GNU bug report logs - #72741
[PATCH 00/32] Astronomy update 2024/08.

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

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 00/32] Astronomy update 2024/08.
Date: Wed, 21 Aug 2024 01:01:29 +0100

Hi Guix!

The last month of not too hot (meteorologly) Summer in rainy island, a new
portion of astro* soft update with continued work on packaging Astropy
affiliated projects and attempt to bring jdaviz - JWST astronomical data
analysis tools in the Jupyter platform, to Guix.


- added [7/7]
  - [X] python-glue-astronomy :: Astronomy-specific plugins for glue
  - [X] python-glue-qt :: Multidimensional data visualization across files
  - [X] python-pvextractor :: Position-Velocity diagram extractor
  - [X] python-pyxsim :: Simulating X-ray observations from astrophysical sources
  - [X] python-soxs :: Simulated Observations of X-ray Sources
  - [X] python-specreduce :: Spectroscopic Reductions
  - [X] python-zodipy :: Zodiacal emission simulations
- updated [20/20]
  - [X] indi :: 2.0.8->2.0.9
  - [X] python-astroplan :: 0.10->0.10.1
  - [X] python-astropy-iers-data :: 0.2024.7.15.0.31.42->0.2024.8.12.0.32.58
  - [X] python-astropy :: 6.1.1->6.1.2
  - [X] python-crds :: 11.17.26->11.18.1
  - [X] python-czml3 :: 1.0.1->1.0.2
  - [X] python-drms :: 0.7.1->0.8.0
  - [X] python-dust-extinction :: 1.4.1->1.5
  - [X] python-glymur :: 0.12.9->0.13.5
  - [X] python-mpl-animators :: 1.1.1->1.2.0
  - [X] python-radiospectra :: 0.5.0->0.6.0
  - [X] python-rad :: 0.20.0->0.21.0
  - [X] python-reproject :: 0.13.1->0.14.0
  - [X] python-roman-datamodels :: 0.20.0->0.21.0
  - [X] python-shapely :: 2.0.2->2.0.5
  - [X] python-specutils :: 1.15.0->1.16.0
  - [X] python-stcal :: 1.7.1->1.8.0
  - [X] python-stpipe :: 0.6.0->0.7.0
  - [X] python-sunpy :: 5.1.5->6.0.1
  - [X] python-viresclient :: 0.11.6->0.12.0

Next month would be a packageing continuation of Astropy affilated project,
IRAF fixing build, bringing more Glue's projects and python-jdaviz packages.

I've found few nice photo stacking software which I'd like to review and add
to Guix Astro collection:
- http://deepskystacker.free.fr/english/index.html
- https://sites.google.com/view/sequator/
- https://pixinsight.com/
- https://www.autostakkert.com/

Build stats:
--8<---------------cut here---------------start------------->8---
> ./pre-inst-env guix build indi <at> 2 python-astroplan python-astropy
  python-astropy-iers-data python-crds python-czml3 python-drms
  python-dust-extinction python-glue-astronomy python-glue-core python-glue-qt
  python-glymur python-mpl-animators python-pvextractor python-pyxsim python-rad
  python-radiospectra python-reproject python-roman-datamodels python-shapely
  python-soxs python-specreduce python-specutils python-stcal python-stpipe
  python-sunkit-image python-sunpy python-viresclient python-zodipy

/gnu/store/6af53igxjnd5vyz51jqmnnlg4c40k91y-python-zodipy-1.0.0
/gnu/store/nvp43bv8qn2rrr7dvw3l5addy8khv6ha-python-viresclient-0.12.0
/gnu/store/mzd3mc0hr8k933rpbqmmy7kj15fd53j3-python-sunpy-6.0.1
/gnu/store/p1gs601ywhzxsd2drwl5xhxn3rx1xxl2-python-sunkit-image-0.5.1
/gnu/store/53qgbk6id2pmqmswks5k1lff30iwa4ai-python-stpipe-0.7.0
/gnu/store/sdsa5n72kam3j53vrg93qkg5935iq0nc-python-stcal-1.8.0
/gnu/store/pa4ks97sg8ppl717bsh6f3h52yk7np60-python-specutils-1.16.0
/gnu/store/zz5whq4cb0wbjd74075b6cz0qnp6psyc-python-specreduce-1.4.1
/gnu/store/dnb7qvd83xr797qf6m4kdqcwq6rf3hcj-python-soxs-4.8.5
/gnu/store/bb842x6lsnic8gqk4yhjk9dmpcsh7agm-python-shapely-2.0.5
/gnu/store/ynnw3p9w7blaw98vv3zrxs2vhqaszx53-python-roman-datamodels-0.21.0
/gnu/store/abpgjd0vmb0apprcyjn5ym25qf832731-python-reproject-0.14.0
/gnu/store/ncpf8wfp6lrnma9izmhyn7c5xrgmdbpf-python-radiospectra-0.6.0
/gnu/store/bw4p64whsrbysfz6871ngsp0agl4zmq3-python-rad-0.21.0
/gnu/store/xbn5iwhzn1zmnal4bvgvipn95mvid9qf-python-pyxsim-4.4.1
/gnu/store/flvjwavcpigc7ynqbarhb5zpa1jmn533-python-pvextractor-0.4
/gnu/store/9srbj6y4304pn2p6d856iih5hvknhv0b-python-mpl-animators-1.2.0
/gnu/store/h4vlbqhlj7vkxnkwrvz50vm9wavqf9hg-python-glymur-0.13.5
/gnu/store/686wjz46v8rcr5602jw74mhikplha41b-python-glue-qt-0.3.1
/gnu/store/m2vwmhxbv8m7v6svlqpp7lv103r8s5i8-python-glue-core-1.21.1
/gnu/store/ldzd0l7mv9dah7hr1r9c1rxsycjd8a2n-python-glue-astronomy-0.10.0
/gnu/store/360s666ahrkm2a1ngrrigrz49nd3sjyf-python-dust-extinction-1.5
/gnu/store/vgv6kifi0gs8b0wbw1520s1b234mfm2l-python-drms-0.8.0
/gnu/store/jbhrlbr36680wdv50m76alfslp875rnp-python-czml3-1.0.2
/gnu/store/88lvc2qi8qw5r5z3wnj085ka5dh5bd14-python-crds-11.18.1
/gnu/store/2s713db6bl9dv4nvw4y2dvmsq5s1qrdw-python-astropy-iers-data-0.2024.8.12.0.32.58
/gnu/store/ag27r2wlzj1dgkbqjm8h3r8mdwg1fk6d-python-astropy-6.1.2
/gnu/store/35cfqa5gvyvlg8zqldl1bnqajr2p5m4v-python-astroplan-0.10.1
/gnu/store/7z51y785f31mnrhsbbwfjassbav5v1fl-indi-2.0.9
--8<---------------cut here---------------end--------------->8---

Dependent build stats:
--8<---------------cut here---------------start------------->8---
> ./pre-inst-env guix refresh --list-dependent indi <at> 2 python-astroplan
  python-astropy python-astropy-iers-data python-crds python-czml3 python-drms
  python-dust-extinction python-glue-astronomy python-glue-core python-glue-qt
  python-glymur python-mpl-animators python-pvextractor python-pyxsim python-rad
  python-radiospectra python-reproject python-roman-datamodels python-shapely
  python-soxs python-specreduce python-specutils python-stcal python-stpipe
  python-sunkit-image python-sunpy python-viresclient python-zodipy

Building the following 33 packages would ensure 99 dependent packages are
rebuilt: scamp <at> 2.10.0 python-regularizepsf <at> 0.3.4 python-zodipy <at> 1.0.0
python-sncosmo <at> 2.11.1 python-kanon <at> 0.6.6 python-naima <at> 0.10.0
python-viresclient <at> 0.12.0 python-cesium <at> 0.12.1 python-asdf-zarr <at> 0.0.4
python-asdf-compression <at> 0.0.1-0.57cc7e7 python-astroalign <at> 2.5.1
python-aplpy <at> 2.1.0 python-poliastro <at> 0.17.0 python-astroplan <at> 0.10.1
python-glue-qt <at> 0.3.1 python-pandapipes <at> 0.10.0 python-liana-py <at> 1.1.0
python-pandera <at> 0.18.0 python-overpass <at> 0.7 python-osmnx <at> 1.9.3 python-verde <at> 1.8.0
cura <at> 4.13.1 python-quadpy <at> 0.16.10 python-cplot <at> 0.9.3 python-statmorph <at> 0.5.7
ginga-qt5 <at> 5.1.0 python-commonroad-route-planner <at> 2022.3 python-pyxsim <at> 4.4.1
python-sunkit-image <at> 0.5.1 python-sbpy <at> 0.4.0 python-jwst-reffiles <at> 1.0.1
python-glue-astronomy <at> 0.10.0 python-radiospectra <at> 0.6.0

/gnu/store/ncpf8wfp6lrnma9izmhyn7c5xrgmdbpf-python-radiospectra-0.6.0
/gnu/store/ldzd0l7mv9dah7hr1r9c1rxsycjd8a2n-python-glue-astronomy-0.10.0
/gnu/store/crdk1jx6c8pigjvjfx63jqzi2i75h102-python-jwst-reffiles-1.0.1
/gnu/store/cwv3rrczylad5l5v5qf7hymp35g1zayw-python-sbpy-0.4.0
/gnu/store/p1gs601ywhzxsd2drwl5xhxn3rx1xxl2-python-sunkit-image-0.5.1
/gnu/store/xbn5iwhzn1zmnal4bvgvipn95mvid9qf-python-pyxsim-4.4.1
/gnu/store/krfnvbq40zzlszjmz4in3js8an81sqf1-python-commonroad-route-planner-2022.3
/gnu/store/22501ww4h1mbiid4pb0m467spncxp3cd-ginga-qt5-5.1.0
/gnu/store/dddwr4hyqgals4w3fyzksvzxcdzp5a6i-python-statmorph-0.5.7
/gnu/store/1019lwlarinzkl0g86ym5zm0a04854cg-python-cplot-0.9.3
/gnu/store/nd2s0xh2xdinprvvk3w53vdb39ay89hv-python-quadpy-0.16.10
/gnu/store/irpd0kqf441d9ims14aglan659f9d3zf-cura-4.13.1
/gnu/store/0jmfsf6s02arc9f9ds7l179bwnnq9bhl-python-verde-1.8.0
/gnu/store/zdv03gnx1bhqhrdy1bx88lf22danbqfb-python-osmnx-1.9.3
/gnu/store/qw6wi859w7lhdh7jr8n9vz9s6wrhynbv-python-overpass-0.7
/gnu/store/k7d4549rqkwgq7c5llp992dv202j80l8-python-pandera-0.18.0
/gnu/store/nnbxppbgwhj1wl133s94ypl9sqm58091-python-liana-py-1.1.0
/gnu/store/9zxrdkx6k2hswblkxkxkcz95dnccf8wq-python-pandapipes-0.10.0
/gnu/store/686wjz46v8rcr5602jw74mhikplha41b-python-glue-qt-0.3.1
/gnu/store/35cfqa5gvyvlg8zqldl1bnqajr2p5m4v-python-astroplan-0.10.1
/gnu/store/fxg99dydd7873ixn68d19c6z46c5yyjv-python-poliastro-0.17.0
/gnu/store/rb8nnjvcbllasnj3wapfmr97d4yn52qj-python-aplpy-2.1.0
/gnu/store/8zln2va5j0ic0nryzqy37kfa4qxxjdgn-python-astroalign-2.5.1
/gnu/store/wbfw2079iy0d597lx9bn1x76x9ic1i53-python-asdf-compression-0.0.1-0.57cc7e7
/gnu/store/4z72lpw3j8qd4px6g8qmmr08ghbgfs0f-python-asdf-zarr-0.0.4
/gnu/store/q7s2vnmwxifbj8vg7g5578q3s7h64w55-python-cesium-0.12.1
/gnu/store/nvp43bv8qn2rrr7dvw3l5addy8khv6ha-python-viresclient-0.12.0
/gnu/store/jwfbs4m1zl1m9i25w854cwr57l14gsl9-python-naima-0.10.0
/gnu/store/bvsxab4y9glqq7barz8xg8r3pg278y1h-python-kanon-0.6.6
/gnu/store/l1263y5x4pswazf2fgy3ia4qv1ji9bw6-python-sncosmo-2.11.1
/gnu/store/6af53igxjnd5vyz51jqmnnlg4c40k91y-python-zodipy-1.0.0
/gnu/store/vhl3mx7vr2ipxwpavjqy5kzf3sw15kc6-python-regularizepsf-0.3.4
/gnu/store/aa63pkhckcy0z0gvldgbr641xi9l3cp4-scamp-2.10.0
--8<---------------cut here---------------end--------------->8---

Sharlatan Hellseher (32):
  gnu: indi-2.0: Adjust package style.
  gnu: indi-2.0: Update to 2.0.9.
  gnu: python-astroplan: Update to 0.10.1.
  gnu: python-astropy-iers-data: Update to 0.2024.8.12.0.32.58.
  gnu: python-astropy: Update to 6.1.2.
  gnu: python-crds: Update to 11.18.1.
  gnu: python-czml3: Update to 1.0.2.
  gnu: python-drms: Update to 0.8.0.
  gnu: python-dust-extinction: Update to 1.5.
  gnu: python-glue-core: Adjust inputs.
  gnu: python-glymur: Update to 0.13.5.
  gnu: python-mpl-animators: Update to 1.2.0.
  gnu: python-rad: Update to 0.21.0.
  gnu: python-radiospectra: Update to 0.6.0.
  gnu: python-reproject: Update to 0.14.0.
  gnu: python-roman-datamodels: Update to 0.21.0.
  gnu: python-specutils: Update to 1.16.0.
  gnu: python-shapely: Update to 2.0.5.
  gnu: python-shapely: Adjust home page.
  gnu: python-stcal: Update to 1.8.0.
  gnu: python-stpipe: Update to 0.7.0.
  gnu: python-sunpy: Update to 6.0.1.
  gnu: python-viresclient: Update to 0.12.0.
  gnu: Add python-soxs.
  gnu: Add python-pyxsim.
  gnu: Add python-specreduce.
  gnu: Add python-glue-astronomy.
  gnu: Add python-pvextractor.
  gnu: Add python-glue-qt.
  gnu: Add python-sunkit-image.
  gnu: Add python-zodipy.
  gnu: python-sunkit-image: Disable more failing tests.

 gnu/packages/astronomy.scm  | 578 ++++++++++++++++++++++++++++++------
 gnu/packages/python-xyz.scm |  10 +-
 2 files changed, 497 insertions(+), 91 deletions(-)


base-commit: 8b4d6b5a6255b22bde69ee1e6642ebcebaf81a94
-- 
2.41.0

Message #8 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 01/32] gnu: indi-2.0: Adjust package style.
Date: Wed, 21 Aug 2024 01:03:03 +0100

* gnu/packages/astronomy.scm (indi-2.0): Apply G-expressions.
[arguments] <tests>: Enable tests on all architectures.
<parallel-tests>: Disable it to make tests more stable.
<configure-flags>: Build all tests, do not set "Release" build type.
<phases>: Add 'patch-udev-rule phase. Refresh custom 'check phase to
include integration tests.'
[inputs]: Add kmod.

Change-Id: I46223344b042e2516065a4382fb0feb36645ebf9
---
 gnu/packages/astronomy.scm | 46 +++++++++++++++++++++-----------------
 1 file changed, 26 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 212650630c..c7c244ed96 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -61,6 +61,7 @@ (define-module (gnu packages astronomy)
   #:use-module (gnu packages jupyter)
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages libusb)
+  #:use-module (gnu packages linux)
   #:use-module (gnu packages lua)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
@@ -4316,26 +4317,30 @@ (define-public indi-2.0
         (base32 "1rsy6ihwl3fnv502pmycx0xry9qn1qfz13kwdifcf2075wqd1lx9"))))
     (build-system cmake-build-system)
     (arguments
-     ;; TODO: fix failing tests on aarch64-system.
-     `(#:tests? ,(not (or (%current-target-system) (target-aarch64?)))
-       #:configure-flags
-       (let ((out (assoc-ref %outputs "out")))
-         (list
-          "-DINDI_BUILD_UNITTESTS=ON"
-          "-DCMAKE_BUILD_TYPE=Release"
-          (string-append "-DCMAKE_INSTALL_PREFIX=" out)
-          (string-append "-DUDEVRULES_INSTALL_DIR=" out "/lib/udev/rules.d")))
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (with-directory-excursion "test"
-                 (invoke "ctest")))))
-         (add-before 'install 'set-install-directories
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (mkdir-p (string-append out "/lib/udev/rules.d"))))))))
+     (list
+      #:parallel-tests? #f  ; Socket address collisions between tests
+      #:configure-flags
+      #~(list "-DINDI_BUILD_UNITTESTS=ON"
+              "-DINDI_BUILD_INTEGTESTS=ON"
+              "-DCMAKE_INSTALL_LIBDIR=lib"
+              (string-append "-DCMAKE_INSTALL_PREFIX=" #$output)
+              (string-append "-DUDEVRULES_INSTALL_DIR=" #$output "/lib/udev/rules.d"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-udev-rules
+            (lambda _
+              (substitute* (list "drivers/auxiliary/99-indi_auxiliary.rules"
+                                 "drivers/video/80-dbk21-camera.rules")
+                (("/bin/sh") (which "sh"))
+                (("/sbin/modprobe")
+                 (string-append #$(this-package-input "kmod") "/bin/modprobe")))))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (with-directory-excursion "integs"
+                  (invoke "ctest" "-V" "--output-on-failure"))
+                (with-directory-excursion "test"
+                  (invoke "ctest" "-V"))))))))
     (native-inputs
      (list googletest))
     (inputs
@@ -4343,6 +4348,7 @@ (define-public indi-2.0
            curl
            fftw
            gsl
+           kmod
            libev
            libjpeg-turbo
            libnova
-- 
2.41.0

Message #11 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 02/32] gnu: indi-2.0: Update to 2.0.9.
Date: Wed, 21 Aug 2024 01:03:04 +0100

* gnu/packages/astronomy.scm (indi-2.0): Update to 2.0.9.

Change-Id: I332cb8b17a16adc920f34b8d45c366d42055c054
---
 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 c7c244ed96..81f31eb163 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4305,7 +4305,7 @@ (define-public imppg
 (define-public indi-2.0
   (package
     (name "indi")
-    (version "2.0.8")
+    (version "2.0.9")
     (source
      (origin
        (method git-fetch)
@@ -4314,7 +4314,7 @@ (define-public indi-2.0
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1rsy6ihwl3fnv502pmycx0xry9qn1qfz13kwdifcf2075wqd1lx9"))))
+        (base32 "08wmw7mrxx1zc89yka3c52djmpvlb8zimq8yzs95gh3p7r5jfpq9"))))
     (build-system cmake-build-system)
     (arguments
      (list
-- 
2.41.0

Message #14 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 03/32] gnu: python-astroplan: Update to 0.10.1.
Date: Wed, 21 Aug 2024 01:03:05 +0100

* gnu/packages/astronomy.scm (python-astroplan): Update to 0.10.1.

Change-Id: I7968e02a1525ab8f2440b0192db566ffdfad935a
---
 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 81f31eb163..95073889b8 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2002,13 +2002,13 @@ (define-public python-astropy-iers-data
 (define-public python-astroplan
   (package
     (name "python-astroplan")
-    (version "0.10")
+    (version "0.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astroplan" version))
        (sha256
-        (base32 "0nl7yi0h5nn4id1jifd8hpwzqdarq9z2iq56x0j2kmj3472cjw0n"))))
+        (base32 "0nb97fz0mlypdlvs09wyh0z7mxw0d6aqqkd9yfzhlqz1fwrprn9r"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #17 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 04/32] gnu: python-astropy-iers-data: Update to
 0.2024.8.12.0.32.58.
Date: Wed, 21 Aug 2024 01:03:06 +0100

* gnu/packages/astronomy.scm (python-astropy-iers-data): Update to 0.2024.8.12.0.32.58.

Change-Id: I6eaafc0de734180c96ae35bb1c90344a54d9afa3
---
 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 95073889b8..dac36ebeba 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1961,13 +1961,13 @@ (define-public python-astropy-iers-data
     ;; In case of changing the source method git-fetch, consider to check the
     ;; tag as it's not following the PyPI version, see
     ;; <https://github.com/astropy/astropy-iers-data/issues/17>.
-    (version "0.2024.7.15.0.31.42")
+    (version "0.2024.8.12.0.32.58")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy_iers_data" version))
        (sha256
-        (base32 "18wpqjyjqpxhp1x9rh1dxqmmif2amsbwwbw0zwfjh0dyrbb28c3h"))))
+        (base32 "1xw4s6vyl29miccbs3ylyichj1rcmzmya3lmh27f173n7k2zb5g0"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #20 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 05/32] gnu: python-astropy: Update to 6.1.2.
Date: Wed, 21 Aug 2024 01:03:07 +0100

* gnu/packages/astronomy.scm (python-astropy): Update to 6.1.2.

Change-Id: Ia0c01d57201e45fc2def7323a363bde852e22fa7
---
 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 dac36ebeba..83811a73bf 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1813,13 +1813,13 @@ (define-public stellarium
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "6.1.1")
+    (version "6.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "0f31wgjg22phcx8fw7p612qp3v2ak7nziisnsnwaqc0wj5fz9ip5"))
+        (base32 "0fhx9zjsqp7z8z8phafpbwpb46idrbsamkfg42l8j0z94i73s452"))
        (modules '((guix build utils)))
        (snippet
         '(begin
-- 
2.41.0

Message #23 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 06/32] gnu: python-crds: Update to 11.18.1.
Date: Wed, 21 Aug 2024 01:03:08 +0100

* gnu/packages/astronomy.scm (python-crds): Update to 11.18.1.

Change-Id: I26c7c8c81c58d44ffac5c38ac2783c49f63fad37
---
 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 83811a73bf..5ff5e02811 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2351,13 +2351,13 @@ (define-public python-cmyt
 (define-public python-crds
   (package
     (name "python-crds")
-    (version "11.17.26")
+    (version "11.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "crds" version))
        (sha256
-        (base32 "1qw1j3gz8l2z4ra33hl4zblc90kvwjf2ajb343n0xmf7lzs1gwc7"))))
+        (base32 "0k0q76mc9a18lrjqah8yb7v97dmhlwhsxyqr9r5rk0w4iqi6j7pp"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #26 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 07/32] gnu: python-czml3: Update to 1.0.2.
Date: Wed, 21 Aug 2024 01:03:09 +0100

* gnu/packages/astronomy.scm (python-czml3): Update to 1.0.2.
[native-inputs]: Remove python-pytest-cov.

Change-Id: I580ccbe9f87e6ba2d01e4181d4e491640c6dcf09
---
 gnu/packages/astronomy.scm | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 5ff5e02811..91271e665f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2396,7 +2396,7 @@ (define-public python-crds
 (define-public python-czml3
   (package
     (name "python-czml3")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method git-fetch)
@@ -2405,17 +2405,12 @@ (define-public python-czml3
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1vm9ajpnwxncvsl1ix3jarqyi14b0703g12wsr8b0agkrjlpmvmx"))))
+        (base32 "0gsdffn5w7j1aridvmx4xh6axvmbmqjwawacc8fnshpcyh4md5pn"))))
     (build-system pyproject-build-system)
     (propagated-inputs
-     (list python-attrs
-           python-dateutil
-           python-w3lib))
+     (list python-attrs python-dateutil python-w3lib))
     (native-inputs
-     (list python-astropy
-           python-pytest
-           python-pytest-cov
-           python-pytest-mypy))
+     (list python-astropy python-pytest python-pytest-mypy))
     (home-page "https://github.com/poliastro/czml3")
     (synopsis "Python library to write CZML")
     (description
-- 
2.41.0

Message #29 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 08/32] gnu: python-drms: Update to 0.8.0.
Date: Wed, 21 Aug 2024 01:03:10 +0100

* gnu/packages/astronomy.scm (python-drms): Update to 0.8.0.
[native-inputs]: Remove python-pytest.

Change-Id: Id42d08c1b6e8921cd8fb9e4b58b71a2e133f6679
---
 gnu/packages/astronomy.scm | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 91271e665f..b3ca5074c3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2422,20 +2422,18 @@ (define-public python-czml3
 (define-public python-drms
   (package
     (name "python-drms")
-    (version "0.7.1")
+    (version "0.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "drms" version))
        (sha256
-        (base32 "01q00zwpbhik9lgbc42z6q791ybxc41rxgrj04fpcfkl3hcl0nyr"))))
+        (base32 "19lqy510d7iyxfz445h2rn4d0rvmd4d3lnjmvbkvv270ckpfw09f"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-astropy
-           python-pytest-astropy
-           python-pytest
-           python-setuptools-scm))
-    (propagated-inputs (list python-numpy python-pandas))
+     (list python-astropy python-pytest-astropy python-setuptools-scm))
+    (propagated-inputs
+     (list python-numpy python-pandas))
     (home-page "https://sunpy.org")
     (synopsis "Access astronomical HMI, AIA and MDI data with Python")
     (description
-- 
2.41.0

Message #32 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 09/32] gnu: python-dust-extinction: Update to 1.5.
Date: Wed, 21 Aug 2024 01:03:11 +0100

* gnu/packages/astronomy.scm (python-dust-extinction): Update to 1.5.

Change-Id: Icb7e5f62cc25ecf11729a47b83331f0170a44e0b
---
 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 b3ca5074c3..0febff6867 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2488,13 +2488,13 @@ (define-public python-drizzle
 (define-public python-dust-extinction
   (package
     (name "python-dust-extinction")
-    (version "1.4.1")
+    (version "1.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "dust_extinction" version))
        (sha256
-        (base32 "00vyglyq2209y0mp0d5vipqrfjxp4qb8x8nx8ic2x4s19xq8ds88"))))
+        (base32 "0f0g6gh4kj83xfv0cdp30dahs80pnhsj7c6ryz3f59qf6d5zqard"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      (list python-astropy python-scipy))
-- 
2.41.0

Message #35 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 10/32] gnu: python-glue-core: Adjust inputs.
Date: Wed, 21 Aug 2024 01:03:12 +0100

* gnu/packages/astronomy.scm (python-glue-core): Add missing inputs
highlighted in sanity-check on python-glue-astronomy.
[propagated-inputs]: Add python-h5py and python-pillow.

Change-Id: I6b63152f4b80aa708d882e2b8b598480a620bfca
---
 gnu/packages/astronomy.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 0febff6867..c3d912ca21 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1166,6 +1166,7 @@ (define-public python-glue-core
            python-dill
            python-echo
            python-fast-histogram
+           python-h5py
            python-ipython
            python-matplotlib
            python-mpl-scatter-density
@@ -1173,6 +1174,7 @@ (define-public python-glue-core
            python-openpyxl
            python-pandas
            ;; python-pyavm ; optional, not packed
+           python-pillow
            python-scikit-image
            python-scipy
            python-setuptools
-- 
2.41.0

Message #38 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 11/32] gnu: python-glymur: Update to 0.13.5.
Date: Wed, 21 Aug 2024 01:03:13 +0100

* gnu/packages/python-xyz.scm (python-glymur): Update to 0.13.5.

Change-Id: I307a4325f051faf2f2e46dd29878e6599b12f237
---
 gnu/packages/python-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a5553007dd..6caa9ab7bc 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -2219,7 +2219,7 @@ (define-public python-gh-md-to-html
 (define-public python-glymur
   (package
     (name "python-glymur")
-    (version "0.12.9")
+    (version "0.13.5")
     (source
      (origin
        (method git-fetch)   ; no tests data in PyPi package
@@ -2228,7 +2228,7 @@ (define-public python-glymur
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0awyav7071nn9z2g4mmpg33y0y0nfandfr6nr3j5vyb8hnprcmns"))))
+        (base32 "1n2n7bj5w29w5y2gcl4hxhqf85n0j2crkln9i0mprq3xw8finxpx"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #41 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 12/32] gnu: python-mpl-animators: Update to 1.2.0.
Date: Wed, 21 Aug 2024 01:03:14 +0100

* gnu/packages/astronomy.scm (python-mpl-animators): Update to 1.2.0.
[arguments]: <#:phases>: Add 'set-home phase.
[native-inputs]: Add python-pytest-doctestplus and python-pytest-xdist.

Change-Id: I6cbdc2e51e0841540c0944ceeb3e154ba2907ca7
---
 gnu/packages/astronomy.scm | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c3d912ca21..51dd065109 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2641,17 +2641,29 @@ (define-public python-kanon
 (define-public python-mpl-animators
   (package
     (name "python-mpl-animators")
-    (version "1.1.1")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "mpl_animators" version))
        (sha256
-        (base32 "078dshs383ny182dac0spg7z0iilcwa0fnwv1vizsr6p1d3ar98b"))))
+        (base32 "0xxzwxp2zss2s5ci6d349nfdc4hcbm10pqmf5zf14yn66plc1r4k"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+         (add-before 'check 'set-home
+           (lambda _
+             ;; Relax matplotlib warning: ... because the default path
+             ;; (/homeless-shelter/.config/matplotlib) is not a writable
+             ;; directory ...
+             (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-pytest
+           python-pytest-doctestplus
            python-pytest-mpl
+           python-pytest-xdist
            python-setuptools-scm))
     (propagated-inputs
      (list python-astropy
-- 
2.41.0

Message #44 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 13/32] gnu: python-rad: Update to 0.21.0.
Date: Wed, 21 Aug 2024 01:03:15 +0100

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

Change-Id: Ic3d5d8d643b60a9b279813cc47b45e44389b2bc3
---
 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 51dd065109..ec0ec25c20 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5272,13 +5272,13 @@ (define-public python-gwcs
 (define-public python-rad
   (package
     (name "python-rad")
-    (version "0.20.0")
+    (version "0.21.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "rad" version))
        (sha256
-        (base32 "05b7qjhahzfjdp820m3qm69wrzb73njjqrzkk7hxkd8gbrbp0mj1"))))
+        (base32 "0b2gfsyccfx9dmmh725h7qjh5rxabg5w1j52yzfi8b0a8nmg6j6a"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #47 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 14/32] gnu: python-radiospectra: Update to 0.6.0.
Date: Wed, 21 Aug 2024 01:03:16 +0100

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

Change-Id: Ic8dbd5a7ac6cfad8c83830c095e60416e9c97a81
---
 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 ec0ec25c20..e505b4abcb 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5336,13 +5336,13 @@ (define-public python-radio-beam
 (define-public python-radiospectra
   (package
     (name "python-radiospectra")
-    (version "0.5.0")
+    (version "0.6.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "radiospectra" version))
        (sha256
-        (base32 "0nw71a7i875lfwbwhpc80nvwalb7iq3fynfkbngx6f6jb3v10dgs"))))
+        (base32 "1mqdh90hpq7sc9lybmc7y33g84vswf7w0r5hs57rf3a9hzfxad90"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #50 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 15/32] gnu: python-reproject: Update to 0.14.0.
Date: Wed, 21 Aug 2024 01:03:17 +0100

* gnu/packages/astronomy.scm (python-reproject): Update to 0.14.0.
[propagated-inputs]: Remove python-click.
[native-inputs]: Remove python-pytest; add python-asdf, python-gwcs and
python-pyvo.

Change-Id: If3434c59635fb818923f1bc7e292d494166d50be
---
 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 e505b4abcb..a9dd4360c4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3119,13 +3119,13 @@ (define-public python-regularizepsf
 (define-public python-reproject
   (package
     (name "python-reproject")
-    (version "0.13.1")
+    (version "0.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "reproject" version))
        (sha256
-        (base32 "1xk809h2j3zj37l5lx4l87zanf9zxbxajcrff2b2f2i0jpnmxqv3"))))
+        (base32 "1h5v74da32ai9dkhcdn3xx4h05awlxhhnrsdjj1sb644c1vlyg6x"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3162,7 +3162,6 @@ (define-public python-reproject
      (list python-asdf
            python-astropy
            python-astropy-healpix
-           python-click
            python-cloudpickle
            python-dask
            python-fsspec
@@ -3175,9 +3174,11 @@ (define-public python-reproject
     (native-inputs
      (list python-cython-3
            python-extension-helpers
-           python-pytest
+           python-asdf
+           python-gwcs
            python-pytest-astropy
            python-pytest-xdist
+           python-pyvo
            ;; python-sunpy ; circular dependencies, test optional
            python-setuptools-scm))
     (home-page "https://reproject.readthedocs.io")
-- 
2.41.0

Message #53 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 16/32] gnu: python-roman-datamodels: Update to 0.21.0.
Date: Wed, 21 Aug 2024 01:03:18 +0100

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

Change-Id: I0cde48b566ef594ec5a83d7a8f1b5d6fc65acaa8
---
 gnu/packages/astronomy.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a9dd4360c4..3124422f08 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5374,18 +5374,18 @@ (define-public python-radiospectra
 (define-public python-roman-datamodels
   (package
     (name "python-roman-datamodels")
-    (version "0.20.0")
+    (version "0.21.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "roman_datamodels" version))
        (sha256
-        (base32 "1918wnssf478w168mhv009jkirmny8hyfxrkwvl8iish36dcqagh"))))
+        (base32 "00hwyxixdk3i48nhqnn7pnkkp3fran6fn8kzwx2w4bjkwv8cd126"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
-      #~(list "-n" "auto")
+      #~(list "--numprocesses" "auto")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'set-env
-- 
2.41.0

Message #56 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 17/32] gnu: python-specutils: Update to 1.16.0.
Date: Wed, 21 Aug 2024 01:03:19 +0100

* gnu/packages/astronomy.scm (python-specutils): Update to 1.16.0.

Change-Id: Ic9796b2ab717e64ee00658b76a0e0e470a89100e
---
 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 3124422f08..bf43123538 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3477,13 +3477,13 @@ (define-public python-spectral-cube
 (define-public python-specutils
   (package
     (name "python-specutils")
-    (version "1.15.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "specutils" version))
        (sha256
-        (base32 "0gx90dn9vmbvd7a53xb7a51jabskrad52g7imgy0ih1jchdls2pj"))))
+        (base32 "1bv1f0bpyc8pgxywcmhd3rpmnx0l604iqn4cx6isa9jfp6gnd0z3"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #59 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 18/32] gnu: python-shapely: Update to 2.0.5.
Date: Wed, 21 Aug 2024 01:03:20 +0100

* gnu/packages/python-xyz.scm (python-shapely): Update to 2.0.5.

Change-Id: Ia5a49492a5bf02e514d8f3524dc3c26227660901
---
 gnu/packages/python-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6caa9ab7bc..589928bb28 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -2607,13 +2607,13 @@ (define-public python-rasterio
 (define-public python-shapely
   (package
     (name "python-shapely")
-    (version "2.0.2")
+    (version "2.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "shapely" version))
        (sha256
-        (base32 "1rs90q4ys5cav0hz1dq72wq2mk4aqlqqbfjrnb2zzfkiq42cq4qp"))))
+        (base32 "0cpyziixzdj7xqkya4k6fwr0qmrw8k84fsrx6p5sdgw6qxmkdwmz"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #62 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 19/32] gnu: python-shapely: Adjust home page.
Date: Wed, 21 Aug 2024 01:03:21 +0100

Permanent redirect from <https://github.com/Toblerity/Shapely> to
<https://github.com/shapely/shapely>.

* gnu/packages/python-xyz.scm (python-shapely) [home-page]: Fix lint
warning.

Change-Id: Ifa78b15647e58a832a5da108f0fbe9f51fdb21df
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 589928bb28..0a9afc958c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -2629,7 +2629,7 @@ (define-public python-shapely
      (list geos))
     (propagated-inputs
      (list python-numpy))
-    (home-page "https://github.com/Toblerity/Shapely")
+    (home-page "https://github.com/shapely/shapely")
     (synopsis "Library for the manipulation and analysis of geometric objects")
     (description "Shapely is a Python package for manipulation and analysis of
 planar geometric objects.  It is based on the @code{GEOS} library.")
-- 
2.41.0

Message #65 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 20/32] gnu: python-stcal: Update to 1.8.0.
Date: Wed, 21 Aug 2024 01:03:22 +0100

* gnu/packages/astronomy.scm (python-stcal): Update to 1.8.0.
[arguments] <#:test-flags>: Disable some tests requiring network access.
<#:phases>: Add 'patch-slope-fitter phase.
[propagated-inputs]: Add python-drizzle, python-requests,
python-scikit-image, and python-tweakwcs.
[native-inputs]: Remove python-pytest-cov.

Change-Id: Ibe7737a99dc8ef6a5219769e9ecbac1a0327d062
---
 gnu/packages/astronomy.scm | 28 ++++++++++++++++++++++++----
 1 file changed, 24 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index bf43123538..1bb8356346 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3703,18 +3703,35 @@ (define-public python-stsci-stimage
 (define-public python-stcal
   (package
     (name "python-stcal")
-    (version "1.7.1")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stcal" version))
        (sha256
-        (base32 "003ygbfa25awvy2zjfxd1k4f1aklsvd53sdk7qa0w42v6ys2kabs"))))
+        (base32 "0vcq1462wdfi96qqsd5bidx38bbpnpcm18j6s761jz8ymi6vifap"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~(list "-k" (string-append
+                    ;; 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"))
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-slope-fitter
+            (lambda _
+              (substitute* "src/stcal/ramp_fitting/src/slope_fitter.c"
+                ;; It's failing to build, it looks like Guix's NumPy does not
+                ;; contain the variable: error: ‘NPY_NTYPES_LEGACY’ undeclared
+                ;; (first use in this function)
+                ((".*NPY_NTYPES_LEGACY.*") ""))))
           (add-before 'build 'silent-check-for-opencv
             (lambda _
               ;; XXX: Can't detect opencv-python version. The input opencv
@@ -3729,14 +3746,17 @@ (define-public python-stcal
      (list opencv ;Provides OpenCV-Python
            python-asdf
            python-astropy
+           python-drizzle
            python-gwcs
            python-numpy
-           python-scipy))
+           python-requests
+           python-scikit-image
+           python-scipy
+           python-tweakwcs))
     (native-inputs
      (list python-cython-3
            python-psutil
            python-pytest
-           python-pytest-cov
            python-pytest-doctestplus
            python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/stcal")
-- 
2.41.0

Message #68 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 21/32] gnu: python-stpipe: Update to 0.7.0.
Date: Wed, 21 Aug 2024 01:03:23 +0100

* gnu/packages/astronomy.scm (python-stpipe): Update to 0.7.0.
[arguments] <#:test-flags>: Remove them as all tests now pass without
issues.

Change-Id: I2eadddc3c80b960d99ec899bc8cfd14cec33c117
---
 gnu/packages/astronomy.scm | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 1bb8356346..49b26e0e8b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3812,13 +3812,13 @@ (define-public python-stdatamodels
 (define-public python-stpipe
   (package
     (name "python-stpipe")
-    (version "0.6.0")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stpipe" version))
        (sha256
-        (base32 "0iipbz5ydxxxk44q8ab0ylk7jpxjfhag4vgkhvpj67zs4s45sd8a"))
+        (base32 "0kxm0vllyi3z149q3g3xpfl0c0wpviiyfh55rv0x6zvs0px6c81j"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -3828,10 +3828,6 @@ (define-public python-stpipe
              (("from astropy.extern.configobj import validate") "import validate")
              (("from astropy.extern.configobj.configobj import ") "from configobj import ")
              (("from astropy.extern.configobj.validate import ") "from validate import "))))))
-    (arguments
-     (list
-      ;; See https://github.com/spacetelescope/stpipe/issues/114
-      #:test-flags #~(list "-k" "not test_roman_datamodel")))
     (build-system pyproject-build-system)
     (propagated-inputs
      (list python-asdf
@@ -3839,7 +3835,8 @@ (define-public python-stpipe
            python-crds
            python-stdatamodels))
     (native-inputs
-     (list python-pytest
+     (list ;; python-jwst ; cycle:  python-stpipe -> python-jwst -> python-stpipe
+           python-pytest
            python-pytest-doctestplus
            python-pytest-openfiles
            python-setuptools-scm))
-- 
2.41.0

Message #71 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 22/32] gnu: python-sunpy: Update to 6.0.1.
Date: Wed, 21 Aug 2024 01:03:24 +0100

* gnu/packages/astronomy.scm (python-sunpy): Update to 6.0.1.
[propagated-inputs]: Remove python-jplephem and python-sqlalchemy; add python-pyerfa.
[native-inputs]: Remove python-pytest and python-pytest-doctestplus; add
python-jplephem.

Change-Id: I5e291fdb0fcf19e107a390fc68dec9fb9a8395bb
---
 gnu/packages/astronomy.scm | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 49b26e0e8b..fc0d348d26 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3222,13 +3222,13 @@ (define-public python-sgp4
 (define-public python-sunpy
   (package
     (name "python-sunpy")
-    (version "5.1.5")
+    (version "6.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sunpy" version))
        (sha256
-        (base32 "1jdkkcv247chsj08wrxxv0m577ji5cg7mxx5pw7q0ahmnq93xk2p"))))
+        (base32 "1yp7x26fzxs66bfvzaim8ns5q6514l66mbz5gabhlxb9pp8i6i85"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3247,10 +3247,11 @@ (define-public python-sunpy
       #~(modify-phases %standard-phases
           (add-after 'unpack 'relax-requirements
             (lambda _
-              (substitute* "setup.cfg"
-                ;; It's already updated in master branch, but not released yet.
-                ;; drms>=0.6.1,<0.7.0
-                (("0.7.0") "0.7.2"))))
+              (substitute* "pyproject.toml"
+                ;; packaging>=23.0
+                ((">=23.0") ">=21.3")
+                ;; numpy>=1.23.5
+                ((">=1.23.5") ">=1.23.2"))))
           (add-before 'install 'writable-compiler
             (lambda _
               (make-file-writable "sunpy/_compiler.c")))
@@ -3266,10 +3267,10 @@ (define-public python-sunpy
            python-aiohttp
            python-extension-helpers
            python-hvpy
+           python-jplephem
+           ;; python-mplcairo ; Not packed yet in Guix
            python-packaging
-           python-pytest
            python-pytest-astropy
-           python-pytest-doctestplus
            python-pytest-mock
            python-pytest-mpl
            python-pytest-xdist
@@ -3288,16 +3289,15 @@ (define-public python-sunpy
            python-h5netcdf
            python-h5py
            python-hypothesis
-           python-jplephem
            python-matplotlib
            python-mpl-animators
            python-numpy
            python-pandas
+           python-pyerfa
            python-reproject
            python-scikit-image
            python-scipy
            ;; python-spiceypy ; Not packed yet in Guix, long jorney.
-           python-sqlalchemy
            python-tqdm
            python-zeep))
     (home-page "https://sunpy.org")
-- 
2.41.0

Message #74 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 23/32] gnu: python-viresclient: Update to 0.12.0.
Date: Wed, 21 Aug 2024 01:03:25 +0100

* gnu/packages/astronomy.scm (python-viresclient): Update to 0.12.0.

Change-Id: I560f0172f327c09c15a559ae8940abcb9718f0dd
---
 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 fc0d348d26..451ad9019e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5512,13 +5512,13 @@ (define-public python-tweakwcs
 (define-public python-viresclient
   (package
     (name "python-viresclient")
-    (version "0.11.6")
+    (version "0.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "viresclient" version))
        (sha256
-        (base32 "1npn5ka0cflvl6ngf5b08z59dh79hnyh5v2z4sf0872q9zkwmjjw"))))
+        (base32 "1y3g59yh3ic5288f2n9r6bj7b0w3vfdfcnqfg1va0z7w9jnk55j1"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-flit-core python-pytest))
-- 
2.41.0

Message #77 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 24/32] gnu: Add python-soxs.
Date: Wed, 21 Aug 2024 01:03:26 +0100

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

Change-Id: Ie5712f2d8d26f78d6eee997689fabaa113b04a9e
---
 gnu/packages/astronomy.scm | 50 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 451ad9019e..21de65f8d3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1273,6 +1273,56 @@ (define-public python-sncosmo
 to make such analysis both as flexible and clear as possible.")
     (license license:bsd-3)))
 
+(define-public python-soxs
+  (package
+    (name "python-soxs")
+    (version "4.8.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "soxs" version))
+       (sha256
+        (base32 "1m5q3i7hk7jqdpd46h13c4a16b74p0k4mqkxhs43b4vi95h70qrj"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX: Tests require additional data, check if it may be packed
+      ;; separately, see tests/ci_install.sh.
+      #:tests? #f
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'set-home
+            (lambda _
+              ;; To address sanity check warning: UserWarning: unable to write
+              ;; new config file.
+              (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-appdirs
+           python-astropy
+           python-h5py
+           python-numpy
+           python-pooch
+           python-pyyaml
+           python-regions
+           python-scipy
+           python-tqdm))
+    (native-inputs
+     (list python-cython
+           python-setuptools-scm))
+    (home-page "https://hea-www.cfa.harvard.edu/soxs/")
+    (synopsis "Simulated Observations of X-ray Sources")
+    (description
+     "SOXS is a software suite which can create simulated X-ray observations
+of astrophysical sources with almost any existing or planned X-ray
+observatory.  The goal of SOXS is to provide a comprehensive set of tools to
+design source models and convolve them with simulated models of X-ray
+instruments.  This package was originally developed to support the
+@url{https://www.lynxobservatory.org/,Lynx X-ray Observatory} mission concept,
+but has evolved to support other missions as well.")
+    ;; SOXS is licensed under the terms of the Modified BSD License (also
+    ;; known as New or Revised BSD).
+    (license license:bsd-3)))
+
 (define-public wcslib
   (package
     (name "wcslib")
-- 
2.41.0

Message #80 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 25/32] gnu: Add python-pyxsim.
Date: Wed, 21 Aug 2024 01:03:27 +0100

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

Change-Id: I65be8702f12f26aed6ed9bff9c246ac3400aa1db
---
 gnu/packages/astronomy.scm | 53 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 21de65f8d3..53b50db7cd 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1196,6 +1196,59 @@ (define-public python-glue-core
 across many files.")
     (license license:bsd-3)))
 
+(define-public python-pyxsim
+  (package
+    (name "python-pyxsim")
+    (version "4.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyxsim" version))
+       (sha256
+        (base32 "1vviy9hk2z3h0fi6c8207ps5pklsjn0a77pqq6wa4sa1n07clc8i"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX: Tests require additional data, check if it may be packed
+      ;; separately, see tests/ci_install.sh.
+      #:tests? #f
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'set-home
+            (lambda _
+              ;; To address sanity check warning: UserWarning: unable to write
+              ;; new config file.
+              (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-astropy
+           python-h5py
+           python-numpy
+           python-scipy
+           python-soxs
+           python-tqdm
+           python-unyt
+           python-yt))
+    (native-inputs
+     (list python-cython-3
+           python-setuptools-scm))
+    (home-page "https://hea-www.cfa.harvard.edu/~jzuhone/pyxsim/")
+    (synopsis "Simulating X-ray observations from astrophysical sources")
+    (description
+     "pyXSIM is a Python package for simulating X-ray emission from
+astrophysical sources.
+
+X-rays probe the high-energy universe, from hot galaxy clusters to compact
+objects such as neutron stars and black holes and many interesting sources in
+between.  pyXSIM makes it possible to generate synthetic X-ray observations of
+these sources from a wide variety of models, whether from grid-based
+simulation codes such as FLASH, Enzo, and Athena, to particle-based codes such
+as Gadget and AREPO, and even from datasets that have been created “by
+hand”,such as from NumPy arrays.  pyXSIM also provides facilities for
+manipulating the synthetic observations it produces in various ways, as well
+as ways to export the simulated X-ray events to other software packages to
+simulate the end products of specific X-ray observatories.")
+    (license license:bsd-3)))
+
 (define-public python-sncosmo
   (package
     (name "python-sncosmo")
-- 
2.41.0

Message #83 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 26/32] gnu: Add python-specreduce.
Date: Wed, 21 Aug 2024 01:03:28 +0100

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

Change-Id: Ia6468aeb8bb65cd3d9ff0a8f854e393069ba6f4f
---
 gnu/packages/astronomy.scm | 53 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 53b50db7cd..6f7fecd8e4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1376,6 +1376,59 @@ (define-public python-soxs
     ;; known as New or Revised BSD).
     (license license:bsd-3)))
 
+(define-public python-specreduce
+  (package
+    (name "python-specreduce")
+    (version "1.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "specreduce" version))
+       (sha256
+        (base32 "14ba4ws2z3kpw007f3hpslgp5i6dx082xhql4aim7j82211gpj6s"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; TODO: Try to link some test data availale in
+      ;; specification-specreduce-data package.
+      #~(list "-k" (string-append
+                    "not specreduce.calibration_data.get_pypeit_data_path"
+                    " and not specreduce.calibration_data.get_reference_file_path"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-pypojrect-toml
+            (lambda _
+              (substitute* "pyproject.toml"
+                ;; TypeError: Configuration.__init__() got an unexpected
+                ;; keyword argument 'version_file'
+                (("version_file = .*") ""))))
+         (add-before 'check 'set-home
+           (lambda _
+             ;; Relax matplotlib warning: ... because the default path
+             ;; (/homeless-shelter/.config/matplotlib) is not a writable
+             ;; directory ...
+             (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-astropy
+           python-gwcs
+           python-matplotlib
+           python-photutils
+           python-specutils
+           python-synphot))
+    (native-inputs
+     (list python-photutils
+           python-setuptools-scm
+           python-pytest-astropy))
+    (home-page "https://specreduce.readthedocs.io/")
+    (synopsis "Spectroscopic Reductions")
+    (description
+     "This package implements functionality of spectroscopic reduction in
+observations from Optical and @acronym{Near-infrared spectroscopy,NIR}
+instruments.")
+    (license (list license:bsd-3     ; licenses/LICENSE.rst, same as python-astropy
+                   license:expat)))) ; licenses/KOSMOS_LICENSE
+
 (define-public wcslib
   (package
     (name "wcslib")
-- 
2.41.0

Message #86 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 27/32] gnu: Add python-glue-astronomy.
Date: Wed, 21 Aug 2024 01:03:29 +0100

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

Change-Id: Ia11da145d30b221497b71b8ffa49b9522ca547a7
---
 gnu/packages/astronomy.scm | 41 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6f7fecd8e4..fe74008f7e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1149,6 +1149,47 @@ (define-public ginga-qt5
        (prepend python-pyqt)))
     (synopsis "Qt5 image viewer build based on python-ginga library")))
 
+(define-public python-glue-astronomy
+  (package
+    (name "python-glue-astronomy")
+    (version "0.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "glue-astronomy" version))
+       (sha256
+        (base32 "1bra11i55g687ykzll5clp7mf3l9kc0x11wqc3gwfi98qx8fgpqz"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "--pyargs" "glue_astronomy"
+              ;; XXX: Findout why these tests fail to load:
+              ;; E ModuleNotFoundError: No module named 'glue.qglue'
+              ;; E ImportError: cannot import name 'make_2dspec_image' from
+              ;; 'specreduce.utils.synth_data'
+              "--ignore=glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py"
+              "--ignore=glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py"
+              "--ignore=glue_astronomy/translators/tests/test_trace.py"
+              "--ignore=glue_astronomy/translators/tests/test_trace.py")))
+    (propagated-inputs
+     (list python-astropy
+           python-glue-core
+           python-regions
+           python-specreduce
+           python-spectral-cube
+           python-specutils))
+    (native-inputs
+     (list python-mock
+           python-pytest-astropy
+           python-setuptools-scm))
+    (home-page "https://github.com/glue-viz/glue-astronomy")
+    (synopsis "Astronomy-specific plugins for glue")
+    (description
+     "The glue-astronomy plugin for glue provides a collection of
+astronomy-specific functionality")
+    (license license:bsd-3)))
+
 (define-public python-glue-core
   (package
     (name "python-glue-core")
-- 
2.41.0

Message #89 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 28/32] gnu: Add python-pvextractor.
Date: Wed, 21 Aug 2024 01:03:30 +0100

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

Change-Id: I43589099c662cd73ac234a8581be6a559d2ddd6c
---
 gnu/packages/astronomy.scm | 48 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index fe74008f7e..38f9db1c8c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1237,6 +1237,54 @@ (define-public python-glue-core
 across many files.")
     (license license:bsd-3)))
 
+(define-public python-pvextractor
+  (package
+    (name "python-pvextractor")
+    (version "0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pvextractor" version))
+       (sha256
+        (base32 "1kl33vg5rxmdwlk36pn8zqa7k7f43fb7w417fym6ygp86mci2spd"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags #~(list "--pyargs" "pvextractor")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; See <https://github.com/radio-astro-tools/pvextractor/issues/124>.
+         (add-after 'unpack 'patch-regexp
+           (lambda _
+             (substitute* "pvextractor/pvregions.py"
+               (("coordre = re.compile.*")
+                "coordre = re.compile(\"^[a-z]*\\\\((.*)\\\\)\")\n"))))
+           (add-before 'check 'prepare-x
+             (lambda _
+               (system "Xvfb &")
+               (setenv "DISPLAY" ":0")
+               (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-astropy
+           python-matplotlib
+           python-numpy
+           python-pyqt-6
+           python-qtpy
+           python-scipy
+           python-spectral-cube))
+    (native-inputs
+     (list python-pytest-astropy
+           python-setuptools-scm
+           xorg-server-for-tests))
+    (home-page "http://pvextractor.readthedocs.io")
+    (synopsis "Position-Velocity diagram extractor")
+    (description
+     "The concept of the pvextractor package is simple - given a path defined
+in sky coordinates, and a spectral cube, extract a slice of the cube along
+that path, and along the spectral axis, producing a position-velocity or
+position-frequency slice.")
+    (license license:bsd-3)))
+
 (define-public python-pyxsim
   (package
     (name "python-pyxsim")
-- 
2.41.0

Message #92 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 29/32] gnu: Add python-glue-qt.
Date: Wed, 21 Aug 2024 01:03:31 +0100

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

Change-Id: I44a58be6282a76bbd20e5501012a41b87563c5c3
---
 gnu/packages/astronomy.scm | 42 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 38f9db1c8c..4c96098145 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1237,6 +1237,48 @@ (define-public python-glue-core
 across many files.")
     (license license:bsd-3)))
 
+(define-public python-glue-qt
+  (package
+    (name "python-glue-qt")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "glue-qt" version))
+       (sha256
+        (base32 "15ycykhg02xmsrlyv90qxckssmrq355qaqmz7p8nnqygm0gyrnx1"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+           (add-before 'check 'prepare-x
+             (lambda _
+               (system "Xvfb &")
+               (setenv "DISPLAY" ":0")
+               (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-astropy
+           python-echo
+           python-glue-core
+           python-ipykernel
+           python-ipython
+           python-matplotlib
+           python-numpy
+           python-pvextractor
+           python-qtconsole
+           python-qtpy
+           python-scipy))
+    (native-inputs
+     (list python-objgraph
+           python-pytest
+           python-setuptools-scm
+           xorg-server-for-tests))
+    (home-page "http://glueviz.org")
+    (synopsis "Multidimensional data visualization across files")
+    (description "Multidimensional data visualization across files.")
+    (license license:bsd-3)))
+
 (define-public python-pvextractor
   (package
     (name "python-pvextractor")
-- 
2.41.0

Message #95 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 30/32] gnu: Add python-sunkit-image.
Date: Wed, 21 Aug 2024 01:03:32 +0100

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

Change-Id: I3213dc2dc2be23407db9316f5ed84a9d248cbee2
---
 gnu/packages/astronomy.scm | 44 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 4c96098145..e36a3b57ce 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1560,6 +1560,50 @@ (define-public python-specreduce
     (license (list license:bsd-3     ; licenses/LICENSE.rst, same as python-astropy
                    license:expat)))) ; licenses/KOSMOS_LICENSE
 
+(define-public python-sunkit-image
+  (package
+    (name "python-sunkit-image")
+    (version "0.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sunkit_image" version))
+       (sha256
+        (base32 "1wzii7dy0yb2lx0k8m3iak5vxc0wbybj5cdkvrk93sr14k9crqds"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; XXX: Check with upstram: assert False.
+      #:test-flags #~(list "-k" "not test_fnrgf")
+      #:phases
+      #~(modify-phases %standard-phases
+         (add-before 'check 'set-home
+           (lambda _
+             ;; For tests: Permission denied: '/homeless-shelter'
+             (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list python-astropy
+           python-matplotlib
+           python-numpy
+           python-scikit-image
+           python-scipy
+           python-sunpy))
+    (native-inputs
+     (list python-astroscrappy
+           python-beautifulsoup4
+           python-dask
+           python-drms
+           python-importlib-resources
+           python-pytest-astropy
+           python-pytest-mpl
+           python-setuptools-scm
+           python-zeep))
+    (home-page "http://docs.sunpy.org/projects/sunkit-image/")
+    (synopsis "Solar Physics image processing toolbox")
+    (description
+     "This package provides an image processing toolbox for Solar Physics.")
+    (license license:bsd-2)))
+
 (define-public wcslib
   (package
     (name "wcslib")
-- 
2.41.0

Message #98 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 31/32] gnu: Add python-zodipy.
Date: Wed, 21 Aug 2024 01:03:33 +0100

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

Change-Id: I15a7603330ee0ca19ec6073ac312e15f44db1a2b
---
 gnu/packages/astronomy.scm | 40 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e36a3b57ce..11c0ca306e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -6017,6 +6017,46 @@ (define-public python-yt-astro-analysis
 @end itemize")
     (license (list license:bsd-3 license:lgpl3))))
 
+(define-public python-zodipy
+  (package
+    (name "python-zodipy")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch) ;; no tests in the PyPI tarball
+       (uri (git-reference
+             (url "https://github.com/Cosmoglobe/zodipy")
+             (commit (string-append "v." version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "08hwicpv3wfpccr2cj1vxb8iy7av12yjs3prq0zw7qc89imrgrbn"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              (substitute* "pyproject.toml"
+                ;; numpy = "^1.26.4"
+                (("1.26.4") "1.23.2")
+                ;; scipy = "^1.13.0"
+                (("1.13.0") "1.12.0")))))))
+    (propagated-inputs
+     (list python-astropy
+           python-jplephem
+           python-numpy
+           python-scipy))
+    (native-inputs
+     (list python-poetry-core
+           python-pytest))
+    (home-page "https://github.com/Cosmoglobe/zodipy")
+    (synopsis "Zodiacal emission simulations")
+    (description
+     "ZodiPy is an package for simulating zodiacal light in intensity for
+arbitrary solar system observers.")
+    (license license:gpl3+)))
+
 (define-public qfits
   (package
     (name "qfits")
-- 
2.41.0

Message #101 received at 72741 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 32/32] gnu: python-sunkit-image: Disable more failing tests.
Date: Wed, 21 Aug 2024 01:03:34 +0100

* gnu/packages/astronomy.scm (python-sunkit-image) [arguments]
<#:test-flags>: Disable 2 more failing tests.

Change-Id: Id42ab4da383120eda01e4b025e5df6af8d3ae528
---
 gnu/packages/astronomy.scm | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 11c0ca306e..5c43d43f12 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1574,13 +1574,17 @@ (define-public python-sunkit-image
     (arguments
      (list
       ;; XXX: Check with upstram: assert False.
-      #:test-flags #~(list "-k" "not test_fnrgf")
+      #:test-flags
+      #~(list "-k" (string-append
+                    "not test_fnrgf"
+                    " and not test_calculate_solar_rotate_shift"
+                    " and not test_mapsequence_solar_derotate"))
       #:phases
       #~(modify-phases %standard-phases
-         (add-before 'check 'set-home
-           (lambda _
-             ;; For tests: Permission denied: '/homeless-shelter'
-             (setenv "HOME" "/tmp"))))))
+          (add-before 'check 'set-home
+            (lambda _
+              ;; For tests: Permission denied: '/homeless-shelter'
+              (setenv "HOME" "/tmp"))))))
     (propagated-inputs
      (list python-astropy
            python-matplotlib
-- 
2.41.0

Message #106 received at 72741-done <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 72741-done <at> debbugs.gnu.org
Subject: [PATCH 00/32] Astronomy update 2024/08.
Date: Tue, 27 Aug 2024 17:06:09 +0100

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

Pushed as 1e69ac70c7..0cf4de40a2 to master

--
Oleg

[signature.asc (application/pgp-signature, inline)]

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