received at 76480 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 51/51] gnu: python-jwst-reffiles: Enable tests and
 sanity-check.
Date: Fri, 21 Feb 2025 21:49:45 +0000

* gnu/packages/astronomy.scm (python-jwst-reffiles) [arguments]
<tests?>: Enable them.
<test-flags>: Skip one failing test.
<phases>: Enable 'sanity-check.
[native-inputs]: Remove python-stsci-stimage.

Change-Id: Idcbcd4fd955ccfdfec88325d557ca979cb66a2dc
---
 gnu/packages/astronomy.scm | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9ce7ca50f8e..65890c3e9c8 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4517,25 +4517,17 @@ (define-public python-jwst-reffiles
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; FIXME: Invistigate why it failes on python-jwst side where the
-      ;; python-tweakwcs is built just fine:
-      ;;
-      ;; <...>/tweakwcs/matchutils.py:18: in <module>
-      ;; from stsci.stimage import xyxymatch
-      ;; E   ModuleNotFoundError: No module named 'stsci.stimage'
-      #:tests? #f
-      #:phases
-      #~(modify-phases %standard-phases
-          (delete 'sanity-check))))
+      ;; One test fails with error: FileNotFoundError: [Errno 2] No such file
+      ;; or directory.
+      #:test-flags #~(list "-k" "not test_calib_prep_steps")))
+    (native-inputs
+     (list python-pytest))
     (propagated-inputs
      (list python-astropy
            python-jwst
            python-matplotlib
            python-numpy
            python-scipy))
-    (native-inputs
-     (list python-pytest
-           python-stsci-stimage))
     (home-page "https://github.com/spacetelescope/jwst_reffiles")
     (synopsis "Tool for JWST's CRDS-formatted reference files creation")
     (description
-- 
2.47.1

Reply sent to Sharlatan Hellseher <sharlatanus <at> gmail.com>:
You have taken responsibility. (Fri, 28 Feb 2025 22:56:01 GMT) Full text and rfc822 format available.

Notification sent to Sharlatan Hellseher <sharlatanus <at> gmail.com>:
bug acknowledged by developer. (Fri, 28 Feb 2025 22:56:02 GMT) Full text and rfc822 format available.

Message #163 received at 76480-done <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76480-done <at> debbugs.gnu.org
Subject: [PATCH 00/51] Astro update 2025/02
Date: Fri, 28 Feb 2025 22:54:56 +0000

[Message part 1 (text/plain, inline)]

Pushed to master:

3d34fde47f9 * master origin/master astro-update gnu: python-jwst-reffiles: Enable tests and sanity-check.
e95358b8cb8 * gnu: python-jwst: Update to 1.17.1.
307431484ec * gnu: python-stcal: Update to 1.11.1.
efaf99a21e0 * gnu: python-poliastro: Disable more failing tests.
647337b5291 * gnu: Add python-astrocut.
1dea1431baf * gnu: Add python-s3path.
7f71a7a8aeb * gnu: Add python-sndata.
3731cc50126 * gnu: Add python-mpsplines.
4fd8bd03eab * gnu: Add python-lofar-h5plot.
a244d5b9316 * gnu: Add python-losoto.
62e5dc3a81e * gnu: Add python-glfw.
78bd8d84520 * gnu: Add python-esutil.
165c090c614 * gnu: Add python-cmocean.
7895f144b67 * gnu: python-viresclient: Update to 0.12.2.
1b914f5b96f * gnu: python-sunkit-image: Update to 0.6.0.
9c136c2755f * gnu: python-stsci-stimage: Update to 0.2.10.
86bdc9ca175 * gnu: python-soxs: Update to 5.0.0.
f261b628fa4 * gnu: python-spherical-geometry: Remove bundled libqd source.
a2202e93f72 * gnu: python-specreduce: Simplify.
5270127cafa * gnu: python-sncosmo: Update to 2.12.0.
9423215aae4 * gnu: python-sgp4: Update to 2.24.
25787dc106d * gnu: python-sep-pjw: Update to 1.3.8.
3dad8e1d312 * gnu: python-sep-pjw: Simplify.
ff6676600c8 * gnu: python-roman-datamodels: Update to 0.23.1.
6feca4a9ffc * gnu: python-rad: Update to 0.23.1.
a1991143df8 * gnu: python-pyvo: Update to 1.6.1.
d08fa792fc4 * gnu: python-ndcube: Update to 2.3.1.
9ddd1861aea * gnu: python-halotools: Update to 0.9.3.
58fe8c97081 * gnu: python-tweakwcs: Skip 2 tests.
95d4ab9e63c * gnu: python-gwcs: Update to 0.24.0.
6d20e9de90d * gnu: python-glue-core: Update to 1.22.0.
085c7d556f2 * gnu: python-mpl-scatter-density: Update to 0.8.
9973e999330 * gnu: python-fitsio: Update to 1.2.5.
379683b80a4 * gnu: python-ephem: Update to 4.2.
c0159aee5f2 * gnu: python-extinction: Fix source and home-page URL.
7a129cd0a41 * gnu: python-drms: Update to 0.9.0.
381b069d4b6 * gnu: python-drizzle: Update to 2.0.1.
fdb19ee1dcf * gnu: python-czml3: Update to 2.3.4.
e1cf7d5900d * gnu: python-cmyt: Update to 2.0.2.
f0436f51984 * gnu: python-astroquery: Update to 0.4.9.post1.
b5d9088af29 * gnu: python-astropy-iers-data: Update to 0.2025.2.17.0.34.13.
f59a0dd715c * gnu: python-astropy-healpix: Update to 1.1.2.
6d6bcb631d6 * gnu: python-astropy: Simplify check phase.
9187e166e51 * gnu: python-asdf-astropy: Update to 0.7.1.
0e05a3b4175 * gnu: python-asdf: Update to 4.1.0.
d12eccaa523 * gnu: scamp: Update to 2.13.1.
f286fb6f636 * gnu: libxisf: Update to 0.2.13.
7c5ad11461c * gnu: libsep: Update to 1.4.0.
d77dc6a018f * gnu: indi-2.0: Update to 2.1.2.1.
bbde0b9d9fe * gnu: Add python-casacore.
11284f55f63 * gnu: casacore: Update to 3.6.1.

--
Oleg

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This bug report was last modified 3 days ago.

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Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.

GNU bug report logs - #76480 [PATCH 00/51] Astro update 2025/02

GNU bug report logs - #76480
[PATCH 00/51] Astro update 2025/02