[bug#71084] [PATCH 00/26] Astronomy update 2024/05.

[bug#71084] [PATCH 00/26] Astronomy update 2024/05.

[Sharlatan Hellseher]

Hi Guix!

The spring is nearly over, but the number of updates and new packages
still coming with astro* soft update. With my gardening of the module
it's 100% covered with pyproject-build-system for each Python project
packed there and 100% built at least on x86_64 architecture.

I would like to add python-pyspedas - Python-based Space Physics
Environment Data Analysis Software, but it depends on
<https://cdaweb.gsfc.nasa.gov/WebServices/REST> which is licensed under
<https://en.wikipedia.org/wiki/NASA_Open_Source_Agreement>, so I'm doubt
if it's acceptable or not to include to Guix main channel.

This time some of the main highlights are:
- Bringing python-yt to Guix
- All python packages are build with pyproject-build-system
- All packages are buildable at least on x86_64 architecture

- added [4/4]
  - [X] python-yt :: Toolkit for analysis and visualization of
    volumetric data
  - [X] python-geopack ::  to add python-pyspedas
  - [X] python-comm :: Python Comm implementation for the Jupyter kernel
    protocol; to refresh python-ipywidgets
  - [X] python-viresclient :: Python package which connects to a VirES
    server, of which there are two: VirES for Swarm
    <https://vires.services> and VirES for Aeolus
    <https://aeolus.services>; to add python-pyspedas

- updated [15/15]
  - [X] calceph :: 3.5.5->4.0.0
  - [X] python-astropy-iers-data :: 0.2024.4.15.2.45.49->0.2024.5.13.0.30.12
  - [X] python-astropy :: 6.0.1->6.1.0
  - [X] python-astroscrappy :: 1.1.0->1.2.0
  - [X] python-ccdproc ::  2.4.1->2.4.2
  - [X] python-cdflib :: 1.2.6->1.3.1
  - [X] python-crds :: 11.17.20->11.17.22
  - [X] python-dust-extinction :: 1.3->1.4
  - [X] python-jplephem :: 2.21->2.22
  - [X] python-rad :: 0.19.2->0.20.0
  - [X] python-ewah-bool-utils :: 1.1.0->1.2.0
  - [X] python-roman-datamodels :: 0.19.1->0.20.0
  - [X] python-specutils :: 1.14.0->1.15.0
  - [X] python-stsci-image :: 2.3.5->2.3.7
  - [X] python-sunpy :: 5.1.2->5.1.3

After python-yt is available in Guix I would start preparing more Astropy
affiliated projects some of them looks very nice:
- python-tangos :: The Agile Numerical Galaxy Organisation System
- python-jdaviz :: JWST astronomical data analysis tools in the Jupyter platform

I also would like to bring IRAF project to Guix
<https://github.com/iraf-community>, it's quite old C/Fortran based
project now maintained by Ole Streicher (maintainer of
https://salsa.debian.org/debian-astro-team)

Build stats:

--8<---------------cut here---------------start------------->8---
./pre-inst-env guix build calceph python-astropy
python-astropy-iers-data python-astroscrappy python-ccdproc
python-cdflib python-comm python-crds python-dust-extinction
python-ephem python-ewah-bool-utils python-geopack python-jplephem
python-more-itertools@10.2.0 python-pyvo python-rad
python-roman-datamodels python-sep python-sgp4 python-specutils
python-stsci-image python-sunpy python-unyt python-viresclient python-yt

/gnu/store/lr7m7ka3i0317jg7m9ysn0g96k1yab9f-python-yt-4.3.1
/gnu/store/nw3ic2scsqp8060clzsxnf8xhchslpcl-python-viresclient-0.11.6
/gnu/store/ymbksv1p22rdn9fc1n7mwylpykmkdlg5-python-unyt-3.0.1
/gnu/store/n10j56jpgwcbqrvx7ii98y2pc536wy3f-python-sunpy-5.1.3
/gnu/store/jk3fphkvc4iahjsbc77mdxzdx79x9xa0-python-stsci-image-2.3.7
/gnu/store/myxavg0514pn9x0dz9bnpiyd6v00m9lg-python-specutils-1.15.0
/gnu/store/6v18fgiz99d5aj02q9z4y2smyxqja255-python-sgp4-2.23
/gnu/store/nw9n46c8x4iggz46sl2zwx4c8cvic5lg-python-sep-1.2.1
/gnu/store/z5l3g9d13g8x8dpsskgy3binhvicjfbi-python-roman-datamodels-0.20.0
/gnu/store/ck4m1qxc3nyhsim151i71afx0ay0zkfj-python-rad-0.20.0
/gnu/store/hbf6457zl31ararwhzlnvkv346f7r27k-python-pyvo-1.5.1
/gnu/store/qww87pdssi9b85kj6ma76f7pfrjbpmll-python-more-itertools-10.2.0
/gnu/store/4c71a65dv847gz1hngd2207alam1kl89-python-jplephem-2.22
/gnu/store/xw075kdkfgl1wf2gdyg65jafms7rpn3d-python-geopack-1.0.10
/gnu/store/nrpkwyxrak55glgqddpx5a5f62ddsyyw-python-ewah-bool-utils-1.2.0
/gnu/store/lryxxm8di55pzg92p5dlx97bw5slc099-python-ephem-4.1.5
/gnu/store/g2mdxjgrn2j1y0lqbifw5ybiq6bwpy0a-python-dust-extinction-1.4
/gnu/store/672rz2imm266pzyhhp9lkfxhs7f1v2lp-python-crds-11.17.22
/gnu/store/90y7ajcl05r6m4w2mhcfkrilzniqwvfc-python-comm-0.2.2
/gnu/store/vck9spqki4rv110v67j60jhqh655y1lr-python-cdflib-1.3.1
/gnu/store/8q4kickgib3cvsq7v8f806b16i4yj3ff-python-ccdproc-2.4.2
/gnu/store/5qlbc8i1yqj9jydmd5cfgkwfj5p9y2hc-python-astroscrappy-1.2.0
/gnu/store/snnhw89cd5x7xrg83x9vzzxx9771wss4-python-astropy-iers-data-0.2024.5.13.0.30.12
/gnu/store/k0v376wnz1l1f1kv4915bggavvywnlbj-python-astropy-6.1.0
/gnu/store/pdfc2v9bd4qlmzdm2d0bqrlbznfgxg8c-calceph-4.0.0
--8<---------------cut here---------------end--------------->8---

Dependent build stats:

--8<---------------cut here---------------start------------->8---
./pre-inst-env guix refresh --list-dependent calceph python-astropy
python-astropy-iers-data python-astroscrappy python-ccdproc
python-cdflib python-comm python-crds python-dust-extinction
python-ephem python-ewah-bool-utils python-geopack python-jplephem
python-more-itertools@10.2.0 python-pyvo python-rad
python-roman-datamodels python-sep python-sgp4 python-specutils
python-stsci-image python-sunpy python-unyt python-viresclient python-yt

Building the following 15 packages would ensure 63 dependent packages
are rebuilt: python-asdf-compression@0.0.1-0.57cc7e7
python-asdf-zarr@0.0.3 python-cesium@0.12.1 python-viresclient@0.11.6
scamp@2.10.0 ginga-qt5@5.0.1 python-poliastro@0.17.0 python-ginga@5.0.1
python-astroplan@0.10 python-aplpy@2.1.0 python-astroalign@2.5.1
python-jwst@1.14.0 python-radiospectra@0.5.0 python-yt@4.3.1
python-pyjanitor@0.27.0

/gnu/store/sfmkwmpihpjv10gqrbbxqzqcsb6q9ncz-python-pyjanitor-0.27.0
/gnu/store/lr7m7ka3i0317jg7m9ysn0g96k1yab9f-python-yt-4.3.1
/gnu/store/vpf2grh18jq4n59z5xk91c680g3hjkg5-python-radiospectra-0.5.0
/gnu/store/8bdpnp17zibddbgsiwyh632h794g7jrq-python-jwst-1.14.0
/gnu/store/5yrrkl1lshnz9vdmnqmlb4kysl3m1b6m-python-astroalign-2.5.1
/gnu/store/l6g5fla44hhs2rdayj9pk9wzl4hdjn6k-python-aplpy-2.1.0
/gnu/store/84gmp7ykakd4zwah9bgm59smq5zwfpj2-python-astroplan-0.10
/gnu/store/5dk6m10zr628rlj3abw965an223gh5m9-python-ginga-5.0.1
/gnu/store/35m97lhq3v26fgy5kcsyrh91sfdbkq59-python-poliastro-0.17.0
/gnu/store/b4nmarr0zzac92f32dq9hk157iszl41r-ginga-qt5-5.0.1
/gnu/store/1ibrbzqh6nm0mlkr0aafm303q2f1qaa9-scamp-2.10.0
/gnu/store/nw3ic2scsqp8060clzsxnf8xhchslpcl-python-viresclient-0.11.6
/gnu/store/0rnjpghin70x95w5psgk3ikj8xqf0iic-python-cesium-0.12.1
/gnu/store/3ycib8ybqxyq07p4f5mf5baa20fnqm1s-python-asdf-zarr-0.0.3
/gnu/store/mcl0lxi5w74b8m21iivrc8grwna1lyx4-python-asdf-compression-0.0.1-0.57cc7e7
--8<---------------cut here---------------end--------------->8---

Sharlatan Hellseher (26):
  gnu: python-sep: Refresh package style.
  gnu: python-ephem: Use pyproject-build-system.
  gnu: python-sgp4: Use pyproject-build-system.
  gnu: packages/astronomy: Minimize import from python build system.
  gnu: calceph: Update to 4.0.0.
  gnu: python-astropy-iers-data: Update to 0.2024.5.13.0.30.12.
  gnu: python-astropy: Update to 6.1.0.
  gnu: python-pyvo: Disable a failing test.
  gnu: python-astroscrappy: Update to 1.2.0.
  gnu: python-dust-extinction: Update to 1.4.
  gnu: python-ccdproc: Update to 2.4.2.
  gnu: python-cdflib: Update to 1.3.1.
  gnu: python-crds: Update to 11.17.22.
  gnu: python-jplephem: Update to 2.22.
  gnu: python-rad: Update to 0.20.0
  gnu: python-roman-datamodels: Update to 0.20.0.
  gnu: python-sunpy: Update to 5.1.3.
  gnu: python-stsci-image: Update to 2.3.7.
  gnu: python-specutils: Update to 1.15.0.
  gnu: python-unyt: Fix version detection.
  gnu: python-ewah-bool-utils: Update to 1.2.0.
  gnu: Add python-viresclient.
  gnu: Add python-geopack.
  gnu: Add python-comm.
  gnu: Add python-more-itertools-next.
  gnu: Add python-yt.

 gnu/packages/astronomy.scm          | 316 +++++++++++++++++++---------
 gnu/packages/geo.scm                |  26 +++
 gnu/packages/jupyter.scm            |  27 +++
 gnu/packages/python-compression.scm |   4 +-
 gnu/packages/python-science.scm     |   2 +-
 gnu/packages/python-xyz.scm         |  35 +++
 6 files changed, 303 insertions(+), 107 deletions(-)


base-commit: 7881d6085146fefda17ed9eefa133b5b5c97af87
-- 
2.41.0

[bug#71084] [PATCH 01/26] gnu: python-sep: Refresh package style.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sep): Refresh package style.
[package]: Swap to package/inherit.
[build-system]: Swap to pyproject-build-system.
[arguments]: <#:test-flags>: Activate tests for Python.
[native-inputs]: Do not modify inherited inputs, override instead. Add
python-pytest.
[propagated-inputs]: Override inputs.
[synopsis]: Add Python specific synopsis.

Change-Id: I86f68972eb51e9d546bcba6ee4f33de726c022e2
---
 gnu/packages/astronomy.scm | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 3701a7e90c..62100c4c51 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4472,19 +4472,16 @@ (define-public python-pysynphot
       (license license:bsd-3))))
 
 (define-public python-sep
-  (package
-    (inherit libsep)
+  (package/inherit libsep
     (name "python-sep")
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     (strip-keyword-arguments
-      '(#:make-flags) (package-arguments libsep)))
+     (list #:test-flags #~(list "test.py")))
     (native-inputs
-     (modify-inputs (package-inputs libsep)
-       (prepend python-cython)))
+     (list python-cython python-pytest))
     (propagated-inputs
-     (modify-inputs (package-inputs libsep)
-       (prepend python-numpy)))))
+     (list  python-numpy))
+    (synopsis "Python library for Source Extraction and Photometry")))
 
 (define-public python-suntime
   (package
-- 
2.41.0

[bug#71084] [PATCH 02/26] gnu: python-ephem: Use pyproject-build-system.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ephem): Adjust indentation.
[build-system]: Swap to pyproject-build-system.

Change-Id: Idc21c004f93f2362a70b2e9fb874ff125fd8c3fa
---
 gnu/packages/astronomy.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 62100c4c51..e78d9b7a40 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2324,13 +2324,13 @@ (define-public python-ephem
   (package
     (name "python-ephem")
     (version "4.1.5")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "ephem" version))
-              (sha256
-               (base32
-                "0ainqbnvw320pc61q5b6ad6f2mhn1pvrlnq489cwfx0m82mahr0c"))))
-    (build-system python-build-system)
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ephem" version))
+       (sha256
+        (base32 "0ainqbnvw320pc61q5b6ad6f2mhn1pvrlnq489cwfx0m82mahr0c"))))
+    (build-system pyproject-build-system)
     (native-inputs (list tzdata))
     (home-page "https://rhodesmill.org/pyephem/")
     (synopsis "Compute positions of the planets and stars")
-- 
2.41.0

[bug#71084] [PATCH 03/26] gnu: python-sgp4: Use pyproject-build-system.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sgp4): [build-system]: Swap to
pyproject-build-system.

Change-Id: Iebaba503a439d858f1e603ab3f7e4bd17be2adb1
---
 gnu/packages/astronomy.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e78d9b7a40..2d9acc5192 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2855,7 +2855,7 @@ (define-public python-sgp4
        (uri (pypi-uri "sgp4" version))
        (sha256
         (base32 "0aalbmldks6ykgkcxwkvnp04q0avhv903m5zwvg8i7zvl99xrbfq"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (propagated-inputs
      (list python-numpy))
     (home-page "https://github.com/brandon-rhodes/python-sgp4")
-- 
2.41.0

[bug#71084] [PATCH 04/26] gnu: packages/astronomy: Minimize import from python build system.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm: Select just pypi-uri from python build
system module.

Change-Id: I1b02cdd24a6456d58136ee126f7bdb2a01dce9b4
---
 gnu/packages/astronomy.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 2d9acc5192..f7683f6d71 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -97,7 +97,7 @@ (define-module (gnu packages astronomy)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
-  #:use-module (guix build-system python)
+  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix build-system pyproject)
   #:use-module (guix download)
   #:use-module (guix gexp)
-- 
2.41.0

[bug#71084] [PATCH 05/26] gnu: calceph: Update to 4.0.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (calceph): Update to 4.0.0.
[source]: Swap to git checkout.
[build-system]: Swap to cmake-build-system.
[properties]: Remove them.

Change-Id: Ic1559a1f956aa90200c911fbee057c55a7fb9874
---
 gnu/packages/astronomy.scm | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index f7683f6d71..c3894c284a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -191,20 +191,21 @@ (define-public aocommon
 (define-public calceph
   (package
     (name "calceph")
-    (version  "3.5.5")
+    (version  "4.0.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://www.imcce.fr/content/medias/recherche/equipes/asd/calceph/calceph-"
-             version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.obspm.fr/imcce_calceph/calceph")
+             (commit (string-append name "_"
+                                    (string-replace-substring version "." "_")))))
        (sha256
-        (base32 "1jiaqyir2qcxzjlhk7f9fhrf6snjsiwxznvzdl996xr6m4lzbb7p"))))
-    (build-system gnu-build-system)
+        (base32 "1yabdq51plg3dijp68xajhsz395gi2fyp5qkvrj3dgv8d4qw52nw"))
+       (file-name (git-file-name name version))))
+    (build-system cmake-build-system)
     (native-inputs
      (list gfortran))
     (home-page "https://www.imcce.fr/inpop/calceph")
-    (properties `((release-monitoring-url . ,home-page)))
     (synopsis "Astronomical library to access the binary planetary ephemeris files")
     (description
      "The CALCEPH Library is designed to access the binary planetary ephemeris files,
-- 
2.41.0

[bug#71084] [PATCH 06/26] gnu: python-astropy-iers-data: Update to 0.2024.5.13.0.30.12.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy-iers-data): Update to 0.2024.5.13.0.30.12.

Change-Id: Iac104aea31b967d902f424f3257a07c30d245007
---
 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 c3894c284a..aec8455b3b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1760,13 +1760,13 @@ (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 "0.2024.4.15.2.45.49")
+    (version "0.2024.5.13.0.30.12")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy_iers_data" version))
        (sha256
-        (base32 "15wran1d5bw1mm3xl3ibp6i5aa7icj9p6g1mqcyp596qmdjnm8wp"))))
+        (base32 "1vs3aqg0mb54bkci646h5pqbnfb50798ajim6xjg7nacpjhr8j3p"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#71084] [PATCH 07/26] gnu: python-astropy: Update to 6.1.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy): Update to 6.1.0.

Change-Id: I72bbbec2df8fb6aba884c0700a977b34b3d8beec
---
 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 aec8455b3b..6b2c124f80 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1614,13 +1614,13 @@ (define-public celestia-gtk
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "6.0.1")
+    (version "6.1.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "175k2h039c0b8rsf0fdphmxbpjrszd138j8z9zkhh1kd6pg7bac9"))
+        (base32 "03wm12bpfifvjbvf7rixv9yr5ya5c9gy9p0dff862mxi21gr2fvc"))
        (modules '((guix build utils)))
        (snippet
         '(begin
-- 
2.41.0

[bug#71084] [PATCH 08/26] gnu: python-pyvo: Disable a failing test.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pyvo) [arguments]: <#:test-flags>:
Disable one failing test.

Change-Id: I662a08126991c7db1f37d9ae04160f5a926d443f
---
 gnu/packages/astronomy.scm | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6b2c124f80..39fc59509c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2709,6 +2709,11 @@ (define-public python-pyvo
        (sha256
         (base32 "0cm6agaf1gvc5bi95wx6a70ngj9vn95rx78fs59vlrmpww7q2807"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; Disable one failing test, see
+      ;; <https://github.com/astropy/pyvo/issues/547>.
+      #:test-flags #~(list "-k" "not test_single_table_description")))
     (native-inputs
      (list python-pytest-astropy python-requests-mock python-setuptools-scm))
     (propagated-inputs
-- 
2.41.0

[bug#71084] [PATCH 09/26] gnu: python-astroscrappy: Update to 1.2.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroscrappy): Update to 1.2.0.
[native-inputs]: Remove python-cython, python-h5py, python-pandas, and
python-scikit-image; add python-cython-3.

Change-Id: I8008d35e94f9076c489709ad241f97dec6e22b2a
---
 gnu/packages/astronomy.scm | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 39fc59509c..48dde56d1e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1936,13 +1936,13 @@ (define-public python-astroquery
 (define-public python-astroscrappy
   (package
     (name "python-astroscrappy")
-    (version "1.1.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astroscrappy" version))
        (sha256
-        (base32 "0shmfilvzpmlwz4fh0bx4kqmzr0y39fgga6vipxb5d1rx1y6q6by"))))
+        (base32 "0r2alg8imr201ykjsvr6y43bzw8mwbc4ddprn8f6qfw9k4hsx8ff"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1958,12 +1958,9 @@ (define-public python-astroscrappy
               (make-file-writable "astroscrappy/_compiler.c")
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
-     (list python-cython
+     (list python-cython-3
            python-extension-helpers
-           python-h5py
-           python-pandas
            python-pytest-astropy
-           python-scikit-image
            python-scipy
            python-setuptools-scm))
     (propagated-inputs (list python-astropy python-numpy))
-- 
2.41.0

[bug#71084] [PATCH 10/26] gnu: python-dust-extinction: Update to 1.4.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-dust-extinction): Update to 1.4.

Change-Id: I335f9ae01c022c6bea229b73f131aab459126809
---
 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 48dde56d1e..d832b738a9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2299,13 +2299,13 @@ (define-public python-drizzle
 (define-public python-dust-extinction
   (package
     (name "python-dust-extinction")
-    (version "1.3")
+    (version "1.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "dust_extinction" version))
        (sha256
-        (base32 "14zy6kyrfi4ash7qg1k3im1zzgr2r7rnaggzk0ar3jlfmsii743k"))))
+        (base32 "0yw2mdsbsmk0cs9wzsmmrnkhriyhj1gir6irjsfxd518fa8bik2k"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      (list python-astropy python-scipy))
-- 
2.41.0

[bug#71084] [PATCH 11/26] gnu: python-ccdproc: Update to 2.4.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ccdproc): Update to 2.4.2.

Change-Id: Ic6be0d26ae6f612c9b57fd88b0458496c28b353a
---
 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 d832b738a9..2065badfa4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2048,13 +2048,13 @@ (define-public python-casa-formats-io
 (define-public python-ccdproc
   (package
     (name "python-ccdproc")
-    (version "2.4.1")
+    (version "2.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ccdproc" version))
        (sha256
-        (base32 "186plgfhrj7wivs053y65jlv1x33y8ii31jdr2rm4s6pl0j7x29z"))))
+        (base32 "14faivm9nihpdwzg0jx1c9zr7jk22gjfjw78raq6h63ypl10i6yx"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-memory-profiler
-- 
2.41.0

[bug#71084] [PATCH 12/26] gnu: python-cdflib: Update to 1.3.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-cdflib): Update to 1.3.1.
[propagated-inputs]: Remove python-attrs.

Change-Id: I13abd2608c18796e6d8d5d37bee0a037fbd2794d
---
 gnu/packages/astronomy.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 2065badfa4..c6baece0f7 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2076,7 +2076,7 @@ (define-public python-ccdproc
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-    (version "1.2.6")
+    (version "1.3.1")
     (source
      (origin
        (method git-fetch)               ; no tests in PyPI release
@@ -2085,7 +2085,7 @@ (define-public python-cdflib
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1wxr35sqsdqzf85xyjh1v8hmwwiyv4cn0lr7q8l1kkngfywq5l2r"))))
+        (base32 "0zmz9wjhlq43lqy5k4fld9cj5k39s1hkkaligrn3kpf9hcbd79qn"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases
@@ -2098,7 +2098,7 @@ (define-public python-cdflib
                  (lambda _
                    (setenv "HOME" (getcwd)))))))
     (propagated-inputs
-     (list python-attrs python-numpy))
+     (list python-numpy))
     (native-inputs
      (list python-astropy
            python-hypothesis
-- 
2.41.0

[bug#71084] [PATCH 13/26] gnu: python-crds: Update to 11.17.22.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-crds): Update to 11.17.22. Adjust
indentation.
[native-inputs]: Remove python-flake8, python-ipython,
python-lockfile, python-mock, python-nose, python-pylint, and
python-pytest.

Change-Id: Idbbece6544755753dce2046292d2552924992959
---
 gnu/packages/astronomy.scm | 45 +++++++++++++++++---------------------
 1 file changed, 20 insertions(+), 25 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c6baece0f7..38b878ab25 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2150,13 +2150,13 @@ (define-public python-cmyt
 (define-public python-crds
   (package
     (name "python-crds")
-    (version "11.17.20")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "crds" version))
-              (sha256
-               (base32
-                "0480jjklv2p60fp892dr4qglwv44k86hx29y8q1c967l9k53wc9f"))))
+    (version "11.17.22")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "crds" version))
+       (sha256
+        (base32 "1i2wh7cgyn7r0fnn7ikfsdqjrcpg46xsk619mhdqywk5yjcxlz9f"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2164,24 +2164,19 @@ (define-public python-crds
       ;; additional test data. See:
       ;; https://github.com/spacetelescope/crds/blob/master/setup_test_cache
       #:tests? #f))
-    (propagated-inputs (list python-asdf
-                             python-astropy
-                             python-boto3
-                             python-filelock
-                             python-numpy
-                             python-parsley
-                             python-pysynphot
-                             python-roman-datamodels
-                             python-stsynphot
-                             python-requests))
-    (native-inputs (list python-flake8
-                         python-ipython
-                         python-lockfile
-                         python-mock
-                         python-nose
-                         python-pylint
-                         python-pytest
-                         python-setuptools-scm))
+    (propagated-inputs
+     (list python-asdf
+           python-astropy
+           python-boto3
+           python-filelock
+           python-numpy
+           python-parsley
+           python-pysynphot
+           python-roman-datamodels
+           python-stsynphot
+           python-requests))
+    (native-inputs
+     (list python-setuptools-scm))
     (home-page "https://hst-crds.stsci.edu")
     (synopsis "Calibration Reference Data System for HST and JWST")
     (description
-- 
2.41.0

[bug#71084] [PATCH 14/26] gnu: python-jplephem: Update to 2.22.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-jplephem): Update to 2.22.

Change-Id: I87c1d7e61438634fa1562c5ab42ca2f90ae588a4
---
 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 38b878ab25..e7ce7e7efc 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4109,13 +4109,13 @@ (define-public sunclock
 (define-public python-jplephem
   (package
     (name "python-jplephem")
-    (version "2.21")
+    (version "2.22")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "jplephem" version))
        (sha256
-        (base32 "0mcdhb22vwbyavcnkcwchj0cxnxsvaw5563v464ipwlm0rhln69l"))))
+        (base32 "0b2rgb7pvwnl72pqjryf9c812mmdxr69fwiym7mnz05l2xrcr6hd"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#71084] [PATCH 15/26] gnu: python-rad: Update to 0.20.0

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-rad): Update to 0.20.0. Adjust
indentation.

Change-Id: I5921c5153ace1032313121c00c73423f3d1e7c84
---
 gnu/packages/astronomy.scm | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e7ce7e7efc..16e5310e74 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4997,13 +4997,13 @@ (define-public python-gwcs
 (define-public python-rad
   (package
     (name "python-rad")
-    (version "0.19.2")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "rad" version))
-              (sha256
-               (base32
-                "08dh9asdjgfmczmqyjplgdvbk3n68qw6akd8h953wq6v3yr4k4rq"))))
+    (version "0.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "rad" version))
+       (sha256
+        (base32 "05b7qjhahzfjdp820m3qm69wrzb73njjqrzkk7hxkd8gbrbp0mj1"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -5012,7 +5012,8 @@ (define-public python-rad
       #:test-flags #~(list "--ignore=tests/test_schemas.py")))
     (native-inputs
      (list python-pytest python-setuptools-scm))
-    (propagated-inputs (list python-asdf python-asdf-astropy))
+    (propagated-inputs
+     (list python-asdf python-asdf-astropy))
     (home-page "https://github.com/spacetelescope/rad")
     (synopsis "Roman Attribute Dictionary")
     (description
-- 
2.41.0

[bug#71084] [PATCH 16/26] gnu: python-roman-datamodels: Update to 0.20.0.

[Sharlatan Hellseher]

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

Change-Id: I6bd533d81a0c8b6f2cc183e274190ff7042e965f
---
 gnu/packages/astronomy.scm | 40 ++++++++++++++++++++------------------
 1 file changed, 21 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 16e5310e74..b7c885c8f2 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5098,13 +5098,13 @@ (define-public python-radiospectra
 (define-public python-roman-datamodels
   (package
     (name "python-roman-datamodels")
-    (version "0.19.1")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "roman_datamodels" version))
-              (sha256
-               (base32
-                "1fp9rwzm5kzm0hjwwmlx7kym7yriyhxbfg2zr3y625pyvwpnl0a8"))))
+    (version "0.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "roman_datamodels" version))
+       (sha256
+        (base32 "1918wnssf478w168mhv009jkirmny8hyfxrkwvl8iish36dcqagh"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -5115,18 +5115,20 @@ (define-public python-roman-datamodels
           (add-after 'unpack 'set-env
             (lambda _
               (setenv "HOME" "/tmp"))))))
-    (propagated-inputs (list python-asdf
-                             python-asdf-astropy
-                             python-astropy
-                             python-gwcs
-                             python-numpy
-                             python-psutil
-                             python-rad))
-    (native-inputs (list python-pytest
-                         python-pytest-doctestplus
-                         python-pytest-env
-                         python-pytest-xdist
-                         python-setuptools-scm))
+    (propagated-inputs
+     (list python-asdf
+           python-asdf-astropy
+           python-astropy
+           python-gwcs
+           python-numpy
+           python-psutil
+           python-rad))
+    (native-inputs
+     (list python-pytest
+           python-pytest-doctestplus
+           python-pytest-env
+           python-pytest-xdist
+           python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/roman_datamodels")
     (synopsis "Roman Datamodels Support")
     (description
-- 
2.41.0

[bug#71084] [PATCH 17/26] gnu: python-sunpy: Update to 5.1.3.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sunpy): Update to 5.1.3.

Change-Id: If025ccc8435202a6bf50cf1e48d1955c51a78a34
---
 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 b7c885c8f2..9df51c03e4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2875,13 +2875,13 @@ (define-public python-sgp4
 (define-public python-sunpy
   (package
     (name "python-sunpy")
-    (version "5.1.2")
+    (version "5.1.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sunpy" version))
        (sha256
-        (base32 "0h62qh74xanj2drikjch7h0a5g4dsaf3v4qxx38vjazmibc37ynp"))))
+        (base32 "0bqpbdgd3blpa4y5f45j5cqn0xdnmqvqnqr1vmqwn5ddlx88z5lh"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#71084] [PATCH 18/26] gnu: python-stsci-image: Update to 2.3.7.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stsci-image): Update to 2.3.7.

Change-Id: Icd3c8d2b893e9eb83820912a0f6afe855330aa97
---
 gnu/packages/astronomy.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9df51c03e4..e86761048f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3229,13 +3229,13 @@ (define-public python-spherical-geometry
 (define-public python-stsci-image
   (package
     (name "python-stsci-image")
-    (version "2.3.5")
+    (version "2.3.7")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "stsci.image" version))
+       (uri (pypi-uri "stsci_image" version))
        (sha256
-        (base32 "1vnp4256nbdvapa69cmm80sjz11ygxa49abr9nbvssj6nyyp5icb"))))
+        (base32 "13sbych5929isrick2035rk31qcb1icm2l6pz7pjqsi45hsffxxm"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#71084] [PATCH 19/26] gnu: python-specutils: Update to 1.15.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-specutils): Update to 1.15.0.

Change-Id: I43f19ce39574a497097f4605dc2a18f6fd6343e9
---
 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 e86761048f..13387c3349 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3130,13 +3130,13 @@ (define-public python-spectral-cube
 (define-public python-specutils
   (package
     (name "python-specutils")
-    (version "1.14.0")
+    (version "1.15.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "specutils" version))
        (sha256
-        (base32 "06l0k8hi4hbfs825cnw948nnkl627g3w48n2pf9rspbvd3vbs2qf"))))
+        (base32 "0gx90dn9vmbvd7a53xb7a51jabskrad52g7imgy0ih1jchdls2pj"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#71084] [PATCH 20/26] gnu: python-unyt: Fix version detection.

[Sharlatan Hellseher]

* gnu/packages/python-science.scm (python-unyt): Fix version detection.
[native-inputs]: Add python-setuptools-scm.

Change-Id: I96e7d2530b15299a39911bebf62b76a9191ea91b
---
 gnu/packages/python-science.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 861badad2e..5e37177712 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1860,7 +1860,7 @@ (define-public python-unyt
                              python-numpy
                              python-sympy))
     ;; Pint is optional, but we do not propagate it due to its size.
-    (native-inputs (list python-pint python-pytest))
+    (native-inputs (list python-pint python-pytest python-setuptools-scm))
     (home-page "https://unyt.readthedocs.io")
     (synopsis "Library for working with data that has physical units")
     (description
-- 
2.41.0

[bug#71084] [PATCH 21/26] gnu: python-ewah-bool-utils: Update to 1.2.0.

[Sharlatan Hellseher]

* gnu/packages/python-compression.scm (python-ewah-bool-utils): Update to 1.2.0.

Change-Id: I7bc50249f2d7e97c64d23054ad176cf0e4af6258
---
 gnu/packages/python-compression.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
index 947dd189d3..96e607bfe9 100644
--- a/gnu/packages/python-compression.scm
+++ b/gnu/packages/python-compression.scm
@@ -200,13 +200,13 @@ (define-public python-cramjam
 (define-public python-ewah-bool-utils
   (package
     (name "python-ewah-bool-utils")
-    (version "1.1.0")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ewah_bool_utils" version))
        (sha256
-        (base32 "11z9vv9m19370j762z100dqhy2ndjzkxk3w9z02lzwadbyibal3h"))))
+        (base32 "1bff3cv5m4n5pwqz0q90dy42vpyrrhylnrkcd49g1dlf3fs6r0pp"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

[bug#71084] [PATCH 22/26] gnu: Add python-viresclient.

[Sharlatan Hellseher]

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

Change-Id: I690a6d8f1fc80dde1605f50d09f540d556fa881b
---
 gnu/packages/astronomy.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 13387c3349..122be3b260 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5214,6 +5214,37 @@ (define-public python-skyfield
 orbit around the Earth.")
     (license license:expat)))
 
+(define-public python-viresclient
+  (package
+    (name "python-viresclient")
+    (version "0.11.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "viresclient" version))
+       (sha256
+        (base32 "1npn5ka0cflvl6ngf5b08z59dh79hnyh5v2z4sf0872q9zkwmjjw"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-flit-core python-pytest))
+    (propagated-inputs
+     (list python-cdflib
+           python-jinja2
+           python-netcdf4
+           python-pandas
+           python-requests
+           python-tables
+           python-tqdm
+           python-xarray))
+    (home-page "https://viresclient.readthedocs.io/en/latest/")
+    (synopsis "Python client for interacting with a VirES server")
+    (description
+     "This package provides a Python client for interacting with a
+@code{VirES} server, of which there are two: VirES for
+@url{https://vires.services, Swarm} and VirES for
+@url{https://aeolus.services, Aeolus}")
+    (license license:expat)))
+
 (define-public python-wiimatch
   (package
     (name "python-wiimatch")
-- 
2.41.0

[bug#71084] [PATCH 23/26] gnu: Add python-geopack.

[Sharlatan Hellseher]

* gnu/packages/geo.scm (python-geopack): New variable.

Change-Id: I674b09030684dd0d9f94b4b87cf96aeea983ee89
---
 gnu/packages/geo.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index c9152fb4f8..69e7b58677 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -959,6 +959,32 @@ (define-public python-fiona
 pyproj, Rtree, and Shapely.")
     (license license:bsd-3)))
 
+(define-public python-geopack
+  (package
+    (name "python-geopack")
+    (version "1.0.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "geopack" version))
+       (sha256
+        (base32 "0mryjp7m4h99qlpvnn40s81sygr73qcv8rkmjp9pcli1gz829kjf"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX Reported upstream <https://github.com/tsssss/geopack/issues/21>.
+      #:tests? #f))
+    (native-inputs
+     (list python-pytest))
+    (propagated-inputs
+     (list python-numpy python-scipy))
+    (home-page "https://github.com/tsssss/geopack")
+    (synopsis "Python version of geopack and Tsyganenko models")
+    (description
+     "Python version of geopack and Tsyganenko models, compatible with
+@code{geopack05} and @code{geopack08}.")
+    (license license:expat)))
+
 (define-public python-geopandas
   (package
     (name "python-geopandas")
-- 
2.41.0

[bug#71084] [PATCH 24/26] gnu: Add python-comm.

[Sharlatan Hellseher]

* gnu/packages/jupyter.scm (python-comm): New variable.

Change-Id: I1bed7b6f54e63db6f47cdbaccd816c56f06045f8
---
 gnu/packages/jupyter.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index ef68521b53..7ff6202665 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr>
 ;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -491,6 +492,32 @@ (define-public python-jupyter-server-mathjax
 Mathjax, the JavaScript display engine for mathematics.")
     (license license:bsd-3)))
 
+(define-public python-comm
+  (package
+    (name "python-comm")
+    (version "0.2.2")
+    (source
+     (origin
+       (method git-fetch)   ; no tests data in PyPi package
+       (uri (git-reference
+             (url "https://github.com/ipython/comm")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "18xsbpd8dgcfbc51xl59nlwaq7jnyzvgzjfj6psscv71894x4lg7"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-hatchling python-pytest python-setuptools-scm))
+    (propagated-inputs
+     (list python-traitlets))
+    (home-page "https://github.com/ipython/comm")
+    (synopsis "Python Comm implementation for the Jupyter kernel protocol")
+    (description
+     "This package provides a way to register a Kernel Comm implementation, as
+per the Jupyter kernel protocol. It also provides a base Comm implementation
+and a default CommManager that can be used.")
+    (license license:bsd-3)))
+
 (define-public python-nbclient
   (package
     (name "python-nbclient")
-- 
2.41.0

[bug#71084] [PATCH 25/26] gnu: Add python-more-itertools-next.

[Sharlatan Hellseher]

* gnu/packages/python-xyz.scm (python-more-itertools-next): New variable.

Change-Id: Ia9deef0c19931356446e2731a315d27ce54e6ab0
---
 gnu/packages/python-xyz.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9d3066cab4..520dcd0b69 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26462,6 +26462,41 @@ (define-public python-more-itertools
 working with iterables.")
     (license license:expat)))
 
+;; Needed for python-yt, older version fails with exception: E ImportError:
+;; cannot import name 'mark_ends' from 'more_itertools'
+;; (<...>more_itertools/__init__.py)
+(define-public python-more-itertools-next
+  (package
+    (inherit python-more-itertools)
+    (name "python-more-itertools")
+    (version "10.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "more-itertools" version))
+       (sha256
+        (base32
+         "1q9rq9g026m4wl6ki2q8pw7xbc02vl34qqw702h9jgixqj0b9k4g"))
+       (snippet
+        ;; distutils.errors.DistutilsOptionError: No configuration found for
+        ;; dynamic 'description'. Some dynamic fields need to be specified via
+        ;; `tool.setuptools.dynamic`others must be specified via the equivalent
+        ;; attribute in `setup.py`.
+        '(delete-file "setup.py"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "python" "-m" "unittest")))))))
+    (native-inputs
+     (list python-flit-core))
+    (propagated-inputs
+     (list python-six))))
+
 (define-public python-latexcodec
   (package
     (name "python-latexcodec")
-- 
2.41.0

[bug#71084] [PATCH 26/26] gnu: Add python-yt.

[Sharlatan Hellseher]

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

Change-Id: Ic8331de39e0a5e875aef8d49b7597c269b2b155e
---
 gnu/packages/astronomy.scm | 79 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 122be3b260..c1fe5b0a47 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5268,6 +5268,85 @@ (define-public python-wiimatch
 using (multivariate) polynomials.")
     (license license:bsd-3)))
 
+(define-public python-yt
+  (package
+    (name "python-yt")
+    (version "4.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "yt" version))
+       (sha256
+        (base32 "03jy35vyniyd1pd3sv0zpd2f3ks2iyqw65xv28ids8nw6v1vavbv"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:build-backend "setuptools.build_meta"
+      #:test-flags
+      #~(list "-n" "auto")
+      #:phases
+      #~(modify-phases %standard-phases
+         (add-after 'unpack 'relax-requirements
+           (lambda _
+             (substitute* "pyproject.toml"
+               ;; XXX: Updating ipywidgets requires long chain of rebuilds,
+               ;; maybe for python-team.
+               ;;
+               ;; ipywidgets>=8.0.0
+               ((">=8.0.0") ">=7.6.3"))))
+          (add-before 'check 'prepare-test-environment
+            (lambda _
+              (setenv "HOME" "/tmp")
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (propagated-inputs
+     (list python-cmyt
+           python-ewah-bool-utils
+           python-ipywidgets
+           python-matplotlib
+           python-more-itertools-next
+           python-numpy
+           python-packaging
+           python-pillow
+           python-tomli-w
+           python-tqdm
+           python-unyt))
+    (native-inputs
+     (list python-cython-3
+           python-nose
+           python-nose-exclude
+           python-nose-timer
+           python-pyaml
+           python-pytest
+           python-pytest-mpl
+           python-pytest-xdist
+           python-setuptools
+           python-sympy))
+    (home-page "http://yt-project.org/")
+    (synopsis "Analyzing and visualizing volumetric data framework")
+    (description
+     "This package provides a structured, variable-resolution meshes,
+ unstructured meshes, and discrete or sampled data such as particles.  Focused on
+ driving physically-meaningful inquiry, it has been applied in domains such as
+ astrophysics, seismology, nuclear engineering, molecular dynamics, and
+ oceanography.")
+    (license (list
+              ;; COPYING.txt: for Python code.
+              ;;
+              ;; yt uses a shared copyright model. Each contributor maintains
+              ;; copyright over their contributions to yt. But, it is important
+              ;; to note that these contributions are typically only changes to
+              ;; the repositories. Thus, the yt source code, in its entirety is
+              ;; not the copyright of any single person or institution. Instead,
+              ;; it is the collective copyright of the entire yt Development
+              ;; Team. If individual contributors want to maintain a record of
+              ;; what changes/contributions they have specific copyright on,
+              ;; they should indicate their copyright in the commit message of
+              ;; the change, when they commit the change to one of the yt
+              ;; repositories.
+              license:bsd-3
+              ;; yt/frontends/artio/artio_headers/LICENSE: for C code.
+              license:lgpl3))))
+
 (define-public unsio
   ;; There is no versioned tag, use the latest commit.
   (let ((commit "25e52468298e1194c9726ef5dba9d5fbb46870f5")
-- 
2.41.0

bug#71084: [PATCH 00/26] Astronomy update 2024/05.

[Andrew Tropin via Guix-patches via]

[-- Attachment #1: Type: text/plain, Size: 8867 bytes --]

On 2024-05-20 23:11, Sharlatan Hellseher wrote:

> Hi Guix!
>
> The spring is nearly over, but the number of updates and new packages
> still coming with astro* soft update. With my gardening of the module
> it's 100% covered with pyproject-build-system for each Python project
> packed there and 100% built at least on x86_64 architecture.
>
> I would like to add python-pyspedas - Python-based Space Physics
> Environment Data Analysis Software, but it depends on
> <https://cdaweb.gsfc.nasa.gov/WebServices/REST> which is licensed under
> <https://en.wikipedia.org/wiki/NASA_Open_Source_Agreement>, so I'm doubt
> if it's acceptable or not to include to Guix main channel.
>
> This time some of the main highlights are:
> - Bringing python-yt to Guix
> - All python packages are build with pyproject-build-system
> - All packages are buildable at least on x86_64 architecture
>
> - added [4/4]
>   - [X] python-yt :: Toolkit for analysis and visualization of
>     volumetric data
>   - [X] python-geopack ::  to add python-pyspedas
>   - [X] python-comm :: Python Comm implementation for the Jupyter kernel
>     protocol; to refresh python-ipywidgets
>   - [X] python-viresclient :: Python package which connects to a VirES
>     server, of which there are two: VirES for Swarm
>     <https://vires.services> and VirES for Aeolus
>     <https://aeolus.services>; to add python-pyspedas
>
> - updated [15/15]
>   - [X] calceph :: 3.5.5->4.0.0
>   - [X] python-astropy-iers-data :: 0.2024.4.15.2.45.49->0.2024.5.13.0.30.12
>   - [X] python-astropy :: 6.0.1->6.1.0
>   - [X] python-astroscrappy :: 1.1.0->1.2.0
>   - [X] python-ccdproc ::  2.4.1->2.4.2
>   - [X] python-cdflib :: 1.2.6->1.3.1
>   - [X] python-crds :: 11.17.20->11.17.22
>   - [X] python-dust-extinction :: 1.3->1.4
>   - [X] python-jplephem :: 2.21->2.22
>   - [X] python-rad :: 0.19.2->0.20.0
>   - [X] python-ewah-bool-utils :: 1.1.0->1.2.0
>   - [X] python-roman-datamodels :: 0.19.1->0.20.0
>   - [X] python-specutils :: 1.14.0->1.15.0
>   - [X] python-stsci-image :: 2.3.5->2.3.7
>   - [X] python-sunpy :: 5.1.2->5.1.3
>
> After python-yt is available in Guix I would start preparing more Astropy
> affiliated projects some of them looks very nice:
> - python-tangos :: The Agile Numerical Galaxy Organisation System
> - python-jdaviz :: JWST astronomical data analysis tools in the Jupyter platform
>
> I also would like to bring IRAF project to Guix
> <https://github.com/iraf-community>, it's quite old C/Fortran based
> project now maintained by Ole Streicher (maintainer of
> https://salsa.debian.org/debian-astro-team)
>
> Build stats:
>
> --8<---------------cut here---------------start------------->8---
> ./pre-inst-env guix build calceph python-astropy
> python-astropy-iers-data python-astroscrappy python-ccdproc
> python-cdflib python-comm python-crds python-dust-extinction
> python-ephem python-ewah-bool-utils python-geopack python-jplephem
> python-more-itertools@10.2.0 python-pyvo python-rad
> python-roman-datamodels python-sep python-sgp4 python-specutils
> python-stsci-image python-sunpy python-unyt python-viresclient python-yt
>
> /gnu/store/lr7m7ka3i0317jg7m9ysn0g96k1yab9f-python-yt-4.3.1
> /gnu/store/nw3ic2scsqp8060clzsxnf8xhchslpcl-python-viresclient-0.11.6
> /gnu/store/ymbksv1p22rdn9fc1n7mwylpykmkdlg5-python-unyt-3.0.1
> /gnu/store/n10j56jpgwcbqrvx7ii98y2pc536wy3f-python-sunpy-5.1.3
> /gnu/store/jk3fphkvc4iahjsbc77mdxzdx79x9xa0-python-stsci-image-2.3.7
> /gnu/store/myxavg0514pn9x0dz9bnpiyd6v00m9lg-python-specutils-1.15.0
> /gnu/store/6v18fgiz99d5aj02q9z4y2smyxqja255-python-sgp4-2.23
> /gnu/store/nw9n46c8x4iggz46sl2zwx4c8cvic5lg-python-sep-1.2.1
> /gnu/store/z5l3g9d13g8x8dpsskgy3binhvicjfbi-python-roman-datamodels-0.20.0
> /gnu/store/ck4m1qxc3nyhsim151i71afx0ay0zkfj-python-rad-0.20.0
> /gnu/store/hbf6457zl31ararwhzlnvkv346f7r27k-python-pyvo-1.5.1
> /gnu/store/qww87pdssi9b85kj6ma76f7pfrjbpmll-python-more-itertools-10.2.0
> /gnu/store/4c71a65dv847gz1hngd2207alam1kl89-python-jplephem-2.22
> /gnu/store/xw075kdkfgl1wf2gdyg65jafms7rpn3d-python-geopack-1.0.10
> /gnu/store/nrpkwyxrak55glgqddpx5a5f62ddsyyw-python-ewah-bool-utils-1.2.0
> /gnu/store/lryxxm8di55pzg92p5dlx97bw5slc099-python-ephem-4.1.5
> /gnu/store/g2mdxjgrn2j1y0lqbifw5ybiq6bwpy0a-python-dust-extinction-1.4
> /gnu/store/672rz2imm266pzyhhp9lkfxhs7f1v2lp-python-crds-11.17.22
> /gnu/store/90y7ajcl05r6m4w2mhcfkrilzniqwvfc-python-comm-0.2.2
> /gnu/store/vck9spqki4rv110v67j60jhqh655y1lr-python-cdflib-1.3.1
> /gnu/store/8q4kickgib3cvsq7v8f806b16i4yj3ff-python-ccdproc-2.4.2
> /gnu/store/5qlbc8i1yqj9jydmd5cfgkwfj5p9y2hc-python-astroscrappy-1.2.0
> /gnu/store/snnhw89cd5x7xrg83x9vzzxx9771wss4-python-astropy-iers-data-0.2024.5.13.0.30.12
> /gnu/store/k0v376wnz1l1f1kv4915bggavvywnlbj-python-astropy-6.1.0
> /gnu/store/pdfc2v9bd4qlmzdm2d0bqrlbznfgxg8c-calceph-4.0.0
> --8<---------------cut here---------------end--------------->8---
>
> Dependent build stats:
>
> --8<---------------cut here---------------start------------->8---
> ./pre-inst-env guix refresh --list-dependent calceph python-astropy
> python-astropy-iers-data python-astroscrappy python-ccdproc
> python-cdflib python-comm python-crds python-dust-extinction
> python-ephem python-ewah-bool-utils python-geopack python-jplephem
> python-more-itertools@10.2.0 python-pyvo python-rad
> python-roman-datamodels python-sep python-sgp4 python-specutils
> python-stsci-image python-sunpy python-unyt python-viresclient python-yt
>
> Building the following 15 packages would ensure 63 dependent packages
> are rebuilt: python-asdf-compression@0.0.1-0.57cc7e7
> python-asdf-zarr@0.0.3 python-cesium@0.12.1 python-viresclient@0.11.6
> scamp@2.10.0 ginga-qt5@5.0.1 python-poliastro@0.17.0 python-ginga@5.0.1
> python-astroplan@0.10 python-aplpy@2.1.0 python-astroalign@2.5.1
> python-jwst@1.14.0 python-radiospectra@0.5.0 python-yt@4.3.1
> python-pyjanitor@0.27.0
>
> /gnu/store/sfmkwmpihpjv10gqrbbxqzqcsb6q9ncz-python-pyjanitor-0.27.0
> /gnu/store/lr7m7ka3i0317jg7m9ysn0g96k1yab9f-python-yt-4.3.1
> /gnu/store/vpf2grh18jq4n59z5xk91c680g3hjkg5-python-radiospectra-0.5.0
> /gnu/store/8bdpnp17zibddbgsiwyh632h794g7jrq-python-jwst-1.14.0
> /gnu/store/5yrrkl1lshnz9vdmnqmlb4kysl3m1b6m-python-astroalign-2.5.1
> /gnu/store/l6g5fla44hhs2rdayj9pk9wzl4hdjn6k-python-aplpy-2.1.0
> /gnu/store/84gmp7ykakd4zwah9bgm59smq5zwfpj2-python-astroplan-0.10
> /gnu/store/5dk6m10zr628rlj3abw965an223gh5m9-python-ginga-5.0.1
> /gnu/store/35m97lhq3v26fgy5kcsyrh91sfdbkq59-python-poliastro-0.17.0
> /gnu/store/b4nmarr0zzac92f32dq9hk157iszl41r-ginga-qt5-5.0.1
> /gnu/store/1ibrbzqh6nm0mlkr0aafm303q2f1qaa9-scamp-2.10.0
> /gnu/store/nw3ic2scsqp8060clzsxnf8xhchslpcl-python-viresclient-0.11.6
> /gnu/store/0rnjpghin70x95w5psgk3ikj8xqf0iic-python-cesium-0.12.1
> /gnu/store/3ycib8ybqxyq07p4f5mf5baa20fnqm1s-python-asdf-zarr-0.0.3
> /gnu/store/mcl0lxi5w74b8m21iivrc8grwna1lyx4-python-asdf-compression-0.0.1-0.57cc7e7
> --8<---------------cut here---------------end--------------->8---
>
> Sharlatan Hellseher (26):
>   gnu: python-sep: Refresh package style.
>   gnu: python-ephem: Use pyproject-build-system.
>   gnu: python-sgp4: Use pyproject-build-system.
>   gnu: packages/astronomy: Minimize import from python build system.
>   gnu: calceph: Update to 4.0.0.
>   gnu: python-astropy-iers-data: Update to 0.2024.5.13.0.30.12.
>   gnu: python-astropy: Update to 6.1.0.
>   gnu: python-pyvo: Disable a failing test.
>   gnu: python-astroscrappy: Update to 1.2.0.
>   gnu: python-dust-extinction: Update to 1.4.
>   gnu: python-ccdproc: Update to 2.4.2.
>   gnu: python-cdflib: Update to 1.3.1.
>   gnu: python-crds: Update to 11.17.22.
>   gnu: python-jplephem: Update to 2.22.
>   gnu: python-rad: Update to 0.20.0
>   gnu: python-roman-datamodels: Update to 0.20.0.
>   gnu: python-sunpy: Update to 5.1.3.
>   gnu: python-stsci-image: Update to 2.3.7.
>   gnu: python-specutils: Update to 1.15.0.
>   gnu: python-unyt: Fix version detection.
>   gnu: python-ewah-bool-utils: Update to 1.2.0.
>   gnu: Add python-viresclient.
>   gnu: Add python-geopack.
>   gnu: Add python-comm.
>   gnu: Add python-more-itertools-next.
>   gnu: Add python-yt.
>
>  gnu/packages/astronomy.scm          | 316 +++++++++++++++++++---------
>  gnu/packages/geo.scm                |  26 +++
>  gnu/packages/jupyter.scm            |  27 +++
>  gnu/packages/python-compression.scm |   4 +-
>  gnu/packages/python-science.scm     |   2 +-
>  gnu/packages/python-xyz.scm         |  35 +++
>  6 files changed, 303 insertions(+), 107 deletions(-)
>
>
> base-commit: 7881d6085146fefda17ed9eefa133b5b5c97af87

Merged, thank you for the keeping guix astronomy on bleeding edge :)

-- 
Best regards,
Andrew Tropin

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