GNU bug report logs - #66778
[PATCH 00/19] gnu: Astronomy 2023/10 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 2023/10 updates.
Date: Fri, 27 Oct 2023 23:08:49 +0100

Hi Guix,

Please review October's patch series updating and improving packages related
to (gnu packages astronomy).

Patch series was built without issues and did not introduce regression for
dependent packages.

./pre-inst-env guix build --rounds=2 erfa glnemo2 imppg libxisf python-asdf python-astroalign python-astropy python-cdflib python-crds python-ephem python-jwst python-pyerfa python-pynbody python-pytest-astropy python-pytest-doctestplus python-pytest-remotedata python-spherical-geometry

/gnu/store/3yh8r1vxrlnqs008ma5424yaacp0r0d3-python-spherical-geometry-1.2.22
/gnu/store/s04bn2j8kq71a0vmip763an7cxic9642-python-pytest-remotedata-0.4.1
/gnu/store/k22abqi9lzyfpv0cppzcl8gbgbas1pzq-python-pytest-doctestplus-1.0.0
/gnu/store/is5amhbdchfwgr8937p0cni7g1rbd71a-python-pytest-astropy-0.11.0
/gnu/store/daqa4jcszyxv09g2wrvgir9pz3vdj7xj-python-pynbody-1.4.1
/gnu/store/vlv5q4f28an5valrjc0ikinskpbiqy6r-python-pyerfa-2.0.1.1
/gnu/store/6b2f0646f6hppqjfldhnrqpxm1sn9anc-python-jwst-1.12.5
/gnu/store/pi1iw8fchz4lygjq0kfrn98crz81mwi2-python-ephem-4.1.5
/gnu/store/a3qfyskrf0y5kisj8igvxc7g5a3531fr-python-crds-11.17.7
/gnu/store/wwih8y7vxlzmj7pgy71rfqldm8hhcpkw-python-cdflib-1.2.3
/gnu/store/4iyzv925fvgzmb26fhm7d655dar81x6d-python-astropy-5.3.4
/gnu/store/2wnw8y49l6addfcwrhbq10040dgv1k2y-python-astroalign-2.5.0
/gnu/store/17fwh5dagk576brmyih01r2awf3hzsa6-python-asdf-3.0.0
/gnu/store/ij7xzk0077p7g2kx92ys7xazqb8rp4zg-libxisf-0.2.10
/gnu/store/sn3z4kxsxdf57iljwmdyd3z789gafqgg-imppg-0.6.5
/gnu/store/a9a2nchr6raf1715ak36vqjjz4hk3s0q-glnemo2-1.21.0
/gnu/store/5jw73r8vinkfgakcyqx8d4drqpg9v81z-erfa-2.0.1

./pre-inst-env guix build $(./pre-inst-env guix refresh --list-dependent erfa glnemo2 imppg libxisf python-asdf python-astroalign python-astropy python-cdflib python-crds python-ephem python-jwst python-pyerfa python-pynbody python-pytest-astropy python-pytest-doctestplus python-pytest-remotedata python-spherical-geometry |awk -F: '{print $2}')

/gnu/store/6b2f0646f6hppqjfldhnrqpxm1sn9anc-python-jwst-1.12.5
/gnu/store/wcb81q01y8d1qlmvwlsad3x7sjzl7yj8-beets-bandcamp-0.1.4
/gnu/store/p5hcj2glkjbjfwh67330r6nnaz1v5aka-emacs-calibredb-2.12.0
/gnu/store/a7b6srwgixrwl4842r2snh4j6dfvlngk-python-sunpy-5.0.1
/gnu/store/2wnw8y49l6addfcwrhbq10040dgv1k2y-python-astroalign-2.5.0
/gnu/store/rwsay49d8a6zbrvkl9mir110qwk1lqbr-python-tslearn-0.6.2
/gnu/store/6f1gviws0sxjyxzgy0a7dz1zhy9ac9k7-python-regions-0.7
/gnu/store/wkxqrwzb1hh7qhl5gxh1nj8p68wziv2f-python-poliastro-0.17.0
/gnu/store/17fwh5dagk576brmyih01r2awf3hzsa6-python-asdf-3.0.0
/gnu/store/5najcxfg77ap8hnnv3lkqlzhk58brzp5-python-casa-formats-io-0.2.1
/gnu/store/7za8zq0ip3admdyzj2ry1fkwr47rzm1g-python-pytorch-lightning-2.0.2
/gnu/store/fig4v3b0y0awbg3rhfa6wiwzhyqaw74i-julia-astrotime-0.7.0

Sharlatan Hellseher (19):
  gnu: glnemo2: Fix home-page.
  gnu: imppg: Use standard configure phase.
  gnu: python-spherical-geometry: Simplify package.
  gnu: python-spherical-geometry: Enable tests.
  gnu: python-pynbody: Update to 1.4.1.
  gnu: python-cdflib: Update to 1.2.2.
  gnu: python-astroalign: Update to 2.5.0.
  gnu: erfa: Update to 2.0.1.
  gnu: python-pyerfa: Update to 2.0.1.1.
  gnu: libxisf: Update to 0.2.10.
  gnu: python-astropy: Update to 5.3.4.
  gnu: python-cdflib: Update to 1.2.3.
  gnu: python-crds: Update to 11.17.7.
  gnu: python-ephem: Update to 4.1.5.
  gnu: python-jwst: Update to 1.12.5.
  gnu: python-pytest-remotedata: Update to 0.4.1.
  gnu: python-pytest-doctestplus: Update to 1.0.0.
  gnu: python-pytest-astropy: Update to 0.11.0.
  gnu: python-asdf: Update to 3.0.0.

 gnu/packages/astronomy.scm    | 142 +++++++++++++++++++---------------
 gnu/packages/python-check.scm |  12 +--
 2 files changed, 85 insertions(+), 69 deletions(-)


base-commit: 50f514762bf35b029eb89518c5ab5b3d1bf27f48
-- 
2.41.0

Message #8 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 01/19] gnu: glnemo2: Fix home-page.
Date: Fri, 27 Oct 2023 23:14:44 +0100

* gnu/packages/astronomy.scm (glnemo2): Fix home-page to point to actual
project's one.
---
 gnu/packages/astronomy.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 764a674a6d..0eaa734e84 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -869,7 +869,7 @@ (define-public glnemo2
            libtirpc
            qtbase-5
            zlib))
-    (home-page "https://projets.lam.fr/projects/unsio/wiki")
+    (home-page "https://projets.lam.fr/projects/glnemo2/wiki/Wiki")
     (synopsis "3D interactive visualization program for n-body like particles")
     (description
      "GLNEMO2 is an interactive 3D visualization program which displays
-- 
2.41.0

Message #11 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 02/19] gnu: imppg: Use standard configure phase.
Date: Fri, 27 Oct 2023 23:14:45 +0100

* gnu/packages/astronomy.scm (imppg): Use G-expressions.
[arguments]{phases}: Use 'configure standard phase instead of
replacement.
---
 gnu/packages/astronomy.scm | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 0eaa734e84..63b502be81 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3100,19 +3100,8 @@ (define-public imppg
         (base32 "0a6wb1a9adwd01dmy0r03xxp8iz9y7mvh30088ajilhj4lf90vxa"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f                      ;no test provided
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'configure
-           (lambda* (#:key outputs #:allow-other-keys)
-             (mkdir-p "build")
-             (chdir "build")
-             (invoke
-              "cmake"
-              "-G" "Unix Makefiles"
-              "-DCMAKE_BUILD_TYPE=Release"
-              (string-append "-DCMAKE_INSTALL_PREFIX=" (assoc-ref outputs "out"))
-              ".."))))))
+     (list ;; No test provided
+      #:tests? #f))
     (native-inputs
      (list boost pkg-config))
     (inputs
-- 
2.41.0

Message #14 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 03/19] gnu: python-spherical-geometry: Simplify package.
Date: Fri, 27 Oct 2023 23:14:46 +0100

* gnu/packages/astronomy.scm (python-spherical-geometry):
[arguments]{phases}<preparations>: Switch to
SETUPTOOLS_SCM_PRETEND_VERSION evnar instead modifying setup.py.
---
 gnu/packages/astronomy.scm | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 63b502be81..18cf562e12 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2480,12 +2480,7 @@ (define-public python-spherical-geometry
       #~(modify-phases %standard-phases
           (add-after 'unpack 'preparations
             (lambda _
-              ;; Fixing: setuptools-scm was unable to detect version for ...
-              (substitute* "setup.py"
-                (("use_scm_version=True")
-                 (format #f "version=~s" #$version))
-                (("setup_requires=\\['setuptools_scm'\\],.*")
-                 ""))
+              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
               ;; Use our own libraries in place of bundles.
               (setenv "USE_SYSTEM_QD" "1"))))))
     (native-inputs
-- 
2.41.0

Message #17 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 04/19] gnu: python-spherical-geometry: Enable tests.
Date: Fri, 27 Oct 2023 23:14:47 +0100

* gnu/packages/astronomy.scm (python-spherical-geometry): Enable tests.
[build-system]: Switch to pyproject-build-system.
[arguments]{phases}: Add 'build-extensions phase.
---
 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 18cf562e12..3b85d4ec9e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2470,19 +2470,22 @@ (define-public python-spherical-geometry
        (file-name (git-file-name name version))
        (sha256
         (base32 "0kzcncqir4v7nhk9lxj9gxr32p3krkaqa58y2i4kksgxxy24qw4z"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list
-      ;; NOTE: (Sharlatan-20220523T231348+0100): Tests depends on old Python2
-      ;; libarry `sphere'
-      #:tests? #f
+      ;; XXX: Disable one failing test
+      ;; See https://github.com/spacetelescope/spherical_geometry/issues/252
+      #:test-flags #~(list "-k" "not test_overlap")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'preparations
             (lambda _
               (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
               ;; Use our own libraries in place of bundles.
-              (setenv "USE_SYSTEM_QD" "1"))))))
+              (setenv "USE_SYSTEM_QD" "1")))
+          (add-before 'check 'build-extensions
+            (lambda _
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest
            python-setuptools-scm))
-- 
2.41.0

Message #20 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 05/19] gnu: python-pynbody: Update to 1.4.1.
Date: Fri, 27 Oct 2023 23:14:48 +0100

* gnu/packages/astronomy.scm (python-pynbody): Update to 1.4.1.
[source]: Switch to git-fetch.
---
 gnu/packages/astronomy.scm | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 3b85d4ec9e..9cdf264389 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3403,13 +3403,21 @@ (define-public python-pyerfa
 (define-public python-pynbody
   (package
     (name "python-pynbody")
-    (version "1.3.1")
+    (version "1.4.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "pynbody" version))
+       (method git-fetch) ;PyPi doesn't have not prebuit version.
+       (uri (git-reference
+             (url "https://github.com/pynbody/pynbody")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1yp7ja66zqmbnh7bbwbyimxq1nkrmjrcif2rzfm1hswm0fp2fbga"))))
+        (base32 "1vl1yif3bsazcil6saghrpa4qsg47fnr7xnkjpqnp44b7ipww27r"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Symlink goes to not existing directory.
+        #~(for-each delete-file '("docs/testdata"
+                                  "docs/tutorials/example_code/testdata")))))
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags #~(list
-- 
2.41.0

Message #23 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 06/19] gnu: python-cdflib: Update to 1.2.2.
Date: Fri, 27 Oct 2023 23:14:49 +0100

* gnu/packages/astronomy.scm (python-cdflib): Update to 1.2.2.
---
 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 9cdf264389..26de338752 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1730,7 +1730,7 @@ (define-public python-ccdproc
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method git-fetch)   ; no tests in pypi archive
@@ -1739,7 +1739,7 @@ (define-public python-cdflib
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0v73fl69pxbk52ilhj2593zmn3qhqy4hrrwby8m9z2sq3fd5xk0v"))))
+        (base32 "0ri3bqammmf0a9j9y6p4vym63ibgz8fsa0n46al9jv8iwfbs7bp7"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases
-- 
2.41.0

Message #26 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 07/19] gnu: python-astroalign: Update to 2.5.0.
Date: Fri, 27 Oct 2023 23:14:50 +0100

* gnu/packages/astronomy.scm (python-astroalign): Update to 2.5.0.
---
 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 26de338752..249ef80afb 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3997,7 +3997,7 @@ (define-public python-roman-datamodels
 (define-public python-astroalign
   (package
     (name "python-astroalign")
-    (version "2.4.2")
+    (version "2.5.0")
     (source
      (origin
        ;; There are no tests in the PyPI tarball.
@@ -4007,7 +4007,7 @@ (define-public python-astroalign
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0hly20a65540hr3l1lsd1i4d90a0vdrbwnn6zx3z8s89ha9lq3pb"))))
+        (base32 "0br1v2l48jx214a1bcdr8wz1wggcswcbz4cqv8d19fd46fc4qlhy"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-astropy
-- 
2.41.0

Message #29 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 08/19] gnu: erfa: Update to 2.0.1.
Date: Fri, 27 Oct 2023 23:14:51 +0100

* gnu/packages/astronomy.scm (erfa): Update to 2.0.1.
---
 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 249ef80afb..bc44f3cbab 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -649,7 +649,7 @@ (define-public qfits
 (define-public erfa
   (package
     (name "erfa")
-    (version "2.0.0")
+    (version "2.0.1")
     (source
      (origin
        (method git-fetch)
@@ -658,7 +658,7 @@ (define-public erfa
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0s9dpj0jdkqcg552f00jhd722czji4pffabmpys5pgi6djckq4f4"))))
+        (base32 "1hxjbcvdlq4871r17fphbaf3bd8dsjagp1rdb3j8v6kr4f1dil9n"))))
     (build-system gnu-build-system)
     (native-inputs
      (list automake autoconf libtool pkg-config))
-- 
2.41.0

Message #32 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 09/19] gnu: python-pyerfa: Update to 2.0.1.1.
Date: Fri, 27 Oct 2023 23:14:52 +0100

* gnu/packages/astronomy.scm (python-pyerfa): Update to 2.0.1.1.
---
 gnu/packages/astronomy.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index bc44f3cbab..bd146afd3c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3358,13 +3358,13 @@ (define-public python-jwst
 (define-public python-pyerfa
   (package
     (name "python-pyerfa")
-    (version "2.0.0.3")
+    (version "2.0.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyerfa" version))
        (sha256
-        (base32 "0f8zykzxjsiwv5ibdn5asla2ng2xl0xdkrcrrd61j31mb3xbnzyp"))
+        (base32 "0swsdkipnk73iflsa7qbaw89wahbnfyvplqaxwi0yfrxippp9b6v"))
        (modules '((guix build utils)))
        (snippet
         #~(begin
@@ -3375,6 +3375,7 @@ (define-public python-pyerfa
      (list
       ;; Disable only one failing test:
       ;; AttributeError: __warningregistry__
+      ;; See https://github.com/liberfa/pyerfa/issues/126
       #:test-flags #~(list "-k" "not test_errwarn_reporting")
       #:phases
       #~(modify-phases %standard-phases
-- 
2.41.0

Message #35 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 10/19] gnu: libxisf: Update to 0.2.10.
Date: Fri, 27 Oct 2023 23:14:53 +0100

* gnu/packages/astronomy.scm (libxisf): Update to 0.2.10.
---
 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 bd146afd3c..51053b1d58 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2892,7 +2892,7 @@ (define-public libpasastro
 (define-public libxisf
   (package
     (name "libxisf")
-    (version "0.2.9")
+    (version "0.2.10")
     (source
      (origin
        (method git-fetch)
@@ -2901,7 +2901,7 @@ (define-public libxisf
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "02cxv86h0ng4kmvyjkf7cr2ak2i3vpf0q0ik7jg4nmqjsidcs796"))))
+        (base32 "0q5qipn8887yhrk9pmi4fksxxmqas3w2aw2p194yhzkjapxk2k9h"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags #~(list "-DUSE_BUNDLED_LIBS=OFF")))
-- 
2.41.0

Message #38 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 11/19] gnu: python-astropy: Update to 5.3.4.
Date: Fri, 27 Oct 2023 23:14:54 +0100

* gnu/packages/astronomy.scm (python-astropy): Update to 5.3.4.
[arguments]{phases}: Disable one failing test, reported upstream.
---
 gnu/packages/astronomy.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 51053b1d58..937da94b03 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1412,13 +1412,13 @@ (define-public celestia-gtk
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "5.3.3")
+    (version "5.3.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "1fwk7x4q1hgdf9m8q613c6q7045sam1g934vgqv588ksbngxyc03"))
+        (base32 "1n7iwvjari4xv37094cpiapmjhhm57b04hi4r40wqb5czbigg46l"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -1473,7 +1473,9 @@ (define-public python-astropy
                              "not remote_data"
                              ;; XXX: Check why this tests failing.
                              " and not test_ignore_sigint"
-                             " and not test_parquet_filter"))))))))
+                             " and not test_parquet_filter"
+                             ;; See https://github.com/astropy/astropy/issues/15537
+                             " and not test_pvstar"))))))))
     (native-inputs
      (list pkg-config
            python-colorlog
-- 
2.41.0

Message #41 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 13/19] gnu: python-crds: Update to 11.17.7.
Date: Fri, 27 Oct 2023 23:14:56 +0100

* gnu/packages/astronomy.scm (python-crds): Update to 11.17.7.
---
 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 f19c5dfbdd..b9bff73a35 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1781,13 +1781,13 @@ (define-public python-cdflib
 (define-public python-crds
   (package
     (name "python-crds")
-    (version "11.17.6")
+    (version "11.17.7")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "crds" version))
               (sha256
                (base32
-                "1sbfl45rx21g622vm8baqv0ydcdixf1jdjgydn07sxl7kn15fa4g"))))
+                "10cxhb1xss21p992bfd5jm8bix1n12h0fd8m5sp6bcsgn6zs94v0"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #44 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 14/19] gnu: python-ephem: Update to 4.1.5.
Date: Fri, 27 Oct 2023 23:14:57 +0100

* gnu/packages/astronomy.scm (python-ephem): Update to 4.1.5.
---
 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 b9bff73a35..e18d86f191 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1942,13 +1942,13 @@ (define-public python-drizzle
 (define-public python-ephem
   (package
     (name "python-ephem")
-    (version "4.1.4")
+    (version "4.1.5")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ephem" version))
               (sha256
                (base32
-                "0q67z79lgwdylxagbsjm42xvsmk5jmgvghy36m2n5lb2446rz9bk"))))
+                "0ainqbnvw320pc61q5b6ad6f2mhn1pvrlnq489cwfx0m82mahr0c"))))
     (build-system python-build-system)
     (native-inputs (list tzdata))
     (home-page "https://rhodesmill.org/pyephem/")
-- 
2.41.0

Message #47 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 15/19] gnu: python-jwst: Update to 1.12.5.
Date: Fri, 27 Oct 2023 23:14:58 +0100

* gnu/packages/astronomy.scm (python-jwst): Update to 1.12.5.
---
 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 e18d86f191..c5a6f59e87 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3293,13 +3293,13 @@ (define-public python-jplephem
 (define-public python-jwst
   (package
     (name "python-jwst")
-    (version "1.12.3")
+    (version "1.12.5")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "jwst" version))
               (sha256
                (base32
-                "0bw7i0pmpdgk2zf47d57g45hm3yb4wbrf1p19z9vg555qv4f4kr5"))))
+                "0blrl00lz1snhcnr7j59nh05rnpqxdnfp8hhgagkr50h85q4smrn"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #50 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 12/19] gnu: python-cdflib: Update to 1.2.3.
Date: Fri, 27 Oct 2023 23:14:55 +0100

* gnu/packages/astronomy.scm (python-cdflib): Update to 1.2.3.
---
 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 937da94b03..f19c5dfbdd 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1732,7 +1732,7 @@ (define-public python-ccdproc
 (define-public python-cdflib
   (package
     (name "python-cdflib")
-    (version "1.2.2")
+    (version "1.2.3")
     (source
      (origin
        (method git-fetch)   ; no tests in pypi archive
@@ -1741,7 +1741,7 @@ (define-public python-cdflib
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0ri3bqammmf0a9j9y6p4vym63ibgz8fsa0n46al9jv8iwfbs7bp7"))))
+        (base32 "0vpgcbc9pmx0qqfia1frnwq3jkgfp8y3ikqdnzs5bs1sr13p9p3w"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:phases
-- 
2.41.0

Message #53 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 16/19] gnu: python-pytest-remotedata: Update to 0.4.1.
Date: Fri, 27 Oct 2023 23:14:59 +0100

* gnu/packages/python-check (python-pytest-remotedata): Update to 0.4.1.
---
 gnu/packages/python-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 0ccae07093..ef1db87102 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -735,13 +735,13 @@ (define-public python-pytest-openfiles
 (define-public python-pytest-remotedata
   (package
     (name "python-pytest-remotedata")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-remotedata" version))
        (sha256
-        (base32 "1j5106j331cfdyfcwzrbs3yby84mq1b0kddfysq12z2dwdcca8dy"))))
+        (base32 "0ndvnj9zghfj17haphrygiri9iy38wb8lwq1xdkfvlfd73v8ph05"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.41.0

Message #56 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 17/19] gnu: python-pytest-doctestplus: Update to 1.0.0.
Date: Fri, 27 Oct 2023 23:15:00 +0100

* gnu/packages/python-check (python-pytest-doctestplus): Update to 1.0.0.
---
 gnu/packages/python-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index ef1db87102..9dafae0d67 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -568,13 +568,13 @@ (define-public python-pytest-arraydiff
 (define-public python-pytest-doctestplus
   (package
     (name "python-pytest-doctestplus")
-    (version "0.12.1")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-doctestplus" version))
        (sha256
-        (base32 "10ciqylgziihxwxryxvxgmkqgws51pqcarn0gbh1d4cxx55rx5vs"))))
+        (base32 "17ylfnrcvvp6sd13bfj40jl40paqmjsbywysszb3xqgdr86l8l7n"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags
-- 
2.41.0

Message #59 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 18/19] gnu: python-pytest-astropy: Update to 0.11.0.
Date: Fri, 27 Oct 2023 23:15:01 +0100

* gnu/packages/python-check (python-pytest-astropy): Update to 0.11.0.
---
 gnu/packages/python-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 9dafae0d67..4e955d2528 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -510,13 +510,13 @@ (define-public python-pytest-astropy-header
 (define-public python-pytest-astropy
   (package
     (name "python-pytest-astropy")
-    (version "0.10.0")
+    (version "0.11.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-astropy" version))
        (sha256
-        (base32 "04g2rh261s3s6ym8mwi4iv2a6anbgwvwzcvkyilfck6yxrncdqw5"))))
+        (base32 "1d9rcxnc57rjp96xag1gq725pwl11b3k5hdaz7c3w5lixncsmbjf"))))
     (build-system python-build-system)
     (arguments (list #:tests? #f)) ; there are no tests
     (native-inputs
-- 
2.41.0

Message #62 received at 66778 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 66778 <at> debbugs.gnu.org
Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Subject: [PATCH 19/19] gnu: python-asdf: Update to 3.0.0.
Date: Fri, 27 Oct 2023 23:15:02 +0100

* gnu/packages/astronomy.scm (python-asdf-3.0): New variable, migrated
from python-asdf.
[arguments]: Move it from here ...
[native-inputs]: Remove python-astronomy, python-pytest-openfiles.
[propagated-inputs]: Add python-attrs. Remove
python-importlib-resources, python-jsonschema.

(python-asdf-2.15): New variable. Inherited from python-asdf-3.0.
[arguments]: ... to here.

(python-asdf): Set it to use python-asdf-2.15 as 3.0.0 includes some
breaking changes which may not testes in dependent projects.
---
 gnu/packages/astronomy.scm | 48 ++++++++++++++++++++++++++------------
 1 file changed, 33 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c5a6f59e87..ea69ad6542 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3598,32 +3598,23 @@ (define-public python-tweakwcs
 @code{FITS WCS} and @code{JWST gWCS} are supported.")
     (license license:bsd-3)))
 
-(define-public python-asdf
+(define-public python-asdf-3.0
   (package
     (name "python-asdf")
-    (version "2.15.0")
+    (version "3.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf" version))
        (sha256
-        (base32 "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8"))))
+        (base32 "1a6lf75q9w8fsyq3hn6a7fyldkkyqxddlq21fwdfjwij40dzh3s8"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list #:test-flags
-           #~(list "-k" (string-append
-                         "not test_overwrite"
-                         " and not test_tagging_scalars"
-                         " and not test_info_command"
-                         " and not test_array_inline_threshold_recursive"))))
     (native-inputs
-     (list python-astropy
-           python-fsspec
+     (list python-fsspec
            python-packaging
            python-psutil
            python-pytest
            python-pytest-doctestplus
-           python-pytest-openfiles
            python-pytest-remotedata
            python-semantic-version
            python-setuptools-scm))
@@ -3631,10 +3622,9 @@ (define-public python-asdf
      (list python-asdf-standard
            python-asdf-transform-schemas
            python-asdf-unit-schemas
+           python-attrs ;; for vendorized jsonschema
            python-importlib-metadata
-           python-importlib-resources
            python-jmespath
-           python-jsonschema
            python-lz4
            python-numpy
            python-pyyaml))
@@ -3646,6 +3636,34 @@ (define-public python-asdf
 implementation of the ASDF Standard.")
     (license license:bsd-3)))
 
+(define-public python-asdf-2.15
+  (package
+    (inherit python-asdf-3.0)
+    (version "2.15.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "asdf" version))
+       (sha256
+        (base32 "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8"))))
+    (arguments
+     (list #:test-flags
+           #~(list "-k" (string-append
+                         "not test_overwrite"
+                         " and not test_tagging_scalars"
+                         " and not test_info_command"
+                         " and not test_array_inline_threshold_recursive"))))
+    (native-inputs
+     (modify-inputs (package-native-inputs python-asdf-3.0)
+       (prepend python-astropy python-pytest-openfiles)))
+    (propagated-inputs
+     (modify-inputs (package-propagated-inputs python-asdf-3.0)
+       (prepend python-jsonschema python-importlib-resources)))))
+
+(define-public python-asdf
+  ;; Default version of ASDF..
+  python-asdf-2.15)
+
 (define-public python-asdf-standard
   (package
     (name "python-asdf-standard")
-- 
2.41.0

Message #65 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: Andreas Enge <andreas <at> enge.fr>, Eric Bavier <bavier <at> posteo.net>,
 Efraim Flashner <efraim <at> flashner.co.il>, guix-patches <at> gnu.org,
 66778-done <at> debbugs.gnu.org
Subject: Re: [bug#66778] [PATCH 00/19] gnu: Astronomy 2023/10 updates.
Date: Sun, 05 Nov 2023 18:29:15 +0000

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

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

> Hi Guix,
>
> Please review October's patch series updating and improving packages related
> to (gnu packages astronomy).

...

> Sharlatan Hellseher (19):
>   gnu: glnemo2: Fix home-page.
>   gnu: imppg: Use standard configure phase.
>   gnu: python-spherical-geometry: Simplify package.
>   gnu: python-spherical-geometry: Enable tests.
>   gnu: python-pynbody: Update to 1.4.1.
>   gnu: python-cdflib: Update to 1.2.2.
>   gnu: python-astroalign: Update to 2.5.0.
>   gnu: erfa: Update to 2.0.1.
>   gnu: python-pyerfa: Update to 2.0.1.1.
>   gnu: libxisf: Update to 0.2.10.
>   gnu: python-astropy: Update to 5.3.4.
>   gnu: python-cdflib: Update to 1.2.3.
>   gnu: python-crds: Update to 11.17.7.
>   gnu: python-ephem: Update to 4.1.5.
>   gnu: python-jwst: Update to 1.12.5.
>   gnu: python-pytest-remotedata: Update to 0.4.1.
>   gnu: python-pytest-doctestplus: Update to 1.0.0.
>   gnu: python-pytest-astropy: Update to 0.11.0.
>   gnu: python-asdf: Update to 3.0.0.
>
>  gnu/packages/astronomy.scm    | 142 +++++++++++++++++++---------------
>  gnu/packages/python-check.scm |  12 +--
>  2 files changed, 85 insertions(+), 69 deletions(-)
>
>
> base-commit: 50f514762bf35b029eb89518c5ab5b3d1bf27f48

These look good to me, I've pushed them to master as
7995a474eab286a0eb05b065716ecd026a681d56.

Thanks,

Chris

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