[bug#74497] [PATCH 00/46] Astro update 2024/11.

[bug#74497] [PATCH 00/46] Astro update 2024/11.

[Sharlatan Hellseher]

November updates are delayed, but still on the track with monthly Astro soft
update!

There were a multiple technical whoopsies; I've nearly lost all changes during
git rebase but with some wizardy and archaeology in git logs files resurrected
all changes for this month, ah ye maybe it was due to some very cold whether
^.^ let's see what we have.

The main highlights:
- Astropy is on the latest release (6.1.6) at the time it was checked this month.
- NASA's Common Data Format (CDF) project is now packed and available for
  review, license looks FOSS compatible and not restrictive for modification
  or distribution.
- Prepared one Julia package from JuliaAstro collection it may open the door
  for more dependent packages.
- Added more transit packages related to Astropy affiliated packages,
- And, eh.., a lot of Python updates on python-team branch bringing a NumPy of
  1.24.4 and the latest Pandas.
- Maintenance comments, Python Nose (a test framework), is deprecated so all
  references to that package were removed in the whole (gnu packages
  astronomy) module, no regression was introduced.

The log:
- added [10/10]
  - [X] cdf :: NASA's Common Data Format library and tools
  - [X] julia-astroangles :: Lightweight string parsing and representation of angles
  - [X] python-cosmopy :: Cosmological calculator in Python
  - [X] python-george :: Fast Gaussian Processes for regression
  - [X] python-hasasia :: Pulsar timing array sensitivity curves calculation in Python
  - [X] python-holodeck :: MBH Binary Population Synthesis for Gravitational Wave Calculations
  - [X] python-kalepy :: Kernel Density Estimation (KDE) and sampling
  - [X] python-puremagic :: Pure Python implementation of magic file detection
  - [X] python-spisea :: Stellar Population Synthesis Modeling
  - [X] python-vispy :: Interactive scientific visualization in Python
- updated [31/31]
  - [X] imppg :: 0.6.5->1.9.2-beta
  - [X] libpasastro :: 1.4.2->1.4.3
  - [X] python-aplpy :: 2.1.0->2.2.0
  - [X] python-asdf-astropy :: 0.6.1->0.7.0
  - [X] python-astroalign :: 2.6.0->2.6.1
  - [X] python-astrodendro :: 0.2.0-0.3181c36->0.3.1
  - [X] python-astropy-iers-data :: 0.2024.10.14.0.32.55->0.2024.11.18.0.35.2
  - [X] python-astropy :: 6.1.4->6.1.6
  - [X] python-bayesicfitting :: 3.2.1->3.2.2
  - [X] python-cdflib :: 1.3.1->1.3.2
  - [X] python-crds :: 12.0.4->12.0.6
  - [X] python-drizzle :: 1.15.3->2.0.0
  - [X] python-ginga :: 5.1.0->5.2.0
  - [X] python-jwst :: 1.16.0->1.16.1
  - [X] python-ndcube :: 2.2.3->2.2.4
  - [X] python-photutils :: 2.0.1->2.0.2
  - [X] python-pyerfa :: 2.0.1.4->2.0.1.5
  - [X] python-pyvo :: 1.5.3->1.6
  - [X] python-rad :: 0.21.0->0.22.0
  - [X] python-regularizepsf :: 0.4.0->1.0.2
  - [X] python-reproject :: 0.14.0->0.14.1
  - [X] python-roman-datamodels :: 0.21.0->0.22.0
  - [X] python-sep-pjw :: 1.3.6->1.3.7
  - [X] python-sncosmo :: 2.11.1->2.11.2
  - [X] python-specutils :: 1.18.0->1.19.0
  - [X] python-statmorph :: 0.5.7->0.6.0
  - [X] python-stcal :: 1.9.0->1.10.0
  - [X] python-stdatamodels :: 2.1.1->2.1.2
  - [X] python-stsynphot :: 1.3.0->1.4.0
  - [X] python-synphot :: 1.4.0->1.5.0
  - [X] python-yt :: 4.3.1->4.4.0

The next month plan is to continue with python-team refresh, prepare more
Astropy affiliated projects and try to pack more C/C++/Julia astro libraries.

The build stats:
--8<---------------cut here---------------start------------->8---
> ./pre-inst-env guix build cdf gpredict imppg julia-astroangles libpasastro
python-aplpy python-asdf-astropy python-astroalign python-astrodendro
python-astrodendro python-astropy python-astropy-iers-data
python-bayesicfitting python-cdflib python-cosmopy python-crds python-drizzle
python-gatspy python-george python-ginga python-hasasia python-holodeck
python-jwst python-kalepy python-ndcube python-photutils python-puremagic
python-pyerfa python-pyvo python-rad python-regularizepsf python-reproject
python-roman-datamodels python-sep-pjw python-sncosmo python-specutils
python-spisea python-statmorph python-stcal python-stdatamodels
python-stsynphot python-synphot python-vispy python-yt
python-yt-astro-analysis

/gnu/store/3bsx8l3csbv4hqaxflg8py839ks5pwdn-python-yt-astro-analysis-1.1.3
/gnu/store/bfs45ibqsphgrl6k823xkiajcfsq93vx-python-yt-4.4.0
/gnu/store/gqkvnia7k3b06l17r1fcdwyamydgkn80-python-vispy-0.14.3
/gnu/store/z628savshf01410q2l49m7l9afkadki2-python-synphot-1.5.0
/gnu/store/xxsd293w7jscgb5dzjf0rpdjkawq6nj7-python-stsynphot-1.4.0
/gnu/store/dqwy05ixdkwcnhc80xayq2zyhsflprhw-python-stdatamodels-2.1.2
/gnu/store/1jpmd9nbf0vkpqmpb5np5ws3m32g2zx4-python-stcal-1.10.0
/gnu/store/lb5yrql1gqsngkshiqqg9i3v4n86lj6p-python-statmorph-0.6.0
/gnu/store/840lqs45bxcmq9skdaajhhcwvffqxrz3-python-spisea-2.1.11
/gnu/store/kvmp1fpn4h9w0mq199d4g3yjars50k88-python-specutils-1.19.0
/gnu/store/zd1nmwpyb48z1j9s4hp731ha4knkflpm-python-sncosmo-2.11.2
/gnu/store/hbn6acz583a0yy6582m96phy2ygcsjrh-python-sep-pjw-1.3.7
/gnu/store/arx0n6x85d1qr129hcm75pn846hls14j-python-roman-datamodels-0.22.0
/gnu/store/cz0lvb8far97pbz0n5k9lidiz763gbd8-python-reproject-0.14.1
/gnu/store/sgyaa3d657pbb0g41hp2pz8czx2qhna3-python-regularizepsf-1.0.2
/gnu/store/988lg2m0qm2vknm3pw3f48zmzwavv2lh-python-rad-0.22.0
/gnu/store/il2738qks33l4jbgvjndqgxg2gsqszzf-python-pyvo-1.6
/gnu/store/7l0jqyirimmvpn4hiz0jx9wb1bi24yff-python-pyerfa-2.0.1.5
/gnu/store/d6qgcqq5iw1h92z8dzaqkdz0wzi79rsq-python-puremagic-1.28
/gnu/store/kfq7wl7b4fkj7ygq8mz5bds09m13vm0f-python-photutils-2.0.2
/gnu/store/jd0y8sibm7nxq573k7yyr6bip5kk6hc5-python-ndcube-2.2.4
/gnu/store/0n6d2bhj99w3a2qng32nmnjwc4s03yn3-python-kalepy-1.4.3
/gnu/store/5a20zwyfw5x0qpggcrhpr021nxhfvakn-python-jwst-1.16.1
/gnu/store/wp99hv94cq8xhdgs3hzwnnf67dbafxr4-python-holodeck-1.5.2
/gnu/store/apd47hrbv5cmnwbfar4bgkm4nb8bd536-python-hasasia-1.2.3
/gnu/store/jv5i8g9fzw27nvfpdjzxf82gr9n47ki9-python-ginga-5.2.0
/gnu/store/jd256ihvhhjsxgkiz1adinxr36id3c9l-python-george-0.4.3
/gnu/store/jx46k743fvr06ldr6hk30sf7l8d8kw8i-python-gatspy-0.3
/gnu/store/9yyggm4y92a811qxxpbq53kx74zr14bg-python-drizzle-2.0.0
/gnu/store/v405g563z5yig2jmpj8ndp0ny69nda8z-python-crds-12.0.6
/gnu/store/8yf4hv86kr32303l9ddlpcx4fyg8niim-python-cosmopy-3.6
/gnu/store/3p5if19nkljfi175b314gvhp2vfsm5yg-python-cdflib-1.3.2
/gnu/store/7bw0ki2ys5z3108z23smfmv2jic70zxv-python-bayesicfitting-3.2.2
/gnu/store/j4n4pbqp3i251gb1n9j65vh3c99a5505-python-astropy-iers-data-0.2024.11.18.0.35.2
/gnu/store/dfxc2hfdh3q8jr19c2y7cr9cs1335sky-python-astropy-6.1.6
/gnu/store/jb7xxy4x0yvrsqjd32sl8d7zn3liz9v2-python-astrodendro-0.3.1
/gnu/store/a9dwgq3szkhc7an5rrc63ry7zbcry7ry-python-astroalign-2.6.1
/gnu/store/rjr4di1xnb3hlwbjvi8dki0iarh7bg3z-python-asdf-astropy-0.7.0
/gnu/store/iq17m1nm30d5avl587w2kkq6z755mras-python-aplpy-2.2.0
/gnu/store/6vn7icwbh768m3n5nw9yljjxg9flxh46-libpasastro-1.4.3
/gnu/store/bjjfal1f4cilh9px4j6f8j6b8bavhqaj-julia-astroangles-0.1.3
/gnu/store/chza2dzfgksj7immxhzklcjhlavf3sib-imppg-1.9.2-beta
/gnu/store/qnsdmyvcs8ic6f9pfs6bxjgi2qbxga88-gpredict-2.2.1
/gnu/store/vljrinjr0z9vmkyaslym5sd85ff3pfqr-cdf-3.9.1
--8<---------------cut here---------------end--------------->8---

Dependent build stats:
--8<---------------cut here---------------start------------->8---
Building the following 30 packages would ensure 90 dependent packages are
rebuilt: python-zodipy@1.1.0 python-kanon@0.6.6
python-asdf-compression@0.0.1-0.57cc7e7 python-asdf-zarr@0.0.4
python-viresclient@0.12.0 python-naima@0.10.0 python-halotools@0.9.1
scamp@2.10.0 python-spisea@2.1.11 python-holodeck@1.5.2 python-statmorph@0.6.0
python-cesium@0.12.1 python-sncosmo@2.11.2 python-coolest@0.1.9
python-astroplan@0.10.1 ginga-qt5@5.2.0 python-poliastro@0.17.0
python-sunkit-image@0.5.1 python-radiospectra@0.6.0 python-aplpy@2.2.0
python-glue-qt@0.3.1 python-regularizepsf@1.0.2 python-astroalign@2.6.1
python-acstools@3.7.2 python-jwst-reffiles@1.0.1 python-webbpsf@1.4.0
python-sbpy@0.5.0 python-glue-astronomy@0.10.0 python-pyxsim@4.4.2
python-yt-astro-analysis@1.1.3

/gnu/store/3bsx8l3csbv4hqaxflg8py839ks5pwdn-python-yt-astro-analysis-1.1.3
/gnu/store/6dc49c7ilmc5hf1vs92xb1dn4w7gd5d6-python-pyxsim-4.4.2
/gnu/store/3kp6r7l17vj9fcf05q6s7cm5cqgqcqvj-python-glue-astronomy-0.10.0
/gnu/store/qk8g8xvvvfs4hwikdl67s7dw9n1d7dy8-python-sbpy-0.5.0
/gnu/store/5xjv5mxdfl8hg0a1k1znqbmy4639kv7l-python-webbpsf-1.4.0
/gnu/store/p6hyqmc2xa9hwyizdxzrns3q67w5zcaj-python-jwst-reffiles-1.0.1
/gnu/store/r251pnwzxci80k0h65gnn2i0n54hmnn3-python-acstools-3.7.2
/gnu/store/a9dwgq3szkhc7an5rrc63ry7zbcry7ry-python-astroalign-2.6.1
/gnu/store/sgyaa3d657pbb0g41hp2pz8czx2qhna3-python-regularizepsf-1.0.2
/gnu/store/97yv077si7l5zg5bv9gy8yanpmnm4562-python-glue-qt-0.3.1
/gnu/store/iq17m1nm30d5avl587w2kkq6z755mras-python-aplpy-2.2.0
/gnu/store/zj8hynzhz30pq9k12skh1frq69sl0wgf-python-radiospectra-0.6.0
/gnu/store/6blzi1a3rbq2jaavmavk649kidk4l8p9-python-sunkit-image-0.5.1
/gnu/store/8sq46a6kf18whw4sv9wfgjkby31mhgmn-python-poliastro-0.17.0
/gnu/store/3yv90jx56jw86wsbv0rl5had92qk1a37-ginga-qt5-5.2.0
/gnu/store/cizh2ban80d7xblkgzs839p06b421h7k-python-astroplan-0.10.1
/gnu/store/nk0v1wgwvgkap9y97id31fm4fym206h6-python-coolest-0.1.9
/gnu/store/zd1nmwpyb48z1j9s4hp731ha4knkflpm-python-sncosmo-2.11.2
/gnu/store/cl06nnk6w83xlyhq9jnqmym0fyrfxc71-python-cesium-0.12.1
/gnu/store/lb5yrql1gqsngkshiqqg9i3v4n86lj6p-python-statmorph-0.6.0
/gnu/store/wp99hv94cq8xhdgs3hzwnnf67dbafxr4-python-holodeck-1.5.2
/gnu/store/840lqs45bxcmq9skdaajhhcwvffqxrz3-python-spisea-2.1.11
/gnu/store/4x48kpn4mp3zv3mdhdp21rhy89akhv09-scamp-2.10.0
/gnu/store/8j7mdszrild2qk9n4lgc4lpvy34hd4z4-python-halotools-0.9.1
/gnu/store/k35hrzwffb6qqmrc2bg3hj9f0alk1dsm-python-naima-0.10.0
/gnu/store/4k671l0ziwmlamymb6nfzaj9aalf8grb-python-viresclient-0.12.0
/gnu/store/wl0x68hi7kv3ff47d85bmnzcisz65zkq-python-asdf-zarr-0.0.4
/gnu/store/va019rd8irpryvd5ilia8bjhz2ld0jgr-python-asdf-compression-0.0.1-0.57cc7e7
/gnu/store/5wq804ayfl0k6xjhhsmvaybff3df0qik-python-kanon-0.6.6
/gnu/store/k54zz5jvwvwa8zw9n5hi2sfmx4d0aina-python-zodipy-1.1.0
--8<---------------cut here---------------end--------------->8---

Sharlatan Hellseher (46):
  gnu: Add cdf.
  gnu: Add julia-astroangles.
  gnu: Add python-kalepy.
  gnu: Add python-george.
  gnu: Add python-hasasia.
  gnu: Add python-cosmopy.
  gnu: Add python-holodeck.
  gnu: Add python-vispy.
  gnu: Add python-spisea.
  gnu: gpredict: Update commentary note.
  gnu: healpix-source: Update commentary note.
  gnu: imppg: Update to 1.9.2-beta.
  gnu: libpasastro: Update to 1.4.3.
  gnu: python-asdf-astropy: Update to 0.7.0.
  gnu: python-astropy-iers-data: Update to 0.2024.11.18.0.35.2.
  gnu: python-astropy: Update to 6.1.6.
  gnu: python-bayesicfitting: Update to 3.2.2.
  gnu: python-crds: Update to 12.0.6.
  gnu: python-drizzle: Update to 2.0.0.
  gnu: Add python-puremagic.
  gnu: python-ginga: Update to 5.2.0.
  gnu: python-aplpy: Update to 2.2.0.
  gnu: python-astroalign: Update to 2.6.1.
  gnu: python-astrodendro: Update to 0.3.1.
  gnu: python-astrodendro: Fix indentation.
  gnu: python-cdflib: Update to 1.3.2.
  gnu: python-jwst: Update to 1.16.1.
  gnu: python-ndcube: Update to 2.2.4.
  gnu: python-photutils: Update to 2.0.2.
  gnu: python-pyerfa: Update to 2.0.1.5.
  gnu: python-pyvo: Update to 1.6.
  gnu: python-rad: Update to 0.22.0.
  gnu: python-regularizepsf: Update to 1.0.2.
  gnu: python-reproject: Update to 0.14.1.
  gnu: python-roman-datamodels: Update to 0.22.0.
  gnu: python-sep-pjw: Update to 1.3.7.
  gnu: python-sncosmo: Update to 2.11.2.
  gnu: python-specutils: Update to 1.19.0.
  gnu: python-statmorph: Update to 0.6.0.
  gnu: python-stcal: Update to 1.10.0.
  gnu: python-stdatamodels: Update to 2.1.2.
  gnu: python-stsynphot: Update to 1.4.0.
  gnu: python-synphot: Update to 1.5.0.
  gnu: python-yt: Update to 4.4.0.
  gnu: python-yt-astro-analysis: Adjust inputs.
  gnu: python-gatspy: Adjust inputs.

 gnu/packages/astronomy.scm       | 789 ++++++++++++++++++++-----------
 gnu/packages/julia-xyz.scm       |  25 +
 gnu/packages/python-graphics.scm |  74 ++-
 gnu/packages/python-xyz.scm      |  23 +
 gnu/packages/statistics.scm      |  61 +++
 5 files changed, 697 insertions(+), 275 deletions(-)


base-commit: 36f516bfcdf64185f5d70c21a908283be22a34fd
-- 
2.46.0

[bug#74497] [PATCH 01/46] gnu: Add cdf.

[Sharlatan Hellseher]

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

Change-Id: I596dd3d1050e9276009d7e19fd9e9d1514510230
---
 gnu/packages/astronomy.scm | 52 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 1afdcd15a9..fc34cb7c40 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -460,6 +460,58 @@ (define-public ccfits
     (license (license:non-copyleft "file://License.txt"
                                    "See License.txt in the distribution."))))
 
+(define-public cdf
+  (package
+    (name "cdf")
+    (version "3.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       ;; The archive version is esoteric here, meanwhile it's mentioned as
+       ;; normal semantic version in documentation (eg. 39_1), update the URL
+       ;; URL accordingly.
+       (uri (string-append
+             "https://spdf.gsfc.nasa.gov/pub/software/cdf/dist/"
+             "cdf39_1/linux/cdf39_1-dist-cdf.tar.gz" ))
+       (sha256
+        (base32 "08k6yv6gb0abhqp7dfysll5dgqc7kqbcvyiq4winnilazp6n1n01"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:test-target "test"
+      #:make-flags
+      #~(list "CURSES=no"
+              "ENV=gnu"
+              "FORTRAN=no"
+              "OS=linux"
+              "SHARED=yes"
+              (string-append "INSTALLDIR=" #$output)
+              "all")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; no configure
+          (delete 'configure))))
+    (home-page "https://cdf.gsfc.nasa.gov/")
+    (synopsis "NASA's Common Data Format library and tools")
+    (description
+     "CDF or CDF Library is a scientific data management package which allows
+programmers and application developers to manage and manipulate scalar, vector,
+and multi-dimensional data arrays.
+
+The @acronym{CDF, Common Data Format} is a self-describing data abstraction for
+the storage and manipulation of multidimensional data in a platform- and
+discipline-independent fashion.
+
+This package provides library and binary utilities to manipulate CDF files.")
+    ;; This software may be copied or redistributed as long as it is not sold
+    ;; for profit, see <https://cdf.gsfc.nasa.gov/html/cdf_copyright.html>.
+    ;;
+    ;; There are no license agreements or costs involved in obtaining or using
+    ;; CDF, see <https://cdf.gsfc.nasa.gov/html/faq.html>.
+    (license (license:non-copyleft
+              "file://CDF_copyright.txt"
+              "See CDF_copyright.txt in the distribution."))))
+
 (define-public celestia
   (package
     (name "celestia")
-- 
2.46.0

[bug#74497] [PATCH 02/46] gnu: Add julia-astroangles.

[Sharlatan Hellseher]

* gnu/packages/julia-xyz.scm (julia-astroangles): New variable.

Change-Id: I7d4f977577b5e468eee313e216ed5f3d15f7e598
---
 gnu/packages/julia-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 77385ee6e0..4aedf140bc 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -266,6 +266,31 @@ (define-public julia-arraylayouts
 much wider class of matrix types than Julia's in-built @code{StridedArray}.")
     (license license:expat)))
 
+(define-public julia-astroangles
+  (package
+    (name "julia-astroangles")
+    (version "0.1.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaAstro/AstroAngles.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1hd03kv1dppdzz7i9jv11f4rby5c21sdyhbcf3yvba9vnkkd1gz5"))))
+    (build-system julia-build-system)
+    (native-inputs
+     (list julia-stablerngs))
+    (propagated-inputs
+     (list julia-formatting))
+    (home-page "https://github.com/JuliaAstro/AstroAngles.jl")
+    (synopsis "Lightweight string parsing and representation of angles")
+    (description
+     "This package provides a lightweight string parsing and representation of
+angles.")
+    (license license:expat)))
+
 (define-public julia-astrolib
   (package
     (name "julia-astrolib")
-- 
2.46.0

[bug#74497] [PATCH 02/46] gnu: Add julia-astroangles.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 2367 bytes --]

I haven't looked at the rest of the patch set, but I did look at this
one quickly.

I see that there was a 0.1.4 that was adjusted in the Project.toml but
no release was actually tagged. I don't have a preference between the
0.1.3 or 0.1.4.

StableRNGs and Formatting are only listed in test/Project.toml, is
julia-formatting actually needed as a propagated-input?

This package built without any problems on aarch64.

On Sat, Nov 23, 2024 at 07:50:49PM +0000, Sharlatan Hellseher wrote:
> * gnu/packages/julia-xyz.scm (julia-astroangles): New variable.
> 
> Change-Id: I7d4f977577b5e468eee313e216ed5f3d15f7e598
> ---
>  gnu/packages/julia-xyz.scm | 25 +++++++++++++++++++++++++
>  1 file changed, 25 insertions(+)
> 
> diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
> index 77385ee6e0..4aedf140bc 100644
> --- a/gnu/packages/julia-xyz.scm
> +++ b/gnu/packages/julia-xyz.scm
> @@ -266,6 +266,31 @@ (define-public julia-arraylayouts
>  much wider class of matrix types than Julia's in-built @code{StridedArray}.")
>      (license license:expat)))
>  
> +(define-public julia-astroangles
> +  (package
> +    (name "julia-astroangles")
> +    (version "0.1.3")
> +    (source
> +     (origin
> +       (method git-fetch)
> +       (uri (git-reference
> +             (url "https://github.com/JuliaAstro/AstroAngles.jl")
> +             (commit (string-append "v" version))))
> +       (file-name (git-file-name name version))
> +       (sha256
> +        (base32 "1hd03kv1dppdzz7i9jv11f4rby5c21sdyhbcf3yvba9vnkkd1gz5"))))
> +    (build-system julia-build-system)
> +    (native-inputs
> +     (list julia-stablerngs))
> +    (propagated-inputs
> +     (list julia-formatting))
> +    (home-page "https://github.com/JuliaAstro/AstroAngles.jl")
> +    (synopsis "Lightweight string parsing and representation of angles")
> +    (description
> +     "This package provides a lightweight string parsing and representation of
> +angles.")
> +    (license license:expat)))
> +
>  (define-public julia-astrolib
>    (package
>      (name "julia-astrolib")
> -- 
> 2.46.0
> 
> 
> 

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[-- Attachment #2: signature.asc --]
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[bug#74497] [PATCH 03/46] gnu: Add python-kalepy.

[Sharlatan Hellseher]

* gnu/packages/statistics.scm (python-kalepy): New variable.

Change-Id: I1bdaedd07f6149eeffe115eb30c17035a0ed75fd
---
 gnu/packages/statistics.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 7089030fcc..2f48598f87 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -22,6 +22,7 @@
 ;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
 ;;; Copyright © 2024 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
+;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2385,6 +2386,37 @@ (define-public python-patsy
     ;; and is covered by the PSFL.
     (license (list license:bsd-2 license:psfl))))
 
+(define-public python-kalepy
+  (package
+    (name "python-kalepy")
+    (version "1.4.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "kalepy" version))
+       (sha256
+        (base32 "1a1d98vjkjs8zwx4hdss3gv67jyf25mmsrdc5qi8hpxminkizb6w"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-matplotlib
+           python-numba
+           python-numpy
+           python-scipy
+           python-six))
+    (home-page "https://github.com/lzkelley/kalepy")
+    (synopsis "Kernel Density Estimation (KDE) and sampling")
+    (description
+     "This package performs KDE operations on multidimensional data to
+calculate estimated PDFs (probability distribution functions), and resample
+new data from those PDFs.")
+    ;; MIT   - setup.py
+    ;; GPL3+ - LICENSE
+    (license (list license:gpl3+ license:expat))))
+
 (define-public python-lifelines
   (package
     (name "python-lifelines")
-- 
2.46.0

[bug#74497] [PATCH 04/46] gnu: Add python-george.

[Sharlatan Hellseher]

* gnu/packages/statistics.scm (python-george): New variable.

Change-Id: Iff4de57093cbb954b7cb1e079ca9ef71b964e64e
---
 gnu/packages/statistics.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 2f48598f87..a96e92c780 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -63,6 +63,7 @@ (define-module (gnu packages statistics)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages curl)
@@ -2158,6 +2159,34 @@ (define-public python-altair
      "Vega-Altair is a declarative statistical visualization library for Python.")
     (license license:expat)))
 
+(define-public python-george
+  (package
+    (name "python-george")
+    (version "0.4.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "george" version))
+       (sha256
+        (base32 "1zvbdq50ds820aj06lr2nrzwg121bkd9bg0aq83gvk7lf8yqgp4v"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list cmake-minimal
+           pybind11
+           python-pytest
+           python-scikit-build-core
+           python-setuptools-scm))
+    (propagated-inputs
+     (list python-numpy
+           python-scipy))
+    (home-page "https://george.readthedocs.io")
+    (synopsis "Fast Gaussian Processes for regression")
+    (description
+     "George is a fast and flexible Python library for Gaussian Process (GP)
+Regression, focused on efficiently evaluating the marginalized likelihood of a
+dataset under a GP prior, even as this dataset gets Big.")
+    (license license:expat)))
+
 (define-public python-getdist
   (package
     (name "python-getdist")
-- 
2.46.0

[bug#74497] [PATCH 05/46] gnu: Add python-hasasia.

[Sharlatan Hellseher]

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

Change-Id: Iaf6df32037b9435da2731c080578042f1f03867c
---
 gnu/packages/astronomy.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index fc34cb7c40..cac446a6a3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2447,6 +2447,43 @@ (define-public python-halotools
 from a cosmological simulation.")
     (license license:bsd-3)))
 
+(define-public python-hasasia
+  (package
+    (name "python-hasasia")
+    (version "1.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "hasasia" version))
+       (sha256
+        (base32 "0vs3935c9cqwp44dycxfsv4p9q4zbw8i5z3946928yy0nqmj1aw7"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-astropy
+           python-numpy
+           python-scipy))
+    (home-page "https://github.com/Hazboun6/hasasia")
+    (synopsis "Pulsar timing array sensitivity curves calculation in Python")
+    (description
+     "This package provides a Python package to calculate gravitational-wave
+sensitivity curves for pulsar timing arrays.
+
+Features:
+@itemize
+@item pulsar transmission functions
+@item inverse-noise-weighted transmission functions
+@item individual pulsar sensitivity curves
+@item pulsar timing array sensitivity curves as characteristic strain, strain
+sensitivity or energy density
+@item power-law integrated sensitivity curves
+@item sensitivity sky maps for pulsar timing arrays
+@end itemize")
+    (license license:expat)))
+
 (define-public python-healpy
   (package
     (name "python-healpy")
-- 
2.46.0

[bug#74497] [PATCH 06/46] gnu: Add python-cosmopy.

[Sharlatan Hellseher]

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

Change-Id: I31e54ff51a2f18091baba449da3b00cdf5088b15
---
 gnu/packages/astronomy.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index cac446a6a3..c85c00f8e2 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2013,6 +2013,34 @@ (define-public python-coolest
 lens models possibly obtained from different modeling codes.")
     (license  license:gpl3)))
 
+(define-public python-cosmopy
+  (package
+    (name "python-cosmopy")
+    (version "3.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cosmopy" version))
+       (sha256
+        (base32 "16xlg0vyzdx1h5h28y8az48nhiqvx43yd9s30g3rk9ywl4r1j6h8"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-astropy
+           python-click
+           python-future
+           python-numpy
+           python-scipy))
+    (home-page "https://github.com/lzkelley/cosmopy")
+    (synopsis "Cosmological calculator in Python")
+    (description
+     "This package provides a CLI and Python module to quickly calculate
+cosmological parameters e.g. redshift or luminosity-distance.")
+    (license license:expat)))
+
 (define-public python-czml3
   (package
     (name "python-czml3")
-- 
2.46.0

[bug#74497] [PATCH 07/46] gnu: Add python-holodeck.

[Sharlatan Hellseher]

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

Change-Id: Ie6ba03ff9af00683f33f7ec11cd2915f4cfbd5e3
---
 gnu/packages/astronomy.scm | 54 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 53 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c85c00f8e2..75f13a4bf6 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2019 by Amar Singh <nly@disroot.org>
 ;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
 ;;; Copyright © 2020, 2021 Guillaume Le Vaillant <glv@posteo.net>
-;;; Copyright © 2021-2023 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021-2024 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021, 2022 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
 ;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
@@ -71,6 +71,7 @@ (define-module (gnu packages astronomy)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages netpbm)
   #:use-module (gnu packages onc-rpc)
+  #:use-module (gnu packages parallel)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages photo)
   #:use-module (gnu packages pkg-config)
@@ -2571,6 +2572,57 @@ (define-public python-healpy
 scheme and builds with the HEALPix C++ library.")
     (license license:gpl2+)))
 
+(define-public python-holodeck
+  (package
+    (name "python-holodeck")
+    (version "1.5.2")
+    (source
+     (origin
+       (method git-fetch) ; no tests in the PyPI tarball
+       (uri (git-reference
+             (url "https://github.com/nanograv/holodeck")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0jz54fb6yyling2a756qqahixpn1wgxmhhqmv6pf0iqds019v9k7"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "--numprocesses" (number->string (parallel-job-count)))))
+    (native-inputs
+     (list python-cython
+           python-pytest
+           python-pytest-xdist
+           python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-astropy
+           python-cosmopy
+           python-emcee
+           python-george
+           python-h5py
+           python-hasasia
+           python-healpy
+           python-ipywidgets
+           python-kalepy
+           python-matplotlib
+           python-numpy
+           python-psutil
+           python-schwimmbad
+           python-scipy
+           python-sympy
+           python-tqdm))
+    (home-page "https://github.com/byu-pccl/holodeck")
+    (synopsis "MBH Binary Population Synthesis for Gravitational Wave Calculations")
+    (description
+     "This package provides a comprehensive framework for @acronym{Massive
+Black Hole,MBH} binary population synthesis.  The framework includes modules
+to perform population synthesis using a variety of methodologies from
+semi-analytic models, to cosmological hydrodynamic simulations, and even
+observationally-derived galaxy merger catalogs.")
+    (license license:expat)))
+
 (define-public python-pvextractor
   (package
     (name "python-pvextractor")
-- 
2.46.0

[bug#74497] [PATCH 08/46] gnu: Add python-vispy.

[Sharlatan Hellseher]

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

Change-Id: Icb648d621101e0f4b60ada8c0ebbd3a05eea6fb4
---
 gnu/packages/python-graphics.scm | 74 +++++++++++++++++++++++++++++++-
 1 file changed, 73 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-graphics.scm b/gnu/packages/python-graphics.scm
index 403a3c3b34..bc0c93a8ee 100644
--- a/gnu/packages/python-graphics.scm
+++ b/gnu/packages/python-graphics.scm
@@ -16,15 +16,17 @@ (define-module (gnu packages python-graphics)
   #:use-module (guix packages)
   #:use-module (gnu packages)
   #:use-module (gnu packages audio)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gl)
-  #:use-module (gnu packages base)
   #:use-module (gnu packages gtk)
+  #:use-module (gnu packages maths)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages simulation)
   #:use-module (gnu packages video)
   #:use-module (gnu packages xorg))
 
@@ -235,6 +237,76 @@ (define-public python-pyglet
 music." )
     (license license:bsd-3)))
 
+(define-public python-vispy
+  (package
+    (name "python-vispy")
+    (version "0.14.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "vispy" version))
+       (sha256
+        (base32 "07fkk4bdffn0iq5cprk7ydj978rqc4lvzfcs2vkzgfh8m53vifzg"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; Test requiring network access to download test data from
+      ;; <https://raw.githubusercontent.com/vispy/demo-data/main/CONTRIBUTING.txt>.
+      #~(list "-k" (string-append "not test_read_write_image"
+                                  " and not test_wavefront"
+                                  " and not test_config"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-library-path
+            (lambda _
+              (substitute* (list "vispy/ext/egl.py"
+                                 "vispy/ext/fontconfig.py"
+                                 "vispy/gloo/gl/es2.py"
+                                 "vispy/gloo/gl/gl2.py")
+                (("ctypes\\.util\\.find_library\\('EGL'\\)")
+                 (format #f "'~a/~a'" #$(this-package-input "mesa")
+                         "lib/libEGL.so"))
+                (("ctypes\\.util\\.find_library\\('GL'\\)")
+                 (format #f "'~a/~a'" #$(this-package-input "mesa")
+                         "lib/libGL.so"))
+                (("ctypes\\.util\\.find_library\\('GLESv2'\\)")
+                 (format #f "'~a/~a'" #$(this-package-input "mesa")
+                         "lib/libGLESv2.so"))
+                (("util\\.find_library\\('fontconfig'\\)")
+                 (format #f "'~a/~a'" #$(this-package-input "fontconfig-minimal")
+                         "lib/libfontconfig.so")))))
+          (add-before 'check 'prepare-test-environment
+            (lambda _
+              ;; XXX: Check how to set DPI to run headless tests, fails when
+              ;; DISPLAY is set.
+              ;; E RuntimeError: could not determine DPI
+              (setenv "HOME" "/tmp")
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (native-inputs
+     (list python-cython-3
+           python-pytest
+           python-setuptools
+           python-setuptools-scm))
+    (inputs
+     (list fontconfig
+           mesa))
+    (propagated-inputs
+     (list python-freetype-py
+           python-hsluv
+           python-kiwisolver
+           python-meshio
+           python-numpy
+           python-packaging
+           python-pillow))
+    (home-page "http://vispy.org")
+    (synopsis "Interactive scientific visualization in Python")
+    (description
+     "VisPy is a high-performance interactive 2D/3D data visualization library
+leveraging the computational power of modern Graphics Processing Units (GPUs)
+through the OpenGL library to display very large datasets.")
+    (license license:bsd-3)))
+
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above in alphabetical order.
-- 
2.46.0

[bug#74497] [PATCH 09/46] gnu: Add python-spisea.

[Sharlatan Hellseher]

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

Change-Id: Iecf0f7970cb62b8512eb254d3525a34fc59521be
---
 gnu/packages/astronomy.scm | 68 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 75f13a4bf6..74e57c3ef7 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4914,6 +4914,74 @@ (define-public python-spherical-geometry
     ;; QD_LIBRARY_LICENSE.rst for bandeled QD source
     (license license:bsd-3)))
 
+(define-public python-spisea
+  (package
+    (name "python-spisea")
+    (version "2.1.11")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/astropy/SPISEA")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1xgmbg1c0lijvbsfiicjl2r4y7prm47qnmj86w69wa8xxsz7n2ph"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; Tests require additinal data, see
+      ;; <https://spisea.readthedocs.io/en/latest/getting_started.html>.
+      #:tests? #f
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'preparations
+            (lambda _
+              ;; Tests and sanity check are failed with ImportError: cannot
+              ;; import name 'update_default_config' from
+              ;; 'astropy.config.configuration'.
+              (delete-file "spisea/_astropy_init.py")
+              (with-output-to-file "spisea/__init__.py"
+                (lambda _
+                  (display
+                   (string-append "__version__ = \""
+                                  #$(package-version this-package)
+                                  "\""))))
+              (substitute* "setup.cfg"
+                (("astropy-package-template-example = .*") ""))
+              ;; The version could not be determined from git checkout.
+              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))))))
+    (native-inputs
+     (list python-cython
+           python-extension-helpers
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
+    (propagated-inputs
+     (list python-astropy
+           python-matplotlib
+           python-numpy
+           python-pysynphot
+           python-scipy))
+    (home-page "https://spisea.readthedocs.io/en/stable/index.html")
+    (synopsis "Stellar Population Synthesis Modeling")
+    (description
+     "SPISEA is an python package that generates single-age,
+single-metallicity populations (i.e. star clusters). It gives the user control
+over many parameters:
+
+@itemize
+@item cluster characteristics (age, metallicity, mass, distance)
+@item total extinction, differential extinction, and extinction law
+@item stellar evolution and atmosphere models
+@item stellar multiplicity and Initial Mass Function
+@item initial-Final Mass Relation
+@item photometric filters
+@end itemize")
+    ;; Licensed under a 3-clause BSD style license - see LICENSE.rst
+    ;; spisea/_astropy_init.py:
+    (license (list license:gpl3+ license:bsd-3))))
+
 (define-public python-statmorph
   (package
     (name "python-statmorph")
-- 
2.46.0

[bug#74497] [PATCH 10/46] gnu: gpredict: Update commentary note.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (gpredict): Add a link to new lease request
in upstream bug tracker.

Change-Id: I120430c5e55b1848ea03c07474fa0fa9e80aa505
---
 gnu/packages/astronomy.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 74e57c3ef7..7c6c048520 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -805,7 +805,8 @@ (define-public gnuastro
 
 (define-public gpredict
   ;; The latest tag, 2.3, has no major difference with 2.2.1 and is dated for
-  ;; 2018. Additionally, there is some activity on the master branch.
+  ;; 2018. Additionally, there is some activity on the master branch, see
+  ;; <https://github.com/csete/gpredict/issues/368>.
   (package
     (name "gpredict")
     (version "2.2.1")
-- 
2.46.0

[bug#74497] [PATCH 11/46] gnu: healpix-source: Update commentary note.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (healpix-source): Adjust commentary grammar
and provide example of C++ variant of the package naming.

Change-Id: I5b50b0d7ad1310a96315dc16da1eb384c5bac533
---
 gnu/packages/astronomy.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 7c6c048520..0f19e02dc6 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -862,8 +862,10 @@ (define-public gpredict
     (license license:gpl2+)))
 
 (define* (healpix-source #:key version sha256-base32-hash)
-    ;; The sources of HEALPix containing 6 independent packages (Fortran90,
-    ;; IDL, C, C++, java and python) and distributed togather libsharp.
+    ;; The sources of HEALPix contains 6 independent packages (Fortran90, IDL,
+    ;; C, C++, Java and Python) and distributed together with libsharp.  There
+    ;; is also a fresh C++ tarball which does not follow the naming pattern
+    ;; e.g. healpix_cxx-3.82.1.tar.gz.
      (origin
        (method url-fetch)
        (uri
-- 
2.46.0

[bug#74497] [PATCH 12/46] gnu: imppg: Update to 1.9.2-beta.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (imppg): Update to 1.9.2-beta.
[arguments]<tests>: Enable them.
[inputs]: Add lua.

Change-Id: Idcc043bd1ec9ca76a81451cede3d2e13a902d3cb
---
 gnu/packages/astronomy.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 0f19e02dc6..247ead0320 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -957,7 +957,7 @@ (define-public healpix-cxx
 (define-public imppg
   (package
     (name "imppg")
-    (version "0.6.5")
+    (version "1.9.2-beta")
     (source
      (origin
        (method git-fetch)
@@ -966,15 +966,16 @@ (define-public imppg
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0a6wb1a9adwd01dmy0r03xxp8iz9y7mvh30088ajilhj4lf90vxa"))))
+        (base32 "13kqvl9ay4x0ia7iikxbhg96pp46f1awr382p05gxdvsxksq900v"))))
     (build-system cmake-build-system)
-    (arguments
-     (list ;; No test provided
-      #:tests? #f))
     (native-inputs
      (list boost pkg-config))
     (inputs
-     (list cfitsio freeimage glew wxwidgets-3.0))
+     (list cfitsio
+           freeimage
+           glew
+           lua
+           wxwidgets-3.0))
     (home-page "https://github.com/GreatAttractor/imppg")
     (synopsis "Astronomical Image Post-Proccessor (ImPPG)")
     (description
-- 
2.46.0

[bug#74497] [PATCH 13/46] gnu: libpasastro: Update to 1.4.3.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (libpasastro): Update to 1.4.3.

Change-Id: Ia81332461e42dd8623378edda338f0ad4309a5d5
---
 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 247ead0320..0cd741bea1 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1182,7 +1182,7 @@ (define-public libnova
 (define-public libpasastro
   (package
     (name "libpasastro")
-    (version "1.4.2")
+    (version "1.4.3")
     (source
      (origin
        (method git-fetch)
@@ -1191,7 +1191,7 @@ (define-public libpasastro
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1na3gyb3nzb5gdgccs1653j2gnz6w3v1mqzhyhkx3yqw8bs3q5x0"))))
+        (base32 "16d0kc22a1cn9kl8s0mxnaw0ax6qjq3rwhfifgpf1a3f9qp17115"))))
     (build-system gnu-build-system)
     (arguments
      (list
-- 
2.46.0

[bug#74497] [PATCH 14/46] gnu: python-asdf-astropy: Update to 0.7.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.7.0.
[source]: Adjust the name of package as it changed in PyPI.
[phases]{relax-requirements}: New phase.

Change-Id: I84fbbc2d7612d192f662e60011fa9925021d128d
---
 gnu/packages/astronomy.scm | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 0cd741bea1..5b78017929 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1699,21 +1699,28 @@ (define-public python-asdf
 (define-public python-asdf-astropy
   (package
     (name "python-asdf-astropy")
-    (version "0.6.1")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "asdf-astropy" version))
+       (uri (pypi-uri "asdf_astropy" version))
        (sha256
-        (base32 "1ipjpjiirycj2npicbp39ka7db61vx45j8dm2iis71g5l1rzkblp"))))
+        (base32 "0985bhmhnjzlf8n78r1i1dfhbvq167xqz0667kg3jm0l2177b0f9"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
       #~(list "--numprocesses" (number->string (parallel-job-count)))
-      #:phases #~(modify-phases %standard-phases
-                   (add-before 'check 'set-home-env
-                     (lambda _ (setenv "HOME" "/tmp"))))))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              (substitute* "pyproject.toml"
+                ;; numpy>=1.24, all tests passed successfuly. Scheduled for
+                ;; update in python-team.
+                ((">=1.24") ">=1.23"))))
+          (add-before 'check 'set-home-env
+            (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-coverage
            python-h5py
-- 
2.46.0

[bug#74497] [PATCH 15/46] gnu: python-astropy-iers-data: Update to 0.2024.11.18.0.35.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy-iers-data): Update to 0.2024.11.18.0.35.2.

Change-Id: Ieb60e7c657855311703b4dc4799c276e38dd5e31
---
 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 5b78017929..db4cdbb88f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3354,13 +3354,13 @@ (define-public python-astropy-healpix
 (define-public python-astropy-iers-data
   (package
     (name "python-astropy-iers-data")
-    (version "0.2024.10.14.0.32.55")
+    (version "0.2024.11.18.0.35.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy_iers_data" version))
        (sha256
-        (base32 "1849jbmz1x6x783w9k08a9i3g4f722lqwlnszh4dyr50dyrfbrzg"))))
+        (base32 "1n6j5pa5whcpx2hn7n78a7k2xllwgj5gq4lkb9jimrdvx7p0hl5i"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f)) ; no tests
-- 
2.46.0

[bug#74497] [PATCH 16/46] gnu: python-astropy: Update to 6.1.6.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy): Update to 6.1.6.
[arguments]<test-flags>: Disable one failing test.
[propagated-inputs]: Add python-h5py, python-jplephem, and python-pyarrow.
[native-inputs]: Remove python-colorlog, python-coverage, python-h5py,
python-jplephem, and python-pyarrow; add python-setuptools and
python-wheel.

Change-Id: I44bdf23c84c64952e5ae846ad4b3a9c7173f2c06
---
 gnu/packages/astronomy.scm | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index db4cdbb88f..4a96837e16 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3190,13 +3190,13 @@ (define-public stackistry
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "6.1.4")
+    (version "6.1.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "0d0cnqm0p00ap8wys5jcg9h958c6mizx87wzwvmrpackn3i5h59n"))
+        (base32 "0iv8mkdflfprigv3g6666v80nvg6blwz0989hqw232g7gms57qb3"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -3215,12 +3215,16 @@ (define-public python-astropy
       #:test-flags
       #~(list "--pyargs" "astropy"
               "--numprocesses" (number->string (parallel-job-count))
-              "-k" (string-append
+              "-k" (string-join
                     ;; Skip tests that need remote data.
-                    "not remote_data"
-                    ;; ValueError: The truth value of an array with more than
-                    ;; one element is ambiguous. Use a.any() or a.all()
-                    " and not test_table_comp[t16-t26]"))
+                    (list "not remote_data"
+                          ;; ValueError: The truth value of an array with more than
+                          ;; one element is ambiguous. Use a.any() or a.all()
+                          "test_table_comp[t16-t26]"
+                          ;; UnboundLocalError: local variable 'ihd'
+                          ;; referenced before assignment
+                          "test_delay_doc_updates")
+                    " and not "))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'preparations
@@ -3255,36 +3259,36 @@ (define-public python-astropy
     (native-inputs
      (list nss-certs-for-test
            pkg-config
-           python-colorlog
-           python-coverage
            python-cython-3
            python-extension-helpers
-           python-h5py
            python-ipython
-           python-jplephem
            python-objgraph
            python-pandas
-           python-pyarrow
            python-pytest
            python-pytest-astropy
            python-pytest-astropy-header
            python-pytest-mpl
            python-pytest-xdist
            python-scikit-image
+           python-setuptools
            python-setuptools-scm
            python-sgp4
            python-skyfield
            python-threadpoolctl
-           python-timezonefinder))
+           python-timezonefinder
+           python-wheel))
     (inputs
      (list expat wcslib))
     (propagated-inputs
      (list python-astropy-iers-data
            python-configobj
+           python-h5py
+           python-jplephem
            python-matplotlib
            python-numpy
            python-packaging
            python-ply
+           python-pyarrow
            python-pyerfa
            python-pyyaml
            python-scipy))
-- 
2.46.0

[bug#74497] [PATCH 17/46] gnu: python-bayesicfitting: Update to 3.2.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-bayesicfitting): Update to 3.2.2.

Change-Id: Id956076478a2e670f49703c9890a845cb601a167
---
 gnu/packages/astronomy.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 4a96837e16..a3b2392fa7 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1906,18 +1906,16 @@ (define-public python-astroml
 (define-public python-bayesicfitting
   (package
     (name "python-bayesicfitting")
-    (version "3.2.1")
+    (version "3.2.2")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/dokester/BayesicFitting")
-             ;; Tag style has been changed, see
-             ;; <https://github.com/dokester/BayesicFitting/issues/23>.
-             (commit (string-append "v." version))))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0brqvy4r75vh93lj4jwv8wcrc96ka1v44f5ckjvr65y30plnfwg2"))))
+        (base32 "15zl6r5agfc07lnkrr4qwzx0naql0jblh96j095jyqywd2qnhfsb"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.46.0

[bug#74497] [PATCH 18/46] gnu: python-crds: Update to 12.0.6.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-crds): Update to 12.0.6.

Change-Id: Idc9306fb489d77b7aace78e5ce2563e9eda667c8
---
 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 a3b2392fa7..85ac5844a8 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3708,13 +3708,13 @@ (define-public python-cmyt
 (define-public python-crds
   (package
     (name "python-crds")
-    (version "12.0.4")
+    (version "12.0.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "crds" version))
        (sha256
-        (base32 "1xsw120npgf962p3s9rddi88ppmvr0hs6203dnv05wvq2jyfsymv"))))
+        (base32 "1jm85myp61dckr85rfax32z4cvp4nrdz235486jp225kf765fzdx"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.46.0

[bug#74497] [PATCH 19/46] gnu: python-drizzle: Update to 2.0.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-drizzle): Update to 2.0.0.

Change-Id: Ic90751c48296d3aed3b49a894e6c007436f8223c
---
 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 85ac5844a8..c10fdc14f6 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3779,7 +3779,7 @@ (define-public python-drms
 (define-public python-drizzle
   (package
     (name "python-drizzle")
-    (version "1.15.3")
+    (version "2.0.0")
     (source
      (origin
        (method git-fetch) ;PyPi doesn't have the test data sets
@@ -3788,7 +3788,7 @@ (define-public python-drizzle
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0zxhzvd01jgl4r6ivlxkccaf2shzb0c0ir7l06096iv9n6lff3wx"))))
+        (base32 "1psa98n81wphin15j7k0392rh94dkhnwrjp32lr40gb9ldp52mcm"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.46.0

[bug#74497] [PATCH 20/46] gnu: Add python-puremagic.

[Sharlatan Hellseher]

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

Change-Id: I326d15cdf6eb088f456954c28fd735bc1890840a
---
 gnu/packages/python-xyz.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 3872b511a1..4ec6407571 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12827,6 +12827,29 @@ (define-public python-pure-eval
 abstract syntax tree (AST) nodes without side effects.")
     (license license:expat)))
 
+(define-public python-puremagic
+  (package
+    (name "python-puremagic")
+    (version "1.28")
+    (source
+     (origin
+       (method git-fetch)               ;no tests in PyPI archive
+       (uri (git-reference
+             (url "https://github.com/cdgriffith/puremagic")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0sffrjjqh37ijwnggyvs2rfm4iwaz2m395wqg0x727wv8i0x3f3b"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest))
+    (home-page "https://github.com/cdgriffith/puremagic")
+    (synopsis "Pure Python implementation of magic file detection")
+    (description
+     "This package implements a functionality that will identify a file based
+off it's magic numbers.")
+    (license license:expat)))
+
 (define-public python-ast-decompiler
   (package
     (name "python-ast-decompiler")
-- 
2.46.0

[bug#74497] [PATCH 21/46] gnu: python-ginga: Update to 5.2.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ginga): Update to 5.2.0.
[propagated-inputs]: Add python-puremagic.

Change-Id: Ibdb5e3057365ddd67efa49f0ace39912b330be71
---
 gnu/packages/astronomy.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c10fdc14f6..21adcd42a0 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2238,13 +2238,13 @@ (define-public python-gatspy
 (define-public python-ginga
   (package
     (name "python-ginga")
-    (version "5.1.0")
+    (version "5.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ginga" version))
        (sha256
-        (base32 "0c6vpcz59x889z8ggq6r5ci9cf10m7r9h262r6chx31mzdr010wf"))))
+        (base32 "0gdb4wkz3ivizyb15x86q3z9ms7mlhpakwksp417mgy1av85wssh"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2276,6 +2276,7 @@ (define-public python-ginga
            python-packaging
            python-photutils
            python-pillow
+           python-puremagic
            python-pyyaml
            python-qtpy
            python-scipy
-- 
2.46.0

[bug#74497] [PATCH 22/46] gnu: python-aplpy: Update to 2.2.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-aplpy): Update to 2.2.0.
[arguments]<tests>: Enable them.
<phases>: Add 'set-env phase.
[native-inputs]: Add python-setuptools, python-setuptools-scm, and
python-wheel.

Change-Id: I050d5e174112afe5abd707e784a152feac5cef59
---
 gnu/packages/astronomy.scm | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 21adcd42a0..4f4d2ef504 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1584,21 +1584,28 @@ (define-public python-ads
 (define-public python-aplpy
   (package
     (name "python-aplpy")
-    (version "2.1.0")
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "aplpy" version))
        (sha256
-        (base32 "0ph9jhv4q4i4z6nkqr6hjw9148kdlnayxsn83qgv5dqn0h3nc9r8"))))
+        (base32 "03c8k7y75f5bwm8d08fr5xfaay4d9jzr5sas4j2frs7zrr8aak51"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; FIXME: https://github.com/aplpy/aplpy/issues/492
-      #:tests? #f
+      #:test-flags #~(list "--pyargs" "aplpy")
       #:phases
       #~(modify-phases %standard-phases
-          (delete 'sanity-check))))
+          (add-after 'unpack 'set-env
+            (lambda _
+              (setenv "HOME" "/tmp"))))))
+    (native-inputs
+     (list python-pytest-astropy
+           python-pytest-mpl
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (propagated-inputs
      (list python-astropy
            python-matplotlib
@@ -1609,9 +1616,6 @@ (define-public python-aplpy
            python-reproject
            python-scikit-image
            python-shapely))
-    (native-inputs
-     (list python-pytest-astropy
-           python-pytest-mpl))
     (home-page "http://aplpy.github.io")
     (synopsis "Astronomical Plotting Library in Python")
     (description
-- 
2.46.0

[bug#74497] [PATCH 23/46] gnu: python-astroalign: Update to 2.6.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroalign): Update to 2.6.1.

Change-Id: I2181e07f4e90750e8855ead326bf7d0b97956089
---
 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 4f4d2ef504..7f020a1ba9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1776,7 +1776,7 @@ (define-public python-asdf-zarr
 (define-public python-astroalign
   (package
     (name "python-astroalign")
-    (version "2.6.0")
+    (version "2.6.1")
     (source
      (origin
        ;; There are no tests in the PyPI tarball.
@@ -1786,7 +1786,7 @@ (define-public python-astroalign
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "19dmdnp2hzhzd25601xrfflhxi3j2rgpwf3nl882173wb544cxyq"))))
+        (base32 "1r65n0jx3gvr43c8svswcpvjdjwz85xcvxrrxmvxzv0w2bd6xcc9"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-astropy
-- 
2.46.0

[bug#74497] [PATCH 24/46] gnu: python-astrodendro: Update to 0.3.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astrodendro): Update to 0.3.1.
[source]: Swap to PyPI tarball containing a fresh release.
[phases]: Remove 'set-env-version, no longer required.

Change-Id: I3180990d8a12747b7b301680a705f956a7f47e0c
---
 gnu/packages/astronomy.scm | 26 +++++---------------------
 1 file changed, 5 insertions(+), 21 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 7f020a1ba9..78e9d0c156 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1808,32 +1808,16 @@ (define-public python-astroalign
     (license license:expat)))
 
 (define-public python-astrodendro
-  ;; XXX: 0.2.0 was released 8 years ago and not compatible with Python 3.10,
-  ;; use the latest commit on master branch, see
-  ;; <https://github.com/dendrograms/astrodendro/issues/189>.
-  (let ((commit "3181c36489caa4c62b36b7ec8e06f4da65af6fda")
-        (revision "0"))
     (package
       (name "python-astrodendro")
-      (version (git-version "0.2.0" revision commit))
+      (version "0.3.1")
       (source
        (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/dendrograms/astrodendro")
-               (commit commit)))
+         (method url-fetch)
+         (uri (pypi-uri "astrodendro" version))
          (sha256
-          (base32 "1imahzl0g8r1lxyiz9wi9q4zk519yxgn6qs1nb0ybb34sipjs4kz"))
-         (file-name (git-file-name name version))))
+          (base32 "0pav2rq5q0wyr38g6z8ai4z2iqqc9x04iwll158yvkvgnv352m0i"))))
       (build-system pyproject-build-system)
-      (arguments
-       (list
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-before 'build 'set-env-version
-              (lambda _
-                (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
-                        #$(version-major+minor+point version)))))))
       (native-inputs
        (list python-pytest
              python-setuptools
@@ -1849,7 +1833,7 @@ (define-public python-astrodendro
       (description
        "This package provides an way to compute dendrograms of observed or
 simulated Astronomical data in Python.")
-      (license license:expat))))
+      (license license:expat)))
 
 (define-public python-astroml
   (package
-- 
2.46.0

[bug#74497] [PATCH 25/46] gnu: python-astrodendro: Fix indentation.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astrodendro): Fix indentation.

Change-Id: I3bfe4cd012c55d6affaaab8c0ee8cee3d4f9847c
---
 gnu/packages/astronomy.scm | 50 +++++++++++++++++++-------------------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 78e9d0c156..1a45356bf8 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1808,32 +1808,32 @@ (define-public python-astroalign
     (license license:expat)))
 
 (define-public python-astrodendro
-    (package
-      (name "python-astrodendro")
-      (version "0.3.1")
-      (source
-       (origin
-         (method url-fetch)
-         (uri (pypi-uri "astrodendro" version))
-         (sha256
-          (base32 "0pav2rq5q0wyr38g6z8ai4z2iqqc9x04iwll158yvkvgnv352m0i"))))
-      (build-system pyproject-build-system)
-      (native-inputs
-       (list python-pytest
-             python-setuptools
-             python-setuptools-scm
-             python-wheel))
-      (propagated-inputs
-       (list python-astropy
-             python-h5py
-             python-matplotlib
-             python-numpy))
-      (home-page "https://dendrograms.readthedocs.io/")
-      (synopsis "Astronomical dendrograms computation")
-      (description
-       "This package provides an way to compute dendrograms of observed or
+  (package
+    (name "python-astrodendro")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "astrodendro" version))
+       (sha256
+        (base32 "0pav2rq5q0wyr38g6z8ai4z2iqqc9x04iwll158yvkvgnv352m0i"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
+    (propagated-inputs
+     (list python-astropy
+           python-h5py
+           python-matplotlib
+           python-numpy))
+    (home-page "https://dendrograms.readthedocs.io/")
+    (synopsis "Astronomical dendrograms computation")
+    (description
+     "This package provides an way to compute dendrograms of observed or
 simulated Astronomical data in Python.")
-      (license license:expat)))
+    (license license:expat)))
 
 (define-public python-astroml
   (package
-- 
2.46.0

[bug#74497] [PATCH 26/46] gnu: python-cdflib: Update to 1.3.2.

[Sharlatan Hellseher]

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

Change-Id: Ibd8ed32e12c09b3f9e88a668e92a9c1c9dc9db86
---
 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 1a45356bf8..692c54e66e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3583,7 +3583,7 @@ (define-public python-ccdproc
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-    (version "1.3.1")
+    (version "1.3.2")
     (source
      (origin
        (method git-fetch)               ; no tests in PyPI release
@@ -3592,7 +3592,7 @@ (define-public python-cdflib
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0zmz9wjhlq43lqy5k4fld9cj5k39s1hkkaligrn3kpf9hcbd79qn"))))
+        (base32 "0g723s5xg7vd37vlbjpgpiljd3vxwccslwzcf619zvdnc2xbcw2c"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases
-- 
2.46.0

[bug#74497] [PATCH 27/46] gnu: python-jwst: Update to 1.16.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-jwst): Update to 1.16.1.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Id5c45dccc8f1b06826a3bae09e2b8bc68d6f5a20
---
 gnu/packages/astronomy.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 692c54e66e..546b0c6e0c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5365,13 +5365,13 @@ (define-public python-jplephem
 (define-public python-jwst
   (package
     (name "python-jwst")
-    (version "1.16.0")
+    (version "1.16.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "jwst" version))
               (sha256
                (base32
-                "06krkpfhwpc825bsdl0rffd9qlqw1rl928fwxa7cywds5dahpiyn"))
+                "1bqfgqp4gdm1ky5dvzhzpgygwr710h4mbykp5sb9aw3cw9jg1bk7"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -5431,7 +5431,9 @@ (define-public python-jwst
                          python-pytest-openfiles
                          python-requests-mock
                          ;; python-ruff ; not packed yet in Guix
-                         python-setuptools-scm))
+                         python-setuptools
+                         python-setuptools-scm
+                         python-wheel))
     (home-page "https://jwst-pipeline.readthedocs.io/en/latest/")
     (synopsis
      "Python library for science observations from the James Webb Space Telescope")
-- 
2.46.0

[bug#74497] [PATCH 28/46] gnu: python-ndcube: Update to 2.2.4.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ndcube): Update to 2.2.4.

Change-Id: I326497497ca71d156ead1c45a14d24556fe6bd9b
---
 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 546b0c6e0c..33e20c16f8 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4019,13 +4019,13 @@ (define-public python-naima
 (define-public python-ndcube
   (package
     (name "python-ndcube")
-    (version "2.2.3")
+    (version "2.2.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ndcube" version))
        (sha256
-        (base32 "01sxmy5ki5bcgva5z3m20mg20dfx5n6dkb41kdfcdizqmsw96qmn"))))
+        (base32 "08l4nq43igpic6v3zjnyjq3yy44czg79798rmv5la52hbzbz1kj3"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.46.0

[bug#74497] [PATCH 29/46] gnu: python-photutils: Update to 2.0.2.

[Sharlatan Hellseher]

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

Change-Id: I28b9d14f13157362c4781068c16c22b890c34a24
---
 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 33e20c16f8..a6d0700702 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4084,13 +4084,13 @@ (define-public python-ndcube
 (define-public python-photutils
   (package
     (name "python-photutils")
-    (version "2.0.1")
+    (version "2.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "photutils" version))
        (sha256
-        (base32 "1mcsp5bsg3i6w3v9gf7vhkyhlxsn57hgbs0b94p5c4hcv9fa4y3g"))))
+        (base32 "0lpah7a4wb3r7i8d4gc5bmb34bx3idg921220xhsgdplml77syzh"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.46.0

[bug#74497] [PATCH 30/46] gnu: python-pyerfa: Update to 2.0.1.5.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pyerfa): Update to 2.0.1.5.

Change-Id: I9be430d4acacbbfccb4eaa928863864291ab2649
---
 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 a6d0700702..248ca2af88 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5488,13 +5488,13 @@ (define-public python-jwst-reffiles
 (define-public python-pyerfa
   (package
     (name "python-pyerfa")
-    (version "2.0.1.4")
+    (version "2.0.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyerfa" version))
        (sha256
-        (base32 "1lwx4hril705r2iz4pirgn0wrpv1wk20mr669g03bsij69qsdf5c"))
+        (base32 "1h7nw61wqx9qsznnl8qandixr6c1n3f65hyqwzanav44wi7v5mhp"))
        (modules '((guix build utils)))
        (snippet
         #~(begin
-- 
2.46.0

[bug#74497] [PATCH 31/46] gnu: python-pyvo: Update to 1.6.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pyvo): Update to 1.6.

Change-Id: Iff2f08d372f950193c53f394d73be07b1f0a1de4
---
 gnu/packages/astronomy.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 248ca2af88..50d7b57ad5 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4323,14 +4323,17 @@ (define-public python-pyavm
 (define-public python-pyvo
   (package
     (name "python-pyvo")
-    (version "1.5.3")
+    (version "1.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyvo" version))
        (sha256
-        (base32 "0zlqn7qflv5ipmlqkq85qjgggz84zi67jm45w4ayfapmhh74sa7x"))))
+        (base32 "1ahcazgxhmxscjgz58mxw75k9g0xm7iffnc4lqfbm3h0wqiz8vnv"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags #~(list "--pyargs" "pyvo")))
     (native-inputs
      (list python-pytest-astropy
            python-requests-mock
-- 
2.46.0

[bug#74497] [PATCH 32/46] gnu: python-rad: Update to 0.22.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-rad): Update to 0.22.0.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: If9509ccba985f08a3a6d263316beb263ff055db4
---
 gnu/packages/astronomy.scm | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 50d7b57ad5..23c8a85386 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6259,13 +6259,13 @@ (define-public python-gwcs
 (define-public python-rad
   (package
     (name "python-rad")
-    (version "0.21.0")
+    (version "0.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "rad" version))
        (sha256
-        (base32 "0b2gfsyccfx9dmmh725h7qjh5rxabg5w1j52yzfi8b0a8nmg6j6a"))))
+        (base32 "1p6v49gzbzishy1kdd5g8nbl97qp459s1smb6j94wvif4262zkm8"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -6273,9 +6273,13 @@ (define-public python-rad
       ;; python-rad -> python-roman-datamodels -> python-crds -> python-rad
       #:test-flags #~(list "--ignore=tests/test_schemas.py")))
     (native-inputs
-     (list python-pytest python-setuptools-scm))
+     (list python-pytest
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (propagated-inputs
-     (list python-asdf python-asdf-astropy))
+     (list python-asdf
+           python-asdf-astropy))
     (home-page "https://github.com/spacetelescope/rad")
     (synopsis "Roman Attribute Dictionary")
     (description
-- 
2.46.0

[bug#74497] [PATCH 33/46] gnu: python-regularizepsf: Update to 1.0.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-regularizepsf): Update to 1.0.2.
[source]: Swap to PyPI tarball as a fresh release contains tests now.
[phases]: Remove all custom ones.
[propagated-inputs]: Remove python-dill and python-lmfit.
[native-inputs]: Remove python-cython and python-pytest-runner; add
python-setuptools, python-setuptools-scm, and python-wheel.

Change-Id: I1c17bef1a1a21665b633d22282a9df37155e4f29
---
 gnu/packages/astronomy.scm | 36 ++++++++++--------------------------
 1 file changed, 10 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 23c8a85386..0391c339cb 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4408,44 +4408,28 @@ (define-public python-regions
 (define-public python-regularizepsf
   (package
     (name "python-regularizepsf")
-    (version "0.4.0")
+    (version "1.0.2")
     (source
      (origin
-       (method git-fetch) ; no tests data in the PyPI tarball
-       (uri (git-reference
-             (url "https://github.com/punch-mission/regularizepsf")
-             (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (pypi-uri "regularizepsf" version))
        (sha256
-        (base32 "0b16lscrzd1lribwis19y6dh6qrgddhcinlc2lbwkzzqqkjdnyzi"))))
+        (base32 "1ial8i9nshhpn3lsgnjqm94dfrzxwz2qgpd8bjzmml1ls0j7sm9v"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-         (add-after 'unpack 'relax-requirements
-           (lambda _
-             (substitute* "setup.py"
-               ;; numpy==1.26.4
-               (("==1.26.4") ">=1.23"))))
-          (add-before 'check 'build-extensions
-            (lambda _
-              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (native-inputs
+     (list python-pytest
+           python-pytest-mpl
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (propagated-inputs
      (list python-astropy
-           python-dill
            python-h5py
-           python-lmfit
            python-matplotlib
            python-numpy
            python-scikit-image
            python-scipy
            python-sep-pjw))
-    (native-inputs
-     (list python-cython
-           python-pytest
-           python-pytest-mpl
-           python-pytest-runner))
     (home-page "https://github.com/punch-mission/regularizepsf")
     (synopsis "Point spread function modeling and regularization")
     (description
-- 
2.46.0

[bug#74497] [PATCH 34/46] gnu: python-reproject: Update to 0.14.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-reproject): Update to 0.14.1.

Change-Id: I4d354d42193933cb50440383a544d25f9418749b
---
 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 0391c339cb..d793a63889 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4440,13 +4440,13 @@ (define-public python-regularizepsf
 (define-public python-reproject
   (package
     (name "python-reproject")
-    (version "0.14.0")
+    (version "0.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "reproject" version))
        (sha256
-        (base32 "1h5v74da32ai9dkhcdn3xx4h05awlxhhnrsdjj1sb644c1vlyg6x"))))
+        (base32 "0yg5dga054xdwsx75q204h04gmrw0mgayc74l4rpymcbkckymj2k"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.46.0

[bug#74497] [PATCH 35/46] gnu: python-roman-datamodels: Update to 0.22.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-roman-datamodels): Update to 0.22.0.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I7cfc5aed379c9056f93e1214ec5b06f56edced74
---
 gnu/packages/astronomy.scm | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d793a63889..ac3b00f685 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6359,13 +6359,13 @@ (define-public python-radiospectra
 (define-public python-roman-datamodels
   (package
     (name "python-roman-datamodels")
-    (version "0.21.0")
+    (version "0.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "roman_datamodels" version))
        (sha256
-        (base32 "00hwyxixdk3i48nhqnn7pnkkp3fran6fn8kzwx2w4bjkwv8cd126"))))
+        (base32 "0n50pgs7y0nmrx86qlny27mas2zgx708gm3xfkl7an2nwkdfwfld"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -6376,6 +6376,14 @@ (define-public python-roman-datamodels
           (add-after 'unpack 'set-env
             (lambda _
               (setenv "HOME" "/tmp"))))))
+    (native-inputs
+     (list python-pytest
+           python-pytest-doctestplus
+           python-pytest-env
+           python-pytest-xdist
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (propagated-inputs
      (list python-asdf
            python-asdf-astropy
@@ -6384,12 +6392,6 @@ (define-public python-roman-datamodels
            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
-- 
2.46.0

[bug#74497] [PATCH 36/46] gnu: python-sep-pjw: Update to 1.3.7.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sep-pjw): Update to 1.3.7.

Change-Id: I2adbb4b283ce2b545ce8dcd0671beb88a8fcd3b5
---
 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 ac3b00f685..43832d92d6 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5836,13 +5836,13 @@ (define-public python-sep
 (define-public python-sep-pjw
   (package
     (name "python-sep-pjw")
-    (version "1.3.6")
+    (version "1.3.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sep_pjw" version))
        (sha256
-        (base32 "0ji3khgswidnnqx34js9fyk39kgh4gvf7q8gk2f7r4acaabzja2v"))))
+        (base32 "1z8m2l3ccxj1izdazv7a0hg6zd1495bvby8w114s5ji7fd91vdv7"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.46.0

[bug#74497] [PATCH 37/46] gnu: python-sncosmo: Update to 2.11.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sncosmo): Update to 2.11.2.

Change-Id: I00ec74de18a88782895e185edb063e9508b90d46
---
 gnu/packages/astronomy.scm | 66 ++++++++++++++++++++------------------
 1 file changed, 34 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 43832d92d6..93085adac7 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2794,49 +2794,51 @@ (define-public python-sirilic
 (define-public python-sncosmo
   (package
     (name "python-sncosmo")
-    (version "2.11.1")
+    (version "2.11.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sncosmo" version))
        (sha256
-        (base32 "0nmhrvaw22zxpmykl70a91mc88pxmw0x5fdxjiz3hdzkdbqrg0x9"))))
+        (base32 "1n7kh2qinp04ilf8d26hgjs6c3bdy5vbmppc6ps9jy1q0ll8gi69"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
       ;; Disable tests requireing remote access to download test data.
       #~(list
-         "-k" (string-append "not test_megacampsf_bandpass"
-                             " and not test_builtins_remote_aa"
-                             " and not test_builtins_remote_nm"
-                             " and not test_builtins_remote_um"
-                             " and not test_builtins_remote_wfc3"
-                             " and not test_builtins_megacampsf"
-                             " and not test_builtins_timeseries_ascii"
-                             " and not test_builtins_timeseries_fits"
-                             " and not test_builtins_salt2model"
-                             " and not test_builtins_salt3model"
-                             " and not test_builtins_2011fe"
-                             " and not test_builtins_mlcs2k2"
-                             " and not test_builtins_snemo"
-                             " and not test_builtins_sugar"
-                             " and not test_builtins_magsys_fits"
-                             " and not test_builtins_magsys_csp"
-                             " and not test_builtins_magsys_ab_b12"
-                             " and not test_builtins_magsys_jla"
-                             " and not test_csp_magsystem"
-                             " and not test_compositemagsystem_band_error"
-                             " and not test_G10"
-                             " and not test_C11"
-                             " and not test_salt2source_timeseries_vs_snfit"
-                             " and not test_salt2source_rcov_vs_snfit"
-                             " and not test_bandflux"
-                             " and not test_bandflux_multi"
-                             " and not test_bandflux_zpsys"
-                             " and not test_bandfluxcov"
-                             " and not test_bandmag"
-                             " and not test_sugarsource"))
+         "-k" (string-join
+               (list "not test_megacampsf_bandpass"
+                     "test_builtins_remote_aa"
+                     "test_builtins_remote_nm"
+                     "test_builtins_remote_um"
+                     "test_builtins_remote_wfc3"
+                     "test_builtins_megacampsf"
+                     "test_builtins_timeseries_ascii"
+                     "test_builtins_timeseries_fits"
+                     "test_builtins_salt2model"
+                     "test_builtins_salt3model"
+                     "test_builtins_2011fe"
+                     "test_builtins_mlcs2k2"
+                     "test_builtins_snemo"
+                     "test_builtins_sugar"
+                     "test_builtins_magsys_fits"
+                     "test_builtins_magsys_csp"
+                     "test_builtins_magsys_ab_b12"
+                     "test_builtins_magsys_jla"
+                     "test_csp_magsystem"
+                     "test_compositemagsystem_band_error"
+                     "test_G10"
+                     "test_C11"
+                     "test_salt2source_timeseries_vs_snfit"
+                     "test_salt2source_rcov_vs_snfit"
+                     "test_bandflux"
+                     "test_bandflux_multi"
+                     "test_bandflux_zpsys"
+                     "test_bandfluxcov"
+                     "test_bandmag"
+                     "test_sugarsource")
+               " and not "))
       #:phases
       #~(modify-phases %standard-phases
          (add-after 'unpack 'relax-requirements
-- 
2.46.0

[bug#74497] [PATCH 38/46] gnu: python-specutils: Update to 1.19.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-specutils): Update to 1.19.0.

Change-Id: Ic90ecae2032682f893f7bfd7c4521d02d906fec1
---
 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 93085adac7..76910307c5 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4800,13 +4800,13 @@ (define-public python-spectral-cube
 (define-public python-specutils
   (package
     (name "python-specutils")
-    (version "1.18.0")
+    (version "1.19.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "specutils" version))
        (sha256
-        (base32 "16fwazgk1cbqd9njrmwg4xyxg4qykv8c5mk5bzxwz1q5arjc8cy7"))))
+        (base32 "1iwkrs436z8xrzwl5rkla8nimyfrx5ydklghm41xgzr27nkvqa12"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.46.0

[bug#74497] [PATCH 39/46] gnu: python-statmorph: Update to 0.6.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-statmorph): Update to 0.6.0.
[arguments]<test-flags>: Enable all tests as issue is resolved upstream.
[propagated-inputs]: Remove python-matplotlib.

Change-Id: I48b71e590b9c4da4f09ab578767c05890110e8d4
---
 gnu/packages/astronomy.scm | 28 ++--------------------------
 1 file changed, 2 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 76910307c5..a83cee194b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4976,43 +4976,19 @@ (define-public python-spisea
 (define-public python-statmorph
   (package
     (name "python-statmorph")
-    (version "0.5.7")
+    (version "0.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "statmorph" version))
        (sha256
-        (base32 "06rbwrqlvdzn9innx05kjjmm4mmacd8kwwsfdf5idbwzby5ny5lw"))))
+        (base32 "1575vmk4kl06yxyid7mb1r7llbrmraagvx2b0h5x335ha7irnkjk"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      ;; XXX: Skip most of the tests for now, see
-      ;; <https://github.com/vrodgom/statmorph/issues/11>.
-      #~(list "-k" (string-append "not test_asymmetric"
-                                  " and not test_bright_pixel"
-                                  " and not test_catastrophic"
-                                  " and not test_empty_gini_segmap"
-                                  " and not test_full_gini_segmap"
-                                  " and not test_full_segmap"
-                                  " and not test_insufficient_data"
-                                  " and not test_make_figure"
-                                  " and not test_masked_centroid"
-                                  " and not test_merger"
-                                  " and not test_missing_arguments"
-                                  " and not test_negative_source"
-                                  " and not test_no_psf"
-                                  " and not test_psf"
-                                  " and not test_random_noise"
-                                  " and not test_small_source"
-                                  " and not test_tiny_source"
-                                  " and not test_weightmap"))))
     (native-inputs
      (list python-pytest
            python-setuptools))
     (propagated-inputs
      (list python-astropy
-           python-matplotlib
            python-numpy
            python-photutils
            python-scikit-image
-- 
2.46.0

[bug#74497] [PATCH 40/46] gnu: python-stcal: Update to 1.10.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stcal): Update to 1.10.0.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: If0da286182d27e74af1278a7dfc1e3d54f6b8d23
---
 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 a83cee194b..07ed2ea727 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5110,26 +5110,27 @@ (define-public python-stsci-stimage
 (define-public python-stcal
   (package
     (name "python-stcal")
-    (version "1.9.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stcal" version))
        (sha256
-        (base32 "1n843r19zyjm14iadfbi71ixpk0jrbhaj7h3szy1yhnhrfsrkwar"))))
+        (base32 "1h0vkc3nd77qm2ph1nihpd1n7dzr3d4rw2wga6j7siqjiwmphj3g"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
-      #~(list "-k" (string-append
+      #~(list "-k" (string-join
                     ;; Tests requiring network access.
-                    "not test_absolute_align"
-                    " and not test_relative_align[True]"
-                    " and not test_relative_align[False]"
-                    " and not test_get_catalog"
-                    " and not test_create_catalog"
-                    " and not test_create_catalog_graceful_failure"
-                    " and not test_parse_refcat"))
+                    (list "not test_absolute_align"
+                          "test_relative_align[True]"
+                          "test_relative_align[False]"
+                          "test_get_catalog"
+                          "test_create_catalog"
+                          "test_create_catalog_graceful_failure"
+                          "test_parse_refcat")
+                    " and not "))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-slope-fitter
@@ -5149,6 +5150,14 @@ (define-public python-stcal
             (lambda _
               ;; Cython extensions have to be built before running the tests.
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (native-inputs
+     (list python-cython-3
+           python-psutil
+           python-pytest
+           python-pytest-doctestplus
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (propagated-inputs
      (list opencv ;Provides OpenCV-Python
            python-asdf
@@ -5160,12 +5169,6 @@ (define-public python-stcal
            python-scikit-image
            python-scipy
            python-tweakwcs))
-    (native-inputs
-     (list python-cython-3
-           python-psutil
-           python-pytest
-           python-pytest-doctestplus
-           python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/stcal")
     (synopsis "STScI tools and algorithms used in calibration pipelines")
     (description "STScI tools and algorithms used in calibration pipelines.")
-- 
2.46.0

[bug#74497] [PATCH 41/46] gnu: python-stdatamodels: Update to 2.1.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stdatamodels): Update to 2.1.2.

Change-Id: I59dec6df596c42b48cf6841c4d10857af9c92bd2
---
 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 07ed2ea727..82275ebbda 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5177,13 +5177,13 @@ (define-public python-stcal
 (define-public python-stdatamodels
   (package
     (name "python-stdatamodels")
-    (version "2.1.1")
+    (version "2.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stdatamodels" version))
        (sha256
-        (base32 "08zkr0amc65dj2lr90d2r29cj23f8h0ms94qmmcgcq2r4xlpna10"))))
+        (base32 "0x7fzkda9cr7bsf8hq2q090a73cxk3l3ynipq8lqixfp8c94m3kq"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.46.0

[bug#74497] [PATCH 42/46] gnu: python-stsynphot: Update to 1.4.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stsynphot): Update to 1.4.0.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I9155f517358ecf651a47fe48a676202a2c19bb2f
---
 gnu/packages/astronomy.scm | 38 +++++++++++++++++++++-----------------
 1 file changed, 21 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 82275ebbda..1295b04f6b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5263,13 +5263,13 @@ (define-public python-stpipe
 (define-public python-stsynphot
   (package
     (name "python-stsynphot")
-    (version "1.3.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "stsynphot" version))
-              (sha256
-               (base32
-                "15m3vy39mc7rh1mrxs8d2bs0bx5vv632m6wg8n15fqjzhadqy7j5"))))
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "stsynphot" version))
+       (sha256
+        (base32 "02xaglg1kv3mk6gqjcs1283mmy9b42fgsga8g2z8768lkgwmmg9j"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -5278,16 +5278,20 @@ (define-public python-stsynphot
       ;; Failed to load Vega spectrum from
       ;; /grp/redcat/trds/calspec/alpha_lyr_stis_010.fits;
       #:tests? #f))
-    (propagated-inputs (list python-astropy
-                             python-beautifulsoup4
-                             python-matplotlib
-                             python-numpy
-                             python-scipy
-                             python-synphot))
-    (native-inputs (list python-pytest
-                         python-pytest-astropy
-                         python-pytest-astropy-header
-                         python-setuptools-scm))
+    (native-inputs
+     (list python-pytest
+           python-pytest-astropy
+           python-pytest-astropy-header
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
+    (propagated-inputs
+     (list python-astropy
+           python-beautifulsoup4
+           python-matplotlib
+           python-numpy
+           python-scipy
+           python-synphot))
     (home-page "https://github.com/spacetelescope/stsynphot_refactor")
     (synopsis "Synthetic photometry using Astropy for HST and JWST")
     (description
-- 
2.46.0

[bug#74497] [PATCH 43/46] gnu: python-synphot: Update to 1.5.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-synphot): Update to 1.5.0.
Simplify package.
[arguments]<phases>: Use default 'check phase.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Iccc0c2bedc7075af3da2bc0ffb822787d40d6f41
---
 gnu/packages/astronomy.scm | 25 +++++++++----------------
 1 file changed, 9 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 1295b04f6b..aec9cc330a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5881,36 +5881,29 @@ (define-public python-suntime
 (define-public python-synphot
   (package
     (name "python-synphot")
-    (version "1.4.0")
+    (version "1.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "synphot" version))
        (sha256
-        (base32 "0fk860bxaqbamrq15pkqlbvhbf70y50cra2mgvv9r0cxq37isbi6"))))
+        (base32 "0xifg0fbh2rj3jn5i504c0qh51dlzgr1l2k962nh38synjhq9csc"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key tests? test-flags #:allow-other-keys)
-              (when tests?
-                (invoke "python" "setup.py" "build_ext" "--inplace")
-                ;; Step out of the source directory to avoid interference; we
-                ;; want to run the installed code with extensions etc.
-                (with-directory-excursion "/tmp"
-                  (apply invoke "pytest" "-v" test-flags))))))))
+      #:test-flags #~(list "--pyargs" "synphot")))
+    (native-inputs
+     (list python-pytest
+           python-pytest-astropy
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (propagated-inputs
      (list python-astropy
            python-dust-extinction
            python-numpy
            python-scipy
            python-specutils ))
-    (native-inputs
-     (list python-pytest
-           python-pytest-astropy
-           python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/synphot_refactor")
     (synopsis "Synthetic photometry using Astropy")
     (description
-- 
2.46.0

[bug#74497] [PATCH 44/46] gnu: python-yt: Update to 4.4.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-yt): Update to 4.4.0.
[arguments]<test-flags>: Disable some failing tests and tests requiring
network access.
[propagated-inputs]: Add python-astropy, python-cartopy,
python-glue-core, python-h5py, python-netcdf4, python-pandas,
python-pooch, python-regions, python-requests, and python-xarray.
[native-inputs]: Remove python-nose, python-nose-exclude, and
python-nose-timer; add nss-certs-for-test.

Change-Id: Ia868892b81fb8c5fc72ae20040b5f70ef936ff78
---
 gnu/packages/astronomy.scm | 42 ++++++++++++++++++++++++++++++--------
 1 file changed, 34 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index aec9cc330a..858fb75d45 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6584,19 +6584,30 @@ (define-public python-wiimatch
 (define-public python-yt
   (package
     (name "python-yt")
-    (version "4.3.1")
+    (version "4.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "yt" version))
        (sha256
-        (base32 "03jy35vyniyd1pd3sv0zpd2f3ks2iyqw65xv28ids8nw6v1vavbv"))))
+        (base32 "1mf084wp0wrhi17npzbyz42lh3xwlc2hggr8h4pmighsnafdy58f"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:build-backend "setuptools.build_meta"
       #:test-flags
-      #~(list "--numprocesses" (number->string (parallel-job-count)))
+      #~(list "--numprocesses" (number->string (parallel-job-count))
+              "-k" (string-join
+                    ;; Tests requiring networking.
+                    (list "not test_load_sample_timeout"
+                          "test_unknown_filename"
+                          "test_typo_filename"
+                          "test_data_dir_broken"
+                          "test_registry_byte_size_dtype"
+                          "test_registry_byte_size_sign"
+                          ;; AssertionError: Arrays are not equal
+                          "test_field_cut_off_axis_octree")
+                    " and not "))
       #:phases
       #~(modify-phases %standard-phases
          (add-after 'unpack 'relax-requirements
@@ -6612,10 +6623,8 @@ (define-public python-yt
               (setenv "HOME" "/tmp")
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
-     (list python-cython-3
-           python-nose
-           python-nose-exclude
-           python-nose-timer
+     (list nss-certs-for-test
+           python-cython-3
            python-pyaml
            python-pytest
            python-pytest-mpl
@@ -6634,7 +6643,24 @@ (define-public python-yt
            python-pillow
            python-tomli-w
            python-tqdm
-           python-unyt))
+           python-unyt
+           ;; Optional
+           ;; python-arm-pyart ; not packed yet
+           ;; python-f90nml
+           ;; python-firefly
+           ;; python-miniball
+           ;; python-pyx
+           ;; python-ratarmount
+           python-astropy
+           python-cartopy
+           python-glue-core
+           python-h5py
+           python-netcdf4
+           python-pandas
+           python-pooch
+           python-regions
+           python-requests
+           python-xarray))
     (home-page "http://yt-project.org/")
     (synopsis "Analyzing and visualizing volumetric data framework")
     (description
-- 
2.46.0

[bug#74497] [PATCH 45/46] gnu: python-yt-astro-analysis: Adjust inputs.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-yt-astro-analysis) [native-inputs]:
Remove python-nose; add python-pytest.

Change-Id: I0b08ced355e739f1522cc749ea96db65413dc7b5
---
 gnu/packages/astronomy.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 858fb75d45..999914b3f9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6700,8 +6700,9 @@ (define-public python-yt-astro-analysis
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; Disable test which require MPI setup and failed to run, check why.
-      #:test-flags #~(list "--ignore=test_halo_finders_ts.py")
+      ;; Disable test which requires MPI setup and failed to run, check why.
+      #:test-flags
+      #~(list "--ignore=yt_astro_analysis/halo_analysis/tests/test_halo_finders_ts.py")
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'build-extensions
@@ -6709,9 +6710,9 @@ (define-public python-yt-astro-analysis
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-cython
-           python-nose
-           python-tomli
+           python-pytest
            python-setuptools
+           python-tomli
            python-wheel))
     (propagated-inputs
      (list python-h5py
-- 
2.46.0

[bug#74497] [PATCH 46/46] gnu: python-gatspy: Adjust inputs.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-gatspy) [native-inputs]: Remove
python-nose.

Change-Id: Ifbbaedf62817339743ac2313626cd058134479d9
---
 gnu/packages/astronomy.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 999914b3f9..4370f8e1c3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2210,12 +2210,14 @@ (define-public python-gatspy
           ;; Tests need this
           (add-before 'check 'set-HOME
             (lambda _ (setenv "HOME" "/tmp"))))))
+    (native-inputs
+     (list python-pytest
+           python-setuptools-scm))
     (propagated-inputs
      (list python-astroml
            python-numpy
            python-scipy
            python-supersmoother))
-    (native-inputs (list python-pytest python-nose python-setuptools-scm))
     (home-page "https://github.com/astroml/gatspy")
     (synopsis "General tools for astronomical time series in Python")
     (description
-- 
2.46.0

[bug#74497] [PATCH 00/46] Astro update 2024/11.

[Andreas Enge]

Hello,

Am Sat, Nov 23, 2024 at 07:48:14PM +0000 schrieb Sharlatan Hellseher:
> - NASA's Common Data Format (CDF) project is now packed and available for
>   review, license looks FOSS compatible and not restrictive for modification
>   or distribution.

here is the license text:

"Common Data Format (CDF)
Space Physics Data Facility
NASA/Goddard Space Flight Center

This software may be copied or redistributed as long as it is not sold
for profit, but it can be incorporated into any other substantive
product with or without modifications for profit or non-profit.  If the
software is modified, it must include the following notices:

  - The software is not the original (for protection of the original
    author's reputations from any problems introduced by others)

  - Change history (e.g. date, functionality, etc.)

This copyright notice must be reproduced on each copy made. This software is
provided as is without any express or implied warranties whatsoever."

I would say that "as long as it is not sold for profit" makes it non-free
unfortunately.

But then the next sentence is really strange, since it is somewhat unclear
what "incorporate" and "substantive" mean - can I sell a music CD (which
is substantive) and put a modified version of the software on the same
support (which is maybe not incorporated)?

But even when selling modifications is possible as part of a bigger
product, I think the conclusion remains that the software itself
is not free.

Andreas

[bug#74497] [PATCH 00/46] Astro update 2024/11.

[Sharlatan Hellseher]

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Hi Andreas and Efraim,

Thanks for review.

> I think the conclusion remains that the software itself is not free.
I'll exclude cdf package and maybe propose to Gux science channel instead.

> StableRNGs and Formatting are only listed in test/Project.toml, is
> julia-formatting actually needed as a propagated-input?
I can ammend the package

A question about the series, do I need to adjust it after above comments
are applied and send to the tracker or it would be fine to push directly
after modification?

--
Thanks,
Oleg

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[bug#74497] [PATCH 00/46] Astro update 2024/11.

[Andreas Enge]

Hello Oleg,

Am Wed, Nov 27, 2024 at 08:32:55PM +0000 schrieb Sharlatan Hellseher:
> > I think the conclusion remains that the software itself is not free.
> I'll exclude cdf package and maybe propose to Gux science channel instead.

sounds good!

> A question about the series, do I need to adjust it after above comments
> are applied and send to the tracker or it would be fine to push directly
> after modification?

I would be happy with you sending it directly, since I think you made sure
it all compiles, and QA is not working well right now.

Andreas