[bug#69924] [PATCH 00/49] gnu: Astronomy 2024/02 updates.

[bug#69924] [PATCH 00/49] gnu: Astronomy 2024/02 updates.

[Sharlatan Hellseher]

Hi Guix!

I'm glad to provide patch series for Astronomy 2024/03 updates.

This month includes 29 updates, 5 tests speed up (about 6x times faster), 8
new packages and a few minor modifications.

The series places a basement for including python-yt [1] of v4.2.2. The latest
version requires Cython>=3.0.3 which is not available in Guix yet.

I need to update python-more-itertools to v10.2.0 in python-team branch to
pass the build of python-yt A task for the next cycle as it's update involves
1242 packages to be rebuilt.

- [1] https://yt-project.org/ a package for analyzing and visualizing volumetric data,

Build stats:

--8<---------------cut here---------------start------------->8---
> ./pre-inst-env guix build calcmysky python-asdf python-asdf-astropy
  python-asdf-compression python-asdf-standard python-asdf-zarr python-astroplan
  python-astropy-iers-data python-astroquery python-blosc python-cdflib
  python-cmyt python-crds python-dask python-distributed python-drizzle
  python-ewah-bool-utils python-ginga python-glymur python-gwcs python-hvpy
  python-nose-exclude python-partd python-pydantic-settings python-pynbody
  python-pytest-arraydiff python-pytest-doctestplus python-pytest-examples
  python-pytest-filter-subpackage python-pyvo python-radiospectra
  python-specutils python-stcal python-stdatamodels python-suntime python-zarr
  splash

/gnu/store/6csb9rkf12hg37xmixvq3p6hr3pv4zzz-splash-3.10.3
/gnu/store/gak55qj3zvh4nfvdpvj91ryk0ffrxnzn-python-zarr-2.17.1
/gnu/store/l3iqzifgrp4ikvdf6pj1vsdjyphs1pc9-python-suntime-1.3.2
/gnu/store/yyydzq9ps0x0lyzqxx1xniq937fn4qb3-python-stdatamodels-1.10.0
/gnu/store/dg2j6y6jsckysp6jp94nqdsqcvw5vigl-python-stcal-1.6.1
/gnu/store/jcyryp4rf9fssnmsq3s2fh1qn05x2ipq-python-specutils-1.13.0
/gnu/store/fg9m0fpr18jmvzp6qwbcccdi56y8y9dn-python-radiospectra-0.5.0
/gnu/store/d29ds5w5kzvrdhq5gwz49nmpx0752v84-python-pyvo-1.5.1
/gnu/store/izs8bd415wpsr8b7fmnfgz0pyq930zyn-python-pytest-filter-subpackage-0.2.0
/gnu/store/592dd7z9m1q24gh0vmc6g3sfdxlddwri-python-pytest-examples-0.0.10
/gnu/store/lsa16h2zm9rl0wpr7p9da5f9b16fm4mr-python-pytest-doctestplus-1.2.0
/gnu/store/mh5mlvngjbc0lgpdhvkfcf22gykhrjp9-python-pytest-arraydiff-0.6.1
/gnu/store/j7iz6vrz67yhmzq4i9999zj1smj89kfh-python-pynbody-1.6.0
/gnu/store/5rvjai98yph38mr9hzr5cj36b4lnqcg6-python-pydantic-settings-2.2.1
/gnu/store/5m37mism260hij6mx9z4b606vz22dkfb-python-partd-1.2.0
/gnu/store/8arvnd7nswgswr4j45wfpi61791myh54-python-nose-exclude-0.5.0
/gnu/store/mhqpljvcdkhsdihqx590m967ykyj2ry6-python-hvpy-1.1.0
/gnu/store/s6x5svi7kdq296cssxwqcnhgzpxf7gy2-python-gwcs-0.21.0
/gnu/store/y0fx7jjqlmmhjhiar06nrvwgmggiam32-python-glymur-0.12.9
/gnu/store/nhc1m5ll94nncc60yl5wrxfmhf0fjmmp-python-ginga-5.0.0
/gnu/store/wcqa4viszn1f9rk4xh63w2f8l0nrwbrv-python-ewah-bool-utils-1.1.0
/gnu/store/b8c8s98kz1mql5ycpilv4pbf7b2xa2cj-python-drizzle-1.15.1
/gnu/store/zj3ikp853mlpnbbhsqlfk2ynrkbdbqa1-python-distributed-2023.7.0
/gnu/store/q6x1r63hqm4jd7nj4pwcsk1j8l7hfji9-python-dask-2023.7.0
/gnu/store/p6zqpa4nr6h37yaqvgjprwviay8g231c-python-crds-11.17.19
/gnu/store/pi5zpgnmx3kn2i0j4fgzdi0lm26v8gxq-python-cmyt-2.0.0
/gnu/store/s8jyypyjfhgv4f7jhzqkqq5srwln6hws-python-cdflib-1.2.6
/gnu/store/xvnzkccd0rliyindkmkqff31ba5aq75v-python-blosc-1.11.1
/gnu/store/x57ig7ja2r1q89a09ii7x9hcqhja0dwv-python-astroquery-0.4.7
/gnu/store/kq2wsj7lh5z164k6j1hi16138l010ip4-python-astropy-iers-data-0.2024.3.18.0.29.47
/gnu/store/piyaqjshcy1cs20binbaihn7fn9japz9-python-astroplan-0.9.1
/gnu/store/nazqcp2ijcr1vcbp6ww57wgx43dvvjxk-python-asdf-zarr-0.0.3
/gnu/store/593r1pgvqrbc25w19fggzl9raxj8lmdx-python-asdf-standard-1.1.1
/gnu/store/alk4siv7wcg6kckw8zb87njz1gbngfnx-python-asdf-compression-0.0.1-0.57cc7e7
/gnu/store/j137q7b6s53gwfajs21srdfwcqp06w61-python-asdf-astropy-0.6.0
/gnu/store/3ldncii2czhqnhwbirgnavangidfz17j-python-asdf-3.1.0
/gnu/store/pmxrw3xviiinyqii8wdvqb74jnli1bqj-calcmysky-0.3.2
--8<---------------cut here---------------end--------------->8---

Dependent build stats:

--8<---------------cut here---------------start------------->8---
> ./pre-inst-env guix refresh --list-dependent calcmysky python-asdf
  python-asdf-astropy python-asdf-compression python-asdf-standard
  python-asdf-zarr python-astroplan python-astropy-iers-data python-astroquery
  python-blosc python-cdflib python-cmyt python-crds python-dask
  python-distributed python-drizzle python-ewah-bool-utils python-ginga
  python-glymur python-gwcs python-hvpy python-nose-exclude python-partd
  python-pydantic-settings python-pynbody python-pytest-arraydiff
  python-pytest-doctestplus python-pytest-examples
  python-pytest-filter-subpackage python-pyvo python-radiospectra
  python-specutils python-stcal python-stdatamodels python-suntime python-zarr
  splash

  Building the following 34 packages would ensure 116 dependent packages are
  rebuilt: python-hicexplorer@3.7.2 python-vaex-core@4.13.0
  python-pandera@0.17.2  python-bulkvis@2.0.0-2.00a82a9
  python-fanc@0.9.25 python-cooltools@0.5.1 synapse@1.29.0
  python-sparse@0.14.0 python-pytorch-geometric@2.4.0
  python-asdf-compression@0.0.1-0.57cc7e7 python-cesium@0.12.1
  python-poliastro@0.17.0 python-astroplan@0.9.1 python-ginga@5.0.0
  ginga-qt5@5.0.0 python-asdf-zarr@0.0.3 python-aplpy@2.1.0
  python-radiospectra@0.5.0 python-astroalign@2.5.1 python-jwst@1.13.4
  python-scikit-allel@1.3.5 python-cellbender@0.2.2 python-baltica@1.1.2
  python-demuxem@0.1.7 python-biom-format@2.1.12
  r-doubletcollection@1.1.0-1.c0d62f1 python-episcanpy@0.4.0
  python-multivelo@0.1.2 scregseg@0.1.3 python-ikarus@0.0.2
  python-liana-py@0.1.9 python-magic-impute@1.2.1

/gnu/store/kyqv6dra2x1w8ncv92ag56l79j0zana1-python-magic-impute-1.2.1
/gnu/store/86ir5mvssrpalq60sixqijs20qrr35i6-python-liana-py-0.1.9
/gnu/store/s8pr25467absf8xlg5mcbg2w7grhp0ng-python-ikarus-0.0.2
/gnu/store/maqx4c8y1mcpk5pqyhxycz5kjnr89fnb-scregseg-0.1.3
/gnu/store/3s67w1qg8xvqwq5iz85iiv6n766zjvhs-python-multivelo-0.1.2
/gnu/store/ygr013m84b5dihrdn38im32mgvw6xc8a-python-episcanpy-0.4.0
/gnu/store/narpps8awwgj0qi9x1b3h1sgi5gyk0p3-r-doubletcollection-1.1.0-1.c0d62f1
/gnu/store/673rvspqqc9pkdwha6n8szj0qgn6xp17-python-biom-format-2.1.12
/gnu/store/frhk1isndiszv70i6di2byfac90clgd4-python-demuxem-0.1.7
/gnu/store/yfjx9a00yspk5hyjdh79cdll4r424dzk-python-baltica-1.1.2
/gnu/store/d2spq6v9502v024q87q29dyhllsl6g02-python-cellbender-0.2.2
/gnu/store/m35jyyv0xnzbd0g7d69n4m9d7rxi2i8a-python-scikit-allel-1.3.5
/gnu/store/7hb7qb80rkkh07z5sl1pv1da3sd8920j-python-jwst-1.13.4
/gnu/store/hdqizxxn62kiad6p3iwxn32822nl97vm-python-astroalign-2.5.1
/gnu/store/fg9m0fpr18jmvzp6qwbcccdi56y8y9dn-python-radiospectra-0.5.0
/gnu/store/s92a8cl536bf6xxxya2x1lgddjjk0cm5-python-aplpy-2.1.0
/gnu/store/nazqcp2ijcr1vcbp6ww57wgx43dvvjxk-python-asdf-zarr-0.0.3
/gnu/store/d9d2l3iy8wqy860ffwsiig6qlnb10g30-ginga-qt5-5.0.0
/gnu/store/nhc1m5ll94nncc60yl5wrxfmhf0fjmmp-python-ginga-5.0.0
/gnu/store/piyaqjshcy1cs20binbaihn7fn9japz9-python-astroplan-0.9.1
/gnu/store/xn1cgf16xv1j8swl2yn0l50vnxdwi3kf-python-poliastro-0.17.0
/gnu/store/7576nwzrn2sbx3y25xsg1salla1pvp1p-python-cesium-0.12.1
/gnu/store/alk4siv7wcg6kckw8zb87njz1gbngfnx-python-asdf-compression-0.0.1-0.57cc7e7
/gnu/store/xfw2f3jigxbw25lk7vmzc2491g1vzhz8-python-pytorch-geometric-2.4.0
/gnu/store/a0x8hl2qv3zf2wzxwkm6007gc4j60xpn-python-sparse-0.14.0
/gnu/store/40nxhi9asixxlda020xrpqbjig01yipc-synapse-1.29.0
/gnu/store/ycw6bhvhymqp1k3qbgxl3rzip656ppcn-python-cooltools-0.5.1
/gnu/store/hz3b1l0ppv4ff8jn8s9l6sgj73wj7wjj-python-fanc-0.9.25
/gnu/store/yza59f62kv1zb3z65i3jbjv313ycd5sm-python-bulkvis-2.0.0-2.00a82a9
/gnu/store/34x56fkcmy38vv19qbmhrm6qqfc0l2r5-python-pandera-0.17.2
/gnu/store/wrdm8iaxc4qwsisyvqdh8pwg5wy1mjdf-python-vaex-core-4.13.0
/gnu/store/akdh7xl7jdq4vvknn06fval7j3h4nfqf-python-hicexplorer-3.7.2
--8<---------------cut here---------------end--------------->8---

Introduced regression in tests:
- fanc@0-1.354401e
- python-modin@0.15.1

Sharlatan Hellseher (49):
  gnu: calcmysky: Update to 0.3.2.
  gnu: splash: Update to 3.10.3.
  gnu: python-blosc: Move to python-compression.
  gnu: python-blosc: Simplify package.
  gnu: python-pytest-doctestplus: Update to 1.2.0.
  gnu: python-pytest-arraydiff: Update to 0.6.1.
  gnu: python-pytest-arraydiff: Enable tests.
  gnu: python-pytest-filter-subpackage: Update to 0.2.0.
  gnu: python-zarr: Update to 2.17.1.
  gnu: python-partd: Enable tests.
  gnu: python-zarr: Speed up tests.
  gnu: python-distributed: Speed up tests.
  gnu: python-dask: Speed up tests.
  gnu: python-stdatamodels: Speed up tests.
  gnu: python-glymur: Speed up tests.
  gnu: python-ginga: Update to 5.0.0.
  gnu: python-astropy-iers-data: Update to 0.2024.3.18.0.29.47.
  gnu: python-cdflib: Update to 1.2.6.
  gnu: python-cdflib: Enable all tests.
  gnu: python-asdf-unit-schemas: Update to 0.2.0.
  gnu: python-asdf-standard: Update to 1.1.1.
  gnu: python-asdf-transform-schemas: Update to 0.5.0.
  gnu: python-asdf: Update to 3.1.0.
  gnu: python-asdf-coordinates-schemas: Update to 0.3.0.
  gnu: python-asdf-wcs-schemas: Update to 0.4.0.
  gnu: python-asdf-astropy: Update to 0.6.0
  gnu: python-pyvo: Update to 1.5.1.
  gnu: python-astroquery: Update to 0.4.7.
  gnu: python-gwcs: Update to 0.21.0.
  gnu: python-drizzle: Update to 1.15.1.
  gnu: python-suntime: Update to 1.3.2.
  gnu: python-suntime: Refresh package style.
  gnu: python-radiospectra: Update to 0.5.0.
  gnu: python-glymur: Update to 0.12.9.
  gnu: python-specutils: Update to 1.13.0.
  gnu: python-stcal: Update to 1.6.1.
  gnu: python-stcal: Enable sanity check.
  gnu: python-stdatamodels: Update to 1.10.0.
  gnu: python-crds: Update to 11.17.19.
  gnu: python-pynbody: Update to 1.6.0.
  gnu: Add python-asdf-zarr.
  gnu: Add python-asdf-compression.
  gnu: Add python-astroplan.
  gnu: Add python-nose-exclude.
  gnu: Add python-ewah-bool-utils.
  gnu: Add python-cmyt.
  gnu: Add python-pytest-examples.
  gnu: Add python-pydantic-settings.
  gnu: python-hvpy: Update to 1.1.0.

 gnu/packages/astronomy.scm          | 403 +++++++++++++++++++++-------
 gnu/packages/check.scm              | 105 +++++++-
 gnu/packages/python-check.scm       |  34 ++-
 gnu/packages/python-compression.scm |  82 +++++-
 gnu/packages/python-science.scm     |  14 +-
 gnu/packages/python-xyz.scm         | 169 +++++++-----
 6 files changed, 621 insertions(+), 186 deletions(-)


base-commit: 66b20dc567ed9801ab55209fc412e4db92d7b0b0
-- 
2.41.0

[bug#69924] [PATCH 01/49] gnu: calcmysky: Update to 0.3.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (calcmysky): Update to 0.3.2.

Change-Id: I27d6c833aba5a5d8d398a6170485d0e62223ca1b
---
 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 d7747f051d..8ae25b65e2 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -223,7 +223,7 @@ (define-public calceph
 (define-public calcmysky
   (package
     (name "calcmysky")
-    (version "0.3.1")
+    (version "0.3.2")
     (source
      (origin
        (method git-fetch)
@@ -232,7 +232,7 @@ (define-public calcmysky
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "14jbaf9m9wig2bs7a531dvpmdkqpd09lmyvjvj1s0mhgh9g0x9m2"))))
+        (base32 "1kybjlddrm8x4x5y82qczi6z1d2riv6zcfjzrh7pzg2vwj89izh0"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags
-- 
2.41.0

[bug#69924] [PATCH 02/49] gnu: splash: Update to 3.10.3.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (splash): Update to 3.10.3.

Change-Id: Ic5f812a3c35fd76c0a722616efea2745a080c859
---
 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 8ae25b65e2..724643d17f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1203,7 +1203,7 @@ (define-public siril
 (define-public splash
   (package
     (name "splash")
-    (version "3.10.1")
+    (version "3.10.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1211,7 +1211,7 @@ (define-public splash
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "1cyg7my2lbpai81nfnlj0r7pvral3kjn31dcq2p4982d2xg0dj87"))
+                "077s9if7fmccvhsbp0dhvyqcil46vpbgdm1y6qn6h34r8lfqj9z6"))
               (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
-- 
2.41.0

[bug#69924] [PATCH 03/49] gnu: python-blosc: Move to python-compression.

[Sharlatan Hellseher]

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: Type: text/plain; charset=a, Size: 5579 bytes --]

* gnu/packages/python-xyz.scm (python-blosc): Move from here ...
* gnu/packages/python-compression.scm: ... to here.

Change-Id: Ieed1b399602d0ba64b065d1c03ef0855ac52f71e
---
 gnu/packages/python-compression.scm | 47 ++++++++++++++++++++++++++++-
 gnu/packages/python-xyz.scm         | 44 ---------------------------
 2 files changed, 46 insertions(+), 45 deletions(-)

diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index 691fbd3065..ef289bc4d1 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2017, 2019, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Nikita <nikita@n0.is>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
-;;; Copyright © 2018-2020, 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018-2020, 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020, 2022, 2023 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2021 Brendan Tildesley <mail@brendan.scot>
@@ -38,6 +38,7 @@ (define-module (gnu packages python-compression)
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crates-io)
+  #:use-module (gnu packages cmake)
   #:use-module (gnu packages check)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages pkg-config)
@@ -49,6 +50,50 @@ (define-module (gnu packages python-compression)
   #:use-module (gnu packages rust-apps)
   #:use-module (gnu packages sphinx))
 
+(define-public python-blosc
+  (package
+    (name "python-blosc")
+    (version "1.11.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "blosc" version))
+       (sha256
+        (base32
+         "0xmjs28sgpnb940zrhw010dq2m9d8a5h4fgnjyk6645fgfr1j8f2"))
+       (snippet
+        #~(begin (use-modules (guix build utils))
+                 (delete-file-recursively "blosc/c-blosc")))))
+    (build-system python-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'find-blosc
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   (setenv "USE_SYSTEM_BLOSC" "1")
+                   (setenv "Blosc_ROOT" #$(this-package-input "c-blosc"))))
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python" "-m" "blosc.test")))))))
+    (propagated-inputs
+     (list python-scikit-build python-numpy))
+    (inputs (list c-blosc))
+    (native-inputs (list cmake-minimal))
+    (home-page "https://github.com/blosc/python-blosc")
+    (synopsis "Python wrapper for the Blosc data compressor library")
+    (description "Blosc is a high performance compressor optimized for binary
+data.  It has been designed to transmit data to the processor cache faster
+than the traditional, non-compressed, direct memory fetch approach via a
+@code{memcpy()} system call.
+
+Blosc works well for compressing numerical arrays that contains data with
+relatively low entropy, like sparse data, time series, grids with
+regular-spaced values, etc.
+
+This Python package wraps the Blosc library.")
+    (license license:bsd-3)))
+
 (define-public python-multivolumefile
   (package
     (name "python-multivolumefile")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7ed8c945be..7eacce5caf 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -27394,50 +27394,6 @@ (define-public python-locket
 they use the same path.")
     (license license:bsd-2)))
 
-(define-public python-blosc
-  (package
-    (name "python-blosc")
-    (version "1.11.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "blosc" version))
-       (sha256
-        (base32
-         "0xmjs28sgpnb940zrhw010dq2m9d8a5h4fgnjyk6645fgfr1j8f2"))
-       (snippet
-        #~(begin (use-modules (guix build utils))
-                 (delete-file-recursively "blosc/c-blosc")))))
-    (build-system python-build-system)
-    (arguments
-     (list #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'unpack 'find-blosc
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   (setenv "USE_SYSTEM_BLOSC" "1")
-                   (setenv "Blosc_ROOT" #$(this-package-input "c-blosc"))))
-               (replace 'check
-                 (lambda* (#:key tests? #:allow-other-keys)
-                   (when tests?
-                     (invoke "python" "-m" "blosc.test")))))))
-    (propagated-inputs
-     (list python-scikit-build python-numpy))
-    (inputs (list c-blosc))
-    (native-inputs (list cmake-minimal))
-    (home-page "https://github.com/blosc/python-blosc")
-    (synopsis "Python wrapper for the Blosc data compressor library")
-    (description "Blosc is a high performance compressor optimized for binary
-data.  It has been designed to transmit data to the processor cache faster
-than the traditional, non-compressed, direct memory fetch approach via a
-@code{memcpy()} system call.
-
-Blosc works well for compressing numerical arrays that contains data with
-relatively low entropy, like sparse data, time series, grids with
-regular-spaced values, etc.
-
-This Python package wraps the Blosc library.")
-    (license license:bsd-3)))
-
 (define-public python-partd
   (package
     (name "python-partd")
-- 
2.41.0

[bug#69924] [PATCH 04/49] gnu: python-blosc: Simplify package.

[Sharlatan Hellseher]

* gnu/packages/python-compression.scm (python-blosc) [arguments]
<#:phases>: Swap to simple lambda in 'find-blosc phase as it already
uses this-package-input procedure.

Change-Id: I4d3219d9575b9573b0c384b067855fa927f122da
---
 gnu/packages/python-compression.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index ef289bc4d1..d076a4e161 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -69,7 +69,7 @@ (define-public python-blosc
      (list #:phases
            #~(modify-phases %standard-phases
                (add-after 'unpack 'find-blosc
-                 (lambda* (#:key inputs #:allow-other-keys)
+                 (lambda _
                    (setenv "USE_SYSTEM_BLOSC" "1")
                    (setenv "Blosc_ROOT" #$(this-package-input "c-blosc"))))
                (replace 'check
-- 
2.41.0

[bug#69924] [PATCH 05/49] gnu: python-pytest-doctestplus: Update to 1.2.0.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-pytest-doctestplus): Update to 1.2.0.
[arguments] <#:test-flags>: Disable one more failing test.
[home-page]: Update accordingly with lint warning.

Change-Id: I353a671741cf887c348d627d9e071e3fedcc4edc
---
 gnu/packages/python-check.scm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 51a38bbcbe..99f52b6846 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -604,26 +604,29 @@ (define-public python-pytest-cookies
 (define-public python-pytest-doctestplus
   (package
     (name "python-pytest-doctestplus")
-    (version "1.0.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-doctestplus" version))
        (sha256
-        (base32 "17ylfnrcvvp6sd13bfj40jl40paqmjsbywysszb3xqgdr86l8l7n"))))
+        (base32 "0cmrkgpib869kpy8h8hfkg20w16lakkmbkw8cxdywpmf5wx7dbf5"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags
            #~(list "-k" (string-append
+                         ;; Tests requiring network access.
                          "not test_remote_data_url"
                          " and not test_remote_data_float_cmp"
                          " and not test_remote_data_ignore_whitespace"
                          " and not test_remote_data_ellipsis"
                          " and not test_remote_data_requires"
-                         " and not test_remote_data_ignore_warnings"))))
+                         " and not test_remote_data_ignore_warnings"
+                         ;; Requiring git available.
+                         " and not test_generate_diff_basic"))))
     (native-inputs
      (list python-numpy python-pytest python-setuptools-scm))
-    (home-page "https://github.com/astropy/pytest-doctestplus")
+    (home-page "https://github.com/scientific-python/pytest-doctestplus")
     (synopsis "Pytest plugin with advanced doctest features")
     (description
      "This package contains a plugin for the Pytest framework that provides
-- 
2.41.0

[bug#69924] [PATCH 06/49] gnu: python-pytest-arraydiff: Update to 0.6.1.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-pytest-arraydiff): Update to 0.6.1.

Change-Id: I6dd911eb38597790f66756a77f6086112329a156
---
 gnu/packages/python-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 99f52b6846..fe96bd297c 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -545,13 +545,13 @@ (define-public python-pytest-astropy
 (define-public python-pytest-arraydiff
   (package
     (name "python-pytest-arraydiff")
-    (version "0.5.0")
+    (version "0.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-arraydiff" version))
        (sha256
-        (base32 "1livzfbi7ag17hskd5845dh1kdir24f7jrbw8y2s1pyhzyz4jhbi"))))
+        (base32 "1pk7v96rkypx4ld59f6p8fh5bq371ka8g7bh4h7n4df91x2v2dr9"))))
     (build-system python-build-system)
     (arguments
      ;; Tests require python-astropy, which itself requires this package.
-- 
2.41.0

[bug#69924] [PATCH 07/49] gnu: python-pytest-arraydiff: Enable tests.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-pytest-arraydiff): Enable tests.
[build-system]: Swap to pyproject-build-system.
[arguments] <#:test-flags>: Disable tests requiring python-astropy to
break dependencies cycle.

Change-Id: I0e4b6681d106a999c6fc12c3fd8c8f084762a92e
---
 gnu/packages/python-check.scm | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index fe96bd297c..beb151178d 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -552,13 +552,18 @@ (define-public python-pytest-arraydiff
        (uri (pypi-uri "pytest-arraydiff" version))
        (sha256
         (base32 "1pk7v96rkypx4ld59f6p8fh5bq371ka8g7bh4h7n4df91x2v2dr9"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     ;; Tests require python-astropy, which itself requires this package.
-     ;; Disable tests to avoid the circular dependency problem.
-     '(#:tests? #f))
+     (list
+      #:test-flags
+      #~(list "-k" (string-append
+                    ;; Disable tests requiring python-astropy, to break cycle.
+                    "not test_succeeds_func_fits_hdu"
+                    " and not test_fails"
+                    " and not test_generate"
+                    " and not test_default_format"))))
     (native-inputs
-     (list python-pytest python-setuptools-scm)) ; for sanity-check
+     (list python-pytest python-setuptools-scm))
     (propagated-inputs
      (list python-numpy))
     (home-page "https://github.com/astropy/pytest-arraydiff")
-- 
2.41.0

[bug#69924] [PATCH 08/49] gnu: python-pytest-filter-subpackage: Update to 0.2.0.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-pytest-filter-subpackage): Update to 0.2.0.

Change-Id: I04f000b3a75f671340fbd351b06265b99acb3856
---
 gnu/packages/python-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index beb151178d..bee5a468fa 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -668,13 +668,13 @@ (define-public python-pytest-exploratory
 (define-public python-pytest-filter-subpackage
   (package
     (name "python-pytest-filter-subpackage")
-    (version "0.1.2")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-filter-subpackage" version))
        (sha256
-        (base32 "10hpl3f7g2bm29lakmp8492b7lr0dp90khfni12m4gl02xks7bhz"))))
+        (base32 "0mmgg2n8qk6s2kprycjl70lxcpm43dkapplmkf32i0ai6qdqyiiz"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-- 
2.41.0

[bug#69924] [PATCH 09/49] gnu: python-zarr: Update to 2.17.1.

[Sharlatan Hellseher]

* gnu/packages/python-xyz.scm (python-zarr): Update to 2.17.1.

Change-Id: Id7873b68bb82400f66539d03fe9a357deb61d58c
---
 gnu/packages/python-xyz.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7eacce5caf..2bff593063 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26969,15 +26969,15 @@ (define-public python-asciitree
 (define-public python-zarr
   (package
     (name "python-zarr")
-    (version "2.13.3")
+    (version "2.17.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "zarr" version))
        (sha256
         (base32
-         "135ls2q7zc98pk61a5cnh88j4hnnavcwasrswdjqyqvcc68b096v"))))
-    (build-system python-build-system)
+         "0qb2wj60i7v1c95k6m0pskx20ss6dxrj3ym0d7z4c98jfah3ljsn"))))
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-- 
2.41.0

[bug#69924] [PATCH 10/49] gnu: python-partd: Enable tests.

[Sharlatan Hellseher]

Newer version of the project is migrated to pyproject.toml, this change
may help to prepare for the future upgrade.

* gnu/packages/python-xyz.scm (python-partd) [build-system]: Swap to
pyproject-build-system, allowing to detect tests and run them.

Change-Id: Ia4375b83cea6dcbf7781b3dc40f544261075d2ca
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 2bff593063..799174ab60 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -27405,7 +27405,7 @@ (define-public python-partd
        (sha256
         (base32
          "1sy3vdfyyx3bc5590zb7gwpsmimqz8m992x9hsydq8nmhixqjrxa"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (propagated-inputs
      (list python-blosc
            python-locket
-- 
2.41.0

[bug#69924] [PATCH 11/49] gnu: python-zarr: Speed up tests.

[Sharlatan Hellseher]

* gnu/packages/python-xyz.scm (python-zarr): Use G-expressions.
[arguments] <#:test-flags>: Parallelize tests to speed them up.
<#:phases>: 'disable-service-tests remove trailing #t from
lambda. Use standard 'check phase.
[native-inputs]: Add python-fsspec, python-h5py,
python-pytest-doctestplus, python-pytest-timeout, and
python-pytest-xdist.

Change-Id: I3fc4e2a1649ad9f95ed9e3fe87e3f57ad4f58af8
---
 gnu/packages/python-xyz.scm | 34 ++++++++++++++++++++--------------
 1 file changed, 20 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 799174ab60..360b4db3f1 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26979,23 +26979,29 @@ (define-public python-zarr
          "0qb2wj60i7v1c95k6m0pskx20ss6dxrj3ym0d7z4c98jfah3ljsn"))))
     (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'disable-service-tests
-           (lambda _
-             (setenv "ZARR_TEST_ABS" "0")
-             (setenv "ZARR_TEST_MONGO" "0")
-             (setenv "ZARR_TEST_REDIS" "0")
-             #t))
-         (replace 'check
-           (lambda _
-             (invoke "pytest" "-vv" "-k" "not lmdb")
-             #t)))))
+     (list
+      #:test-flags
+      #~(list "-n" "auto")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'disable-service-tests
+            (lambda _
+              (setenv "ZARR_TEST_ABS" "0")
+              (setenv "ZARR_TEST_MONGO" "0")
+              (setenv "ZARR_TEST_REDIS" "0"))))))
     (propagated-inputs
-     (list python-asciitree python-fasteners python-numcodecs
+     (list python-asciitree
+           python-fasteners
+           python-numcodecs
            python-numpy))
     (native-inputs
-     (list python-pytest python-setuptools-scm))
+     (list python-fsspec
+           python-pytest
+           python-h5py
+           python-pytest-doctestplus
+           python-pytest-timeout
+           python-pytest-xdist
+           python-setuptools-scm))
     (home-page "https://github.com/zarr-developers/zarr-python")
     (synopsis "Chunked, compressed, N-dimensional arrays for Python")
     (description
-- 
2.41.0

[bug#69924] [PATCH 12/49] gnu: python-distributed: Speed up tests.

[Sharlatan Hellseher]

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: Type: text/plain; charset=a, Size: 2223 bytes --]

* gnu/packages/python-science.scm (python-distributed) [arguments]
<#:test-flags>: Add option to run tests in parallel. Disable 3 more
flaky tests.
[native-inputs]: Add python-pytest-xdist. Sort alphabetically.

Change-Id: I588c1a1dc82e3208cc1eeeefbdc58fb080775ac0
---
 gnu/packages/python-science.scm | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index b6a116f16b..a01c68cbc3 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -23,6 +23,7 @@
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
 ;;; Copyright © 2022 jgart <jgart@dismail.de>
 ;;; Copyright © 2023, 2024 Troy Figiel <troy@troyfigiel.com>
+;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1688,7 +1689,8 @@ (define-public python-distributed
     (arguments
      (list
       #:test-flags
-      '(list "-x" "-m"
+      '(list "-n" "auto"
+             "-x" "-m"
              (string-append "not slow"
                             " and not flaky"
                             " and not gpu"
@@ -1814,7 +1816,10 @@ (define-public python-distributed
               ;; These tests are rather flaky
               " and not test_quiet_quit_when_cluster_leaves"
               " and not multiple_clients_restart"
-              " and not test_steal_twice"))
+              " and not test_steal_twice"
+              " and not test_task_groups_update_start_stop"
+              " and not test_web_preload"
+              " and not test_web_preload_worker"))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'versioneer
@@ -1889,10 +1894,11 @@ (define-public python-distributed
            python-urllib3
            python-zict))
     (native-inputs
-     (list python-importlib-metadata
+     (list python-flaky
+           python-importlib-metadata
            python-pytest
            python-pytest-timeout
-           python-flaky
+           python-pytest-xdist
            python-versioneer))
     (home-page "https://distributed.dask.org")
     (synopsis "Distributed scheduler for Dask")
-- 
2.41.0

[bug#69924] [PATCH 13/49] gnu: python-dask: Speed up tests.

[Sharlatan Hellseher]

* gnu/packages/python-xyz.scm (python-dask) [arguments] <#:test-flags>:
Add option to run tests in parallel.
[native-inputs]: Add python-xdist. Reformat as a list.

Change-Id: I9b4b1c53f827e1f5d3edd0908f8e37e1a3bddb71
---
 gnu/packages/python-xyz.scm | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 360b4db3f1..4a9069bbed 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -27488,7 +27488,8 @@ (define-public python-dask
      (list
       ;; Avoid coverage
       #:test-flags
-      #~(list "-m" "not gpu and not slow and not network"
+      #~(list "-n" "auto"
+              "-m" "not gpu and not slow and not network"
               "-k" (string-append
                     ;; This one cannot be interrupted.
                     "not test_interrupt"
@@ -27541,7 +27542,10 @@ (define-public python-dask
            python-pyyaml))
     (native-inputs
      (list python-importlib-metadata
-           python-pytest python-pytest-runner python-pytest-rerunfailures
+           python-pytest
+           python-pytest-rerunfailures
+           python-pytest-runner
+           python-pytest-xdist
            python-versioneer))
     (home-page "https://github.com/dask/dask/")
     (synopsis "Parallel computing with task scheduling")
-- 
2.41.0

[bug#69924] [PATCH 14/49] gnu: python-stdatamodels: Speed up tests.

[Sharlatan Hellseher]

gnu/packages/astronomy.scm (python-stdatamodels): Enable parallel
tests to speed them up.
[arguments] <#:test-flags>: Add "-n" option.
[native-inputs]: Add python-pytest-xdist.

Change-Id: I43390240a4a0db48d9abab4c34d1c1c771028486
---
 gnu/packages/astronomy.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 724643d17f..4b3ebd642e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3181,9 +3181,11 @@ (define-public python-stdatamodels
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; Disable tests requiring access to CRDS servers to download ~500MiB of
-      ;; data.
-      #:test-flags #~(list "-k" "not test_crds_selectors_vs_datamodel")
+      #:test-flags
+      #~(list "-n" "auto"
+              ;; Disable tests requiring access to CRDS servers to download
+              ;; ~500MiB of data.
+              "-k" "not test_crds_selectors_vs_datamodel")
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'set-home
@@ -3199,6 +3201,7 @@ (define-public python-stdatamodels
      (list python-crds
            python-pytest
            python-pytest-doctestplus
+           python-pytest-xdist
            python-scipy
            python-semantic-version
            python-setuptools-scm))
-- 
2.41.0

[bug#69924] [PATCH 15/49] gnu: python-glymur: Speed up tests.

[Sharlatan Hellseher]

* gnu/packages/python-xyz.scm (python-glymur): Enable parallel
tests to speed them up.
[arguments] <#:test-flags>: Add it with "-n" option.
[native-inputs]: Add python-pytest-xdist.

Change-Id: Ied066330cc24a50b47307cefb2694675be8af0a4
---
 gnu/packages/python-xyz.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 4a9069bbed..763345c0c2 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1956,6 +1956,8 @@ (define-public python-glymur
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~(list "-n" "auto")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-library-locations
@@ -1981,7 +1983,9 @@ (define-public python-glymur
               ;; which is patched above.
               (delete-file "tests/test_config.py"))))))
     (native-inputs
-     (list python-pytest python-scikit-image))
+     (list python-pytest
+           python-pytest-xdist
+           python-scikit-image))
     (inputs
      (list openjpeg  ; glymur/lib/openjp2.py
            libtiff)) ; glymur/lib/tiff.py
-- 
2.41.0

[bug#69924] [PATCH 16/49] gnu: python-ginga: Update to 5.0.0.

[Sharlatan Hellseher]

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

Change-Id: I4b6dee90dded7606e823e1a2a6df7a5dead962d4
---
 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 4b3ebd642e..4807f3d190 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -709,13 +709,13 @@ (define-public python-gatspy
 (define-public python-ginga
   (package
     (name "python-ginga")
-    (version "4.1.1")
+    (version "5.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ginga" version))
        (sha256
-        (base32 "0w60w9d2yqhbmggp0dljj5a0sk07gywifjq8nzw3y2v47vzgwqb6"))))
+        (base32 "1kydi6qqsscgsa55fa2za35vr5j8xjn09lfbnb5ajr8yxdgm4n3y"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      (list ;;python-exifread  ; optional, not packed yet in Guix
-- 
2.41.0

[bug#69924] [PATCH 17/49] gnu: python-astropy-iers-data: Update to 0.2024.3.18.0.29.47.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy-iers-data): Update to
0.2024.3.18.0.29.47.

Change-Id: Ibc243250266bc1a2c3733a05f554389d2f1dac2c
---
 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 4807f3d190..18ff84752b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1698,13 +1698,13 @@ (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 "0.2024.2.19.0.28.47")
+    (version "0.2024.3.18.0.29.47")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy-iers-data" version))
        (sha256
-        (base32 "0j42hkl8z42x5n3aacld9cvacjzg79lqsivm3xn6bv1gjgy69br9"))))
+        (base32 "1mf03iqw09rp6d8hbby33f4jwfjan9gkb1z7xqsjr2jpj7zwpn3y"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#69924] [PATCH 18/49] gnu: python-cdflib: Update to 1.2.6.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-cdflib): Update to 1.2.6.

Change-Id: Iae2e39e756e5e9664a1b524aa1155d128dc0292c
---
 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 18ff84752b..0ac26b1e7d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1927,7 +1927,7 @@ (define-public python-ccdproc
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-    (version "1.2.4")
+    (version "1.2.6")
     (source
      (origin
        (method git-fetch)   ; no tests in pypi archive
@@ -1936,7 +1936,7 @@ (define-public python-cdflib
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0pjd4dwwlza2592zgdccw1s341s3ikg44pwsr1gk8vjix40m46fr"))))
+        (base32 "1wxr35sqsdqzf85xyjh1v8hmwwiyv4cn0lr7q8l1kkngfywq5l2r"))))
     (build-system pyproject-build-system)
     (arguments
      ;; Disable shaky test.
-- 
2.41.0

[bug#69924] [PATCH 19/49] gnu: python-cdflib: Enable all tests.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-cdflib) [arguments] <#:test-flags>:
Remove it to enable all tests.

Change-Id: I0fd44c117519efb306573d5ec603c430dbb1dc8c
---
 gnu/packages/astronomy.scm | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 0ac26b1e7d..382da91b4c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1930,7 +1930,7 @@ (define-public python-cdflib
     (version "1.2.6")
     (source
      (origin
-       (method git-fetch)   ; no tests in pypi archive
+       (method git-fetch)               ; no tests in PyPI release
        (uri (git-reference
              (url "https://github.com/MAVENSDC/cdflib")
              (commit version)))
@@ -1939,10 +1939,7 @@ (define-public python-cdflib
         (base32 "1wxr35sqsdqzf85xyjh1v8hmwwiyv4cn0lr7q8l1kkngfywq5l2r"))))
     (build-system pyproject-build-system)
     (arguments
-     ;; Disable shaky test.
-     ;; See https://github.com/MAVENSDC/cdflib/issues/234
-     (list #:test-flags #~(list "-k" "not test_compute_cdfepoch16")
-           #:phases
+     (list #:phases
            #~(modify-phases %standard-phases
                (add-before 'build 'set-env-version
                  (lambda _
-- 
2.41.0

[bug#69924] [PATCH 20/49] gnu: python-asdf-unit-schemas: Update to 0.2.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-unit-schemas): Update to 0.2.0.

Change-Id: Ib767a5b3e1d58205e18eb71465a1505d6ba7a7eb
---
 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 382da91b4c..808cbb46d6 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4463,14 +4463,14 @@ (define python-asdf-time-schemas
 (define python-asdf-unit-schemas
   (package
     (name "python-asdf-unit-schemas")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf_unit_schemas" version))
        (sha256
         (base32
-         "16grpx3a9h0v1wirp0zqrfsxm867v5c0xyr98pylzziy45kqvds2"))))
+         "0h24gvm1wip4gh3fw5ki8kwnvcy8gw6b6pajw3i1zvriamdw95fr"))))
     (build-system pyproject-build-system)
     (arguments
      ;; Dependency cycle with python-asdf
-- 
2.41.0

[bug#69924] [PATCH 21/49] gnu: python-asdf-standard: Update to 1.1.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-standard): Update to 1.1.1.
[arguments] <#:phases>: Swap 'remove-blocking-tests phases to use <#:test-flags>.
<#:test-flags>: Add more file to ignore to break cycle with python-asdf.

Change-Id: I8c80d4371adf55de77ef718a21bf8599d0fce17e
---
 gnu/packages/astronomy.scm | 21 ++++++++++-----------
 1 file changed, 10 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 808cbb46d6..8619dac066 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4297,25 +4297,24 @@ (define-public python-asdf
 (define-public python-asdf-standard
   (package
     (name "python-asdf-standard")
-    (version "1.0.3")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf_standard" version))
        (sha256
         (base32
-         "0i7xdjwn5prg2hcnf1zhw57mszc68jjr5sv4rimpzcg7f2dgzn5g"))))
+         "00k1fzc8y8j0ar1chq0nqyfw8bgkkjgrkm32ibn0kz2vn715nlq1"))))
     (build-system pyproject-build-system)
     (arguments
-     (list #:phases #~(modify-phases %standard-phases
-                        (add-before 'check 'remove-blocking-tests
-                          (lambda _
-                            ;; Remove tests require python-asdf where
-                            ;; python-asdf require python-asdf-standard,
-                            ;; break circular dependencies.
-                            (for-each delete-file
-                                      (list "tests/test_manifests.py"
-                                            "tests/test_integration.py")))))))
+     (list
+      #:test-flags
+      ;; Remove tests requiring python-asdf where python-asdf requires
+      ;; python-asdf-standard, break circular dependencies.
+      #~(list "--ignore=tests/test_asdf_schema.py"
+              "--ignore=tests/test_integration.py"
+              "--ignore=tests/test_manifests.py"
+              "--ignore=tests/test_yaml_schema.py")))
     (native-inputs (list python-astropy
                          python-jsonschema
                          python-pypa-build
-- 
2.41.0

[bug#69924] [PATCH 22/49] gnu: python-asdf-transform-schemas: Update to 0.5.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-transform-schemas): Update to 0.5.0.

Change-Id: Ibf122fa98260de9a472a9c2786f85e1f1098fa19
---
 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 8619dac066..ff45ca1434 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4337,13 +4337,13 @@ (define-public python-asdf-standard
 (define python-asdf-transform-schemas
   (package
     (name "python-asdf-transform-schemas")
-    (version "0.4.0")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf_transform_schemas" version))
        (sha256
-        (base32 "1jlls8mirwarf8d67gaix39d8zcx1rx8fmr9qdzrbyrmxqzxqzyy"))))
+        (base32 "0as6dcf9dmxjh24gwdmqwbbrk56fhgsmzwi7af4llwvm4mw4rkw2"))))
     (build-system pyproject-build-system)
     (arguments
      ;; Dependency cycle with python-asdf
-- 
2.41.0

[bug#69924] [PATCH 23/49] gnu: python-asdf: Update to 3.1.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf): Update to 3.1.0.
[arguments] <#:phases>: Add 'fix-test-setup phase.
<#:test-arguments>: Move "-p no:legacypath" option from pyproject.toml
to here.

Change-Id: Ief5734d97d483d2e7af3ea59d702fd4697eb048a
---
 gnu/packages/astronomy.scm | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ff45ca1434..57585619dc 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4254,18 +4254,26 @@ (define-public python-tweakwcs
 (define-public python-asdf
   (package
     (name "python-asdf")
-    (version "3.0.1")
+    (version "3.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf" version))
        (sha256
-        (base32 "1jsk7b4mx04l0a08j832vnl309dba3gjnha9mbd61dzs9ridrfna"))))
+        (base32 "0fa6y3gmqc0y3nz0h68vq3a84pvx6gc5zp33wg8a4n9b4kipm464"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
-      #~(list "-n" "auto")))
+      #~(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
+            (lambda _
+              (substitute* "pyproject.toml"
+                ((".*:legacypath.*") "")))))))
     (native-inputs
      (list python-fsspec
            python-packaging
-- 
2.41.0

[bug#69924] [PATCH 24/49] gnu: python-asdf-coordinates-schemas: Update to 0.3.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-coordinates-schemas): Update to 0.3.0.

Change-Id: Iad7848823f4b6c996aeb74919cbf252014126075
---
 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 57585619dc..9e6aec9b8c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4369,13 +4369,13 @@ (define python-asdf-transform-schemas
 (define python-asdf-coordinates-schemas
   (package
     (name "python-asdf-coordinates-schemas")
-    (version "0.2.0")
+    (version "0.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf_coordinates_schemas" version))
        (sha256
-        (base32 "1x6mipg76c6qldq8s2p2wpsq0cpr9b5krp62xskljdz1f84abyg3"))))
+        (base32 "0kk0rlzv0kkcw6fiwvps4n0x05867xc9hxyyzica31zcvhan12y9"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#69924] [PATCH 25/49] gnu: python-asdf-wcs-schemas: Update to 0.4.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-wcs-schemas): Update to 0.4.0.
[propagated-inputs]: Remove python-asdf-unit-schemas; add python-asdf-coordinates-schemas.

Change-Id: I491f3f7b96b11a1ac894a30aa304d3042299de99
---
 gnu/packages/astronomy.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9e6aec9b8c..c3aa9a2ad5 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4532,13 +4532,13 @@ (define-public python-asdf-astropy
 (define python-asdf-wcs-schemas
   (package
     (name "python-asdf-wcs-schemas")
-    (version "0.3.0")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf_wcs_schemas" version))
        (sha256
-        (base32 "1r9ls2skgwq6my68nfwfah1s0q6bm2qq97s0h79vwh997jy97rai"))))
+        (base32 "1d08ng890xc1ilf3y1hrimx09x990wvg9g18n0ijwvpilnw49fy0"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -4550,9 +4550,9 @@ (define python-asdf-wcs-schemas
            python-semantic-version
            python-setuptools-scm))
     (propagated-inputs
-     (list python-asdf-standard
-           python-asdf-transform-schemas
-           python-asdf-unit-schemas))
+     (list python-asdf-coordinates-schemas
+           python-asdf-standard
+           python-asdf-transform-schemas))
     (home-page "https://github.com/asdf-format/asdf-wcs-schemas")
     (synopsis "ASDF WCS Schemas")
     (description
-- 
2.41.0

[bug#69924] [PATCH 26/49] gnu: python-asdf-astropy: Update to 0.6.0

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.6.0.

Change-Id: I5eca1d6c113b053b8353ed43e7dfc2c7165a3139
---
 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 c3aa9a2ad5..d580bac681 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4492,13 +4492,13 @@ (define python-asdf-unit-schemas
 (define-public python-asdf-astropy
   (package
     (name "python-asdf-astropy")
-    (version "0.5.0")
+    (version "0.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf-astropy" version))
        (sha256
-        (base32 "061y7r1d2fqlr8a6gyaffqa3z5m0ymljahhvxzcb71355xkqig7v"))))
+        (base32 "0cxwknkjkgiavwmsz3vzk88c3spdi1cj4kwp62hgj92g2mh5k0zh"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#69924] [PATCH 27/49] gnu: python-pyvo: Update to 1.5.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pyvo): Update to 1.5.1.

Change-Id: I51228822626a0fac9013580a7bfb7160980ac8fb
---
 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 d580bac681..b3ce51c8df 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2512,13 +2512,13 @@ (define-public python-pyavm
 (define-public python-pyvo
   (package
     (name "python-pyvo")
-    (version "1.5")
+    (version "1.5.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyvo" version))
        (sha256
-        (base32 "1kyd4jbspldfpwwvwxfmhq2cxqp4kfbcsiyk4gjs0ib65idxdr45"))))
+        (base32 "0cm6agaf1gvc5bi95wx6a70ngj9vn95rx78fs59vlrmpww7q2807"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest-astropy python-requests-mock python-setuptools-scm))
-- 
2.41.0

[bug#69924] [PATCH 28/49] gnu: python-astroquery: Update to 0.4.7.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroquery): Update to 0.4.7.
[arguments] <#:test-flags>: Disable one failing test.
<#:phases>: Remove 'prepare-test-environment phase. Add custom 'check
phase.

Change-Id: I159a9d765de7f8de00c4bf226febfc90d2ba6c76
---
 gnu/packages/astronomy.scm | 35 +++++++++++++++++++----------------
 1 file changed, 19 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b3ce51c8df..efd70f5500 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1739,34 +1739,37 @@ (define-public python-astropy-iers-data
 (define-public python-astroquery
   (package
     (name "python-astroquery")
-    (version "0.4.6")
+    (version "0.4.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astroquery" version))
        (sha256
-        (base32 "1vhkzsqlgn3ji5by2rdf2gwklhbyzvpzb1iglalhqjkkrdaaaz1h"))))
+        (base32 "1jbyfhqk74wsdjxzqi0hcrgc7ha4q8cyjx96nv6w9bjg1b5vlzq4"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
       #~(list "--pyargs" "astroquery"
-              "-m" "not remote_data")
+              "-m" "not remote_data"
+              ;; Some tests failed with parallel run, see
+              ;; <https://github.com/astropy/astroquery/issues/2968>.
+              ;; "-n" "auto"
+              "-k" (string-append
+                    ;; Failed: DID NOT RAISE <class
+                    ;; 'astropy.utils.exceptions.AstropyDeprecationWarning'>
+                    "not test_raises_deprecation_warning"))
       #:phases
       #~(modify-phases %standard-phases
-          (add-before 'check 'prepare-test-environment
-            (lambda _
-              (setenv "HOME" (getcwd)) ; some tests need a writable home
-              ;; 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?
+                ;; Some tests require write access to $HOME.
+                (setenv "HOME" "/tmp")
+                ;; 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-beautifulsoup4
-- 
2.41.0

[bug#69924] [PATCH 29/49] gnu: python-gwcs: Update to 0.21.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-gwcs): Update to 0.21.0.

Change-Id: I3e634366c4eaf36b76dd7e3e120fb3ed0b21dcab
---
 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 efd70f5500..d6bda35700 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4567,13 +4567,13 @@ (define python-asdf-wcs-schemas
 (define-public python-gwcs
   (package
     (name "python-gwcs")
-    (version "0.20.0")
+    (version "0.21.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "gwcs" version))
        (sha256
-        (base32 "1vhvs0mcwrw0128q9pd9v21wl173lspj5rvygqr19ljncralbx73"))))
+        (base32 "1fn5l4v236bl7xqi1is40c2q57dji8by98iwqcndfnmjwqf7zllc"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-jsonschema
-- 
2.41.0

[bug#69924] [PATCH 30/49] gnu: python-drizzle: Update to 1.15.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-drizzle): Update to 1.15.1.

Change-Id: I263ef052f61f0b6088be408b208fa31d55050429
---
 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 d6bda35700..d4d474155a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2087,7 +2087,7 @@ (define-public python-drms
 (define-public python-drizzle
   (package
     (name "python-drizzle")
-    (version "1.15.0")
+    (version "1.15.1")
     (source
      (origin
        (method git-fetch) ;PyPi doesn't have the test data sets
@@ -2096,7 +2096,7 @@ (define-public python-drizzle
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "06qh3b60xvm5f2p09l2njwwsh0n95s54r730fyfn66w8mvr1jk82"))))
+        (base32 "14l3d3bx73r7cxhcl1cfh1q088qh5wq5pz5fs9dx7w79kp8mp6pg"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#69924] [PATCH 31/49] gnu: python-suntime: Update to 1.3.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-suntime): Update to 1.3.2.

Change-Id: I0af01462f3732ce9ece89a3d8bd8533563ece929
---
 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 d4d474155a..db220857f5 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4155,13 +4155,13 @@ (define-public python-sep
 (define-public python-suntime
   (package
     (name "python-suntime")
-    (version "1.2.5")
+    (version "1.3.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "suntime" version))
               (sha256
                (base32
-                "0ja64w293wjx76q3z18ikx4rdihwkbj6pnjpbs82ycyyzhfnbpz4"))))
+                "1kyd1r6zcs0jmh5gq74adrnb1h7dfr1mzjq4k4vbngfiga8gfd28"))))
     (build-system python-build-system)
     (propagated-inputs (list python-dateutil))
     (home-page "https://github.com/SatAgro/suntime")
-- 
2.41.0

[bug#69924] [PATCH 32/49] gnu: python-suntime: Refresh package style.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-suntime): Re-indent package.
[build-system]: Swap to pyproject-build-system
[description]: Concatenate small paragraphs into single one.

Change-Id: I368f042eeab2f49c6f41b2ccf0c9a69c8abfec17
---
 gnu/packages/astronomy.scm | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index db220857f5..2986079221 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4156,21 +4156,21 @@ (define-public python-suntime
   (package
     (name "python-suntime")
     (version "1.3.2")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "suntime" version))
-              (sha256
-               (base32
-                "1kyd1r6zcs0jmh5gq74adrnb1h7dfr1mzjq4k4vbngfiga8gfd28"))))
-    (build-system python-build-system)
-    (propagated-inputs (list python-dateutil))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "suntime" version))
+       (sha256
+        (base32 "1kyd1r6zcs0jmh5gq74adrnb1h7dfr1mzjq4k4vbngfiga8gfd28"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-dateutil))
     (home-page "https://github.com/SatAgro/suntime")
     (synopsis "Sunset and sunrise time calculation python library")
     (description
-     "Python library doing sunrise and sunset time calculation.
-
-Takes a WGS84 (GPS) latitude/longitude as input as well as an UTC or local
-datetime object.")
+     "Python library doing sunrise and sunset time calculation.  Takes a
+WGS84 (GPS) latitude/longitude as input as well as an UTC or local datetime
+object.")
     (license license:lgpl3+)))
 
 (define-public python-synphot
-- 
2.41.0

[bug#69924] [PATCH 33/49] gnu: python-radiospectra: Update to 0.5.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-radiospectra): Update to 0.5.0.

Change-Id: I9146be6756530e5bda59ea53e3200ed8403fd672
---
 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 2986079221..ec890c8928 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4670,13 +4670,13 @@ (define-public python-radio-beam
 (define-public python-radiospectra
   (package
     (name "python-radiospectra")
-    (version "0.4.0")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "radiospectra" version))
        (sha256
-        (base32 "0gq61ywk7li0gxwmp4hp2hc4zbrlqgn8zy0sz24qh55kn5l5gxjr"))))
+        (base32 "0nw71a7i875lfwbwhpc80nvwalb7iq3fynfkbngx6f6jb3v10dgs"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#69924] [PATCH 34/49] gnu: python-glymur: Update to 0.12.9.

[Sharlatan Hellseher]

* gnu/packages/python-xyz.scm (python-glymur): Update to 0.12.9.

Change-Id: Ifb84738df85cb6142fc5ecafa164a6dc4148a69e
---
 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 763345c0c2..6d587dc017 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1943,7 +1943,7 @@ (define-public python-gh-md-to-html
 (define-public python-glymur
   (package
     (name "python-glymur")
-    (version "0.12.8")
+    (version "0.12.9")
     (source
      (origin
        (method git-fetch)   ; no tests data in PyPi package
@@ -1952,7 +1952,7 @@ (define-public python-glymur
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0mfyn9j7h13242d41vg12acw55yl2mv6lmgi265hfp11k7g52b6n"))))
+        (base32 "0awyav7071nn9z2g4mmpg33y0y0nfandfr6nr3j5vyb8hnprcmns"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#69924] [PATCH 35/49] gnu: python-specutils: Update to 1.13.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-specutils): Update to 1.13.0.

Change-Id: Ic935f471fd9f5e27745c370940e3f70f715d2ca4
---
 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 ec890c8928..bdf65d0693 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2933,13 +2933,13 @@ (define-public python-spectral-cube
 (define-public python-specutils
   (package
     (name "python-specutils")
-    (version "1.12.0")
+    (version "1.13.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "specutils" version))
        (sha256
-        (base32 "10nq00q71cyj0p74g3kyzb4hrwkbvhsd6m5zvxifc035rfnvc2qv"))))
+        (base32 "0cfsigvsa0i7z2nq9ci9gxccp074kqsgr01xi2npk8xf7cjisrfq"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#69924] [PATCH 36/49] gnu: python-stcal: Update to 1.6.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stcal): Update to 1.6.1.

Change-Id: Ifca867967c302234d38bbe4fa6fcd2a1d61914cf
---
 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 bdf65d0693..431bd0346e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3128,13 +3128,13 @@ (define-public python-stsci-stimage
 (define-public python-stcal
   (package
     (name "python-stcal")
-    (version "1.6.0")
+    (version "1.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stcal" version))
        (sha256
-        (base32 "12skkbc59alw3asvw36x7nvibx68ccfiqdlgs8b5cvdns5j47f9n"))))
+        (base32 "1rwvzjpidz0sfp52mqgs25599hbvxyc4gdc1yk0kdm8aynhdwi82"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#69924] [PATCH 37/49] gnu: python-stcal: Enable sanity check.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stcal) [arguments] <#:phases>:
Revert 'sanity-check phase. Add 'silent-check-for-opencv phase.

Change-Id: Ifd3ae01d261fe6dba8f5e75d4a5134510d826a57
---
 gnu/packages/astronomy.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 431bd0346e..4d1bbcec87 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3140,9 +3140,12 @@ (define-public python-stcal
      (list
       #:phases
       #~(modify-phases %standard-phases
-          ;; XXX: Can't detect opencv-python version. The input opencv might
-          ;; not set the version correctly.
-          (delete 'sanity-check)
+          (add-before 'build 'silent-check-for-opencv
+            (lambda _
+              ;; XXX: Can't detect opencv-python version. The input opencv
+              ;; might not set the version correctly.
+              (substitute* "pyproject.toml"
+                ((".*opencv-python-headless.*") ""))))
           (add-before 'check 'build-extensions
             (lambda _
               ;; Cython extensions have to be built before running the tests.
-- 
2.41.0

[bug#69924] [PATCH 38/49] gnu: python-stdatamodels: Update to 1.10.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stdatamodels): Update to 1.10.0.

Change-Id: I69f98de3e98d22c636ec726ab3ce17f5d96fbb51
---
 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 4d1bbcec87..85c511bbb8 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3174,13 +3174,13 @@ (define-public python-stcal
 (define-public python-stdatamodels
   (package
     (name "python-stdatamodels")
-    (version "1.9.1")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stdatamodels" version))
        (sha256
-        (base32 "0h1v5c96c4q44b2npq9953x44dr6pwmkr1s05wfixdv95arqd8v0"))))
+        (base32 "00zc7z3f2fjvmms2h7176wnzjb025v0aasc6fiib9055sk34bc94"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#69924] [PATCH 39/49] gnu: python-crds: Update to 11.17.19.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-crds): Update to 11.17.19.

Change-Id: I455e3d6aeb0188d13c02e1c57aa3793689c0de5c
---
 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 85c511bbb8..9ddbd8eb1d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1979,13 +1979,13 @@ (define-public python-cdflib
 (define-public python-crds
   (package
     (name "python-crds")
-    (version "11.17.16")
+    (version "11.17.19")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "crds" version))
               (sha256
                (base32
-                "0j84l7132mvwww2y83h2dgz5qw792ilp3hml4h12n7ydks0w0534"))))
+                "1x48yw6jnz7dw0myc86ds0qaki6v1anqaihd5qzrxwrrl61kyp6x"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#69924] [PATCH 40/49] gnu: python-pynbody: Update to 1.6.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pynbody): Update to 1.6.0.
[arguments] <#:test-flags>: Disable more tests.

Change-Id: Icfb65fccbd1e7694a64aa52caa7b905e1b9a1a87
---
 gnu/packages/astronomy.scm | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9ddbd8eb1d..ec23671430 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3981,7 +3981,7 @@ (define-public python-pyerfa
 (define-public python-pynbody
   (package
     (name "python-pynbody")
-    (version "1.5.2")
+    (version "1.6.0")
     (source
      (origin
        (method git-fetch) ;PyPi doesn't have not prebuit version.
@@ -3990,7 +3990,7 @@ (define-public python-pynbody
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "175i99zwnnwglndr71paiadrx3xq3icxjgdqfv3xxpyn7fx4dzab"))
+        (base32 "00isg6nsqzgjqpkczwvrcmj3ndzav3bfzla0a72b44cgdj20wyv8"))
        (modules '((guix build utils)))
        (snippet
         ;; Symlink goes to not existing directory.
@@ -4005,6 +4005,7 @@ (define-public python-pynbody
                            ;;    https://github.com/pynbody/pynbody/blob/ \
                            ;;    f4bd482dc47532831b3ec115c7cb07149d61bfc5/ \
                            ;;    .github/workflows/build-test.yaml#L41
+                           ;; See <https://github.com/pynbody/pynbody/issues/778>
                            "--ignore=tests/copy_on_access_test.py"
                            "--ignore=tests/gravity_test.py"
                            "--ignore=tests/adaptahop_test.py"
@@ -4027,7 +4028,20 @@ (define-public python-pynbody
                            "--ignore=tests/sph_smooth_test.py"
                            "--ignore=tests/subfind_test.py"
                            "--ignore=tests/subfindhdf_gadget4_test.py"
-                           "--ignore=tests/tipsy_test.py")
+                           "--ignore=tests/tipsy_test.py"
+                           "-k"
+                           (string-append
+                            "not test_div_curl_smoothing"
+                            " and not test_float_kd"
+                            " and not test_kd_delete"
+                            " and not test_kd_issue_88"
+                            " and not test_kdtree_from_existing_kdtree"
+                            " and not test_kdtree_shared_mem"
+                            " and not test_neighbour_list"
+                            " and not test_particles_in_sphere"
+                            " and not test_periodic_smoothing"
+                            " and not test_smooth"
+                            " and not test_smooth_WendlandC2"))
            #:phases
            #~(modify-phases %standard-phases
                (add-before 'build 'set-compiler
-- 
2.41.0

[bug#69924] [PATCH 41/49] gnu: Add python-asdf-zarr.

[Sharlatan Hellseher]

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

Change-Id: If26b31aeeb90a595a4d384755ba9060101ee4c8a
---
 gnu/packages/astronomy.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ec23671430..2a4ef61159 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4509,6 +4509,31 @@ (define python-asdf-unit-schemas
     (description "This package provides ASDF schemas for validating unit tags.")
     (license license:bsd-3)))
 
+(define-public python-asdf-zarr
+  (package
+    (name "python-asdf-zarr")
+    (version "0.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "asdf_zarr" version))
+       (sha256
+        (base32 "0ax7c9xarh6fi2yxm1z2p90mc3d57q23a7wc8av30xg8ririrl4s"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-asdf python-fsspec python-zarr))
+    (native-inputs
+     (list python-pytest python-semantic-version python-setuptools-scm))
+    (home-page "https://github.com/asdf-format/asdf-zarr")
+    (synopsis "Asdf extension to support Zarr arrays")
+    (description
+     "This package includes an extension for the Python library asdf to add
+support for reading and writing chunked
+@url{https://zarr.readthedocs.io/en/stable/,Zarr} arrays, a file storage
+format for chunked, compressed, N-dimensional arrays based on an open-source
+specification.")
+    (license license:bsd-3)))
+
 (define-public python-asdf-astropy
   (package
     (name "python-asdf-astropy")
-- 
2.41.0

[bug#69924] [PATCH 42/49] gnu: Add python-asdf-compression.

[Sharlatan Hellseher]

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

Change-Id: I221990d2f25f31dd5272a3ccc4c603da8dac353b
---
 gnu/packages/astronomy.scm | 44 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 2a4ef61159..7849624540 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4322,6 +4322,50 @@ (define-public python-asdf
 implementation of the ASDF Standard.")
     (license license:bsd-3)))
 
+(define-public python-asdf-compression
+  ;; TODO: No release, change to tag when it's ready.
+  (let ((commit "57cc7e76fb4163be3e99fb740b36b5ec5ae96e49")
+        (revision "0"))
+    (package
+      (name "python-asdf-compression")
+      (version (git-version "0.0.1" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/asdf-format/asdf-compression")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1g6iiyls950k66dmd0pbqqdvz74kksc4j191n0ik6fhjnkiwifgs"))))
+      (build-system pyproject-build-system)
+      (arguments
+       (list
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before 'build 'set-version
+              (lambda _
+                (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" "0.0.1"))))))
+      (native-inputs
+       (list python-numpy
+             python-pytest
+             python-semantic-version
+             python-setuptools-scm))
+      (propagated-inputs
+       (list python-asdf
+             python-blosc
+             python-lz4
+             python-zstandard))
+      (home-page "https://github.com/asdf-format/asdf-fits-schemas")
+      (synopsis "ASDF extension to support various compression algorithms")
+      (description
+       "This package includes a plugin for the Python library ASDF to add
+support for reading and writing various compression algorithms including:
+@url{https://www.blosc.org/python-blosc/reference.html,Blosc},
+@url{https://python-lz4.readthedocs.io/en/stable/lz4.frame.html,LZ4 Frame},
+@url{http://facebook.github.io/zstd/,Zstandard}.")
+      (license license:bsd-3))))
+
 (define-public python-asdf-standard
   (package
     (name "python-asdf-standard")
-- 
2.41.0

[bug#69924] [PATCH 43/49] gnu: Add python-astroplan.

[Sharlatan Hellseher]

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

Change-Id: Ia13998c3ccfaab57a9d0670dbd7b4e1c1b92b57a
---
 gnu/packages/astronomy.scm | 80 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 7849624540..a898b98515 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1736,6 +1736,86 @@ (define-public python-astropy-iers-data
 celestial-to-terrestrial coordinate transformations.")
     (license license:bsd-3)))
 
+(define-public python-astroplan
+  (package
+    (name "python-astroplan")
+    (version "0.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "astroplan" version))
+       (sha256
+        (base32 "0jrgii0f11ckxvywinr9kcsljxnpnkh7hv5638wxwcb1iyjmx36r"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "astroplan/tests"
+              "-k" (string-append
+                    ;; Test requiring newer python-pytz
+                    "not test_timezone"
+                    ;; Disable tests requiring remote data.
+                    " and not test_FixedTarget_from_name"
+                    " and not test_altitude_constraint"
+                    " and not test_at_night_basic"
+                    " and not test_caches_shapes"
+                    " and not test_compare_airmass_constraint_and_observer"
+                    " and not test_compare_altitude_constraint_and_observer"
+                    " and not test_docs_example"
+                    " and not test_eclipses"
+                    " and not test_eq_observer"
+                    " and not test_event_observable"
+                    " and not test_galactic_plane_separation"
+                    " and not test_get_skycoord"
+                    " and not test_hash_observer"
+                    " and not test_is_night"
+                    " and not test_local_time_constraint_hawaii_tz"
+                    " and not test_local_time_constraint_utc"
+                    " and not test_moon_illumination"
+                    " and not test_moon_separation"
+                    " and not test_observability_table"
+                    " and not test_observer_lon_lat_el"
+                    " and not test_regression_airmass_141"
+                    " and not test_regression_shapes"
+                    " and not test_sun_separation"
+                    " and not test_tonight")
+              "--ignore=astroplan/tests/test_scheduling.py")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'prepare-test-environment
+            (lambda _
+              (setenv "HOME" "/tmp")
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (propagated-inputs
+     (list python-astropy
+           python-astroquery
+           python-matplotlib
+           python-numpy
+           python-pytz
+           python-six))
+    (native-inputs
+     (list python-pytest-astropy
+           python-pytest-mpl
+           python-setuptools-scm))
+    (home-page "https://github.com/astropy/astroplan")
+    (synopsis "Observation planning package for astronomers")
+    (description
+     "This package provides a flexible toolbox for observation planning and
+scheduling.  When complete, the goal is to be easy for Python beginners and new
+observers to to pick up, but powerful enough for observatories preparing nightly
+and long-term schedules.
+
+Features:
+@itemize
+@item calculate rise/set/meridian transit times, alt/az positions for targets at
+observatories anywhere on Earth
+@item built-in plotting convenience functions for standard observation planning
+plots (airmass, parallactic angle, sky maps)
+@item determining observability of sets of targets given an arbitrary set of
+constraints (i.e., altitude, airmass, moon separation/illumination, etc.)
+@end itemize")
+      (license license:bsd-3)))
+
 (define-public python-astroquery
   (package
     (name "python-astroquery")
-- 
2.41.0

[bug#69924] [PATCH 44/49] gnu: Add python-nose-exclude.

[Sharlatan Hellseher]

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: Type: text/plain; charset=a, Size: 2301 bytes --]

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

Change-Id: I5c91b682163890c822f7d4a548e92fdd287d78a2
---
 gnu/packages/check.scm | 33 ++++++++++++++++++++++++++++++++-
 1 file changed, 32 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index bd1f2d1b65..9ce21b05ba 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -39,7 +39,7 @@
 ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr>
 ;;; Copyright © 2022 Maxime Devos <maximedevos@telenet.be>
 ;;; Copyright © 2022, 2023 David Elsing <david.elsing@posteo.net>
-;;; Copyright © 2022, 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2022-2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2022 jgart <jgart@dismail.de>
 ;;; Copyright © 2023 Luis Felipe López Acevedo <luis.felipe.la@protonmail.com>
 ;;; Copyright © 2023 Timo Wilken <guix@twilken.net>
@@ -2941,6 +2941,37 @@ (define-public python-rednose
 @command{nosetests} command of the Python Nose unit test framework.")
     (license license:bsd-3)))
 
+(define-public python-nose-exclude
+  (package
+    (name "python-nose-exclude")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "nose-exclude" version))
+       (sha256
+        (base32 "0123x1lyv5b2p9civcfg8vilj2ga3q7p2ks1hq25z0gb3ssai3zp"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'disable-test
+            (lambda _
+              ;; Disable failing test: AssertionError.
+              (substitute* '("test_dirs/build/test.py"
+                            "test_dirs/test_not_me/test.py")
+                (("def test_i_should_never_run")
+                 "def off_i_should_never_run")))))))
+    (propagated-inputs
+     (list python-nose))
+    (home-page "https://github.com/kgrandis/nose-exclude")
+    (synopsis "Exclude specific directories from nosetests runs")
+    (description
+     "@code{nose-exclude} is a Nose plugin that allows you to easily specify
+directories to be excluded from testing.")
+    (license license:lgpl2.1+)))
+
 (define-public python-nose-random
   (package
     (name "python-nose-random")
-- 
2.41.0

[bug#69924] [PATCH 45/49] gnu: Add python-ewah-bool-utils.

[Sharlatan Hellseher]

* gnu/packages/python-compression.scm (python-ewah-bool-utils): New variable.

Change-Id: Ib9730d599f66bc2b864bfd305135e367f89ba9dd
---
 gnu/packages/python-compression.scm | 35 +++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index d076a4e161..16e9fc7a4b 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -196,6 +196,41 @@ (define-public python-cramjam
 @end itemize")
     (license license:expat)))
 
+(define-public python-ewah-bool-utils
+  (package
+    (name "python-ewah-bool-utils")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ewah_bool_utils" version))
+       (sha256
+        (base32 "11z9vv9m19370j762z100dqhy2ndjzkxk3w9z02lzwadbyibal3h"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'build-extensions
+            (lambda _
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (native-inputs
+     (list python-cython python-pytest))
+    (propagated-inputs
+     (list python-numpy))
+    (home-page "https://github.com/yt-project/ewah_bool_utils")
+    (synopsis "EWAH Bool Array compression")
+    (description "This package provide a Python wrapper to @acronym{EWAH,
+ Enhanced Word-Aligned Hybrid} compression bitarray method.")
+    (license (list
+              ;; LICENSE: for Python code.
+              license:bsd-3
+              ;; XXX: Check if it's possible to have it as a dedicated package
+              ;; and link here..
+              ;; ewah_bool_utils/cpp/LICENSE: for C++ bundle, sourced from
+              ;; <https://github.com/lemire/EWAHBoolArray>.
+              license:asl2.0))))
+
 (define-public python-pybcj
   (package
     (name "python-pybcj")
-- 
2.41.0

[bug#69924] [PATCH 46/49] gnu: Add python-cmyt.

[Sharlatan Hellseher]

* gnu/packages/python-xyz.scm (python-cmyt): New variable.

Change-Id: I45caa38fc391fe7890f87f41b18d3cfa8da07c80
---
 gnu/packages/astronomy.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a898b98515..14b2c37343 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2056,6 +2056,31 @@ (define-public python-cdflib
 @end itemize")
     (license license:expat)))
 
+(define-public python-cmyt
+  (package
+    (name "python-cmyt")
+    (version "2.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cmyt" version))
+       (sha256
+        (base32 "1zabmckr1z637pfqqvlkj0asfqqvx2x92163dby8x0c8yiqgdvjb"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-colorspacious python-pytest python-pytest-mpl))
+    (propagated-inputs
+     (list python-matplotlib python-numpy))
+    (home-page "https://yt-project.org/")
+    (synopsis "Matplotlib colormaps from the yt project")
+    (description
+     "This package provides a range of colormaps designed for scientific
+use with Matplotlib.  It includes perceptually uniform sequential colormaps such
+as @code{abre}, @code{dusk}, @code{kepl}, and @code{octarine}, as well as
+monochromatic sequential colormaps like @code{blue}, @code{green}, and
+@code{red}, and others (@code{algae}, @code{pastel}, and @code{xray}).")
+    (license license:bsd-3)))
+
 (define-public python-crds
   (package
     (name "python-crds")
-- 
2.41.0

[bug#69924] [PATCH 47/49] gnu: Add python-pytest-examples.

[Sharlatan Hellseher]

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

Change-Id: I8199a7d7294c3b04134474f9f116468ac327cba8
---
 gnu/packages/check.scm | 72 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 9ce21b05ba..fee330a1ce 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1377,6 +1377,78 @@ (define-public python-pytest-dotenv
 from a .env file before running tests.")
     (license license:expat)))
 
+(define-public python-pytest-examples
+  (package
+    (name "python-pytest-examples")
+    (version "0.0.10")
+    (source
+     (origin
+       ;; No tests in the PyPI tarball.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/pydantic/pytest-examples")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0lwxgyfj6lnkhmrvb6kzfskpwfz70kxnhnjvyl3l65k568c4wb4c"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-k"
+              (string-append
+               ;; Disable tests requiring pthon-ruff.
+               "not test_ruff"
+               " and not test_ruff_config"
+               " and not test_ruff_offset"
+               " and not test_ruff_ok"
+               " and not test_ruff_error"
+               " and not test_update_files"
+               " and not test_cases_update[simple.md]"
+               " and not test_cases_update[dataclass_indent.md]"
+               " and not test_cases_update[long_python_lines.py]"
+               " and not test_cases_update[simple.py]"
+               " and not test_cases_update[python_class.py]"
+               " and not test_cases_update[call_twice.md]"
+               " and not test_insert_print[example/README.md:3-33]"
+               " and not test_insert_print[example/README.md:37-40]"
+               " and not test_insert_print[example/README.md:44-47]"
+               " and not test_insert_print[example/README.md:49-66]"
+               " and not test_python_self[example/test_example.py:28-31]"
+               " and not test_python_self[example/test_example.py:40-43]"
+               " and not test_python_self_change_docstyle[example/test_example.py:28-31]"
+               " and not test_python_self_change_docstyle[example/test_example.py:40-43]"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              (substitute* "pyproject.toml"
+                ;; XXX: Removing ruff from required packages to pass Sanity
+                ;; check, add it back when it's available.
+                (("'ruff>=0.0.258',") "")
+                ;; black>=23
+                ((">=23") ">22")))))))
+    (propagated-inputs
+     ;; TODO: Add python-ruff once it has been packaged.
+     (list python-black python-pytest))
+    (native-inputs
+     (list python-hatchling))
+    (home-page "https://pypi.org/project/pytest-examples/")
+    (synopsis "Pytest plugin for testing examples in docstrings and markdown files")
+    (description
+     "Pytest-examples provides functionality for testing Python code examples
+in docstrings and markdown files, with its main features being:
+
+@itemize
+@item lint code examples using ruff and black
+@item run code examples
+@item run code examples and check print statements are inlined correctly in
+the code
+@item It can also update code examples in place to format them and insert or
+update print statements
+@end itemize")
+    (license license:expat)))
+
 (define-public python-pytest-httpserver
   (package
     (name "python-pytest-httpserver")
-- 
2.41.0

[bug#69924] [PATCH 48/49] gnu: Add python-pydantic-settings.

[Sharlatan Hellseher]

* gnu/packages/python-xyz.scm (python-pydantic-settings): New variable.

Change-Id: I410edc37f17a293f3d40ce9a2ab6416ea35bae39
---
 gnu/packages/python-xyz.scm | 65 +++++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6d587dc017..285507971a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7603,6 +7603,71 @@ (define-public python-pydantic-cli
 Interfaces} via data models provided in the JSON format.")
     (license license:expat)))
 
+(define-public python-pydantic-settings
+  (package
+    (name "python-pydantic-settings")
+    (version "2.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pydantic_settings" version))
+       (sha256
+        (base32 "1vf58f398ngk6wpf0jn51ghw65mjs3m03yn06h25jlsmx6jzdf80"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-k" (string-append
+                    ;; Disable tests requiring python-ruff.
+                    "not test_docs_examples[docs/index.md:24-83]"
+                    " and not test_docs_examples[docs/index.md:113-137]"
+                    " and not test_docs_examples[docs/index.md:148-156]"
+                    " and not test_docs_examples[docs/index.md:173-183]"
+                    " and not test_docs_examples[docs/index.md:193-201]"
+                    " and not test_docs_examples[docs/index.md:212-243]"
+                    " and not test_docs_examples[docs/index.md:286-317]"
+                    " and not test_docs_examples[docs/index.md:331-372]"
+                    " and not test_docs_examples[docs/index.md:430-439]"
+                    " and not test_docs_examples[docs/index.md:453-459]"
+                    " and not test_docs_examples[docs/index.md:514-522]"
+                    " and not test_docs_examples[docs/index.md:547-549]"
+                    " and not test_docs_examples[docs/index.md:553-585]"
+                    " and not test_docs_examples[docs/index.md:620-645]"
+                    " and not test_docs_examples[docs/index.md:654-732]"
+                    " and not test_docs_examples[docs/index.md:738-772]"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              (substitute* "pyproject.toml"
+                ;; hatchling.build failed on this line with error:
+                ;; ValueError: Unknown classifier in field
+                ;; `project.classifiers`: Framework :: Pydantic :: 2
+                (("'Framework :: Pydantic :: 2',") "")
+                ;; python-dotenv>=0.21.0
+                ((">=0.21.0") ">=0.20.0"))))
+          (add-before 'check 'set-home
+            (lambda _
+              ;; FileNotFoundError: [Errno 2] No such file or directory:
+              ;; '/homeless-shelter/
+              (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-dotenv
+           python-pydantic-2
+           python-pyaml
+           python-tomli))
+    (native-inputs
+     (list python-hatchling
+           python-pytest
+           python-pytest-examples
+           python-pytest-mock))
+    (home-page "https://docs.pydantic.dev/latest/usage/pydantic_settings/")
+    (synopsis "Settings management using Pydantic")
+    (description
+     "Pydantic Settings provides optional Pydantic features for loading a
+settings or config class from environment variables or secrets files.")
+    (license license:expat)))
+
 (define-public python-pydoc-markdown
   (package
     (name "python-pydoc-markdown")
-- 
2.41.0

[bug#69924] [PATCH 49/49] gnu: python-hvpy: Update to 1.1.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-hvpy): Update to 1.1.0.
[propagated-inputs]: Remove python-pydantic; add python-pydantic-2 and
python-pydantic-settings.

Change-Id: Id567cff01204d2e8d71bc49ec9ffc88b2bbb3f4e
---
 gnu/packages/astronomy.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 14b2c37343..bde29f7990 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2305,18 +2305,20 @@ (define-public python-extinction
 (define-public python-hvpy
   (package
     (name "python-hvpy")
-    (version "1.0.1")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "hvpy" version))
        (sha256
-        (base32 "0r0asyflz2sw9zn5vgs138nh81m0rbwbakmrncbc1ghdr3g6jahv"))))
+        (base32 "0bly1bgp0axxhzzf5imqsgmms41z8cxbjahxsibvb55dk94gwig6"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f)) ; Requires HTTP(S) access to api.beta.helioviewer.org
-    (propagated-inputs (list python-pydantic python-requests))
-    (native-inputs (list python-pytest python-pytest-astropy))
+    (propagated-inputs
+     (list python-pydantic-2 python-pydantic-settings python-requests))
+    (native-inputs
+     (list python-pytest python-pytest-astropy))
     (home-page "https://helioviewer.org/")
     (synopsis "Helioviewer Python API Wrapper")
     (description "@code{hvpy} is a Python API wrapper around the formal
-- 
2.41.0

bug#69924: [PATCH 00/49] gnu: Astronomy 2024/02 updates.

[Sharlatan Hellseher]

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--
Oleg

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