GNU bug report logs - #65814
[PATCH 00/19] gnu: Astronomy 2023/08 updates.

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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 00/19] gnu: Astronomy 2023/08 updates.
Date: Thu,  7 Sep 2023 23:31:40 +0100

Hi Guix!

Easy to win not breaking patch series which updates and improve some
Astronomy related packages. python-tslearn is updated as well to fix build
after python-astropy update.

Regards,
Oleg

> ./pre-inst-env guix build $(./pre-inst-env guix refresh --list-dependent python-astropy python-stdatamodels python-roman-datamodels python-rad python-pyvo python-photutils python-jwst python-fitsio python-crds python-bayesicfitting python-sunpy python-cdflib python-astropy-healpix splash libxisf | awk -F: '{print $2}')
> /gnu/store/jdndwsfpfyfz42xd6nidx1jxfgcms851-python-sunpy-5.0.0
> /gnu/store/2fk97dy9jf99ds6bf6f8q9drj9kl5xmj-python-astroalign-2.4.2
> /gnu/store/4f5f60jzk712dxdidgafvr58d7ncrqk2-python-jwst-1.11.4
> /gnu/store/1rrs1ngidi5d91gwyc642faax3fbmlmh-python-poliastro-0.17.0
> /gnu/store/34kmwg37dmb9b2rya0zbps0n72rbhv80-python-tslearn-0.6.2
> /gnu/store/p0bwy15kjbcj30scbwangnvzzir12a52-python-regions-0.7

Sharlatan Hellseher (19):
  gnu: libxisf: Update to 0.2.9.
  gnu: libxisf: Extend description.
  gnu: splash: Update to 3.8.4.
  gnu: python-astropy-healpix: Update to 1.0.0.
  gnu: python-cdflib: Update to 1.1.0.
  gnu: python-cdflib: Fix version detection.
  gnu: python-sunpy: Enable more tests.
  gnu: python-bayesicfitting: Update to 3.2.0.
  gnu: python-crds: Update to 11.17.4.
  gnu: python-fitsio: Update to 1.2.0.
  gnu: python-jwst: Update to 1.11.4.
  gnu: python-photutils: Update to 1.9.0.
  gnu: python-pyvo: Update to 1.4.2.
  gnu: python-rad: Update to 0.17.1.
  gnu: python-roman-datamodels: Update to 0.17.1.
  gnu: python-roman-datamodels: Remove all test constrains.
  gnu: python-stdatamodels: Update to 1.8.0.
  gnu: python-astropy: Update to 5.3.3.
  gnu: python-tslearn: Update to 0.6.2.

 gnu/packages/astronomy.scm        | 144 +++++++++++++++---------------
 gnu/packages/machine-learning.scm |   4 +-
 2 files changed, 74 insertions(+), 74 deletions(-)


base-commit: 6113e0529d61df7425f64e30a6bf77f7cfdfe5a5
-- 
2.41.0

Message #8 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 01/19] gnu: libxisf: Update to 0.2.9.
Date: Thu,  7 Sep 2023 23:32:09 +0100

* gnu/packages/astronomy.scm (libxisf): Update to 0.2.9.
---
 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 e8499bb4b4..624c17eade 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2790,7 +2790,7 @@ (define-public libpasastro
 (define-public libxisf
   (package
     (name "libxisf")
-    (version "0.2.8")
+    (version "0.2.9")
     (source
      (origin
        (method git-fetch)
@@ -2799,7 +2799,7 @@ (define-public libxisf
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1j2bg53hrr2yc55qa6549vcpj7qjnwmxjcdgc98w3ygnrjy7n7v0"))))
+        (base32 "02cxv86h0ng4kmvyjkf7cr2ak2i3vpf0q0ik7jg4nmqjsidcs796"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags #~(list "-DUSE_BUNDLED_LIBS=OFF")))
-- 
2.41.0

Message #11 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 02/19] gnu: libxisf: Extend description.
Date: Thu,  7 Sep 2023 23:32:10 +0100

* gnu/packages/astronomy.scm (libxisf)[description]: Explain acronym.
Add essential links to the mentioned standard and the service.
---
 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 624c17eade..278b82512c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2810,8 +2810,11 @@ (define-public libxisf
     (home-page "https://nouspiro.space/?page_id=306")
     (synopsis "Astronomical library to load and write XISF file format")
     (description
-     "LibXISF is C++ library that can read and write XISF files produced by
-PixInsight.  It implements XISF 1.0 specification.")
+     "LibXISF is C++ library that can read and write @acronym{XISF,Extensible
+Image Serialization Format} files produced by @url{https://pixinsight.com/,
+PixInsight}.  It implements
+@url{https://pixinsight.com/doc/docs/XISF-1.0-spec/XISF-1.0-spec.html, XISF
+1.0 specification}.")
     (license license:gpl3+)))
 
 (define-public missfits
-- 
2.41.0

Message #14 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 04/19] gnu: python-astropy-healpix: Update to 1.0.0.
Date: Thu,  7 Sep 2023 23:32:12 +0100

* gnu/packages/astronomy.scm (python-astropy-healpix): Update to 1.0.0.
---
 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 3a590c1ef2..307b70871b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1460,13 +1460,13 @@ (define-public python-astropy
 (define-public python-astropy-healpix
   (package
     (name "python-astropy-healpix")
-    (version "0.7")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy_healpix" version))
        (sha256
-        (base32 "1n1svmd41iv944zf4anbnsigd47zr4dfjf49vrc7m6928gmq9hw8"))))
+        (base32 "18zfmdv0vs0yawirq8c2mpjxx7bvy66z0rlcyc1n6s0fl5ifz0pl"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #17 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 03/19] gnu: splash: Update to 3.8.4.
Date: Thu,  7 Sep 2023 23:32:11 +0100

* gnu/packages/astronomy.scm (splash): Update to 3.8.4.
---
 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 278b82512c..3a590c1ef2 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1011,7 +1011,7 @@ (define-public siril
 (define-public splash
   (package
     (name "splash")
-    (version "3.8.2")
+    (version "3.8.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1019,7 +1019,7 @@ (define-public splash
                     (commit (string-append "v" version))))
               (sha256
                (base32
-                "0y6l135g0a3hvvh8w8sfdh1kfq2g0gbp0dgjhnmwid8bwwcjvw8v"))
+                "1l18sqz5mpab9wb5hlbfy18wfwq6fpijc3p9wa5bv6lrcymvpirp"))
               (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments
-- 
2.41.0

Message #20 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 05/19] gnu: python-cdflib: Update to 1.1.0.
Date: Thu,  7 Sep 2023 23:32:13 +0100

* gnu/packages/astronomy.scm (python-cdflib): Update to 1.1.0.
---
 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 307b70871b..95b29ec2ea 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1643,7 +1643,7 @@ (define-public python-ccdproc
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-    (version "1.0.5")
+    (version "1.1.0")
     (source
      (origin
        (method git-fetch)   ; no tests in pypi archive
@@ -1652,7 +1652,7 @@ (define-public python-cdflib
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1pkda9gmpjhbqxl2jj5q9rjx77lv5c908mgf20lw3rz4nvfaa2wn"))))
+        (base32 "0qxf13vmfiblcazxdk2b765b02ys57amawvrwlkj9d5x9f5s6061"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases
-- 
2.41.0

Message #23 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 06/19] gnu: python-cdflib: Fix version detection.
Date: Thu,  7 Sep 2023 23:32:14 +0100

* gnu/packages/astronomy.scm (python-cdflib): Fix version detection
during build Wheel package.
[arguments]: Add new phase 'set-env-version.
[native-inputs]: Add python-setuptools-scm.
---
 gnu/packages/astronomy.scm | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 95b29ec2ea..335c075a68 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1657,6 +1657,10 @@ (define-public python-cdflib
     (arguments
      (list #:phases
            #~(modify-phases %standard-phases
+               (add-before 'build 'set-env-version
+                 (lambda _
+                   (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
+                           #$version)))
                (add-before 'check 'set-home-env
                  (lambda _
                    (setenv "HOME" (getcwd)))))))
@@ -1668,6 +1672,7 @@ (define-public python-cdflib
            python-pytest
            python-pytest-cov
            python-pytest-remotedata
+           python-setuptools-scm
            python-xarray))
     (home-page "https://github.com/MAVENSDC/cdflib")
     (synopsis "Python library to deal with NASA's CDF astronmical data format")
-- 
2.41.0

Message #26 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 07/19] gnu: python-sunpy: Enable more tests.
Date: Thu,  7 Sep 2023 23:32:15 +0100

* gnu/packages/astronomy.scm (python-sunpy): Enable tests detecting
python-cdflib metadata. Update annotation for still disabled tests.
---
 gnu/packages/astronomy.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 335c075a68..c69b38dae5 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2252,11 +2252,10 @@ (define-public python-sunpy
       #:test-flags
       #~(list "-k" (string-append
                     ;; XXX: Failed: DID NOT RAISE <class 'ModuleNotFoundError'>
+                    ;; It struggles to find python-opencsv package info with
+                    ;; 'importlib.metadata'
                     "not test_main_nonexisting_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"))
+                    " and not test_main_stdlib_module"))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'install 'writable-compiler
-- 
2.41.0

Message #29 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 09/19] gnu: python-crds: Update to 11.17.4.
Date: Thu,  7 Sep 2023 23:32:17 +0100

* gnu/packages/astronomy.scm (python-crds): Update to 11.17.4.
---
 gnu/packages/astronomy.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 453571325f..cf524a2f6c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1692,13 +1692,13 @@ (define-public python-cdflib
 (define-public python-crds
   (package
     (name "python-crds")
-    (version "11.17.0")
+    (version "11.17.4")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "crds" version))
               (sha256
                (base32
-                "0sdz1k4hrgrc2jwihp9ns7lx23kcz7f90c222q7aaqf9g3vvpqlr"))))
+                "0bk6cyd2il7ibqwky6m5kkgs9shrlzyfpnp2rh9jx0xa9habf7zm"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1710,7 +1710,6 @@ (define-public python-crds
                              python-astropy
                              python-boto3
                              python-filelock
-                             python-lxml
                              python-numpy
                              python-parsley
                              python-pysynphot
-- 
2.41.0

Message #32 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 08/19] gnu: python-bayesicfitting: Update to 3.2.0.
Date: Thu,  7 Sep 2023 23:32:16 +0100

* gnu/packages/astronomy.scm (python-bayesicfitting): Update to 3.2.0.
---
 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 c69b38dae5..453571325f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1582,7 +1582,7 @@ (define-public python-astroscrappy
 (define-public python-bayesicfitting
   (package
     (name "python-bayesicfitting")
-    (version "3.1.1")
+    (version "3.2.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1591,7 +1591,7 @@ (define-public python-bayesicfitting
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "07y9dr9wxhxrvhk0jjakhbyrgal60i92m7z7q14fp12k8x0gl69l"))))
+                "0q6v7w9b1xzam0qn5vsl5wrdp1fkfpsn411pzd8wyy9giznpajxi"))))
     (build-system python-build-system)
     (arguments
      (list #:phases #~(modify-phases %standard-phases
-- 
2.41.0

Message #35 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 10/19] gnu: python-fitsio: Update to 1.2.0.
Date: Thu,  7 Sep 2023 23:32:18 +0100

* gnu/packages/astronomy.scm (python-fitsio): Update to 1.2.0.
[arguments]{phases}: Swap 'unbundle-cfitsio to 'set-env as there is
support for system CFitsio library provided.
[inputs]: Add zlib.
---
 gnu/packages/astronomy.scm | 33 +++++++++++++++------------------
 1 file changed, 15 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index cf524a2f6c..2064a05c64 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -534,45 +534,42 @@ (define-public python-astroml
 (define-public python-fitsio
   (package
     (name "python-fitsio")
-    (version "1.1.10")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "fitsio" version))
        (sha256
-        (base32 "0dv2vjj8qn3rq5sr99x5yjjch5h867c8q7zh73i67dzdsk7ix0jf"))
+        (base32 "04fbg1ffj7qrlzw50xzzkfnlk6qjjqq96j0im7phprmwb1rbvzzh"))
        (modules '((guix build utils)))
        (snippet
-        ;; Remove the bundled cfitsio
+        ;; Remove the bundled cfitsio. When update the package check the
+        ;; current bundled version.
         #~(begin
-            (delete-file-recursively "cfitsio3490")
+            (delete-file-recursively "cfitsio-4.2.0")
             (substitute* "MANIFEST.in"
-              (("recursive-include cfitsio3490.*$\n") ""))))))
+              (("recursive-include cfitsio-4.2.0.*$\n") ""))))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'unbundle-cfitsio
+          (add-before 'build 'set-env
             (lambda _
-              (let* ((cfitsio #$(this-package-input "cfitsio"))
-                     (includedir (string-append "\"" cfitsio "/include\""))
-                     (libdir (string-append "\"" cfitsio "/lib\"")))
-                ;; Use Guix' cfitsio instead of the bundled one
-                (substitute* "setup.py"
-                  (("self.use_system_fitsio = False") "pass")
-                  (("self.system_fitsio_includedir = None") "pass")
-                  (("self.system_fitsio_libdir = None") "pass")
-                  (("self.use_system_fitsio") "True")
-                  (("self.system_fitsio_includedir") includedir)
-                  (("self.system_fitsio_libdir") libdir)))))
+              (setenv "FITSIO_USE_SYSTEM_FITSIO" "True")
+              (setenv "FITSIO_SYSTEM_FITSIO_INCLUDEDIR"
+                      (string-append
+                       #$(this-package-input "cfitsio") "/include"))
+              (setenv "FITSIO_SYSTEM_FITSIO_LIBDIR"
+                      (string-append
+                       #$(this-package-input "cfitsio") "/lib"))))
           (add-before 'check 'build-extensions
             (lambda _
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest))
     (inputs
-     (list curl cfitsio))
+     (list curl cfitsio zlib))
     (propagated-inputs
      (list python-numpy))
     (home-page "https://github.com/esheldon/fitsio")
-- 
2.41.0

Message #38 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 11/19] gnu: python-jwst: Update to 1.11.4.
Date: Thu,  7 Sep 2023 23:32:19 +0100

* gnu/packages/astronomy.scm (python-jwst): Update to 1.11.4.
[propagated-inputs]: Add python-asdf-transform-schemas, python-jplephem.
[native-inputs]: Remove python-codecov, python-flake8.
---
 gnu/packages/astronomy.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 2064a05c64..2c8e16f550 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3181,13 +3181,13 @@ (define-public python-jplephem
 (define-public python-jwst
   (package
     (name "python-jwst")
-    (version "1.10.2")
+    (version "1.11.4")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "jwst" version))
               (sha256
                (base32
-                "1lmfyw2y7c84rs9xqavah9aidj478ijiiijlz6fag11xqn1vs98y"))))
+                "1q3kpdjr8j1y8hkpidy80aqxsp3k13sz4j5aagq3wnzvpnds3x73"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3204,11 +3204,13 @@ (define-public python-jwst
     (propagated-inputs (list opencv
                              python-asdf
                              python-asdf-astropy
+                             python-asdf-transform-schemas
                              python-astropy
                              python-bayesicfitting
                              python-crds
                              python-drizzle
                              python-gwcs
+                             python-jplephem
                              python-jsonschema
                              python-numpy
                              python-photutils
@@ -3226,9 +3228,7 @@ (define-public python-jwst
                              python-stsci-imagestats
                              python-tweakwcs
                              python-wiimatch))
-    (native-inputs (list python-codecov
-                         python-colorama
-                         python-flake8
+    (native-inputs (list python-colorama
                          python-pytest
                          python-pytest-cov
                          python-pytest-doctestplus
-- 
2.41.0

Message #41 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 12/19] gnu: python-photutils: Update to 1.9.0.
Date: Thu,  7 Sep 2023 23:32:20 +0100

* gnu/packages/astronomy.scm (python-photutils): Update to 1.9.0.
---
 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 2c8e16f550..14424fae70 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1925,13 +1925,13 @@ (define-public python-mpl-animators
 (define-public python-photutils
   (package
     (name "python-photutils")
-    (version "1.7.0")
+    (version "1.9.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "photutils" version))
        (sha256
-        (base32 "1bq4ma402lpa5d6l85awlc23kasxf40nq8hgi3iyrilnfikan0jz"))))
+        (base32 "0gjvrmcb10lyqx3h9521zqskqngd5xcp3l9h2b02mk1p7q54mzdy"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #44 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 13/19] gnu: python-pyvo: Update to 1.4.2.
Date: Thu,  7 Sep 2023 23:32:21 +0100

* gnu/packages/astronomy.scm (python-pyvo): 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 14424fae70..95c585079c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2084,13 +2084,13 @@ (define-public python-poppy
 (define-public python-pyvo
   (package
     (name "python-pyvo")
-    (version "1.4.1")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyvo" version))
        (sha256
-        (base32 "17acv1yhz1jrsx9f35nr1vg276ibaivh4i243qkmp6abzvfyg907"))))
+        (base32 "1jwmgpavw80mf9sigfz5p2cqh6vz5mvm11ziqmdp5zdccn42kzk6"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest-astropy python-requests-mock python-setuptools-scm))
-- 
2.41.0

Message #47 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 14/19] gnu: python-rad: Update to 0.17.1.
Date: Thu,  7 Sep 2023 23:32:22 +0100

* gnu/packages/astronomy.scm (python-rad): Update to 0.17.1.
[arguments]{tests?}: Disable them to break dependencies cycle.
[native-inputs]: Remove python-astropy, python-pytest,
python-pytest-doctestplus, python-pytest-openfiles.
---
 gnu/packages/astronomy.scm | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 95c585079c..a402c63e9f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3807,22 +3807,20 @@ (define-public python-gwcs
 (define-public python-rad
   (package
     (name "python-rad")
-    (version "0.15.0")
+    (version "0.17.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "rad" version))
               (sha256
                (base32
-                "0j51pkywxdaqrfz162rdsywlvx1mbb2h0gi5framvhf25i1im7mb"))))
+                "11jhh3qmd00g8sn6hcfshbpb2qy1rfj0xkxn30pd63lqazg4ra3p"))))
     (build-system pyproject-build-system)
     (arguments
-     (list #:test-flags #~(list "-k" "not remote_data")))
-    (native-inputs (list python-astropy
-                         python-pytest
-                         python-pytest-doctestplus
-                         python-pytest-openfiles
-                         python-semantic-version
-                         python-setuptools-scm))
+     (list
+      ;; XXX: Tests introduce dependencies cycle, breaking it by disable them.
+      ;; python-rad -> python-roman-datamodels -> python-crds -> python-rad
+      #:tests? #f))
+    (native-inputs (list python-semantic-version python-setuptools-scm))
     (propagated-inputs (list python-asdf python-asdf-astropy))
     (home-page "https://github.com/spacetelescope/rad")
     (synopsis "Roman Attribute Dictionary")
-- 
2.41.0

Message #50 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 15/19] gnu: python-roman-datamodels: Update to 0.17.1.
Date: Thu,  7 Sep 2023 23:32:23 +0100

* gnu/packages/astronomy.scm (python-roman-datamodels): Update to
0.17.1.
[arguments]{phases}: Add 'set-env phase to pass tests.
[native-inputs]: Remove python-pytest-openfiles. Add python-pytest-env.
---
 gnu/packages/astronomy.scm | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a402c63e9f..d1b34def8f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3835,13 +3835,13 @@ (define-public python-rad
 (define-public python-roman-datamodels
   (package
     (name "python-roman-datamodels")
-    (version "0.15.0")
+    (version "0.17.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "roman_datamodels" version))
               (sha256
                (base32
-                "0frhm1cqqd8934yizhm4fy78y38q2w9ncm4rv1n74hfypkyis4ap"))))
+                "1y12cp8172i4a314gmhpi86jw6pfylz1adh0rzr5zqmvd3mrjqlj"))))
     (build-system pyproject-build-system)
     (arguments
      ;; XXX: Check how to make all tests enabled, probably some more inner
@@ -3850,7 +3850,12 @@ (define-public python-roman-datamodels
      (list #:test-flags #~(list "-k"
                                 (string-append "not test_will_validate"
                                  " and not test_will_strict_validate"
-                                 " and not test_nuke_validation"))))
+                                 " and not test_nuke_validation"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-env
+            (lambda _
+              (setenv "HOME" "/tmp"))))))
     (propagated-inputs (list python-asdf
                              python-asdf-astropy
                              python-asdf-standard
@@ -3859,8 +3864,10 @@ (define-public python-roman-datamodels
                              python-numpy
                              python-psutil
                              python-rad))
-    (native-inputs (list python-pytest python-pytest-doctestplus
-                         python-pytest-openfiles python-semantic-version
+    (native-inputs (list python-pytest
+                         python-pytest-doctestplus
+                         python-pytest-env
+                         python-semantic-version
                          python-setuptools-scm))
     (home-page "https://github.com/spacetelescope/roman_datamodels")
     (synopsis "Roman Datamodels Support")
-- 
2.41.0

Message #53 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 16/19] gnu: python-roman-datamodels: Remove all test
 constrains.
Date: Thu,  7 Sep 2023 23:32:24 +0100

* gnu/packages/astronomy.scm (python-roman-datamodels): Remove all test
constrains. All of 1115 passed.
---
 gnu/packages/astronomy.scm | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d1b34def8f..fb501e421c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3844,13 +3844,7 @@ (define-public python-roman-datamodels
                 "1y12cp8172i4a314gmhpi86jw6pfylz1adh0rzr5zqmvd3mrjqlj"))))
     (build-system pyproject-build-system)
     (arguments
-     ;; XXX: Check how to make all tests enabled, probably some more inner
-     ;; input chain needs to be upgraded, keep them disabled to make the build
-     ;; green.
-     (list #:test-flags #~(list "-k"
-                                (string-append "not test_will_validate"
-                                 " and not test_will_strict_validate"
-                                 " and not test_nuke_validation"))
+     (list
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'set-env
-- 
2.41.0

Message #56 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 17/19] gnu: python-stdatamodels: Update to 1.8.0.
Date: Thu,  7 Sep 2023 23:32:25 +0100

* gnu/packages/astronomy.scm (python-stdatamodels): Update to 1.8.0.
[propagated-inputs]: Remove python-jsonschema.
[native-inputs]: Remove python-pytest-openfiles.
---
 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 fb501e421c..783f328c4d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2526,13 +2526,13 @@ (define-public python-stcal
 (define-public python-stdatamodels
   (package
     (name "python-stdatamodels")
-    (version "1.7.1")
+    (version "1.8.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "stdatamodels" version))
               (sha256
                (base32
-                "0d7a27myl3xgri3z7yx26mr4dpqnlfhdh5i2ql2miwymi0mx3ij5"))))
+                "003h3f07aqf6s24ivwnps81n2h51k545b236s75l8ppvjrm45xfq"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2546,13 +2546,11 @@ (define-public python-stdatamodels
     (propagated-inputs (list python-asdf
                              python-asdf-astropy
                              python-astropy
-                             python-jsonschema
                              python-numpy
                              python-psutil))
     (native-inputs (list python-crds
                          python-pytest
                          python-pytest-doctestplus
-                         python-pytest-openfiles
                          python-scipy
                          python-semantic-version
                          python-setuptools-scm))
-- 
2.41.0

Message #59 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 18/19] gnu: python-astropy: Update to 5.3.3.
Date: Thu,  7 Sep 2023 23:32:26 +0100

* gnu/packages/astronomy.scm (python-astropy): Update to 5.3.3.
---
 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 783f328c4d..fc61baa92b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1353,13 +1353,13 @@ (define-public celestia-gtk
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "5.3.1")
+    (version "5.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "0x4dh7wx9sn1gy6sl2d54zsd24cgfjwrlk6kfrwpzzrmbsv22lwv"))
+        (base32 "1fwk7x4q1hgdf9m8q613c6q7045sam1g934vgqv588ksbngxyc03"))
        (modules '((guix build utils)))
        (snippet
         '(begin
-- 
2.41.0

Message #62 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 19/19] gnu: python-tslearn: Update to 0.6.2.
Date: Thu,  7 Sep 2023 23:32:27 +0100

* gnu/packages/machine-learning.scm (python-tslearn): Update to 0.6.2.
---
 gnu/packages/machine-learning.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 712abe9aff..e10d3ea056 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1488,7 +1488,7 @@ (define-public python-threadpoolctl
 (define-public python-tslearn
   (package
     (name "python-tslearn")
-    (version "0.6.1")
+    (version "0.6.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1497,7 +1497,7 @@ (define-public python-tslearn
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1fhs8c28hdqsyj8kdhzrmrxrh4w92x6nf3gm026xapp9divvljd6"))))
+                "0l9l21jy78mhajdfwyx8rskw08597vg55ff22bjkv6xrjjr9g4ac"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #65 received at 65814 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 65814 <at> debbugs.gnu.org
Cc: Tobias Geerinckx-Rice <me <at> tobias.gr>
Date: Mon, 18 Sep 2023 19:20:20 +0100

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

Hi,

A gentle ping on this issue, please, let me know if I need to change
anything.

Thanks,
Oleg

[Message part 2 (text/html, inline)]

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

From: Christopher Baines <mail <at> cbaines.net>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: 65814 <at> debbugs.gnu.org, Andreas Enge <andreas <at> enge.fr>,
 Efraim Flashner <efraim <at> flashner.co.il>, guix-patches <at> gnu.org,
 Eric Bavier <bavier <at> posteo.net>
Subject: Re: [bug#65814] [PATCH 09/19] gnu: python-crds: Update to 11.17.4.
Date: Wed, 27 Sep 2023 11:51:13 +0100

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

Sharlatan Hellseher <sharlatanus <at> gmail.com> writes:

> * gnu/packages/astronomy.scm (python-crds): Update to 11.17.4.
> ---
>  gnu/packages/astronomy.scm | 5 ++---
>  1 file changed, 2 insertions(+), 3 deletions(-)
>
> diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
> index 453571325f..cf524a2f6c 100644
> --- a/gnu/packages/astronomy.scm
> +++ b/gnu/packages/astronomy.scm
> @@ -1692,13 +1692,13 @@ (define-public python-cdflib
>  (define-public python-crds
>    (package
>      (name "python-crds")
> -    (version "11.17.0")
> +    (version "11.17.4")
>      (source (origin
>                (method url-fetch)
>                (uri (pypi-uri "crds" version))
>                (sha256
>                 (base32
> -                "0sdz1k4hrgrc2jwihp9ns7lx23kcz7f90c222q7aaqf9g3vvpqlr"))))
> +                "0bk6cyd2il7ibqwky6m5kkgs9shrlzyfpnp2rh9jx0xa9habf7zm"))))
>      (build-system pyproject-build-system)
>      (arguments
>       (list
> @@ -1710,7 +1710,6 @@ (define-public python-crds
>                               python-astropy
>                               python-boto3
>                               python-filelock
> -                             python-lxml
>                               python-numpy
>                               python-parsley
>                               python-pysynphot

This change, assuming it's intentional can be mentioned in the commit
message changelog like:

[propagated-inputs]: Remove python-lxml.

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

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

From: Christopher Baines <mail <at> cbaines.net>
To: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Cc: 65814-done <at> debbugs.gnu.org, guix-patches <at> gnu.org
Subject: Re: [bug#65814] [PATCH 00/19] gnu: Astronomy 2023/08 updates.
Date: Wed, 27 Sep 2023 12:42:07 +0100

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

Sharlatan Hellseher <sharlatanus <at> gmail.com> writes:

> Hi Guix!
>
> Easy to win not breaking patch series which updates and improve some
> Astronomy related packages. python-tslearn is updated as well to fix build
> after python-astropy update.

I think there were some preexisting problems around these packages on
the bordeaux build farm, but I think that's been worked around for
x86_64-linux at least now. Most of the packages involved in this patch
series are still blocked for other systems though.

The changes look good to me and I've pushed these patches to master as
105113f241f5814759d4ff4c7b95376f8b8d450d.

Thanks,

Chris

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

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