[bug#70488] [PATCH 00/47] Astronomy 2024/02 updates.

[bug#70488] [PATCH 00/47] Astronomy 2024/02 updates.

[Sharlatan Hellseher]

Hi Guix!

Mid spring update of astronomical software is ready to be reviewed. This time I've concentrated on
fixing build and check phases of some Python projects which are become complicated to pack with even
so powerful pyproject-build-system (no setup.py, dependencies to higher version of other packages,
requirement to build extension, ... the subject for guix dev mailing list indeed).

Main highlights:
- CFITSIO is updated to the latest 4.4.0 version and all dependent packages were checked.
- Stellarium is updated to the latest 24.1 version.
- A long chain of pended packages depending on plplot now started.
- Fixed issue with python-semantic-version on runtime,
  reported by Iliya Tikhonenko <tikhonenko@mpe.mpg.de>.

- added [5/5]
  - [X] psfex :: Astronomical PSF modelling and quality assessment
  - [X] python-assay :: Python testing framework
  - [X] python-pysiaf :: Handling SIAF for space telescopes
  - [X] python-supersmoother :: Python implementation of Friedman's Supersmoother
  - [X] scamp :: Compute astrometric solutions

- updated [30/30]
  - [X] cfitsio 4.3.1 -> 4.4.0
  - [X] indi 2.0.6 -> 2.0.7
  - [X] libxisf 0.2.11 -> 0.2.12
  - [X] parfive 2.0.2 -> 2.1.0
  - [X] python-asdf 3.1.0 -> 3.2.0
  - [X] python-asdf-astropy 0.6.0 -> 0.6.1
  - [X] python-astroplan 0.9.1 -> 0.10
  - [X] python-astropy 6.0.0 -> 6.0.1
  - [X] python-astropy-healpix 1.0.2 -> 1.0.3
  - [X] python-astropy-iers-data 0.2024.3.18.0.29.47 -> 0.2024.4.15.2.45.49
  - [X] python-bayesicfitting 3.2.0 -> 3.2.1
  - [X] python-casa-formats-io 0.2.2 -> 0.3.0
  - [X] python-crds 11.17.19 -> 11.17.20
  - [X] python-ginga 5.0.0 -> 5.0.1
  - [X] python-jwst 1.13.4 -> 1.14.0
  - [X] python-photutils 1.10.0 -> 1.12.0
  - [X] python-rad 0.19.0 -> 0.19.2
  - [X] python-regions 0.8 -> 0.9
  - [X] python-reproject 0.13.0 -> 0.13.1
  - [X] python-roman-datamodels 0.19.0 -> 0.19.1
  - [X] python-specutils 1.13.0 -> 1.14.0
  - [X] python-stcal 1.6.1 -> 1.7.0
  - [X] python-stdatamodels 1.10.0 -> 1.10.1
  - [X] python-stsci-imagestats 1.8.0 -> 1.8.2
  - [X] python-stsci-stimage 0.2.6 -> 0.2.8
  - [X] python-sunpy 5.1.1 -> 5.1.2
  - [X] python-synphot 1.3.0 -> 1.4.0
  - [X] python-tweakwcs 0.8.6 -> 0.8.7
  - [X] stellarium 23.4 -> 24.1

Plan for the next month to continue with packaging Astropy affiliated packages from the list
available at https://www.astropy.org/affiliated/registry.json, bring more foundation packages like
HELPix, which allow to start a new chain of dependent packages, check what is left to bring
python-yt.

Build stats:

--8<---------------cut here---------------start------------->8---
./pre-inst-env guix build cfitsio indi julia-arnoldimethod libxisf parfive psfex
python-asdf python-asdf-astropy python-assay python-astroplan python-astropy
python-astropy-healpix python-astropy-iers-data python-bayesicfitting
python-casa-formats-io python-crds python-exif-read python-gatspy python-ginga
python-jwst python-photutils python-pysiaf python-pytest-socket python-rad
python-regions python-reproject python-roman-datamodels python-skyfield
python-specutils python-stcal python-stdatamodels python-stsci-image
python-stsci-imagestats python-stsci-stimage python-sunpy python-supersmoother
python-synphot python-tweakwcs scamp stellarium

/gnu/store/vdnd125l2g3mmjng502gpn106f0lxp13-stellarium-24.1
/gnu/store/nfncz84xz8qh61s1zgk4bdsd4fzj18ir-scamp-2.10.0
/gnu/store/8blp5lk2wakaxq7gsj5qp3p9viy5d6ph-python-tweakwcs-0.8.7
/gnu/store/563bcym71ymp57kh6y13b0l4ci3836p1-python-synphot-1.4.0
/gnu/store/7243bmnjb129axdf8hl6ncb2izshg42b-python-supersmoother-0.4
/gnu/store/xmqrb8ylglpyxpd4jllrczvvsxssvrmd-python-sunpy-5.1.2
/gnu/store/zbr0cq0ym2gsa18fzgckkwmf6z25dm94-python-stsci-stimage-0.2.8
/gnu/store/iq15ji3g14lbzs4m0ly3xc5fbgm4zz08-python-stsci-imagestats-1.8.2
/gnu/store/jd7bw41528vxxzzcivb5skbky3wiszpl-python-stsci-image-2.3.5
/gnu/store/inp4vi19lch1517ci16qbnm1gwz757bl-python-stdatamodels-1.10.1
/gnu/store/q5p18dlpqy1080agp82qyqjkq41hrrpa-python-stcal-1.7.0
/gnu/store/fvh7f7si5sphwcl1n9pq98nzqhrmjslj-python-specutils-1.14.0
/gnu/store/zpcg7bby7099qhba8b0sxyl1dq83jh07-python-skyfield-1.48
/gnu/store/avdm2a6swr2c3yjf32rfdzyr5gbqdkfk-python-roman-datamodels-0.19.1
/gnu/store/izavyvszb36v6s9i2scza1anxjxpddaa-python-reproject-0.13.1
/gnu/store/7y5k2vh9n48bdd1vb8dri6lkc10r063a-python-regions-0.9
/gnu/store/k4gnfhws4bndjx4np6kmjxx4gapvgc52-python-rad-0.19.2
/gnu/store/wmri5wxmg5bhfva5kb09gx50bw3r1dg7-python-pytest-socket-0.7.0
/gnu/store/3lv3w97y7nm7d2m0q75rbhz994q8759d-python-pysiaf-0.22.0
/gnu/store/8lg6si6056vdp8ld520cyijpcs2pdvyf-python-photutils-1.12
/gnu/store/ca27y6dvrinvd90vhnd35b6pk60vsd1z-python-jwst-1.14.0
/gnu/store/0b1rld810g6qw61zfwxakm00y87hqyn9-python-ginga-5.0.1
/gnu/store/ch54g171q6dldmql8zy563d8rpka4b92-python-gatspy-0.3
/gnu/store/ar89f5lwrfb0jvkyfz50y8liccp84wwx-python-exif-read-3.0.0
/gnu/store/gcmashvb9arz03khxcw89frisvm92r99-python-crds-11.17.20
/gnu/store/iwwll5ma1zp5nma63l669z0j9a8z01yz-python-casa-formats-io-0.3.0
/gnu/store/1kj9s25w82n0rbv8nza3g04hdk5a8b3n-python-bayesicfitting-3.2.1
/gnu/store/j21bfrydd1ps24dv7agdrgjwb1ccxach-python-astropy-iers-data-0.2024.4.15.2.45.49
/gnu/store/gdxnfqryw4vk907jx3c38i6nkjbl4qkb-python-astropy-healpix-1.0.3
/gnu/store/gv5fvf68qdw0vzbcwmpys5y65rd8sjgs-python-astropy-6.0.1
/gnu/store/fdadfm1rgwhaz1na24lw797fchlnp7yf-python-astroplan-0.10
/gnu/store/0cnax1fn7qgp2dklsinfxsp529qymyms-python-assay-0.0.0-0.74617d7
/gnu/store/vsi6cqg75cnj5davswqm3m549gwn2q13-python-asdf-astropy-0.6.1
/gnu/store/scak8mnw103qycklyl6w5hz10yad39fs-python-asdf-3.2.0
/gnu/store/9c6n5zkd3wfchad9i0vaf3is3c56fk0v-psfex-3.24.2
/gnu/store/2c7ni6jxjvhwkrjh7fnvxnfb7k6lcrs1-parfive-2.1.0
/gnu/store/n2pg13iaqz8mwwny285921qlrc0576p0-libxisf-0.2.12
/gnu/store/wa8lgfra92xbwa59xixzpmlyk911k5ni-indi-2.0.7
/gnu/store/w0gnn3301ms307zdjshwpvcp7d0akj5p-cfitsio-4.4.0
--8<---------------cut here---------------end--------------->8---

Dependent build stats:

--8<---------------cut here---------------start------------->8---
./pre-inst-env guix refresh --list-dependent cfitsio indi libxisf parfive psfex
python-asdf python-asdf-astropy python-assay python-astroplan python-astropy
python-astropy-healpix python-astropy-iers-data python-bayesicfitting
python-casa-formats-io python-crds python-exif-read python-gatspy python-ginga
python-jwst python-photutils python-pysiaf python-pytest-socket python-rad
python-regions python-reproject python-roman-datamodels python-skyfield
python-specutils python-stcal python-stdatamodels python-stsci-image
python-stsci-imagestats python-stsci-stimage python-sunpy python-supersmoother
python-synphot python-tweakwcs scamp stellarium
python-tweakwcs scamp stellarium

Building the following 28 packages would ensure 86 dependent packages are
rebuilt: sextractor@2.28.0 indi@2.0.7 imppg@0.6.5 stellarium@24.1 alfa@2.2
julia-wcs@0.6.2 phd2@2.6.13 swarp@2.41.5 glnemo2@1.21.0 gnuastro@0.22
aoflagger@3.4.0 siril@1.2.1 splash@3.10.3 julia-fitsio@0.17.1 gwenview@23.08.5
labplot@2.10.1 python-astroplan@0.10 python-poliastro@0.17.0
python-asdf-compression@0.0.1-0.57cc7e7 python-ginga@5.0.1 ginga-qt5@5.0.1
python-asdf-zarr@0.0.3 python-aplpy@2.1.0 python-astroalign@2.5.1 scamp@2.10.0
python-radiospectra@0.5.0 python-cesium@0.12.1 python-jwst@1.14.0

/gnu/store/ca27y6dvrinvd90vhnd35b6pk60vsd1z-python-jwst-1.14.0
/gnu/store/53ca7byad86s8b76wf9lf6psdzqfjwr5-python-cesium-0.12.1
/gnu/store/dhyinp5s58zpj6fbl3n1v4wa14nhn229-python-radiospectra-0.5.0
/gnu/store/nfncz84xz8qh61s1zgk4bdsd4fzj18ir-scamp-2.10.0
/gnu/store/cxk4zw7vcqlwm6bk8fkkjhgjb4dfw6lk-python-astroalign-2.5.1
/gnu/store/23iywrrc0nvih9pnbsya1786fxviyidy-python-aplpy-2.1.0
/gnu/store/7920xfflxbdb5316yg56xrf34mgar2y4-python-asdf-zarr-0.0.3
/gnu/store/0jky435fla7hdxj3wqs04zqjrfv9h5m0-ginga-qt5-5.0.1
/gnu/store/0b1rld810g6qw61zfwxakm00y87hqyn9-python-ginga-5.0.1
/gnu/store/ahrjhknayszzxfwc872yg682kp6qm3xl-python-asdf-compression-0.0.1-0.57cc7e7
/gnu/store/dyyqx64jydq5k50rwwg2al5i8z52s0sc-python-poliastro-0.17.0
/gnu/store/fdadfm1rgwhaz1na24lw797fchlnp7yf-python-astroplan-0.10
/gnu/store/bnjhapnqsvynnxsc2zz7zcx4sk0m181z-labplot-2.10.1
/gnu/store/60nzh7pwbm11kkhxrhz6zlgz0qf9qiql-gwenview-23.08.5
/gnu/store/1gr204bg17xav3ncvjxhgqlmyg2q6n8l-julia-fitsio-0.17.1
/gnu/store/gvg3ffdgzkc110dzvsbcwgmzb901pa17-splash-3.10.3
/gnu/store/175jp1zq70h556ffn9166r8z77vy8q14-siril-1.2.1
/gnu/store/s4j9iyz6hi8cs8rx9h6wzxvn6zpicy38-aoflagger-3.4.0
/gnu/store/9fjpdh4facjj1my62hw58syqwns157hs-gnuastro-0.22
/gnu/store/isjd84aik55lpyfay3s7kfaw2c0fx9y4-glnemo2-1.21.0
/gnu/store/diyb7zv44188k8wfm98vlsh4r9fjnm8a-swarp-2.41.5
/gnu/store/qv1wyfwis43gbvkf39rr6mhn150c1939-phd2-2.6.13
/gnu/store/gvkcx2v2cs32rjxjkc2xahdh2aa8kkfa-julia-wcs-0.6.2
/gnu/store/8yp0p9xy59n5ci2xn2zzirwlw825b09w-alfa-2.2
/gnu/store/vdnd125l2g3mmjng502gpn106f0lxp13-stellarium-24.1
/gnu/store/7bkl0yjh3dhrfma5aadg0j5d78vazy5b-imppg-0.6.5
/gnu/store/wa8lgfra92xbwa59xixzpmlyk911k5ni-indi-2.0.7
/gnu/store/palpxpc470pl7vq8qflkv8l1brj61dlf-sextractor-2.28.0
--8<---------------cut here---------------end--------------->8---

Sharlatan Hellseher (47):
  gnu: cfitsio: Update to 4.4.0.
  gnu: stellarium: Update to 24.1.
  gnu: indi-2.0: Update to 2.0.7.
  gnu: libxisf: Update to 0.2.12.
  gnu: python-pytest-socket: Update to 0.7.0.
  gnu: parfive: Update to 2.1.0.
  gnu: python-exif-read: Update to 3.0.0.
  gnu: Add python-pysiaf.
  gnu: Add python-supersmoother.
  gnu: python-asdf: Update to 3.2.0.
  gnu: python-asdf-astropy: Update to 0.6.1.
  gnu: python-astropy-iers-data: Update to 0.2024.4.15.2.45.49.
  gnu: python-astropy: Symplify package.
  gnu: python-astropy: Update to 6.0.1.
  gnu: python-astropy-healpix: Update to 1.0.3.
  gnu: python-jwst: Update to 1.14.0.
  gnu: python-stcal: Update to 1.7.0.
  gnu: python-stdatamodels: Update to 1.10.1.
  gnu: python-stsci-imagestats: Update to 1.8.2.
  gnu: python-stsci-image: Refresh package style.
  gnu: python-synphot: Add custom check phase.
  gnu: python-synphot: Update to 1.4.0.
  gnu: python-tweakwcs: Adjust indentation.
  gnu: python-tweakwcs: Update to 0.8.7.
  gnu: python-ginga: Update to 5.0.1.
  gnu: python-ginga: Set HOME for sanity check.
  gnu: python-gatspy: Refresh package style.
  gnu: python-bayesicfitting: Refresh package style.
  gnu: python-bayesicfitting: Update to 3.2.1.
  gnu: Add python-assay.
  gnu: python-skyfield: Enable tests.
  gnu: python-sunpy: Update to 5.1.2.
  gnu: python-astroplan: Update to 0.10.
  gnu: python-rad: Update to 0.19.2.
  gnu: python-regions: Update to 0.9.
  gnu: python-roman-datamodels: Update to 0.19.1.
  gnu: python-casa-formats-io: Update to 0.3.0.
  gnu: python-specutils: Update to 1.14.0.
  gnu: python-photutils: Update to 1.12.
  gnu: python-reproject: Update to 0.13.1.
  gnu: python-reproject: Enable tests.
  gnu: python-asdf: Adjust inputs.
  gnu: python-crds: Update to 11.17.20.
  gnu: python-stsci-stimage: Update to 0.2.8.
  gnu: python-stsci-stimage: Adjust test steps.
  gnu: Add scamp.
  gnu: Add psfex.

 gnu/packages/astronomy.scm      | 709 +++++++++++++++++++++-----------
 gnu/packages/python-check.scm   |  65 ++-
 gnu/packages/python-science.scm |  25 ++
 gnu/packages/python-web.scm     |   4 +-
 gnu/packages/python-xyz.scm     |   4 +-
 5 files changed, 544 insertions(+), 263 deletions(-)


base-commit: 43a4215cad8c6da357f895569c0cedf5e854cee0
-- 
2.41.0

bug#70488: [PATCH 00/47] Astronomy 2024/02 updates.

[Sharlatan Hellseher]

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Closing, wrong subject name.

--
Oleg

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[bug#70489] [PATCH 01/47] gnu: cfitsio: Update to 4.4.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (cfitsio): Update to 4.4.0.

Change-Id: Iac79d04b1cfb59038578939266bc4b948fb3c908
---
 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 6cd0bb7348..0aa2efaabc 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -451,7 +451,7 @@ (define-public ccfits
 (define-public cfitsio
   (package
     (name "cfitsio")
-    (version "4.3.1")
+    (version "4.4.0")
     (source
      (origin
        (method url-fetch)
@@ -459,7 +459,7 @@ (define-public cfitsio
              "https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/"
              "cfitsio-" version ".tar.gz"))
        (sha256
-        (base32 "1gk2a07ypmc8rcngakcarprznq7hi3xr9szfv3hy2yv80ppci9s7"))))
+        (base32 "1abb4ky6pjyi9f9ly8qjmkb5h25d5xxqlrxrgjg86q77bbwhr44m"))))
     (build-system gnu-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 02/47] gnu: stellarium: Update to 24.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (stellarium): Update to 24.1.

Change-Id: I53dea0e03a3b7c4d78b4946a2bbc9a13f9fbec6f
---
 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 0aa2efaabc..d82966932d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1345,7 +1345,7 @@ (define-public stackistry
 (define-public stellarium
   (package
     (name "stellarium")
-    (version "23.4")
+    (version "24.1")
     (source
      (origin
        (method git-fetch)
@@ -1354,7 +1354,7 @@ (define-public stellarium
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "11l3lql3cxj7s7q7n74qd4rhbjy374b4c0lpm0dr8s85mfrq6fmc"))))
+        (base32 "15r8vg1xb4q8vwy10dfs4543bg6r3463sgrpkqk6fpxx46d8axxp"))))
     (build-system cmake-build-system)
     ;; TODO: Complete documentation build and split into dedicated outputs.
     (arguments
-- 
2.41.0

[bug#70489] [PATCH 03/47] gnu: indi-2.0: Update to 2.0.7.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (indi-2.0): Update to 2.0.7.

Change-Id: Ia134449cc18a0c70dcba962b0ea51e2341d34e98
---
 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 d82966932d..d8af86b449 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3804,7 +3804,7 @@ (define-public imppg
 (define-public indi-2.0
   (package
     (name "indi")
-    (version "2.0.6")
+    (version "2.0.7")
     (source
      (origin
        (method git-fetch)
@@ -3813,7 +3813,7 @@ (define-public indi-2.0
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0j1yr8wz6q6xi4dskv3yyhm0valsyfhcw1n8xpfgzbzbdzc8biyw"))))
+        (base32 "0w3494by88g0sz92adgvy75g7f1609ilsblink9z37n02v83dfxi"))))
     (build-system cmake-build-system)
     (arguments
      ;; TODO: fix failing tests on aarch64-system.
-- 
2.41.0

[bug#70489] [PATCH 04/47] gnu: libxisf: Update to 0.2.12.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (libxisf): Update to 0.2.12.

Change-Id: Ide88155581b317cdb74683f49d2ec8b87c6bc5de
---
 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 d8af86b449..917b838e7a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3557,7 +3557,7 @@ (define-public libpasastro
 (define-public libxisf
   (package
     (name "libxisf")
-    (version "0.2.11")
+    (version "0.2.12")
     (source
      (origin
        (method git-fetch)
@@ -3566,7 +3566,7 @@ (define-public libxisf
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "02lnlsdg7f6pbcfk9amzh2k42wsb19d97yp2jq122lzivx9inwn1"))))
+        (base32 "1bvf3x0xdipkg28c75j6jav3b2llbqvfa6lkwiacxxlzmj0226s2"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags #~(list "-DUSE_BUNDLED_LIBS=OFF")))
-- 
2.41.0

[bug#70489] [PATCH 05/47] gnu: python-pytest-socket: Update to 0.7.0.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-pytest-socket): Update to 0.7.0.

Change-Id: I879064eba2f4d93d2e2b519ebdf613685d5b5df9
---
 gnu/packages/python-check.scm | 31 +++++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index b39709d960..777791cb6c 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -420,13 +420,17 @@ (define-public python-vcrpy
 (define-public python-pytest-socket
   (package
     (name "python-pytest-socket")
-    (version "0.5.1")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "pytest-socket" version))
-              (sha256
-               (base32
-                "1dkr86nxkxc0ka3rdnpmk335m8gl1zh1sy8i7w4w1jsidbf82jvw"))))
+    (version "0.7.0")
+    (source
+     (origin
+       ;; There are no tests in the PyPI tarball.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/miketheman/pytest-socket")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1m6s07gvljq82hiajzy1v123kpkciziiqdjqfnas169rmzg0bmnp"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -440,7 +444,18 @@ (define-public python-pytest-socket
                     " and not test_httpx_fails"
                     " and not test_disabled_urllib_fails"
                     " and not test_urllib_succeeds_by_default"
-                    " and not test_enabled_urllib_succeeds"))))
+                    " and not test_enabled_urllib_succeeds"
+                    " and not test_single_cli_arg_connect_disabled_hostname_resolved"))
+     #:phases
+       #~(modify-phases %standard-phases
+           ;; See <https://github.com/miketheman/pytest-socket/issues/308>
+         (add-after 'unpack 'fix-tests
+           (lambda _
+             (substitute* (list "tests/test_async.py"
+                                "tests/test_socket.py"
+                                "tests/test_precedence.py")
+               (("from tests.common import assert_socket_blocked")
+                "from common import assert_socket_blocked")))))))
     (native-inputs (list python-httpx
                          python-poetry-core
                          python-pypa-build
-- 
2.41.0

[bug#70489] [PATCH 06/47] gnu: parfive: Update to 2.1.0.

[Sharlatan Hellseher]

* gnu/packages/python-web.scm (parfive): Update to 2.1.0.

Change-Id: I6207150e012c03943d4553854123831d1bba3e55
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 5a532f8460..fb6abb9d80 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1378,13 +1378,13 @@ (define-public httpie
 (define-public parfive
   (package
     (name "parfive")
-    (version "2.0.2")
+    (version "2.1.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "parfive" version))
               (sha256
                (base32
-                "0pf8rzfwxpkn84xzb4v8m1fy3k7kjlh8f9ln4y5xqlnbqpwi30lh"))))
+                "13nw2y7wjzj6w049av6ff4d0zxgbhkrgck0xyh676c114hcv8v6d"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 07/47] gnu: python-exif-read: Update to 3.0.0.

[Sharlatan Hellseher]

* gnu/packages/python-xyz.scm (python-exif-read): Update to 3.0.0.

Change-Id: I19e0a19041aa943a9f3ecf262077328d52ef4d1d
---
 gnu/packages/python-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index bac90b1e07..6011b4137f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5181,13 +5181,13 @@ (define-public python-pyrsistent
 (define-public python-exif-read
   (package
     (name "python-exif-read")
-    (version "2.1.2")
+    (version "3.0.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ExifRead" version))
               (sha256
                (base32
-                "1b90jf6m9vxh9nanhpyvqdq7hmfx5iggw1l8kq10jrs6xgr49qkr"))))
+                "191c7sa0rca8wkspfq8nlfa6davh743mqkzrcayz5gcx2rja7i8a"))))
     (build-system python-build-system)
     (arguments `(#:tests? #f)) ; no tests
     (home-page "https://github.com/ianare/exif-py")
-- 
2.41.0

[bug#70489] [PATCH 08/47] gnu: Add python-pysiaf.

[Sharlatan Hellseher]

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

Change-Id: Ide732d666bccad885ed3e8c78d62df7e74524b9a
---
 gnu/packages/astronomy.scm | 39 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 917b838e7a..55561c98e7 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4209,6 +4209,45 @@ (define-public python-pyregion
 @end itemize")
     (license license:expat)))
 
+(define-public python-pysiaf
+  (package
+    (name "python-pysiaf")
+    (version "0.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pysiaf" version))
+       (sha256
+        (base32 "08wb98k9k4f04455da5ns9rif8pl9r3ih537w1yj393hkjjiyzfz"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-n" "auto"
+              ;; Disable 2 failing tests, see
+              ;; <https://github.com/spacetelescope/pysiaf/issues/338>
+              "-k" (string-append "not test_write_jwst_siaf_xlsx"
+                                  " and not test_write_jwst_siaf_xml" ))))
+    (propagated-inputs
+     (list python-astropy
+           python-lxml
+           python-matplotlib
+           python-numpy
+           python-numpydoc
+           python-openpyxl
+           python-requests
+           python-scipy))
+    (native-inputs
+     (list python-pytest python-pytest-xdist))
+    (home-page "https://pysiaf.readthedocs.io/")
+    (synopsis "Handling SIAF for space telescopes")
+    (description
+     "@code{pysiaf} is a python package to access, interpret, maintain, and
+generate @acronym{Handling of Science Instrument Aperture Files, SIAF}, in
+particular for JWST.  Tools for applying the frame transformations, plotting,
+comparison, and validation are provided.")
+    (license license:bsd-3)))
+
 (define-public python-pysynphot
   ;; XXX: 2.0.0 was released in 2021 there are a lot of changes since that
   ;; time and it failed to build with python-astropy 6.0.0, use the latest
-- 
2.41.0

[bug#70489] [PATCH 09/47] gnu: Add python-supersmoother.

[Sharlatan Hellseher]

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

Change-Id: I8fb43d746757014e3b773c07458b777b893adb4a
---
 gnu/packages/python-science.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 862e101f6a..b39dc5bc5b 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -2449,6 +2449,31 @@ (define-public python-simple-pid
 proportional-integral-derivative} controller.")
     (license license:expat)))
 
+(define-public python-supersmoother
+  (package
+    (name "python-supersmoother")
+    (version "0.4")
+    (source
+     (origin
+       (method git-fetch)        ; no package in PyPI
+       (uri (git-reference
+             (url "https://github.com/jakevdp/supersmoother")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1lkj8l2mpki6x2pxcwlrplx63lhi8h9v2rzxgjfb0cppsfr8m1wp"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-numpy))
+    (native-inputs (list python-scipy))
+    (home-page "http://github.com/jakevdp/supersmoother")
+    (synopsis "Python implementation of Friedman's Supersmoother")
+    (description
+     "This package provides an efficient implementation of
+@url{https://www.slac.stanford.edu/pubs/slacpubs/3250/slac-pub-3477.pdf,
+Friedman's SuperSmoother} based in Python.  It makes use of numpy for fast
+numerical computation.")
+    (license license:bsd-2)))
+
 (define-public python-opt-einsum
   (package
     (name "python-opt-einsum")
-- 
2.41.0

[bug#70489] [PATCH 10/47] gnu: python-asdf: Update to 3.2.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf): Update to 3.2.0.
[arguments] <#:phases>: Replace 'fix-tests-setup with
'patch-pyprojectct-toml phase and add one more substitution rule.
[propagated-inputs]: Remove python-asdf-unit-schemas.

Change-Id: I9e7a0282ed0a9eb82a20988762792e10ae33496b
---
 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 55561c98e7..b06638c49c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4418,13 +4418,13 @@ (define-public python-tweakwcs
 (define-public python-asdf
   (package
     (name "python-asdf")
-    (version "3.1.0")
+    (version "3.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf" version))
        (sha256
-        (base32 "0fa6y3gmqc0y3nz0h68vq3a84pvx6gc5zp33wg8a4n9b4kipm464"))))
+        (base32 "1wj556g15gwp6ir5hg083l15sifdsf23giqkx0jbn4lgdwjffbgr"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -4432,12 +4432,15 @@ (define-public python-asdf
       #~(list "-n" "auto" "-p" "no:legacypath")
       #:phases
       #~(modify-phases %standard-phases
-          ;; ImportError: Error importing plugin " no:legacypath": No module
-          ;; named ' no:legacypath'
-          (add-before 'check 'fix-tests-setup
+          (add-after 'unpack 'patch-pypojrect-toml
             (lambda _
               (substitute* "pyproject.toml"
-                ((".*:legacypath.*") "")))))))
+                ;; ImportError: Error importing plugin " no:legacypath": No
+                ;; module named ' no:legacypath'
+                ((".*:legacypath.*") "")
+                ;; TypeError: Configuration.__init__() got an unexpected
+                ;; keyword argument 'version_file'
+                (("version_file = \"asdf/_version.py\"") "")))))))
     (native-inputs
      (list python-fsspec
            python-packaging
@@ -4451,7 +4454,6 @@ (define-public python-asdf
     (propagated-inputs
      (list python-asdf-standard
            python-asdf-transform-schemas
-           python-asdf-unit-schemas
            python-attrs ;; for vendorized jsonschema
            python-importlib-metadata
            python-jmespath
-- 
2.41.0

[bug#70489] [PATCH 11/47] gnu: python-asdf-astropy: Update to 0.6.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.6.1.

Change-Id: I06f00006fcba1d0e385e6bc3f82f7a85403d94a9
---
 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 b06638c49c..749c581571 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4727,13 +4727,13 @@ (define-public python-asdf-zarr
 (define-public python-asdf-astropy
   (package
     (name "python-asdf-astropy")
-    (version "0.6.0")
+    (version "0.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf-astropy" version))
        (sha256
-        (base32 "0cxwknkjkgiavwmsz3vzk88c3spdi1cj4kwp62hgj92g2mh5k0zh"))))
+        (base32 "1ipjpjiirycj2npicbp39ka7db61vx45j8dm2iis71g5l1rzkblp"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 12/47] gnu: python-astropy-iers-data: Update to 0.2024.4.15.2.45.49.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy-iers-data): Update to 0.2024.4.15.2.45.49.

Change-Id: Iaf902a0f506f149682868d0df0710d400b21f7e6
---
 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 749c581571..567cb54685 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1696,13 +1696,13 @@ (define-public python-astropy-iers-data
     ;; In case of changing the source method git-fetch, consider to check the
     ;; tag as it's not following the PyPI version, see
     ;; <https://github.com/astropy/astropy-iers-data/issues/17>.
-    (version "0.2024.3.18.0.29.47")
+    (version "0.2024.4.15.2.45.49")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "astropy-iers-data" version))
+       (uri (pypi-uri "astropy_iers_data" version))
        (sha256
-        (base32 "1mf03iqw09rp6d8hbby33f4jwfjan9gkb1z7xqsjr2jpj7zwpn3y"))))
+        (base32 "15wran1d5bw1mm3xl3ibp6i5aa7icj9p6g1mqcyp596qmdjnm8wp"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 13/47] gnu: python-astropy: Symplify package.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy): Simplify package.
[build-system]: Swap to pyproject-build-system.
[arguments] <#:phases>: Merge 'prepare-test-environment into custom
'check phase and move test arguments to <#:test-arguments>.

Change-Id: I80098c3eb4e9d95ef2c651d5416196165be3f7c0
---
 gnu/packages/astronomy.scm | 47 ++++++++++++++++++--------------------
 1 file changed, 22 insertions(+), 25 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 567cb54685..fc3c652132 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1565,9 +1565,20 @@ (define-public python-astropy
            ;; see https://github.com/astropy/astropy/pull/14311
            (with-directory-excursion "cextern"
              (for-each delete-file-recursively '("expat" "wcslib")))))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~(list "--pyargs" "astropy"
+              "-n" "auto"
+              "-k" (string-append
+                    ;; Skip tests that need remote data.
+                    "not remote_data"
+                    ;; E astropy.samp.errors.SAMPProxyError:
+                    ;; <SAMPProxyError 1: 'Timeout expired!'>
+                    " and not test_main"
+                    ;; E ModuleNotFoundError: No module named 'wofz'
+                    " and not test_pickle_functional"))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'preparations
@@ -1587,32 +1598,18 @@ (define-public python-astropy
           (add-before 'install 'writable-compiler
             (lambda _
               (make-file-writable "astropy/_compiler.c")))
-          (add-before 'check 'prepare-test-environment
-            (lambda _
-              ;; Some tests require a writable home.
-              (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)))))
-          ;; TODO: The swap to pyproject-build-system introduced all tests
-          ;; failed due to pytest could not load conftest.py, find out how
-          ;; to resolve it and migrate completely to pyproject-build-system.
           (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
               (when tests?
-                (invoke "python" "-m" "pytest" "--pyargs" "astropy"
-                        ;; with    -n : 133.00s
-                        ;; without -n : 326.14s
-                        "-n" (number->string (parallel-job-count))
-                        "-k" (string-append
-                              ;; Skip tests that need remote data.
-                              "not remote_data"
-                              ;; E astropy.samp.errors.SAMPProxyError:
-                              ;; <SAMPProxyError 1: 'Timeout expired!'>
-                              " and not test_main"
-                              ;; E ModuleNotFoundError: No module named 'wofz'
-                              " and not test_pickle_functional"))))))))
+                (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))))))))
     (native-inputs
      (list pkg-config
            python-colorlog
-- 
2.41.0

[bug#70489] [PATCH 14/47] gnu: python-astropy: Update to 6.0.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy): Update to 6.0.1.
[arguments]: <#:test-flags>: Enable recently failing tests; disable some
new one.
[propagated-inputs]: Add python-matplotlib and python-scipy.
[native-inputs]: Remove python-matplotlib and python-scipy; add
python-threadpoolctl.

Change-Id: Iaa48c84565d11c944444ecd1fd77291f4b3c8c3c
---
 gnu/packages/astronomy.scm | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index fc3c652132..7fcb1a678d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1546,13 +1546,13 @@ (define-public celestia-gtk
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "6.0.0")
+    (version "6.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "1nbpqx7ibm8zsyyy17y5rmfjamwz6mv0sy4drlisap9hald81k83"))
+        (base32 "175k2h039c0b8rsf0fdphmxbpjrszd138j8z9zkhh1kd6pg7bac9"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -1574,11 +1574,9 @@ (define-public python-astropy
               "-k" (string-append
                     ;; Skip tests that need remote data.
                     "not remote_data"
-                    ;; E astropy.samp.errors.SAMPProxyError:
-                    ;; <SAMPProxyError 1: 'Timeout expired!'>
-                    " and not test_main"
-                    ;; E ModuleNotFoundError: No module named 'wofz'
-                    " and not test_pickle_functional"))
+                    ;; ValueError: The truth value of an array with more than
+                    ;; one element is ambiguous. Use a.any() or a.all()
+                    " and not test_table_comp[t16-t26]"))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'preparations
@@ -1619,7 +1617,6 @@ (define-public python-astropy
            python-h5py
            python-ipython
            python-jplephem
-           python-matplotlib
            python-objgraph
            python-pandas
            python-pyarrow
@@ -1629,21 +1626,23 @@ (define-public python-astropy
            python-pytest-mpl
            python-pytest-xdist
            python-scikit-image
-           python-scipy
            python-setuptools-scm
            python-sgp4
            python-skyfield
+           python-threadpoolctl
            python-timezonefinder))
     (inputs
      (list expat wcslib))
     (propagated-inputs
      (list python-astropy-iers-data
            python-configobj
+           python-matplotlib
            python-numpy
            python-packaging
            python-ply
            python-pyerfa
-           python-pyyaml))
+           python-pyyaml
+           python-scipy))
     (home-page "https://www.astropy.org/")
     (synopsis "Core package for Astronomy in Python")
     (description
-- 
2.41.0

[bug#70489] [PATCH 15/47] gnu: python-astropy-healpix: Update to 1.0.3.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy-healpix): Update to 1.0.3.

Change-Id: Iffc1d537bd8b3ec10fbb5ddb7c2fd6251813ccde
---
 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 7fcb1a678d..6908be0694 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1654,13 +1654,13 @@ (define-public python-astropy
 (define-public python-astropy-healpix
   (package
     (name "python-astropy-healpix")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy_healpix" version))
        (sha256
-        (base32 "0fij80ws16xzbph8z9v27w54dnc3vry8fk9p3mvxrglnjgnscvq5"))))
+        (base32 "0ilpwwvdnd4nchivwnbiy1hl07hd2mdg4wb90r2p05kvr5z2lpfy"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 16/47] gnu: python-jwst: Update to 1.14.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-jwst): Update to 1.14.0.
[propagated-inputs]: Remove python-asdf-transform-schemas; add
python-importlib-metadata, python-packaging, python-pysiaf, and
python-synphot.

Change-Id: I0310e0680457a7851d07fa14406edf079000fcd5
---
 gnu/packages/astronomy.scm | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6908be0694..374229bcf4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3969,13 +3969,13 @@ (define-public python-jplephem
 (define-public python-jwst
   (package
     (name "python-jwst")
-    (version "1.13.4")
+    (version "1.14.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "jwst" version))
               (sha256
                (base32
-                "0n5cfjayg15kf5p6pns7k2zfcldqz1464ndbldgzanc33fp9wnfz"))))
+                "0knl2x0z3djsln8mi3a4bkxjz49iwmnr1v6wwsk13zvpkfq21vv4"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3992,19 +3992,21 @@ (define-public python-jwst
     (propagated-inputs (list opencv
                              python-asdf
                              python-asdf-astropy
-                             python-asdf-transform-schemas
                              python-astropy
                              python-bayesicfitting
                              python-crds
                              python-drizzle
                              python-gwcs
+                             python-importlib-metadata
                              python-jplephem
                              python-jsonschema
                              python-numpy
+                             python-packaging
                              python-photutils
                              python-poppy
                              python-psutil
                              python-pyparsing
+                             python-pysiaf
                              python-requests
                              python-scikit-image
                              python-scipy
@@ -4014,6 +4016,7 @@ (define-public python-jwst
                              python-stpipe
                              python-stsci-image
                              python-stsci-imagestats
+                             python-synphot
                              python-tweakwcs
                              python-wiimatch))
     (native-inputs (list python-colorama
@@ -4022,6 +4025,7 @@ (define-public python-jwst
                          python-pytest-doctestplus
                          python-pytest-openfiles
                          python-requests-mock
+                         ;; python-ruff ; not packed yet in Guix
                          python-setuptools-scm))
     (home-page "https://jwst-pipeline.readthedocs.io/en/latest/")
     (synopsis
-- 
2.41.0

[bug#70489] [PATCH 17/47] gnu: python-stcal: Update to 1.7.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stcal): Update to 1.7.0.
[native-inputs]: Remove python-pytest-openfiles.

Change-Id: Ib33bb72ff73fcf569a2519b3353260461b63c143
---
 gnu/packages/astronomy.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 374229bcf4..cb5be9393d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3229,13 +3229,13 @@ (define-public python-stsci-stimage
 (define-public python-stcal
   (package
     (name "python-stcal")
-    (version "1.6.1")
+    (version "1.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stcal" version))
        (sha256
-        (base32 "1rwvzjpidz0sfp52mqgs25599hbvxyc4gdc1yk0kdm8aynhdwi82"))))
+        (base32 "04ippj90dn2671xg4rvncf7jsbpcflr7dr6jc2h52z7xfd1msb4d"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3264,7 +3264,6 @@ (define-public python-stcal
            python-pytest
            python-pytest-cov
            python-pytest-doctestplus
-           python-pytest-openfiles
            python-semantic-version
            python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/stcal")
-- 
2.41.0

[bug#70489] [PATCH 18/47] gnu: python-stdatamodels: Update to 1.10.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stdatamodels): Update to 1.10.1.

Change-Id: Ib1626de00fbd060212b125c3a52e116aa126727e
---
 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 cb5be9393d..32949d0a13 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3274,13 +3274,13 @@ (define-public python-stcal
 (define-public python-stdatamodels
   (package
     (name "python-stdatamodels")
-    (version "1.10.0")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stdatamodels" version))
        (sha256
-        (base32 "00zc7z3f2fjvmms2h7176wnzjb025v0aasc6fiib9055sk34bc94"))))
+        (base32 "1h0imp6j9qrjadhvvqcgrx6dq94qhi0023c8c8r2wddhqrh0h5lg"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 19/47] gnu: python-stsci-imagestats: Update to 1.8.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stsci-imagestats): Update to 1.8.2.

Change-Id: I13bb6eab789a8aa365f6bf0f0f892d8a17e3cc66
---
 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 32949d0a13..b7f7127c24 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3162,13 +3162,13 @@ (define-public python-stsci-image
 (define-public python-stsci-imagestats
   (package
     (name "python-stsci-imagestats")
-    (version "1.8.0")
+    (version "1.8.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "stsci.imagestats" version))
               (sha256
                (base32
-                "01jqqrhcna0ghin48bbcza57d12371ny4l4pqws89irwdhd8xr0r"))))
+                "1nmya85bf2747c9ggya6my5b1slk6g2a7bk16rdv8r5a4ah9hda5"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 20/47] gnu: python-stsci-image: Refresh package style.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stsci-image): Adjust indentation.
[description]: Fix grammar.

Change-Id: I1f4bf751720a3be324644bf417104e36510c62a6
---
 gnu/packages/astronomy.scm | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b7f7127c24..4fea09067c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3135,28 +3135,28 @@ (define-public python-stsci-image
   (package
     (name "python-stsci-image")
     (version "2.3.5")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "stsci.image" version))
-              (sha256
-               (base32
-                "1vnp4256nbdvapa69cmm80sjz11ygxa49abr9nbvssj6nyyp5icb"))))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "stsci.image" version))
+       (sha256
+        (base32 "1vnp4256nbdvapa69cmm80sjz11ygxa49abr9nbvssj6nyyp5icb"))))
     (build-system pyproject-build-system)
     (arguments
-     (list #:phases #~(modify-phases %standard-phases
-                        (add-before 'check 'build-extensions
-                          (lambda _
-                            ;; Cython extensions have to be built before running
-                            ;; the tests.
-                            (invoke "python" "setup.py" "build_ext"
-                                    "--inplace"))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'build-extensions
+            (lambda _
+              ;; Cython extensions have to be built before running the tests.
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-pytest python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/stsci.image")
     (synopsis "Image array manipulation functions")
     (description
-     "This package provides Python modules of @acronym{STScI, Space Telescope
-Science Institute} image array manipulation functions.")
+     "This package provides a Python module to various @acronym{STScI, Space
+Telescope Science Institute} image array manipulation functions.")
     (license license:bsd-3)))
 
 (define-public python-stsci-imagestats
-- 
2.41.0

[bug#70489] [PATCH 21/47] gnu: python-synphot: Add custom check phase.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-synphot): [arguments] <#:phases>:
Remove 'prepare-test-environment phase; add custom 'check phase.

Change-Id: I9cb6d65c226a555ccd62a3a6c08d00868a66f109
---
 gnu/packages/astronomy.scm | 21 ++++++++-------------
 1 file changed, 8 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 4fea09067c..7ca051aa79 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4348,19 +4348,14 @@ (define-public python-synphot
      (list
       #:phases
       #~(modify-phases %standard-phases
-          (add-before 'check 'prepare-test-environment
-            (lambda _
-              (invoke "python" "setup.py" "build_ext" "--inplace")
-              ;; To solve pytest/conftest issue. Pytest tries to load all
-              ;; files with word 'test' in them.
-              ;;
-              ;; ImportError while loading conftest ...
-              ;; _pytest.pathlib.ImportPathMismatchError: ...
-              ;;
-              (call-with-output-file "pytest.ini"
-                (lambda (port)
-                  (format port "[pytest]
-python_files = test_*.py"))))))))
+          (replace 'check
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
+              (when tests?
+                (invoke "python" "setup.py" "build_ext" "--inplace")
+                ;; 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))))))))
     (propagated-inputs
      (list python-astropy
            python-dust-extinction
-- 
2.41.0

[bug#70489] [PATCH 22/47] gnu: python-synphot: Update to 1.4.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-synphot): Update to 1.4.0.

Change-Id: I070381de76cfe1bf057d1c8032d2145d5c346fa2
---
 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 7ca051aa79..c868cd824e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4336,13 +4336,13 @@ (define-public python-suntime
 (define-public python-synphot
   (package
     (name "python-synphot")
-    (version "1.3.0")
+    (version "1.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "synphot" version))
        (sha256
-        (base32 "0a54bfrx9aar66040324sw9qdjz5lg67y28sjsxhyv9h3gppc7c0"))))
+        (base32 "0fk860bxaqbamrq15pkqlbvhbf70y50cra2mgvv9r0cxq37isbi6"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 23/47] gnu: python-tweakwcs: Adjust indentation.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-tweakwcs): Adjust indentation.

Change-Id: Ic8c79addbd0253c2364382e6a0e632945eafb05a
---
 gnu/packages/astronomy.scm | 40 ++++++++++++++++++++------------------
 1 file changed, 21 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c868cd824e..a43f21f0b1 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4379,26 +4379,28 @@ (define-public python-tweakwcs
   (package
     (name "python-tweakwcs")
     (version "0.8.6")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "tweakwcs" version))
-              (sha256
-               (base32
-                "1j75i02xzd36gp7pf6gks6nmp4ivi9cbphya4l69py5p62iaab99"))))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "tweakwcs" version))
+       (sha256
+        (base32 "1j75i02xzd36gp7pf6gks6nmp4ivi9cbphya4l69py5p62iaab99"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-astropy
-                             python-gwcs
-                             python-numpy
-                             python-packaging
-                             python-spherical-geometry
-                             python-stsci-imagestats
-                             python-stsci-stimage))
-    (native-inputs (list python-codecov
-                         python-pytest
-                         python-pytest-cov
-                         python-scipy
-                         python-semantic-version
-                         python-setuptools-scm))
+    (propagated-inputs
+     (list python-astropy
+           python-gwcs
+           python-numpy
+           python-packaging
+           python-spherical-geometry
+           python-stsci-imagestats
+           python-stsci-stimage))
+    (native-inputs
+     (list python-codecov
+           python-pytest
+           python-pytest-cov
+           python-scipy
+           python-semantic-version
+           python-setuptools-scm))
     (home-page "https://tweakwcs.readthedocs.io/en/latest/")
     (synopsis
      "Algorithms for matching and aligning catalogs and for tweaking the WCS")
-- 
2.41.0

[bug#70489] [PATCH 24/47] gnu: python-tweakwcs: Update to 0.8.7.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-tweakwcs): Update to 0.8.7.

Change-Id: I2ef8f29839a99ec3b40efc34a61f57bc32216c8e
---
 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 a43f21f0b1..f57165050f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4378,13 +4378,13 @@ (define-public python-synphot
 (define-public python-tweakwcs
   (package
     (name "python-tweakwcs")
-    (version "0.8.6")
+    (version "0.8.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "tweakwcs" version))
        (sha256
-        (base32 "1j75i02xzd36gp7pf6gks6nmp4ivi9cbphya4l69py5p62iaab99"))))
+        (base32 "0cch4z5zmmi1s02n1wdwss8p7qhrzyiajkaik0gga510kgdsvx48"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      (list python-astropy
-- 
2.41.0

[bug#70489] [PATCH 25/47] gnu: python-ginga: Update to 5.0.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ginga): Update to 5.0.1.
[arguments] <#:phases>: Add 'relax-requirements phase.
[propagated-inputs]: Add opencv, python-exif-read python-packaging,
python-pyyaml, and python-tomli.
[native-inputs]: Add python-pytest-astropy-header.

Change-Id: I314bbd9a037b134a03f5a4a174ab878e9523e4b6
---
 gnu/packages/astronomy.scm | 24 +++++++++++++++++++-----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index f57165050f..70e3daa501 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -707,31 +707,45 @@ (define-public python-gatspy
 (define-public python-ginga
   (package
     (name "python-ginga")
-    (version "5.0.0")
+    (version "5.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ginga" version))
        (sha256
-        (base32 "1kydi6qqsscgsa55fa2za35vr5j8xjn09lfbnb5ajr8yxdgm4n3y"))))
+        (base32 "1zw93487a0ilkb5w5qjgrdnavxlmdmjp6c2wyc1wp8qahby9c0xa"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+         (add-after 'unpack 'relax-requirements
+           (lambda _
+             (substitute* "setup.cfg"
+               ;; packaging>=23.1
+               ((">=23.1") ">=21.3")))))))
     (propagated-inputs
-     (list ;;python-exifread  ; optional, not packed yet in Guix
+     (list opencv
            python-astropy
            python-astroquery
            python-dateutil
+           python-exif-read
+           python-fitsio
            python-magic
            python-matplotlib
-           python-fitsio
            python-numpy
+           python-packaging
            python-photutils
            python-pillow
+           python-pyyaml
            python-qtpy
-           python-scipy))
+           python-scipy
+           python-tomli))
     (native-inputs
      (list python-attrs
            python-docutils
            python-pytest-astropy
+           python-pytest-astropy-header
            python-semantic-version
            python-tornado))
     (home-page "https://ejeschke.github.io/ginga/")
-- 
2.41.0

[bug#70489] [PATCH 26/47] gnu: python-ginga: Set HOME for sanity check.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ginga) [arguments] <#:phases>: Add
'set-home phase.

Change-Id: I7fc9b043ae8ac465645215dabc9d8643b8e08fe2
---
 gnu/packages/astronomy.scm | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 70e3daa501..d183a968ed 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -723,7 +723,13 @@ (define-public python-ginga
            (lambda _
              (substitute* "setup.cfg"
                ;; packaging>=23.1
-               ((">=23.1") ">=21.3")))))))
+               ((">=23.1") ">=21.3"))))
+         (add-before 'check 'set-home
+           (lambda _
+             ;; Relax matplotlib warning: ... because the default path
+             ;; (/homeless-shelter/.config/matplotlib) is not a writable
+             ;; directory ...
+             (setenv "HOME" "/tmp"))))))
     (propagated-inputs
      (list opencv
            python-astropy
-- 
2.41.0

[bug#70489] [PATCH 27/47] gnu: python-gatspy: Refresh package style.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-gatspy): Adjust indentetion.
[arguments]: Use #~ qutation style.
<#:test-flags>: Activate tests for supersmoother.
[propagated-inputs]: Add python-supersmoother.

Change-Id: Ibbaae0f87693f5f4aa6e3f92d567881ad58dbfba
---
 gnu/packages/astronomy.scm | 41 +++++++++++++++++++-------------------
 1 file changed, 21 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d183a968ed..bf71843e05 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -675,33 +675,34 @@ (define-public python-gatspy
   (package
     (name "python-gatspy")
     (version "0.3")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "gatspy" version))
-              (sha256
-               (base32
-                "1gw2z6x8nikvnw2gkdl70gr81cwczd1pd7v8ry2kjn6k4kssrfav"))))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "gatspy" version))
+       (sha256
+        (base32 "1gw2z6x8nikvnw2gkdl70gr81cwczd1pd7v8ry2kjn6k4kssrfav"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:phases
-      '(modify-phases %standard-phases
-         ;; Tests need this
-         (add-before 'check 'set-HOME
-           (lambda _ (setenv "HOME" "/tmp"))))
       #:test-flags
-      '(list "-k"
-             (string-append
-              ;; These tests require internet access
-              "not test_download_data.py"
-              ;; XXX: we don't have supersmoother
-              " and not test_supersmoother.py"))))
-    (propagated-inputs (list python-astroml python-numpy python-scipy))
+      ;; These tests require internet access
+      #~(list "-k" "not test_download_data.py")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; Tests need this
+          (add-before 'check 'set-HOME
+            (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-astroml
+           python-numpy
+           python-scipy
+           python-supersmoother))
     (native-inputs (list python-pytest python-nose python-setuptools-scm))
     (home-page "https://github.com/astroml/gatspy")
     (synopsis "General tools for astronomical time series in Python")
-    (description "This package provides general tools for astronomical time
-series in Python.")
+    (description
+     "This package provides general tools for astronomical time series in
+Python.")
     (license license:bsd-2)))
 
 (define-public python-ginga
-- 
2.41.0

[bug#70489] [PATCH 28/47] gnu: python-bayesicfitting: Refresh package style.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-bayesicfitting): Adjust
indentation.
[build-system]: Swap to pyproject-build-system.
[arguments] <#:test-flags>: Add them.
<#:phases>: Use test flags in 'check phase.

Change-Id: Iffc8591199bbaf2a0da95b6b22476e34121dbe79
---
 gnu/packages/astronomy.scm | 42 ++++++++++++++++++++++----------------
 1 file changed, 24 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index bf71843e05..618d0e78bf 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1934,25 +1934,31 @@ (define-public python-bayesicfitting
   (package
     (name "python-bayesicfitting")
     (version "3.2.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/dokester/BayesicFitting")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0q6v7w9b1xzam0qn5vsl5wrdp1fkfpsn411pzd8wyy9giznpajxi"))))
-    (build-system python-build-system)
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dokester/BayesicFitting")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0q6v7w9b1xzam0qn5vsl5wrdp1fkfpsn411pzd8wyy9giznpajxi"))))
+    (build-system pyproject-build-system)
     (arguments
-     (list #:phases #~(modify-phases %standard-phases
-                        (replace 'check
-                          (lambda* (#:key tests? #:allow-other-keys)
-                            (when tests?
-                              (invoke "python" "-m" "unittest" "discover"
-                                      "test")))))))
-    (propagated-inputs (list python-astropy python-future python-matplotlib
-                             python-numpy python-scipy))
+     (list
+      #:test-flags #~(list "-m" "unittest" "discover" "test")
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
+              (when tests?
+                (apply invoke "python" test-flags)))))))
+    (propagated-inputs
+     (list python-astropy
+           python-future
+           python-matplotlib
+           python-numpy
+           python-scipy))
     (home-page "https://www.bayesicfitting.nl")
     (synopsis "Python Toolbox for Astronimical Bayesian fitting")
     (description
-- 
2.41.0

[bug#70489] [PATCH 29/47] gnu: python-bayesicfitting: Update to 3.2.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-bayesicfitting): Update to 3.2.1.

Change-Id: I97bfc44920a3e8f7c2040088f284a38e0a66aa88
---
 gnu/packages/astronomy.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 618d0e78bf..15aa313c41 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1933,16 +1933,18 @@ (define-public python-astroscrappy
 (define-public python-bayesicfitting
   (package
     (name "python-bayesicfitting")
-    (version "3.2.0")
+    (version "3.2.1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/dokester/BayesicFitting")
-             (commit (string-append "v" version))))
+             ;; Tag style has been changed, see
+             ;; <https://github.com/dokester/BayesicFitting/issues/23>.
+             (commit (string-append "v." version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0q6v7w9b1xzam0qn5vsl5wrdp1fkfpsn411pzd8wyy9giznpajxi"))))
+        (base32 "0brqvy4r75vh93lj4jwv8wcrc96ka1v44f5ckjvr65y30plnfwg2"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 30/47] gnu: Add python-assay.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-assay): New variable.

Change-Id: I0ec910d8c37000ff08119a33e3f42af2269fa494
---
 gnu/packages/python-check.scm | 34 +++++++++++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 777791cb6c..6fdfaad6fb 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -9,7 +9,7 @@
 ;;; Copyright © 2020 Edouard Klein <edk@beaver-labs.com>
 ;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020 Tanguy Le Carrour <tanguy@bioneland.org>
-;;; Copyright © 2021-2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021-2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021 Brendan Tildesley <mail@brendan.scot>
 ;;; Copyright © 2021, 2022 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
@@ -61,6 +61,38 @@ (define-module (gnu packages python-check)
   #:use-module (guix packages)
   #:use-module (guix utils))
 
+(define-public python-assay
+  ;; No release yet.
+  (let ((commit "74617d70e77afa09f58b3169cf496679ac5d5621")
+        (revision "0"))
+    (package
+      (name "python-assay")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/brandon-rhodes/assay")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1klxmamj88mn0q348r08zksccgsbch8sp0m4b04s3myrqnslp2nd"))))
+      (build-system pyproject-build-system)
+      (arguments
+       (list
+        #:test-flags #~(list "-m" "assay.tests")
+        #:phases
+        #~(modify-phases %standard-phases
+            (replace 'check
+              (lambda* (#:key tests? test-flags #:allow-other-keys)
+                (when tests?
+                  (apply invoke "python" test-flags)))))))
+      (home-page "https://github.com/brandon-rhodes/assay")
+      (synopsis "Python testing framework")
+      (description
+       "This package provides opiniotated Python test framework prototype.")
+      (license license:expat))))
+
 (define-public python-assertpy
   (package
     (name "python-assertpy")
-- 
2.41.0

[bug#70489] [PATCH 31/47] gnu: python-skyfield: Enable tests.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-skyfield): Enable tests.
[source]: Swap to git checkout containing test data.
[build-system]: Swap to pyproject-build-system.
[native-inputs]: Add python-assay and python-pandas.

Change-Id: Ia4604ab2e44860dcf1294688639d3c54881f8d8c
---
 gnu/packages/astronomy.scm | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 15aa313c41..dbe589ee1a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5048,15 +5048,27 @@ (define-public python-skyfield
     (version "1.48")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "skyfield" version))
+       (method git-fetch) ; PyPI tarball lacks test data
+       (uri (git-reference
+             (url "https://github.com/skyfielders/python-skyfield")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1qaz0k0lkni3y423r66mkvj99bx08qa9xgqp3cs2df70cmdz30cb"))))
-    (build-system python-build-system)
+        (base32 "0l324r4pz7d5w72c7c5akvjx40287hl7sl0qv7swvn2da53vmq0r"))))
+    (build-system pyproject-build-system)
     (arguments
-     ;; XXX: Tests depend on custom test framework
-     ;; https://github.com/brandon-rhodes/assay
-     `(#:tests? #f))
+     (list
+      #:test-flags
+      #~(list "-m" "assay" "--batch" "skyfield.tests")
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
+              (when tests?
+                (with-directory-excursion "ci"
+                  (apply invoke "python" test-flags))))))))
+    (native-inputs
+     (list python-assay python-pandas))
     (propagated-inputs
      (list python-certifi
            python-jplephem
-- 
2.41.0

[bug#70489] [PATCH 32/47] gnu: python-sunpy: Update to 5.1.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sunpy): Update to 5.1.2.

Change-Id: I275445d688dfb3c3c3da18a37d7d21d79814f8ef
---
 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 dbe589ee1a..0371ed6522 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2806,13 +2806,13 @@ (define-public python-sgp4
 (define-public python-sunpy
   (package
     (name "python-sunpy")
-    (version "5.1.1")
+    (version "5.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sunpy" version))
        (sha256
-        (base32 "07rfdj4v29kcb718sgjfsagazvnl11r01ciqjvazr5x3yadfqrwk"))))
+        (base32 "0h62qh74xanj2drikjch7h0a5g4dsaf3v4qxx38vjazmibc37ynp"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 33/47] gnu: python-astroplan: Update to 0.10.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroplan): Update to 0.10.

Change-Id: I80a988262e417f8a5501d02db5e16a93b5d037b4
---
 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 0371ed6522..52f908611b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1754,13 +1754,13 @@ (define-public python-astropy-iers-data
 (define-public python-astroplan
   (package
     (name "python-astroplan")
-    (version "0.9.1")
+    (version "0.10")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astroplan" version))
        (sha256
-        (base32 "0jrgii0f11ckxvywinr9kcsljxnpnkh7hv5638wxwcb1iyjmx36r"))))
+        (base32 "0nl7yi0h5nn4id1jifd8hpwzqdarq9z2iq56x0j2kmj3472cjw0n"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 34/47] gnu: python-rad: Update to 0.19.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-rad): Update to 0.19.2.

Change-Id: I4de8e8228f6d7ae1ae28cac726fcce5f2058f928
---
 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 52f908611b..10eb640e56 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4862,13 +4862,13 @@ (define-public python-gwcs
 (define-public python-rad
   (package
     (name "python-rad")
-    (version "0.19.0")
+    (version "0.19.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "rad" version))
               (sha256
                (base32
-                "0cp3nrv1vq3g61zx6dq36vdlxd5i8g52vg4hwpxakmwvqvc8p3gd"))))
+                "08dh9asdjgfmczmqyjplgdvbk3n68qw6akd8h953wq6v3yr4k4rq"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 35/47] gnu: python-regions: Update to 0.9.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-regions): Update to 0.9.
[arguments] <#:phases>: Add 'create-setup.py phase, rename
'prepare-test-environment to 'build-extensions to reflect purpose.
[native-inputs]: Remove python-cython; add python-cython-3.

Change-Id: Ia634f93336eb7658c4eaeeb7ddb6539c2e0adee3
---
 gnu/packages/astronomy.scm | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 10eb640e56..fe1bc54157 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2667,13 +2667,13 @@ (define-public python-pyvo
 (define-public python-regions
   (package
     (name "python-regions")
-    (version "0.8")
+    (version "0.9")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "regions" version))
        (sha256
-        (base32 "09401pz7926zlci7cznd78hmv9947f6jxyy2afqdqc1xaccpzcq2"))))
+        (base32 "0kvfdzqry3vcvphd7ldmppbgn3ab97hbfzwxfrlxls92yi41h3i6"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2681,14 +2681,21 @@ (define-public python-regions
       #~(list "-n" "auto")
       #:phases
       #~(modify-phases %standard-phases
+          ;; setup.py was removed in 84c80a280431adda00641cda5264c7de18b43b2f
+          ;; for some unknown reason, which caused the package to fail to
+          ;; build. It is being recreated based on that commit.
+          (add-after 'unpack 'create-setup.py
+            (lambda _
+              (call-with-output-file "setup.py"
+                (lambda (port)
+                  (format port "from setuptools import setup
+from extension_helpers import get_extensions
+setup(ext_modules=get_extensions())")))))
           ;; This file is opened in both install and check phases.
-          ;; XXX: Check if it is still required.
           (add-before 'install 'writable-compiler
             (lambda _ (make-file-writable "regions/_compiler.c")))
-          (add-before 'check 'prepare-test-environment
+          (add-before 'check 'build-extensions
             (lambda _
-              (setenv "HOME" "/tmp")
-              (make-file-writable "regions/_compiler.c")
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (propagated-inputs
      (list python-astropy
@@ -2698,7 +2705,7 @@ (define-public python-regions
            python-scipy
            python-shapely))
     (native-inputs
-     (list python-cython
+     (list python-cython-3
            python-extension-helpers
            python-pytest-arraydiff
            python-pytest-astropy
-- 
2.41.0

[bug#70489] [PATCH 36/47] gnu: python-roman-datamodels: Update to 0.19.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-roman-datamodels): Update to 0.19.1.
[propagated-inputs]: Remove python-asdf-standard.

Change-Id: I30e2adef137bb95f37dd7651ebf8c5e6f9e6155f
---
 gnu/packages/astronomy.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index fe1bc54157..14520b0596 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4971,13 +4971,13 @@ (define-public python-radiospectra
 (define-public python-roman-datamodels
   (package
     (name "python-roman-datamodels")
-    (version "0.19.0")
+    (version "0.19.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "roman_datamodels" version))
               (sha256
                (base32
-                "1ym06rj637fq9gxncdrn3phplk5djrzdwqghszis0di1dvsrif4j"))))
+                "1fp9rwzm5kzm0hjwwmlx7kym7yriyhxbfg2zr3y625pyvwpnl0a8"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -4990,7 +4990,6 @@ (define-public python-roman-datamodels
               (setenv "HOME" "/tmp"))))))
     (propagated-inputs (list python-asdf
                              python-asdf-astropy
-                             python-asdf-standard
                              python-astropy
                              python-gwcs
                              python-numpy
-- 
2.41.0

[bug#70489] [PATCH 37/47] gnu: python-casa-formats-io: Update to 0.3.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-casa-formats-io): Update to 0.3.0.

Change-Id: I3f8ca4c981ac31cc955d374b4e4735e53af4c868
---
 gnu/packages/astronomy.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 14520b0596..c5243dc6e9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1973,7 +1973,7 @@ (define-public python-bayesicfitting
 (define-public python-casa-formats-io
   (package
     (name "python-casa-formats-io")
-    (version "0.2.2")
+    (version "0.3.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "casa-formats-io" version))
-- 
2.41.0

[bug#70489] [PATCH 38/47] gnu: python-specutils: Update to 1.14.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-specutils): Update to 1.14.0.

Change-Id: Ied7078bc28d7b995574fb228797f1d046ea52feb
---
 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 c5243dc6e9..ab5ea7394e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3070,13 +3070,13 @@ (define-public python-spectral-cube
 (define-public python-specutils
   (package
     (name "python-specutils")
-    (version "1.13.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "specutils" version))
        (sha256
-        (base32 "0cfsigvsa0i7z2nq9ci9gxccp074kqsgr01xi2npk8xf7cjisrfq"))))
+        (base32 "06l0k8hi4hbfs825cnw948nnkl627g3w48n2pf9rspbvd3vbs2qf"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 39/47] gnu: python-photutils: Update to 1.12.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-photutils): Update to 1.12.
[arguments]: <#:phases>: Add 'create-setup.py phase.

Change-Id: I94908eda0eb7741cb23d2d4dc969c91cdbd08fa2
---
 gnu/packages/astronomy.scm | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ab5ea7394e..dd5864a582 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2426,13 +2426,15 @@ (define-public python-ndcube
 (define-public python-photutils
   (package
     (name "python-photutils")
-    (version "1.10.0")
+    ;; PyPI version for source archive is missing minor 0, See
+    ;; <https://github.com/astropy/photutils/issues/1727>
+    (version "1.12")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "photutils" version))
        (sha256
-        (base32 "148zhdxhlcgj6dxyzaz78bzxw1q44qa9q9sfdqbfbla0s0w2jaay"))))
+        (base32 "0y4kcj6qjnzwjswc0c2iimh11b0jz6b9ianbh58w4gnb4y71lr6r"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2440,6 +2442,16 @@ (define-public python-photutils
       #~(list "-n" "auto")
       #:phases
       #~(modify-phases %standard-phases
+          ;; setup.py was removed in 36c3231ce5b80ad470fa78be2e96df859d2daf41
+          ;; for some unknown reason, which caused the package to fail to
+          ;; build. It is being recreated based on that commit.
+          (add-after 'unpack 'create-setup.py
+            (lambda _
+              (call-with-output-file "setup.py"
+                (lambda (port)
+                  (format port "from setuptools import setup
+from extension_helpers import get_extensions
+setup(ext_modules=get_extensions())")))))
           ;; This file is opened in both install and check phases.
           (add-before 'install 'writable-compiler
             (lambda _ (make-file-writable "photutils/_compiler.c")))
-- 
2.41.0

[bug#70489] [PATCH 40/47] gnu: python-reproject: Update to 0.13.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-reproject): Update to 0.13.1.
[arguments]: <#:phases>: Add 'create-setup.py phase.
[native-inputs]: Remove python-cython; add python-cython-3.

Change-Id: I77845fa1a9748901bc08235ba95060d39b64e467
---
 gnu/packages/astronomy.scm | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index dd5864a582..32c70b9bdf 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2732,13 +2732,13 @@ (define-public python-regions
 (define-public python-reproject
   (package
     (name "python-reproject")
-    (version "0.13.0")
+    (version "0.13.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "reproject" version))
        (sha256
-        (base32 "1qkjbx8xsawhi1gjzqimais3crvkwgbzy1pr51x6anjjln88rgll"))))
+        (base32 "1xk809h2j3zj37l5lx4l87zanf9zxbxajcrff2b2f2i0jpnmxqv3"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2754,6 +2754,17 @@ (define-public python-reproject
       #:tests? #f
       #:phases
       #~(modify-phases %standard-phases
+          ;; setup.py was removed in a659a260bdd7635cddc8f33c4ea04a3b6d8c1f84
+          ;; for some unknown reason, which caused the package to fail to
+          ;; build. It is being recreated based on that commit.
+          ;; TODO: Check how to implement it in python-build-system.
+          (add-after 'unpack 'create-setup.py
+            (lambda _
+              (call-with-output-file "setup.py"
+                (lambda (port)
+                  (format port "from setuptools import setup
+from extension_helpers import get_extensions
+setup(ext_modules=get_extensions())")))))
           (add-before 'install 'writable-compiler
             (lambda _
               (make-file-writable "reproject/_compiler.c")))
@@ -2778,7 +2789,7 @@ (define-public python-reproject
            python-shapely
            python-zarr))
     (native-inputs
-     (list python-cython
+     (list python-cython-3
            python-extension-helpers
            python-pytest-astropy
            python-semantic-version
-- 
2.41.0

[bug#70489] [PATCH 41/47] gnu: python-reproject: Enable tests.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-reproject): Enable tests.
[arguments]: <#:tests-flags>: Add them as seen in tox.ini.
<#:phases>: Rename 'writable-home to 'prepare-test-environment to reflect
purpose and build extension before tests.
[native-inputs]: Add python-xdist.

Change-Id: I7a5454e3ce241b7a54626f8aba27602b4965c25b
---
 gnu/packages/astronomy.scm | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 32c70b9bdf..58bf607059 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2742,16 +2742,11 @@ (define-public python-reproject
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; FIXME: Failing tests
-      ;;
-      ;; reproject/adaptive/core.py:7: in <module>
-      ;; from .deforest import map_coordinates
-      ;; E   ModuleNotFoundError: No module named 'reproject.adaptive.deforest'
-      ;;
-      ;; Project removed setup.py and there is no alternative to `python
-      ;; setup.py build_ext'
-      ;; See: https://github.com/pypa/setuptools/discussions/3388
-      #:tests? #f
+      #:test-flags
+      #~(list "--arraydiff"
+              "--arraydiff-default-format=fits"
+              "--numprocesses" "auto"
+              "--pyargs" "reproject")
       #:phases
       #~(modify-phases %standard-phases
           ;; setup.py was removed in a659a260bdd7635cddc8f33c4ea04a3b6d8c1f84
@@ -2771,9 +2766,11 @@ (define-public python-reproject
           (add-before 'check 'writable-compiler
             (lambda _
               (make-file-writable "reproject/_compiler.c")))
-          (add-before 'check 'writable-home
+          (add-before 'check 'prepare-test-environment
             (lambda _
-              (setenv "HOME" (getcwd)))))))
+              (setenv "HOME" "/tmp")
+              ;; Cython extensions have to be built before running the tests.
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (propagated-inputs
      (list python-asdf
            python-astropy
@@ -2791,9 +2788,11 @@ (define-public python-reproject
     (native-inputs
      (list python-cython-3
            python-extension-helpers
+           python-pytest
            python-pytest-astropy
+           python-pytest-xdist
+           ;; python-sunpy ; circular dependencies, test optional
            python-semantic-version
-           python-pytest
            python-setuptools-scm))
     (home-page "https://reproject.readthedocs.io")
     (synopsis "Astronomical image reprojection in Python")
-- 
2.41.0

[bug#70489] [PATCH 42/47] gnu: python-asdf: Adjust inputs.

[Sharlatan Hellseher]

python-asdf requires python-semantic-version during runtime which may be
reproduced by:

   guix shell python-asdf python -- python3 -c 'import asdf'
   <...>
   ModuleNotFoundError: No module named 'semantic_version'

* gnu/packages/astronomy.scm (python-asdf): Adjust inputs.
[native-inputs]: Remove python-semantic-version.
[propagated-inputs]: Add python-semantic-version.

(python-asdf-astropy, python-asdf-compression, python-asdf-coordinates-schemas,
python-asdf-wcs-schemas, python-asdf-zarr, python-astroalignn, python-ccdproc,
python-crds, python-ginga, python-gwcs, python-photutils, python-rad,
python-reproject, python-roman-datamodels, python-spectral-cube,
python-specutils, python-stcal, python-stdatamodels, python-stpipe,
python-stsynphot, python-sunpy, python-synphot, python-tweakwcs): Remove
python-semantic-version from native or propagated inputs.

Change-Id: I96bf57f77c327f4ff208e0b173e84bcdd4c287da
Reported-by: Iliya Tikhonenko <tikhonenko@mpe.mpg.de>
---
 gnu/packages/astronomy.scm | 41 +++++++++-----------------------------
 1 file changed, 9 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 58bf607059..5cb62466cb 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -522,8 +522,7 @@ (define-public python-aplpy
            python-shapely))
     (native-inputs
      (list python-pytest-astropy
-           python-pytest-mpl
-           python-semantic-version))
+           python-pytest-mpl))
     (home-page "http://aplpy.github.io")
     (synopsis "Astronomical Plotting Library in Python")
     (description
@@ -753,7 +752,6 @@ (define-public python-ginga
            python-docutils
            python-pytest-astropy
            python-pytest-astropy-header
-           python-semantic-version
            python-tornado))
     (home-page "https://ejeschke.github.io/ginga/")
     (synopsis "Scientific image viewer and toolkit for FITS files")
@@ -2014,8 +2012,7 @@ (define-public python-ccdproc
     (build-system pyproject-build-system)
     (native-inputs
      (list python-memory-profiler
-           python-pytest-astropy
-           python-semantic-version))
+           python-pytest-astropy))
     (propagated-inputs
      (list python-astropy
            python-astroscrappy
@@ -2138,7 +2135,6 @@ (define-public python-crds
                          python-nose
                          python-pylint
                          python-pytest
-                         python-semantic-version
                          python-setuptools-scm))
     (home-page "https://hst-crds.stsci.edu")
     (synopsis "Calibration Reference Data System for HST and JWST")
@@ -2481,7 +2477,6 @@ (define-public python-photutils
            python-extension-helpers
            python-pytest-astropy
            python-pytest-xdist
-           python-semantic-version
            python-setuptools-scm))
     (home-page "https://github.com/astropy/photutils")
     (synopsis "Source detection and photometry")
@@ -2792,7 +2787,6 @@ (define-public python-reproject
            python-pytest-astropy
            python-pytest-xdist
            ;; python-sunpy ; circular dependencies, test optional
-           python-semantic-version
            python-setuptools-scm))
     (home-page "https://reproject.readthedocs.io")
     (synopsis "Astronomical image reprojection in Python")
@@ -2909,7 +2903,6 @@ (define-public python-sunpy
            python-reproject
            python-scikit-image
            python-scipy
-           python-semantic-version
            ;; python-spiceypy ; Not packed yet in Guix, long jorney.
            python-sqlalchemy
            python-tqdm
@@ -3069,7 +3062,6 @@ (define-public python-spectral-cube
            python-pytest-astropy
            python-pytest-xdist
            python-regions
-           python-semantic-version
            python-setuptools-scm))
     (home-page "https://spectral-cube.readthedocs.io/en/latest/")
     (synopsis "Library for reading and analyzing astrophysical spectral data cubes")
@@ -3124,7 +3116,6 @@ (define-public python-specutils
     (native-inputs
      (list python-matplotlib
            python-pytest-astropy
-           python-semantic-version
            python-setuptools-scm
            python-spectral-cube))
     (home-page "https://specutils.readthedocs.io/")
@@ -3322,7 +3313,6 @@ (define-public python-stcal
            python-pytest
            python-pytest-cov
            python-pytest-doctestplus
-           python-semantic-version
            python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/stcal")
     (synopsis "STScI tools and algorithms used in calibration pipelines")
@@ -3364,7 +3354,6 @@ (define-public python-stdatamodels
            python-pytest-doctestplus
            python-pytest-xdist
            python-scipy
-           python-semantic-version
            python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/stdatamodels")
     (synopsis
@@ -3390,8 +3379,8 @@ (define-public python-stpipe
       ;; See https://github.com/spacetelescope/stpipe/issues/114
       #:test-flags #~(list "-k" "not test_roman_datamodel")))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-asdf python-astropy python-crds
-                             python-semantic-version python-stdatamodels))
+    (propagated-inputs
+     (list python-asdf python-astropy python-crds python-stdatamodels))
     (native-inputs (list python-pytest python-pytest-doctestplus
                          python-pytest-openfiles python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/stpipe")
@@ -3429,7 +3418,6 @@ (define-public python-stsynphot
     (native-inputs (list python-pytest
                          python-pytest-astropy
                          python-pytest-astropy-header
-                         python-semantic-version
                          python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/stsynphot_refactor")
     (synopsis "Synthetic photometry using Astropy for HST and JWST")
@@ -4423,7 +4411,6 @@ (define-public python-synphot
     (native-inputs
      (list python-pytest
            python-pytest-astropy
-           python-semantic-version
            python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/synphot_refactor")
     (synopsis "Synthetic photometry using Astropy")
@@ -4457,7 +4444,6 @@ (define-public python-tweakwcs
            python-pytest
            python-pytest-cov
            python-scipy
-           python-semantic-version
            python-setuptools-scm))
     (home-page "https://tweakwcs.readthedocs.io/en/latest/")
     (synopsis
@@ -4503,7 +4489,6 @@ (define-public python-asdf
            python-pytest-doctestplus
            python-pytest-remotedata
            python-pytest-xdist
-           python-semantic-version
            python-setuptools-scm))
     (propagated-inputs
      (list python-asdf-standard
@@ -4513,7 +4498,8 @@ (define-public python-asdf
            python-jmespath
            python-lz4
            python-numpy
-           python-pyyaml))
+           python-pyyaml
+           python-semantic-version))
     (home-page "https://github.com/asdf-format/asdf")
     (synopsis "Python tools to handle ASDF files")
     (description
@@ -4549,7 +4535,6 @@ (define-public python-asdf-compression
       (native-inputs
        (list python-numpy
              python-pytest
-             python-semantic-version
              python-setuptools-scm))
       (propagated-inputs
        (list python-asdf
@@ -4648,7 +4633,6 @@ (define python-asdf-coordinates-schemas
     (native-inputs
      (list python-pytest
            python-pytest-xdist
-           python-semantic-version
            python-setuptools-scm))
     (propagated-inputs
      (list python-asdf))
@@ -4767,7 +4751,7 @@ (define-public python-asdf-zarr
     (propagated-inputs
      (list python-asdf python-fsspec python-zarr))
     (native-inputs
-     (list python-pytest python-semantic-version python-setuptools-scm))
+     (list python-pytest python-setuptools-scm))
     (home-page "https://github.com/asdf-format/asdf-zarr")
     (synopsis "Asdf extension to support Zarr arrays")
     (description
@@ -4802,7 +4786,6 @@ (define-public python-asdf-astropy
            python-pandas
            python-pytest-astropy
            python-scipy
-           python-semantic-version
            python-setuptools-scm))
     (propagated-inputs
      (list python-asdf
@@ -4836,7 +4819,6 @@ (define python-asdf-wcs-schemas
      (list python-asdf
            python-pytest
            python-pytest-openfiles
-           python-semantic-version
            python-setuptools-scm))
     (propagated-inputs
      (list python-asdf-coordinates-schemas
@@ -4867,7 +4849,6 @@ (define-public python-gwcs
            python-pytest
            python-pytest-doctestplus
            python-pyyaml
-           python-semantic-version
            python-setuptools-scm))
     (propagated-inputs
      (list python-asdf
@@ -4905,9 +4886,7 @@ (define-public python-rad
       ;; python-rad -> python-roman-datamodels -> python-crds -> python-rad
       #:test-flags #~(list "--ignore=tests/test_schemas.py")))
     (native-inputs
-     (list python-pytest
-           python-semantic-version
-           python-setuptools-scm))
+     (list python-pytest python-setuptools-scm))
     (propagated-inputs (list python-asdf python-asdf-astropy))
     (home-page "https://github.com/spacetelescope/rad")
     (synopsis "Roman Attribute Dictionary")
@@ -5021,7 +5000,6 @@ (define-public python-roman-datamodels
                          python-pytest-doctestplus
                          python-pytest-env
                          python-pytest-xdist
-                         python-semantic-version
                          python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/roman_datamodels")
     (synopsis "Roman Datamodels Support")
@@ -5055,8 +5033,7 @@ (define-public python-astroalign
      (list python-astropy
            python-ccdproc
            python-pillow
-           python-pytest
-           python-semantic-version))
+           python-pytest))
     (propagated-inputs
      (list python-bottleneck
            python-numpy
-- 
2.41.0

[bug#70489] [PATCH 43/47] gnu: python-crds: Update to 11.17.20.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-crds): Update to 11.17.20.

Change-Id: I426241c2e216b0261787117a10ceab36197dff12
---
 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 5cb62466cb..ee9a35fbc9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2104,13 +2104,13 @@ (define-public python-cmyt
 (define-public python-crds
   (package
     (name "python-crds")
-    (version "11.17.19")
+    (version "11.17.20")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "crds" version))
               (sha256
                (base32
-                "1x48yw6jnz7dw0myc86ds0qaki6v1anqaihd5qzrxwrrl61kyp6x"))))
+                "0480jjklv2p60fp892dr4qglwv44k86hx29y8q1c967l9k53wc9f"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 44/47] gnu: python-stsci-stimage: Update to 0.2.8.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stsci-stimage): Update to 0.2.8.

Change-Id: Ib2f8b9544bc732959d87527d2c55f274dab4393b
---
 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 ee9a35fbc9..b4a82f6353 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3242,13 +3242,13 @@ (define-public python-stsci-imagestats
 (define-public python-stsci-stimage
   (package
     (name "python-stsci-stimage")
-    (version "0.2.6")
+    (version "0.2.8")
     (source (origin
               (method url-fetch)
-              (uri (pypi-uri "stsci.stimage" version))
+              (uri (pypi-uri "stsci_stimage" version))
               (sha256
                (base32
-                "0i7xby1gaiplvbqqv8a4f4cw1is8fwj89mix1z3bqrykqi3n24g0"))))
+                "0p188my6djy65a8j6qsc3v0dpr2svqqv90n0pxxzy52vdjiz3w0w"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#70489] [PATCH 45/47] gnu: python-stsci-stimage: Adjust test steps.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stsci-stimage):
[arguments]: <#:test-flags>: Add them. <#:phases>: Fail over to default
'check phase and add 'waf-configure-build phase before check.
[native-inputs]: Remove python-codecov and, python-pytest-cov.
[description]: Fix indentation.

Change-Id: I350c4ced2cb4afaff72d4d4941d198932cd888f5
---
 gnu/packages/astronomy.scm | 29 +++++++++++++++--------------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b4a82f6353..9d82bd4c89 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3242,6 +3242,8 @@ (define-public python-stsci-imagestats
 (define-public python-stsci-stimage
   (package
     (name "python-stsci-stimage")
+    ;; PyPI version was 0.2.8 but the latest version tag on GiHub was 0.2.7,
+    ;; see <https://github.com/spacetelescope/stsci.stimage/issues/38>
     (version "0.2.8")
     (source (origin
               (method url-fetch)
@@ -3252,27 +3254,26 @@ (define-public python-stsci-stimage
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags #~(list "test_c")
       #:phases
       #~(modify-phases %standard-phases
-          ;; Test steps are taken from GitHub Actions.
-          ;; See https://github.com/spacetelescope/stsci.stimage/issues/27
-          (replace 'check
+          ;; Test steps are taken from GitHub Actions, see
+          ;; <https://github.com/spacetelescope/stsci.stimage/issues/27>
+          (add-before 'check 'waf-configure-build
             (lambda _
               (copy-file (string-append
-                #$(this-package-native-input "python-waf") "/bin/waf")
-               "waf")
-              (invoke "python" "waf" "configure" "build" "do_tests"))))))
-    (propagated-inputs (list python-numpy))
+                          #$(this-package-native-input "python-waf") "/bin/waf")
+                         "waf")
+              (invoke "python" "waf" "configure" "build"))))))
+    (propagated-inputs
+     (list python-numpy))
     (native-inputs
-     (list python-codecov
-           python-pytest
-           python-pytest-cov
-           python-setuptools-scm
-           python-waf))
+     (list python-pytest python-setuptools-scm python-waf))
     (home-page "https://stscistimage.readthedocs.io/en/latest/")
     (synopsis "STScI image processing")
-    (description "This package provides an astronomical Python package with
-image processing functions: @code{xyxymatch}, @code{geomap}.")
+    (description
+     "This package provides an astronomical Python package with image
+processing functions: @code{xyxymatch}, @code{geomap}.")
     (license license:bsd-3)))
 
 (define-public python-stcal
-- 
2.41.0

[bug#70489] [PATCH 46/47] gnu: Add scamp.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (scamp): New variable.

Change-Id: If32adb281017858b0e7d5816cecb509af3cec835
---
 gnu/packages/astronomy.scm | 80 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9d82bd4c89..a9e0583f39 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -69,6 +69,7 @@ (define-module (gnu packages astronomy)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages photo)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages plotutils)
   #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
@@ -3771,6 +3772,85 @@ (define-public gpredict
 @end itemize")
     (license license:gpl2+)))
 
+(define-public scamp
+  (package
+    (name "scamp")
+    (version "2.10.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/astromatic/scamp")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0qic52mzw9avf1a1fsr85mlh63b7hq6d4wj2d00zgdllmclj5l9q"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "CPPFLAGS=-fcommon"
+              "--enable-openblas"
+              "--enable-plplot"
+              (string-append "--with-curl-incdir="
+                             #$(this-package-input "curl") "/include")
+              (string-append "--with-curl-libdir="
+                             #$(this-package-input "curl") "/lib")
+              (string-append "--with-fftw-incdir="
+                             #$(this-package-input "fftwf") "/include")
+              (string-append "--with-fftw-libdir="
+                             #$(this-package-input "fftwf") "/lib")
+              (string-append "--with-openblas-incdir="
+                             #$(this-package-input "openblas") "/include")
+              (string-append "--with-openblas-libdir="
+                             #$(this-package-input "openblas") "/lib")
+              (string-append "--with-plplot-incdir="
+                             #$(this-package-input "plplot") "/include")
+              (string-append "--with-plplot-libdir="
+                             #$(this-package-input "plplot") "/lib"))))
+    (native-inputs
+     (list autoconf
+           automake
+           libtool
+           pkg-config
+           python-astropy
+           python-numpy
+           python-wrapper))
+    (inputs
+     (list curl fftwf openblas plplot))
+    (home-page "https://www.astromatic.net/software/scamp/")
+    (synopsis "Compute astrometric solutions")
+    (description
+     "@acronym{Software for Calibrating AstroMetry and Photometry,SCAMP} is a
+software that computes astrometric projection parameters from source catalogues
+derived from @url{http://fits.gsfc.nasa.gov/,FITS} images.  The computed solution
+is expressed according to the
+@url{http://www.atnf.csiro.au/people/mcalabre/WCS/index.html,WCS} standard.  The
+main features of SCAMP are:
+
+@itemize
+@item compatibility with @code{SExtractor} FITS or Multi-Extension FITS
+catalogue format in input
+@item generation of WCS-compliant and @code{SWarp}-compatible FITS image headers
+in output
+@item automatic grouping of catalogues on the sky
+@item selectable on-line astrometric reference catalogue
+@item automatic determination of scale, position angle, flipping and coordinate
+shift using fast pattern-matching
+@item various astrometric calibration modes for single detectors and detector
+arrays
+@item combined astrometric solutions for multi-channel/instrument surveys
+@item highly configurable astrometric distortion polynomials
+@item correction for differential chromatic refraction
+@item proper motion measurements
+@item multi-threaded code that takes advantage of multiple processors
+@item @url{http://www.ivoa.net/documents/VOTable,VOTable}-compliant XML output
+of meta-data
+@item @url{http://en.wikipedia.org/wiki/XSLT,XSLT} filter sheet provided for
+convenient access to metadata from a regular web browser
+@end itemize")
+    (license license:gpl3+)))
+
 (define-public sgp4
   ;; Version tag v1.0 is dated to <2021-01-11>, use the lates commit instead.
   (let ((commit "6a448b4850e5fbf8c1ca03bb5f6013a9fdc1fd91")
-- 
2.41.0

[bug#70489] [PATCH 47/47] gnu: Add psfex.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (psfex): New variable.

Change-Id: I073df933b244811cd09343ea4951f481ad76b075
---
 gnu/packages/astronomy.scm | 45 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a9e0583f39..2afcee9aa0 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1131,6 +1131,51 @@ (define-public phd2
 from Stark Labs.")
     (license license:bsd-3)))
 
+(define-public psfex
+  (package
+    (name "psfex")
+    (version "3.24.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/astromatic/psfex")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0ykgzyxnxjxqk6b8jng006wjilg4fqaxclpfn8plg6brk1qf39sn"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "CPPFLAGS=-fcommon"
+              "--enable-openblas"
+              "--enable-plplot"
+              (string-append "--with-fftw-libdir="
+                             #$(this-package-input "fftw") "/lib")
+              (string-append "--with-fftw-incdir="
+                             #$(this-package-input "fftw") "/include")
+              (string-append "--with-openblas-libdir="
+                             #$(this-package-input "openblas") "/lib")
+              (string-append "--with-openblas-incdir="
+                             #$(this-package-input "openblas") "/include")
+              (string-append "--with-plplot-libdir="
+                             #$(this-package-input "plplot") "/lib")
+              (string-append "--with-plplot-incdir="
+                             #$(this-package-input "plplot") "/include"))))
+    (native-inputs
+     (list autoconf automake libtool pkg-config))
+    (inputs
+     (list openblas fftw fftwf plplot))
+    (home-page "https://www.astromatic.net/software/psfex/")
+    (synopsis "Astronomical PSF modelling and quality assessment")
+    (description
+     "@acronym{PSFEx, PSF Extractor} extracts models of the @acronym{PSF,
+Point Spread Function} from FITS images processed with SExtractor, and
+measures the quality of images.  The generated PSF models can be used for
+model-fitting photometry or morphological analyses.")
+    (license license:gpl3+)))
+
 (define-public sextractor
   (package
     (name "sextractor")
-- 
2.41.0

bug#70489: [PATCH 00/47] Astronomy 2024/04 updates.

[Sharlatan Hellseher]

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Pushed as 3067eb8d60..147f1f2e0d to master.

--
Oleg

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[bug#70489] [PATCH 00/47] Astronomy 2024/04 updates.

[Leo Famulari]

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On Wed, May 01, 2024 at 08:06:30AM +0100, Sharlatan Hellseher wrote:
> 
> Pushed as 3067eb8d60..147f1f2e0d to master.

Thanks for all the astronomy packages! Great fun in there

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