[bug#64201] [PATCH 00/19] gnu: monthly astronomy packages update

[bug#64201] [PATCH 00/19] gnu: monthly astronomy packages update

[Sharlatan Hellseher]

Hi Guix,

I'm about to keep the pace with updating (gnu package astronomy) monthly where
there is an easy win with just updating version and hash.

Some other packages which can be updated need more time and I don't want them
to block the flow, I'll prepare them while this issue is in review.

Here is the first portion where update took less efforts.
o block the flow, I'll prepare them while this issue is in review.

> ./pre-inst-env guix build $(./pre-inst-env guix refresh --list-dependent sextractor python-photutils calceph calcmysky libxisf splash python-astropy python-ccdproc python-cdflib python-drms python-fitsio python-pyerfa python-reproject python-stcal python-stdatamodels python-sunpy python-synphot python-astroalign | awk -F: '{print $2}')
> /gnu/store/z9s8nr3vm6yyp43kggkb39q1gmvrkwcr-python-jwst-1.10.2
> /gnu/store/3hgr6kk5qavqh550q359ldv2djgv9gak-python-sunpy-5.0.0
> /gnu/store/zijm4ac5xnqirymnbx64jfy12jjhi69f-python-astroalign-2.4.2
> /gnu/store/cjv9pj2q5321fkgfsbygzs59n6rj06ph-python-poliastro-0.17.0
> /gnu/store/195cm9x8biczq485kml0nkrl4ly62rqr-python-regions-0.7

Sharlatan Hellseher (20):
  gnu: sextractor: Update to 2.28.0, fix build.
  gnu: python-photutils: Update to 1.8.0.
  gnu: calceph: Update to 3.5.2.
  gnu: calcmysky: Update to 0.3.1.
  gnu: libxisf: Update to 0.2.8.
  gnu: splash: Update to 3.8.2.
  gnu: python-astropy: Update to 5.3.
  gnu: python-ccdproc: Update to 2.4.1.
  gnu: python-cdflib: Update to 1.0.5.
  gnu: python-drms: Update to 0.6.4.
  gnu: python-fitsio: Update to 1.1.9.
  gnu: python-fitsio: Enable tests.
  gnu: python-pyerfa: Update to 2.0.0.3.
  gnu: python-pyerfa: Fix tests.
  gnu: python-reproject: Update to 0.11.0.
  gnu: python-stcal: Update to 1.3.8.
  gnu: python-stdatamodels: Update to 1.6.0.
  gnu: python-sunpy: Update to 5.0.0.
  gnu: python-synphot: Update to 1.2.1.
  gnu: python-astroalign: Fix build.

 gnu/packages/astronomy.scm | 227 +++++++++++++++++++++++--------------
 1 file changed, 139 insertions(+), 88 deletions(-)


base-commit: e4087930f3ad60918689be5f4bca4ce3e22429f5
-- 
2.40.1

[bug#64201] [PATCH 01/20] gnu: sextractor: Update to 2.28.0, fix build.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (sextractor): Update to 2.28.0, fix build.
[arguments]: Use G-expressions, add configure flags for CFitsio
detection.
[inputs]: Remove labels. Add cfitsio.
---
 gnu/packages/astronomy.scm | 34 +++++++++++++++++++---------------
 1 file changed, 19 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index cdb6750f09..787ca01491 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -747,7 +747,7 @@ (define-public phd2
 (define-public sextractor
   (package
     (name "sextractor")
-    (version "2.25.0")
+    (version "2.28.0")
     (source
      (origin
        (method git-fetch)
@@ -756,29 +756,33 @@ (define-public sextractor
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0q69n3nyal57h3ik2xirwzrxzljrwy9ivwraxzv9566vi3n4z5mw"))))
+        (base32 "15v7brjiraj2rdyxiidcgb58b3dqzdd363j31cjrfqhd1wc8ii5j"))))
     (build-system gnu-build-system)
     ;; NOTE: (Sharlatan-20210124T103117+0000): Building with `atlas' is failing
     ;; due to missing shared library which required on configure phase. Switch
     ;; build to use `openblas' instead. It requires FFTW with single precision
     ;; `fftwf'.
     (arguments
-     `(#:configure-flags
-       (list
-        "--enable-openblas"
-        (string-append
-         "--with-openblas-libdir=" (assoc-ref %build-inputs "openblas") "/lib")
-        (string-append
-         "--with-openblas-incdir=" (assoc-ref %build-inputs "openblas") "/include")
-        (string-append
-         "--with-fftw-libdir=" (assoc-ref %build-inputs "fftw") "/lib")
-        (string-append
-         "--with-fftw-incdir=" (assoc-ref %build-inputs "fftw") "/include"))))
+     (list
+      #:configure-flags
+      #~(list
+         "--enable-openblas"
+         (string-append "--with-cfitsio-incdir="
+                        #$(this-package-input "cfitsio") "/include")
+         (string-append "--with-cfitsio-libdir="
+                        #$(this-package-input "cfitsio") "/lib")
+         (string-append "--with-fftw-incdir="
+                        #$(this-package-input "fftwf") "/include")
+         (string-append "--with-fftw-libdir="
+                        #$(this-package-input "fftwf") "/lib")
+         (string-append "--with-openblas-incdir="
+                        #$(this-package-input "openblas") "/include")
+         (string-append "--with-openblas-libdir="
+                        #$(this-package-input "openblas") "/lib"))))
     (native-inputs
      (list autoconf automake libtool))
     (inputs
-     `(("openblas" ,openblas)
-       ("fftw" ,fftwf)))
+     (list cfitsio fftwf openblas))
     (home-page "https://www.astromatic.net/software/sextractor")
     (synopsis "Extract catalogs of sources from astronomical images")
     (description
-- 
2.40.1

[bug#64201] [PATCH 02/20] gnu: python-photutils: Update to 1.8.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-photutils): Update to
1.8.0. Activate more options.
[build-system]: Swap to python-build-system.
[arguments]: Use G-expressions. Rename the phase before check
'writable-compiler to 'build-extensions to reflect it's purpose, add
new step in phase building extensions for testing.
[propagated-inputs]: Add python-bottleneck, python-gwcs,
python-matplotlib, python-scikit-image, python-scikit-learn,
python-scipy, python-shapely, python-tqdm
[native-inputs]: Remove python-pytest-runner. Add
python-semantic-version.
---
 gnu/packages/astronomy.scm | 44 +++++++++++++++++++++++++++-----------
 1 file changed, 31 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 787ca01491..16debb93a0 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -55,6 +55,7 @@ (define-module (gnu packages astronomy)
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages lua)
+  #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
@@ -1701,30 +1702,47 @@ (define-public python-mpl-animators
 (define-public python-photutils
   (package
     (name "python-photutils")
-    (version "1.7.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "photutils" version))
        (sha256
-        (base32 "1bq4ma402lpa5d6l85awlc23kasxf40nq8hgi3iyrilnfikan0jz"))))
-    (build-system python-build-system)
+        (base32 "07khld3la1zwxd36kal6rglgkji4sd65lk4jc3khk0glb5v3kkrc"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:test-target "pytest"
-       #:phases
-       (modify-phases %standard-phases
-         ;; This file is opened in both install and check phases.
-         (add-before 'install 'writable-compiler
-           (lambda _ (make-file-writable "photutils/_compiler.c")))
-         (add-before 'check 'writable-compiler
-           (lambda _ (make-file-writable "photutils/_compiler.c"))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'install 'writable-compiler
+            (lambda _
+              (make-file-writable "photutils/_compiler.c")))
+          (add-before 'check 'build-extensions
+            (lambda _
+              ;; Cython extensions have to be built before running
+              ;; the tests. If it's not build it fails with error:
+              ;;
+              ;; ModuleNotFoundError: No module named
+              ;; 'photutils.geometry.circular_overlap'
+              (make-file-writable "photutils/_compiler.c")
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (propagated-inputs
-     (list python-astropy python-numpy))
+     (list python-astropy
+           python-bottleneck
+           python-gwcs
+           python-matplotlib
+           python-numpy
+           ; python-resterio : Not packed yet
+           python-scikit-image
+           python-scikit-learn
+           python-scipy
+           python-shapely
+           python-tqdm))
     (native-inputs
      (list python-cython
            python-extension-helpers
            python-pytest-astropy
-           python-pytest-runner
+           python-semantic-version
            python-setuptools-scm))
     (home-page "https://github.com/astropy/photutils")
     (synopsis "Source detection and photometry")
-- 
2.40.1

[bug#64201] [PATCH 03/20] gnu: calceph: Update to 3.5.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (calceph): Update to 3.5.2.
---
 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 16debb93a0..3ff4356a61 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -181,7 +181,7 @@ (define-public aocommon
 (define-public calceph
   (package
     (name "calceph")
-    (version  "3.5.1")
+    (version  "3.5.2")
     (source
      (origin
        (method url-fetch)
@@ -189,7 +189,7 @@ (define-public calceph
              "https://www.imcce.fr/content/medias/recherche/equipes/asd/calceph/calceph-"
              version ".tar.gz"))
        (sha256
-        (base32 "078wn773pwf4pg9m0h0l00g4aq744pq1rb6kz6plgdpzp3hhpk1k"))))
+        (base32 "1rnjlaiii4j0agbj4k242p212bqqmqdqa0lni6c3bnhgfnrbjfp4"))))
     (build-system gnu-build-system)
     (native-inputs
      (list gfortran))
-- 
2.40.1

[bug#64201] [PATCH 04/20] gnu: calcmysky: Update to 0.3.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (calcmysky) Update to 0.3.1.
---
 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 3ff4356a61..2bae404d18 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -216,7 +216,7 @@ (define-public calceph
 (define-public calcmysky
   (package
     (name "calcmysky")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method git-fetch)
@@ -225,7 +225,7 @@ (define-public calcmysky
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1lgn937px4am0lggniwby1f1dl3v4l3iigq72rl9rlhx58zv4lj1"))))
+        (base32 "14jbaf9m9wig2bs7a531dvpmdkqpd09lmyvjvj1s0mhgh9g0x9m2"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags
-- 
2.40.1

[bug#64201] [PATCH 05/20] gnu: libxisf: Update to 0.2.8.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (libxisf): Update to 0.2.8.
---
 gnu/packages/astronomy.scm | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 2bae404d18..e1020bf23e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2571,9 +2571,7 @@ (define-public libpasastro
 (define-public libxisf
   (package
     (name "libxisf")
-    ;; TODO: v0.2.2 (current latest) failed to build on configure phase, issue
-    ;; was open directly with author as he hosts source on seflhosted gitea.
-    (version "0.2.1")
+    (version "0.2.8")
     (source
      (origin
        (method git-fetch)
@@ -2582,7 +2580,7 @@ (define-public libxisf
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0fz9mmj1nz5v7hlr53q8na7khadfn1hm0d1gfpzzw3167bqpy2xv"))))
+        (base32 "1j2bg53hrr2yc55qa6549vcpj7qjnwmxjcdgc98w3ygnrjy7n7v0"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags #~(list "-DUSE_BUNDLED_LIBS=OFF")))
-- 
2.40.1

[bug#64201] [PATCH 06/20] gnu: splash: Update to 3.8.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (splash): Update to 3.8.2.
---
 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 e1020bf23e..d6dde400c9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -833,7 +833,7 @@ (define-public siril
 (define-public splash
   (package
     (name "splash")
-    (version "3.7.2")
+    (version "3.8.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -841,7 +841,7 @@ (define-public splash
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "0nsm6rk0bi99xz7wclk0zy4bpqf0qcsdln5cdjb30lhpf37i2fpa"))
+                "0y6l135g0a3hvvh8w8sfdh1kfq2g0gbp0dgjhnmwid8bwwcjvw8v"))
               (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
-- 
2.40.1

[bug#64201] [PATCH 07/20] gnu: python-astropy: Update to 5.3.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy): Update to 5.3.
[snippet]: Remove trailing #t. Prevent cfitsion from deletion.
[inputs]: Remove cfitsio
---
 gnu/packages/astronomy.scm | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d6dde400c9..d21ff42690 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1138,13 +1138,13 @@ (define-public celestia-gtk
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "5.2.2")
+    (version "5.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "170ddflli35mvhf6pla7aizfw8a7ckq66g1mi1br99dx2r3y7ag6"))
+        (base32 "1rg4i5w7mggfvi63j2aj2d2fjikml55bbxswl6n0j8xkqbhlns8z"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -1153,9 +1153,12 @@ (define-public python-astropy
              (for-each delete-file-recursively '("ply" "configobj")))
            ;; Remove cextern bundles. Check bundled versions against available
            ;; in Guix in the future update of astropy.
+           ;;
+           ;; cfitsio build is only available from non-publicly exposed
+           ;; bundled short version. See:
+           ;; https://github.com/astropy/astropy/pull/14311
            (with-directory-excursion "cextern"
-             (for-each delete-file-recursively '("cfitsio" "expat" "wcslib")))
-           #t))))
+             (for-each delete-file-recursively '("expat" "wcslib")))))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -1222,7 +1225,7 @@ (define-public python-astropy
            python-skyfield
            python-timezonefinder))
     (inputs
-     (list cfitsio expat wcslib))
+     (list expat wcslib))
     (propagated-inputs
      (list python-configobj
            python-numpy
-- 
2.40.1

[bug#64201] [PATCH 08/20] gnu: python-ccdproc: Update to 2.4.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ccdproc): Update to 2.4.1.
[native-inputs]: Add python-semantic-version.
---
 gnu/packages/astronomy.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d21ff42690..153fbd3e1a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1398,15 +1398,18 @@ (define-public python-bayesicfitting
 (define-public python-ccdproc
   (package
     (name "python-ccdproc")
-    (version "2.4.0")
+    (version "2.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ccdproc" version))
        (sha256
-        (base32 "0fy1sni87cr05dkljd8wb7vgh7z9agh8wv5kiagxcpbcf8l06jv1"))))
+        (base32 "186plgfhrj7wivs053y65jlv1x33y8ii31jdr2rm4s6pl0j7x29z"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-memory-profiler python-pytest-astropy))
+    (native-inputs
+     (list python-memory-profiler
+           python-pytest-astropy
+           python-semantic-version))
     (propagated-inputs
      (list python-astropy
            python-astroscrappy
-- 
2.40.1

[bug#64201] [PATCH 09/20] gnu: python-cdflib: Update to 1.0.5.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-cdflib): Update to 1.0.5.
---
 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 153fbd3e1a..8a9b368730 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1427,7 +1427,7 @@ (define-public python-ccdproc
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-    (version "0.4.9")
+    (version "1.0.5")
     (source
      (origin
        (method git-fetch)   ; no tests in pypi archive
@@ -1436,7 +1436,7 @@ (define-public python-cdflib
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1k557najk7ln293zwyghnhw48ays3nqf9s94kibsc7r70c2q7p08"))))
+        (base32 "1pkda9gmpjhbqxl2jj5q9rjx77lv5c908mgf20lw3rz4nvfaa2wn"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases
-- 
2.40.1

[bug#64201] [PATCH 10/20] gnu: python-drms: Update to 0.6.4.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-drms): Update to 0.6.4.
---
 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 8a9b368730..59a4c11e53 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1554,13 +1554,13 @@ (define-public python-czml3
 (define-public python-drms
   (package
     (name "python-drms")
-    (version "0.6.3")
+    (version "0.6.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "drms" version))
        (sha256
-        (base32 "1b0w350y4wbgyy19zcf28xbb85mqq6gnhb6ppibbc4hbn2ixbcvj"))))
+        (base32 "0mkrmr55fgca441z7hvsyri6x9cjsh0sfas3hrj0k1k10k8vszbw"))))
     (build-system python-build-system)
     (arguments
      (list
-- 
2.40.1

[bug#64201] [PATCH 11/20] gnu: python-fitsio: Update to 1.1.9.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-fitsio): Update to 1.1.9.
[native-inputs]: Add python-pytest, otherwise it fails to build.
[propagated-inputs]: Move cfitsio from here ...
[inputs]: ... to here, do not propagate as it's required only on build
and link time.
---
 gnu/packages/astronomy.scm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 59a4c11e53..f841005fa0 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -467,13 +467,13 @@ (define-public cfitsio
 (define-public python-fitsio
   (package
     (name "python-fitsio")
-    (version "1.1.8")
+    (version "1.1.9")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "fitsio" version))
        (sha256
-        (base32 "1y80hgvlkjz1bijfyb2j03853yc1kc63yrf9ab7as31ad2r6kxb1"))
+        (base32 "08mmk0ia0glg39z3gx0n3ynja5ix0lqx0166y8yyw44kkilsqkpv"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove the bundled cfitsio
@@ -499,9 +499,12 @@ (define-public python-fitsio
                   (("self.use_system_fitsio") "True")
                   (("self.system_fitsio_includedir") includedir)
                   (("self.system_fitsio_libdir") libdir))))))))
-    (inputs (list curl))
+    (native-inputs
+     (list python-pytest))
+    (inputs
+     (list curl cfitsio))
     (propagated-inputs
-     (list python-numpy cfitsio))
+     (list python-numpy))
     (home-page "https://github.com/esheldon/fitsio")
     (synopsis
      "Python library to read from and write to FITS files")
-- 
2.40.1

[bug#64201] [PATCH 12/20] gnu: python-fitsio: Enable tests.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-fitsio): Enable tests.
[build-system]: Swap to pyproject-build-system.
[arguments]: Add new phase 'tests-preparation
---
 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 f841005fa0..a26eacef75 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -481,7 +481,7 @@ (define-public python-fitsio
             (delete-file-recursively "cfitsio3490")
             (substitute* "MANIFEST.in"
               (("recursive-include cfitsio3490.*$\n") ""))))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list
       #:phases
@@ -498,7 +498,10 @@ (define-public python-fitsio
                   (("self.system_fitsio_libdir = None") "pass")
                   (("self.use_system_fitsio") "True")
                   (("self.system_fitsio_includedir") includedir)
-                  (("self.system_fitsio_libdir") libdir))))))))
+                  (("self.system_fitsio_libdir") libdir)))))
+          (add-before 'check 'tests-preparation
+            (lambda _
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest))
     (inputs
-- 
2.40.1

[bug#64201] [PATCH 13/20] gnu: python-pyerfa: Update to 2.0.0.3.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pyerfa): Update to 2.0.0.3.
---
 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 a26eacef75..829ee6bcd4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3028,13 +3028,13 @@ (define-public python-jwst
 (define-public python-pyerfa
   (package
     (name "python-pyerfa")
-    (version "2.0.0.1")
+    (version "2.0.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyerfa" version))
        (sha256
-        (base32 "0c6y1rm51kj8ahbr1vwbswck3ix77dc3zhc2fkg6w7iczrzn7m1g"))
+        (base32 "0f8zykzxjsiwv5ibdn5asla2ng2xl0xdkrcrrd61j31mb3xbnzyp"))
        (modules '((guix build utils)))
        (snippet
         '(begin
-- 
2.40.1

[bug#64201] [PATCH 14/20] gnu: python-pyerfa: Fix tests.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pyerfa): Fix tests.
[snippet]: Use G-expressions.
[arguments]: Use G-expressions. Add new phase 'tests-preparation.
---
 gnu/packages/astronomy.scm | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 829ee6bcd4..514aa53258 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3037,17 +3037,23 @@ (define-public python-pyerfa
         (base32 "0f8zykzxjsiwv5ibdn5asla2ng2xl0xdkrcrrd61j31mb3xbnzyp"))
        (modules '((guix build utils)))
        (snippet
-        '(begin
-           ;; Remove bundled submodule library.
-           (delete-file-recursively "liberfa")
-           #t))))
-    (build-system python-build-system)
+        #~(begin
+            ;; Remove bundled submodule library.
+            (delete-file-recursively "liberfa")))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'use-system-liberfa
-           (lambda _
-             (setenv "PYERFA_USE_SYSTEM_LIBERFA" "1"))))))
+     (list
+      ;; Disable only one failing test:
+      ;; AttributeError: __warningregistry__
+      #:test-flags #~(list "-k" "not test_errwarn_reporting")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'use-system-liberfa
+            (lambda _
+              (setenv "PYERFA_USE_SYSTEM_LIBERFA" "1")))
+          (add-before 'check 'tests-preparation
+            (lambda _
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest-doctestplus python-pytest python-setuptools-scm))
     (inputs
-- 
2.40.1

[bug#64201] [PATCH 15/20] gnu: python-reproject: Update to 0.11.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-reproject): Update to 0.11.0.
[native-inputs]: Move python-pyvo, python-gwcs, python-shapely from here ...
[propagated-inputs]: ... to here. Add python-click, python-cloudpickle,
python-dask, python-fsspec, python-zarr.
---
 gnu/packages/astronomy.scm | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 514aa53258..4ba1f2eab9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1945,13 +1945,13 @@ (define-public python-regions
 (define-public python-reproject
   (package
     (name "python-reproject")
-    (version "0.10.0")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "reproject" version))
        (sha256
-        (base32 "1ha0a1ja7k09ysd05adffgsapfwzc6m6az34a0av2mhmlwy4zb1q"))))
+        (base32 "0p07qlqinb826m4n5b5invyfyv4z750sai2caqaf598mgj04l61p"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1974,21 +1974,26 @@ (define-public python-reproject
             (lambda _
               (setenv "HOME" (getcwd)))))))
     (propagated-inputs
-     (list python-astropy
+     (list python-asdf
+           python-astropy
            python-astropy-healpix
+           python-click
+           python-cloudpickle
+           python-dask
+           python-fsspec
+           python-gwcs
            python-numpy
-           python-scipy))
+           python-pyvo
+           python-scipy
+           python-shapely
+           python-zarr))
     (native-inputs
-     (list python-asdf
-           python-cython
+     (list python-cython
            python-extension-helpers
-           python-gwcs
            python-pytest-astropy
-           python-pyvo
            python-semantic-version
            python-pytest
-           python-setuptools-scm
-           python-shapely))
+           python-setuptools-scm))
     (home-page "https://reproject.readthedocs.io")
     (synopsis "Astronomical image reprojection in Python")
     (description
-- 
2.40.1

[bug#64201] [PATCH 16/20] gnu: python-stcal: Update to 1.3.8.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stcal): Update to 1.3.8.
---
 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 4ba1f2eab9..da2c56cc5b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2295,13 +2295,13 @@ (define-public python-stsci-stimage
 (define-public python-stcal
   (package
     (name "python-stcal")
-    (version "1.3.7")
+    (version "1.3.8")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "stcal" version))
               (sha256
                (base32
-                "0yy0pwi3krvhxfby6nzgpgyz5il3sl1j29ihbk81dh9fdh3ys2n9"))))
+                "061acpmd158vs7ndj0zflg4gcwgy96c18mkavz572xv5i0k8zyaw"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases #~(modify-phases %standard-phases
-- 
2.40.1

[bug#64201] [PATCH 17/20] gnu: python-stdatamodels: Update to 1.6.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stdatamodels): Update to 1.6.0.
---
 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 da2c56cc5b..7c41853818 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2324,13 +2324,13 @@ (define-public python-stcal
 (define-public python-stdatamodels
   (package
     (name "python-stdatamodels")
-    (version "1.5.0")
+    (version "1.6.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "stdatamodels" version))
               (sha256
                (base32
-                "1lssz5mnkzgraqa9mdg1w39scsikymcp3zpmsjb146r0pqnwnpzw"))))
+                "09cms07kchwjass5qvbcdskvhv1xg8dz62s77rh63j58f2apak59"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.40.1

[bug#64201] [PATCH 18/20] gnu: python-sunpy: Update to 5.0.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sunpy): Update to 5.0.0. Relax some
failing tests.
---
 gnu/packages/astronomy.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 7c41853818..4ddcb58f42 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2035,13 +2035,13 @@ (define-public python-sgp4
 (define-public python-sunpy
   (package
     (name "python-sunpy")
-    (version "4.1.5")
+    (version "5.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sunpy" version))
        (sha256
-        (base32 "1j5g0ivsrc5ji9s7jc3kcbi2injfs3y31pm3priycljwcsxspkpm"))))
+        (base32 "1w75yc8az86pwbf79h083j4kc2ycfk76ky5kzlmcwgp0ih23mhym"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2049,7 +2049,10 @@ (define-public python-sunpy
       #~(list "-k" (string-append
                     ;; XXX: Failed: DID NOT RAISE <class 'ModuleNotFoundError'>
                     "not test_main_nonexisting_module"
-                    " and not test_main_stdlib_module"))
+                    " and not test_main_stdlib_module"
+                    ;; XXX: packaging.version.InvalidVersion: Invalid version: 'unknown'
+                    " and not test_read_cdf"
+                    " and not test_read_empty_cdf"))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'install 'writable-compiler
-- 
2.40.1

[bug#64201] [PATCH 19/20] gnu: python-synphot: Update to 1.2.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-synphot): Update to 1.2.1.
---
 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 4ddcb58f42..b9c8f44c72 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3207,13 +3207,13 @@ (define-public python-suntime
 (define-public python-synphot
   (package
     (name "python-synphot")
-    (version "1.2.0")
+    (version "1.2.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "synphot" version))
               (sha256
                (base32
-                "02pjp1bnbyq7zi1bxqv56nif4ijd8fscmnn9ldrs8yvgsbmgdvlc"))))
+                "10kcdg2gqmi1w2hsjx9hfizwbff3kll10s68hys13nzh4i8b7cc4"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.40.1

[bug#64201] [PATCH 20/20] gnu: python-astroalign: Fix build.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroalign): Fix build.
---
 gnu/packages/astronomy.scm | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b9c8f44c72..6c43003618 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3680,7 +3680,12 @@ (define-public python-astroalign
        (sha256
         (base32 "0hly20a65540hr3l1lsd1i4d90a0vdrbwnn6zx3z8s89ha9lq3pb"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-astropy python-ccdproc python-pillow))
+    (native-inputs
+     (list python-astropy
+           python-ccdproc
+           python-pillow
+           python-pytest
+           python-semantic-version))
     (propagated-inputs
      (list python-bottleneck
            python-numpy
-- 
2.40.1

[bug#64201]

[Sharlatan Hellseher]

[-- Attachment #1: Type: text/plain, Size: 125 bytes --]

Hi Guix,

A gentle ping on this issue - updates and build fixes.
Let me know if I need to rebase or adjust it.

Thanks,
Okeg

[-- Attachment #2: Type: text/html, Size: 282 bytes --]

[bug#64201]

[Sharlatan Hellseher]

[-- Attachment #1: Type: text/plain, Size: 345 bytes --]

Hi Guix,

Would it be more helpful if I'll split this issue into 20 individual ones
to make sure QA is passed.

Thanks,
Oleg

On Mon, 10 Jul 2023, 22:11 Sharlatan Hellseher, <sharlatanus@gmail.com>
wrote:

> Hi Guix,
>
> A gentle ping on this issue - updates and build fixes.
> Let me know if I need to rebase or adjust it.
>
> Thanks,
> Okeg
>

[-- Attachment #2: Type: text/html, Size: 850 bytes --]

[bug#64201]

[Maxim Cournoyer]

Hi Oleg,

Sharlatan Hellseher <sharlatanus@gmail.com> writes:

> Hi Guix,
>
> Would it be more helpful if I'll split this issue into 20 individual ones
> to make sure QA is passed.

I think QA should process them the same, individual or as a series, as
long as they don't entail the rebuild of more than 600 packages.

So no, don't split them individually, it's fine as is, especially if the
later commits build on top of previous ones.

-- 
Thanks,
Maxim

[bug#64201] [PATCH v2 00/22]: gnu: Astronmy June updates.

[Sharlatan Hellseher]

Hi Guix!

Here is V2 of the patch series updating and fixing some of the packages
from (gnu packages astronomy). I try to split large patches into smaller
digestible ones and drop update for python-phoutils to the latest as it hangs
tests on 90% infinitely, I'll try to update it in next update cycle.

What's new comparing to V1:
- Branched from current master
- Large commit split into smaller ones
- All packages updated to the latest verions where possible
- Update of python-photils was excluded due infinity hangs

I've built patch series locally on x86_64, bare in mind to pass them all it
took about 20min+ on 16 threads machine, astrosoft has a large amount of tests
:-)


Building the following 6 packages would ensure 43 dependent packages are
rebuilt: python-regions@0.7 python-tslearn@0.6.1 python-poliastro@0.17.0
python-astroalign@2.4.2 python-sunpy@5.0.0 python-jwst@1.10.2

> ./pre-inst-env guix build $(./pre-inst-env guix refresh --list-dependent sextractor python-photutils calceph calcmysky libxisf splash python-astropy python-ccdproc python-cdflib python-drms python-fitsio python-pyerfa python-reproject python-stcal python-stdatamodels python-sunpy python-synphot python-astroalign|awk -F: '{print $2}')
> /gnu/store/qm3ls7929w0d4j8kqhrmz0w0yfvq5rp2-python-jwst-1.10.2
> /gnu/store/a7sflrsf3692giqqdf3zx1cmzknqk288-python-sunpy-5.0.0
> /gnu/store/1pyfa0ds8df3lssv7j4syvkk7hkxpa9h-python-astroalign-2.4.2
> /gnu/store/4fabnbs2f8ara1lkc71pxdc77ddb1pf7-python-regions-0.7
> /gnu/store/8855dni0axr014wnfq4kbj7rkwmfrgcl-python-poliastro-0.17.0
> /gnu/store/jwwg7qcyhik0997hlispsp8h9xc0j2y5-python-tslearn-0.6.1

Regards,
Oleg

Sharlatan Hellseher (22):
  gnu: sextractor: Update to 2.28.0, fix build.
  gnu: sextractor: Use G-expressions.
  gnu: python-photutils: Update package style.
  gnu: calceph: Update to 3.5.2.
  gnu: calcmysky: Update to 0.3.1.
  gnu: libxisf: Update to 0.2.8.
  gnu: splash: Update to 3.8.2.
  gnu: python-astropy: Update to 5.3.1.
  gnu: python-ccdproc: Update to 2.4.1.
  gnu: python-cdflib: Update to 1.0.5.
  gnu: python-drms: Update to 0.6.4.
  gnu: python-fitsio: Update to 1.1.10.
  gnu: python-fitsio: Enable tests.
  gnu: python-pyerfa: Update to 2.0.0.3.
  gnu: python-pyerfa: Fix tests.
  gnu: python-pyerfa: Use G-expressions.
  gnu: python-reproject: Update to 0.11.0.
  gnu: python-stcal: Update to 1.4.2.
  gnu: python-stdatamodels: Update to 1.7.1.
  gnu: python-sunpy: Update to 5.0.0.
  gnu: python-synphot: Update to 1.2.1.
  gnu: python-astroalign: Fix build.

 gnu/packages/astronomy.scm | 209 ++++++++++++++++++++++---------------
 1 file changed, 124 insertions(+), 85 deletions(-)


base-commit: 005912c595bf7a3329f8aa51a4ccb1d91b6ecd9e
-- 
2.40.1

[bug#64201] [PATCH v2 01/22] gnu: sextractor: Update to 2.28.0, fix build.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (sextractor): Update to 2.28.0, fix build.
[arguments]: Add configure flags for CFitsio detection.
[inputs]: Add cfitsio.
---
 gnu/packages/astronomy.scm | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9351c691d2..4e03e2fcd6 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -832,7 +832,7 @@ (define-public phd2
 (define-public sextractor
   (package
     (name "sextractor")
-    (version "2.25.0")
+    (version "2.28.0")
     (source
      (origin
        (method git-fetch)
@@ -841,7 +841,7 @@ (define-public sextractor
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0q69n3nyal57h3ik2xirwzrxzljrwy9ivwraxzv9566vi3n4z5mw"))))
+        (base32 "15v7brjiraj2rdyxiidcgb58b3dqzdd363j31cjrfqhd1wc8ii5j"))))
     (build-system gnu-build-system)
     ;; NOTE: (Sharlatan-20210124T103117+0000): Building with `atlas' is failing
     ;; due to missing shared library which required on configure phase. Switch
@@ -851,6 +851,10 @@ (define-public sextractor
      `(#:configure-flags
        (list
         "--enable-openblas"
+        (string-append
+         "--with-cfitsio-libdir=" (assoc-ref %build-inputs "cfitsio") "/lib")
+        (string-append
+         "--with-cfitsio-incdir=" (assoc-ref %build-inputs "cfitsio") "/include")
         (string-append
          "--with-openblas-libdir=" (assoc-ref %build-inputs "openblas") "/lib")
         (string-append
@@ -862,7 +866,8 @@ (define-public sextractor
     (native-inputs
      (list autoconf automake libtool))
     (inputs
-     `(("openblas" ,openblas)
+     `(("cfitsio" ,cfitsio)
+       ("openblas" ,openblas)
        ("fftw" ,fftwf)))
     (home-page "https://www.astromatic.net/software/sextractor")
     (synopsis "Extract catalogs of sources from astronomical images")
-- 
2.40.1

[bug#64201] [PATCH v2 02/22] gnu: sextractor: Use G-expressions.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (sextractor): Use G-expressions.
[inputs]: Remove labels.
---
 gnu/packages/astronomy.scm | 35 +++++++++++++++++------------------
 1 file changed, 17 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 4e03e2fcd6..26d4e9621d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -848,27 +848,26 @@ (define-public sextractor
     ;; build to use `openblas' instead. It requires FFTW with single precision
     ;; `fftwf'.
     (arguments
-     `(#:configure-flags
-       (list
-        "--enable-openblas"
-        (string-append
-         "--with-cfitsio-libdir=" (assoc-ref %build-inputs "cfitsio") "/lib")
-        (string-append
-         "--with-cfitsio-incdir=" (assoc-ref %build-inputs "cfitsio") "/include")
-        (string-append
-         "--with-openblas-libdir=" (assoc-ref %build-inputs "openblas") "/lib")
-        (string-append
-         "--with-openblas-incdir=" (assoc-ref %build-inputs "openblas") "/include")
-        (string-append
-         "--with-fftw-libdir=" (assoc-ref %build-inputs "fftw") "/lib")
-        (string-append
-         "--with-fftw-incdir=" (assoc-ref %build-inputs "fftw") "/include"))))
+     (list
+      #:configure-flags
+      #~(list
+         "--enable-openblas"
+         (string-append "--with-cfitsio-incdir="
+                        #$(this-package-input "cfitsio") "/include")
+         (string-append "--with-cfitsio-libdir="
+                        #$(this-package-input "cfitsio") "/lib")
+         (string-append "--with-fftw-incdir="
+                        #$(this-package-input "fftwf") "/include")
+         (string-append "--with-fftw-libdir="
+                        #$(this-package-input "fftwf") "/lib")
+         (string-append "--with-openblas-incdir="
+                        #$(this-package-input "openblas") "/include")
+         (string-append "--with-openblas-libdir="
+                        #$(this-package-input "openblas") "/lib"))))
     (native-inputs
      (list autoconf automake libtool))
     (inputs
-     `(("cfitsio" ,cfitsio)
-       ("openblas" ,openblas)
-       ("fftw" ,fftwf)))
+     (list cfitsio fftwf openblas))
     (home-page "https://www.astromatic.net/software/sextractor")
     (synopsis "Extract catalogs of sources from astronomical images")
     (description
-- 
2.40.1

[bug#64201] [PATCH v2 03/22] gnu: python-photutils: Update package style.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-photutils): Update package style.
[build-system]: Swap to python-build-system.
[arguments]: Use G-expressions. Rename the phase before check
'writable-compiler to 'build-extensions to reflect it's purpose, add
new step in phase building extensions for testing.
[native-inputs]: Remove python-pytest-runner.
---
 gnu/packages/astronomy.scm | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 26d4e9621d..15a52e0744 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1833,23 +1833,29 @@ (define-public python-photutils
        (uri (pypi-uri "photutils" version))
        (sha256
         (base32 "1bq4ma402lpa5d6l85awlc23kasxf40nq8hgi3iyrilnfikan0jz"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:test-target "pytest"
-       #:phases
-       (modify-phases %standard-phases
-         ;; This file is opened in both install and check phases.
-         (add-before 'install 'writable-compiler
-           (lambda _ (make-file-writable "photutils/_compiler.c")))
-         (add-before 'check 'writable-compiler
-           (lambda _ (make-file-writable "photutils/_compiler.c"))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; This file is opened in both install and check phases.
+          (add-before 'install 'writable-compiler
+            (lambda _ (make-file-writable "photutils/_compiler.c")))
+          (add-before 'check 'build-extensions
+            (lambda _
+              ;; Cython extensions have to be built before running
+              ;; the tests. If it's not build it fails with error:
+              ;;
+              ;; ModuleNotFoundError: No module named
+              ;; 'photutils.geometry.circular_overlap'
+              (make-file-writable "photutils/_compiler.c")
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (propagated-inputs
      (list python-astropy python-numpy))
     (native-inputs
      (list python-cython
            python-extension-helpers
            python-pytest-astropy
-           python-pytest-runner
            python-setuptools-scm))
     (home-page "https://github.com/astropy/photutils")
     (synopsis "Source detection and photometry")
-- 
2.40.1

[bug#64201] [PATCH v2 04/22] gnu: calceph: Update to 3.5.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (calceph): Update to 3.5.2.
---
 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 15a52e0744..9a9f6c5e9a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -181,7 +181,7 @@ (define-public aocommon
 (define-public calceph
   (package
     (name "calceph")
-    (version  "3.5.1")
+    (version  "3.5.2")
     (source
      (origin
        (method url-fetch)
@@ -189,7 +189,7 @@ (define-public calceph
              "https://www.imcce.fr/content/medias/recherche/equipes/asd/calceph/calceph-"
              version ".tar.gz"))
        (sha256
-        (base32 "078wn773pwf4pg9m0h0l00g4aq744pq1rb6kz6plgdpzp3hhpk1k"))))
+        (base32 "1rnjlaiii4j0agbj4k242p212bqqmqdqa0lni6c3bnhgfnrbjfp4"))))
     (build-system gnu-build-system)
     (native-inputs
      (list gfortran))
-- 
2.40.1

[bug#64201] [PATCH v2 05/22] gnu: calcmysky: Update to 0.3.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (calcmysky) Update to 0.3.1.
---
 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 9a9f6c5e9a..19f6771945 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -216,7 +216,7 @@ (define-public calceph
 (define-public calcmysky
   (package
     (name "calcmysky")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method git-fetch)
@@ -225,7 +225,7 @@ (define-public calcmysky
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1lgn937px4am0lggniwby1f1dl3v4l3iigq72rl9rlhx58zv4lj1"))))
+        (base32 "14jbaf9m9wig2bs7a531dvpmdkqpd09lmyvjvj1s0mhgh9g0x9m2"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags
-- 
2.40.1

[bug#64201] [PATCH v2 06/22] gnu: libxisf: Update to 0.2.8.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (libxisf): Update to 0.2.8.
---
 gnu/packages/astronomy.scm | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 19f6771945..cbef790ec6 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2684,9 +2684,7 @@ (define-public libpasastro
 (define-public libxisf
   (package
     (name "libxisf")
-    ;; TODO: v0.2.2 (current latest) failed to build on configure phase, issue
-    ;; was open directly with author as he hosts source on seflhosted gitea.
-    (version "0.2.1")
+    (version "0.2.8")
     (source
      (origin
        (method git-fetch)
@@ -2695,7 +2693,7 @@ (define-public libxisf
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0fz9mmj1nz5v7hlr53q8na7khadfn1hm0d1gfpzzw3167bqpy2xv"))))
+        (base32 "1j2bg53hrr2yc55qa6549vcpj7qjnwmxjcdgc98w3ygnrjy7n7v0"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags #~(list "-DUSE_BUNDLED_LIBS=OFF")))
-- 
2.40.1

[bug#64201] [PATCH v2 07/22] gnu: splash: Update to 3.8.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (splash): Update to 3.8.2.
---
 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 cbef790ec6..c32f0fc539 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -917,7 +917,7 @@ (define-public siril
 (define-public splash
   (package
     (name "splash")
-    (version "3.7.2")
+    (version "3.8.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -925,7 +925,7 @@ (define-public splash
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "0nsm6rk0bi99xz7wclk0zy4bpqf0qcsdln5cdjb30lhpf37i2fpa"))
+                "0y6l135g0a3hvvh8w8sfdh1kfq2g0gbp0dgjhnmwid8bwwcjvw8v"))
               (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
-- 
2.40.1

[bug#64201] [PATCH v2 08/22] gnu: python-astropy: Update to 5.3.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy): Update to 5.3.1.
[snippet]: Remove trailing #t. Prevent cfitsion from deletion.
[inputs]: Remove cfitsio.
---
 gnu/packages/astronomy.scm | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c32f0fc539..a18de38fbd 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1262,13 +1262,13 @@ (define-public celestia-gtk
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "5.2.2")
+    (version "5.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "170ddflli35mvhf6pla7aizfw8a7ckq66g1mi1br99dx2r3y7ag6"))
+        (base32 "0x4dh7wx9sn1gy6sl2d54zsd24cgfjwrlk6kfrwpzzrmbsv22lwv"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -1277,9 +1277,12 @@ (define-public python-astropy
              (for-each delete-file-recursively '("ply" "configobj")))
            ;; Remove cextern bundles. Check bundled versions against available
            ;; in Guix in the future update of astropy.
+           ;;
+           ;; cfitsio build is only available from non-publicly exposed
+           ;; bundled short version. See:
+           ;; https://github.com/astropy/astropy/pull/14311
            (with-directory-excursion "cextern"
-             (for-each delete-file-recursively '("cfitsio" "expat" "wcslib")))
-           #t))))
+             (for-each delete-file-recursively '("expat" "wcslib")))))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -1346,7 +1349,7 @@ (define-public python-astropy
            python-skyfield
            python-timezonefinder))
     (inputs
-     (list cfitsio expat wcslib))
+     (list expat wcslib))
     (propagated-inputs
      (list python-configobj
            python-numpy
-- 
2.40.1

[bug#64201] [PATCH v2 09/22] gnu: python-ccdproc: Update to 2.4.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ccdproc): Update to 2.4.1.
[native-inputs]: Add python-semantic-version.
---
 gnu/packages/astronomy.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a18de38fbd..154fa5a0f2 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1522,15 +1522,18 @@ (define-public python-bayesicfitting
 (define-public python-ccdproc
   (package
     (name "python-ccdproc")
-    (version "2.4.0")
+    (version "2.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ccdproc" version))
        (sha256
-        (base32 "0fy1sni87cr05dkljd8wb7vgh7z9agh8wv5kiagxcpbcf8l06jv1"))))
+        (base32 "186plgfhrj7wivs053y65jlv1x33y8ii31jdr2rm4s6pl0j7x29z"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-memory-profiler python-pytest-astropy))
+    (native-inputs
+     (list python-memory-profiler
+           python-pytest-astropy
+           python-semantic-version))
     (propagated-inputs
      (list python-astropy
            python-astroscrappy
-- 
2.40.1

[bug#64201] [PATCH v2 10/22] gnu: python-cdflib: Update to 1.0.5.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-cdflib): Update to 1.0.5.
---
 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 154fa5a0f2..798879b6a3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1551,7 +1551,7 @@ (define-public python-ccdproc
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-    (version "0.4.9")
+    (version "1.0.5")
     (source
      (origin
        (method git-fetch)   ; no tests in pypi archive
@@ -1560,7 +1560,7 @@ (define-public python-cdflib
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1k557najk7ln293zwyghnhw48ays3nqf9s94kibsc7r70c2q7p08"))))
+        (base32 "1pkda9gmpjhbqxl2jj5q9rjx77lv5c908mgf20lw3rz4nvfaa2wn"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases
-- 
2.40.1

[bug#64201] [PATCH v2 11/22] gnu: python-drms: Update to 0.6.4.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-drms): Update to 0.6.4.
---
 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 798879b6a3..884343ae57 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1678,13 +1678,13 @@ (define-public python-czml3
 (define-public python-drms
   (package
     (name "python-drms")
-    (version "0.6.3")
+    (version "0.6.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "drms" version))
        (sha256
-        (base32 "1b0w350y4wbgyy19zcf28xbb85mqq6gnhb6ppibbc4hbn2ixbcvj"))))
+        (base32 "0mkrmr55fgca441z7hvsyri6x9cjsh0sfas3hrj0k1k10k8vszbw"))))
     (build-system python-build-system)
     (arguments
      (list
-- 
2.40.1

[bug#64201] [PATCH v2 12/22] gnu: python-fitsio: Update to 1.1.10.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-fitsio): Update to 1.1.10.
[native-inputs]: Add python-pytest.
[propagated-inputs]: Move cfitsio from here ...
[inputs]: ... to here, do not propagate as it's required only on build
and link time.
---
 gnu/packages/astronomy.scm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 884343ae57..05fa722499 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -506,13 +506,13 @@ (define-public python-astroml
 (define-public python-fitsio
   (package
     (name "python-fitsio")
-    (version "1.1.8")
+    (version "1.1.10")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "fitsio" version))
        (sha256
-        (base32 "1y80hgvlkjz1bijfyb2j03853yc1kc63yrf9ab7as31ad2r6kxb1"))
+        (base32 "0dv2vjj8qn3rq5sr99x5yjjch5h867c8q7zh73i67dzdsk7ix0jf"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove the bundled cfitsio
@@ -538,9 +538,12 @@ (define-public python-fitsio
                   (("self.use_system_fitsio") "True")
                   (("self.system_fitsio_includedir") includedir)
                   (("self.system_fitsio_libdir") libdir))))))))
-    (inputs (list curl))
+    (native-inputs
+     (list python-pytest))
+    (inputs
+     (list curl cfitsio))
     (propagated-inputs
-     (list python-numpy cfitsio))
+     (list python-numpy))
     (home-page "https://github.com/esheldon/fitsio")
     (synopsis
      "Python library to read from and write to FITS files")
-- 
2.40.1

[bug#64201] [PATCH v2 13/22] gnu: python-fitsio: Enable tests.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-fitsio): Enable tests.
[build-system]: Swap to pyproject-build-system.
[arguments]: Add new phase 'build-extensions.
---
 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 05fa722499..6815ba7db0 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -520,7 +520,7 @@ (define-public python-fitsio
             (delete-file-recursively "cfitsio3490")
             (substitute* "MANIFEST.in"
               (("recursive-include cfitsio3490.*$\n") ""))))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list
       #:phases
@@ -537,7 +537,10 @@ (define-public python-fitsio
                   (("self.system_fitsio_libdir = None") "pass")
                   (("self.use_system_fitsio") "True")
                   (("self.system_fitsio_includedir") includedir)
-                  (("self.system_fitsio_libdir") libdir))))))))
+                  (("self.system_fitsio_libdir") libdir)))))
+          (add-before 'check 'build-extensions
+            (lambda _
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest))
     (inputs
-- 
2.40.1

[bug#64201] [PATCH v2 14/22] gnu: python-pyerfa: Update to 2.0.0.3.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pyerfa): Update to 2.0.0.3.
---
 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 6815ba7db0..ac6108eb6c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3151,13 +3151,13 @@ (define-public python-jwst
 (define-public python-pyerfa
   (package
     (name "python-pyerfa")
-    (version "2.0.0.1")
+    (version "2.0.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyerfa" version))
        (sha256
-        (base32 "0c6y1rm51kj8ahbr1vwbswck3ix77dc3zhc2fkg6w7iczrzn7m1g"))
+        (base32 "0f8zykzxjsiwv5ibdn5asla2ng2xl0xdkrcrrd61j31mb3xbnzyp"))
        (modules '((guix build utils)))
        (snippet
         '(begin
-- 
2.40.1

[bug#64201] [PATCH v2 15/22] gnu: python-pyerfa: Fix tests.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pyerfa): Fix tests.
[build-system]: Swap to pyproject-build-system.
[arguments]: Disable a failing test. Add 'build-extensions phase.
---
 gnu/packages/astronomy.scm | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ac6108eb6c..97fce57cd3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3164,13 +3164,19 @@ (define-public python-pyerfa
            ;; Remove bundled submodule library.
            (delete-file-recursively "liberfa")
            #t))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     `(;; Disable only one failing test:
+       ;; AttributeError: __warningregistry__
+       #:test-flags '("-k" "not test_errwarn_reporting")
+       #:phases
        (modify-phases %standard-phases
          (add-before 'build 'use-system-liberfa
            (lambda _
-             (setenv "PYERFA_USE_SYSTEM_LIBERFA" "1"))))))
+             (setenv "PYERFA_USE_SYSTEM_LIBERFA" "1")))
+         (add-before 'check 'build-extensions
+           (lambda _
+             (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest-doctestplus python-pytest python-setuptools-scm))
     (inputs
-- 
2.40.1

[bug#64201] [PATCH v2 16/22] gnu: python-pyerfa: Use G-expressions.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pyerfa): Use G-expressions.
[snippet]: Remove trailing #t.
---
 gnu/packages/astronomy.scm | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 97fce57cd3..6f1910232b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3160,23 +3160,23 @@ (define-public python-pyerfa
         (base32 "0f8zykzxjsiwv5ibdn5asla2ng2xl0xdkrcrrd61j31mb3xbnzyp"))
        (modules '((guix build utils)))
        (snippet
-        '(begin
-           ;; Remove bundled submodule library.
-           (delete-file-recursively "liberfa")
-           #t))))
+        #~(begin
+            ;; Remove bundled submodule library.
+            (delete-file-recursively "liberfa")))))
     (build-system pyproject-build-system)
     (arguments
-     `(;; Disable only one failing test:
-       ;; AttributeError: __warningregistry__
-       #:test-flags '("-k" "not test_errwarn_reporting")
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'use-system-liberfa
-           (lambda _
-             (setenv "PYERFA_USE_SYSTEM_LIBERFA" "1")))
-         (add-before 'check 'build-extensions
-           (lambda _
-             (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+     (list
+      ;; Disable only one failing test:
+      ;; AttributeError: __warningregistry__
+      #:test-flags #~(list "-k" "not test_errwarn_reporting")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'use-system-liberfa
+            (lambda _
+              (setenv "PYERFA_USE_SYSTEM_LIBERFA" "1")))
+          (add-before 'check 'build-extensions
+            (lambda _
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest-doctestplus python-pytest python-setuptools-scm))
     (inputs
-- 
2.40.1

[bug#64201] [PATCH v2 17/22] gnu: python-reproject: Update to 0.11.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-reproject): Update to 0.11.0.
[native-inputs]: Move python-pyvo, python-gwcs, python-shapely from here ...
[propagated-inputs]: ... to here. Add python-click, python-cloudpickle,
python-dask, python-fsspec, python-zarr.
---
 gnu/packages/astronomy.scm | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6f1910232b..1735eaa25e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2058,13 +2058,13 @@ (define-public python-regions
 (define-public python-reproject
   (package
     (name "python-reproject")
-    (version "0.10.0")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "reproject" version))
        (sha256
-        (base32 "1ha0a1ja7k09ysd05adffgsapfwzc6m6az34a0av2mhmlwy4zb1q"))))
+        (base32 "0p07qlqinb826m4n5b5invyfyv4z750sai2caqaf598mgj04l61p"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2087,21 +2087,26 @@ (define-public python-reproject
             (lambda _
               (setenv "HOME" (getcwd)))))))
     (propagated-inputs
-     (list python-astropy
+     (list python-asdf
+           python-astropy
            python-astropy-healpix
+           python-click
+           python-cloudpickle
+           python-dask
+           python-fsspec
+           python-gwcs
            python-numpy
-           python-scipy))
+           python-pyvo
+           python-scipy
+           python-shapely
+           python-zarr))
     (native-inputs
-     (list python-asdf
-           python-cython
+     (list python-cython
            python-extension-helpers
-           python-gwcs
            python-pytest-astropy
-           python-pyvo
            python-semantic-version
            python-pytest
-           python-setuptools-scm
-           python-shapely))
+           python-setuptools-scm))
     (home-page "https://reproject.readthedocs.io")
     (synopsis "Astronomical image reprojection in Python")
     (description
-- 
2.40.1

[bug#64201] [PATCH v2 18/22] gnu: python-stcal: Update to 1.4.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stcal): Update to 1.4.2.
---
 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 1735eaa25e..d7475a98e8 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2408,13 +2408,13 @@ (define-public python-stsci-stimage
 (define-public python-stcal
   (package
     (name "python-stcal")
-    (version "1.3.7")
+    (version "1.4.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "stcal" version))
               (sha256
                (base32
-                "0yy0pwi3krvhxfby6nzgpgyz5il3sl1j29ihbk81dh9fdh3ys2n9"))))
+                "163vyqcd9qv2knf8jik8y449z7ljl2lvbd7im82bq61prgi3z2hj"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases #~(modify-phases %standard-phases
-- 
2.40.1

[bug#64201] [PATCH v2 19/22] gnu: python-stdatamodels: Update to 1.7.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-stdatamodels): Update to 1.7.1.
---
 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 d7475a98e8..cde133bc0b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2437,13 +2437,13 @@ (define-public python-stcal
 (define-public python-stdatamodels
   (package
     (name "python-stdatamodels")
-    (version "1.5.0")
+    (version "1.7.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "stdatamodels" version))
               (sha256
                (base32
-                "1lssz5mnkzgraqa9mdg1w39scsikymcp3zpmsjb146r0pqnwnpzw"))))
+                "0d7a27myl3xgri3z7yx26mr4dpqnlfhdh5i2ql2miwymi0mx3ij5"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.40.1

[bug#64201] [PATCH v2 20/22] gnu: python-sunpy: Update to 5.0.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sunpy): Update to 5.0.0. Relax some
failing tests.
---
 gnu/packages/astronomy.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index cde133bc0b..8cdece9da4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2148,13 +2148,13 @@ (define-public python-sgp4
 (define-public python-sunpy
   (package
     (name "python-sunpy")
-    (version "4.1.5")
+    (version "5.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sunpy" version))
        (sha256
-        (base32 "1j5g0ivsrc5ji9s7jc3kcbi2injfs3y31pm3priycljwcsxspkpm"))))
+        (base32 "1w75yc8az86pwbf79h083j4kc2ycfk76ky5kzlmcwgp0ih23mhym"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2162,7 +2162,10 @@ (define-public python-sunpy
       #~(list "-k" (string-append
                     ;; XXX: Failed: DID NOT RAISE <class 'ModuleNotFoundError'>
                     "not test_main_nonexisting_module"
-                    " and not test_main_stdlib_module"))
+                    " and not test_main_stdlib_module"
+                    ;; XXX: packaging.version.InvalidVersion: Invalid version: 'unknown'
+                    " and not test_read_cdf"
+                    " and not test_read_empty_cdf"))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'install 'writable-compiler
-- 
2.40.1

[bug#64201] [PATCH v2 21/22] gnu: python-synphot: Update to 1.2.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-synphot): Update to 1.2.1.
---
 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 8cdece9da4..c5c17dfb06 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3330,13 +3330,13 @@ (define-public python-suntime
 (define-public python-synphot
   (package
     (name "python-synphot")
-    (version "1.2.0")
+    (version "1.2.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "synphot" version))
               (sha256
                (base32
-                "02pjp1bnbyq7zi1bxqv56nif4ijd8fscmnn9ldrs8yvgsbmgdvlc"))))
+                "10kcdg2gqmi1w2hsjx9hfizwbff3kll10s68hys13nzh4i8b7cc4"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.40.1

[bug#64201] [PATCH v2 22/22] gnu: python-astroalign: Fix build.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroalign): Fix build.
[native-inputs]: Add python-pytest, python-semantic-version.
---
 gnu/packages/astronomy.scm | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c5c17dfb06..54affefa84 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3803,7 +3803,12 @@ (define-public python-astroalign
        (sha256
         (base32 "0hly20a65540hr3l1lsd1i4d90a0vdrbwnn6zx3z8s89ha9lq3pb"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-astropy python-ccdproc python-pillow))
+    (native-inputs
+     (list python-astropy
+           python-ccdproc
+           python-pillow
+           python-pytest
+           python-semantic-version))
     (propagated-inputs
      (list python-bottleneck
            python-numpy
-- 
2.40.1

[bug#64201] [PATCH v2 00/22]: gnu: Astronmy June updates.

[Andreas Enge]

Hello,

I had a bit of time and managed to build everything depending on the first
8 commits (including python-astropy), which I just pushed. Unfortunately QA
is currently overwhelmed and underpowered, so there is no green button, but
some of the packages had actually been compiled for x86_64.

Thanks for your patience,

Andreas

[bug#64201] [PATCH v2 00/22]: gnu: Astronmy June updates.

[Sharlatan Hellseher]

[-- Attachment #1: Type: text/plain, Size: 583 bytes --]

Hi Andreas,

Would it be more reasonable to prepare other series and mark this one as
completed?

I can cover and test patches which failed for you.

Regards,
Oleg

On Mon, 7 Aug 2023, 19:20 Andreas Enge, <andreas@enge.fr> wrote:

> Hello,
>
> I had a bit of time and managed to build everything depending on the first
> 8 commits (including python-astropy), which I just pushed. Unfortunately QA
> is currently overwhelmed and underpowered, so there is no green button, but
> some of the packages had actually been compiled for x86_64.
>
> Thanks for your patience,
>
> Andreas
>
>

[-- Attachment #2: Type: text/html, Size: 1034 bytes --]

bug#64201: [PATCH v2 00/22]: gnu: Astronmy June updates.

[Andreas Enge]

Hello Oleg,

Am Mon, Aug 07, 2023 at 09:11:01PM +0100 schrieb Sharlatan Hellseher:
> Would it be more reasonable to prepare other series and mark this one as
> completed?

thanks for the offer! But your patches are fine; I just tested them one
by one, while some updates needed to go together. If QA had enough computing
power, it would have created a green button and made it all a bit simpler.
We will get there eventually.

Thanks for all these contributions, which I have just pushed, so I am
closing the issue.

You may go ahead with the next series :)

Andreas