[bug#63542] [PATCH 00/19]: gnu: astronomy: May updates.

[bug#63542] [PATCH 00/19]: gnu: astronomy: May updates.

[Sharlatan Hellseher]

Hi Guix!

After core-update was merged and some issues with main packages related to
astronomy was fixed there is a time to update rest of them.

Here I've updated astronomical Python packages and simplify packaging (used
Gexps or pyproject-build-system). I'd like to add all of my pending packages
in the nearest future, I hope it will be useful for community.

> ./pre-inst-env guix build $(./pre-inst-env guix refresh --list-dependent python-asdf-astropy python-gwcs python-sunpy python-spherical-geometry python-sgp4 python-ccdproc python-reproject python-pyvo python-fitsio python-astropy-healpix python-astroquery python-pynbody python-astral python-poppy python-photutils python-ephem python-asdf | awk -F: '{print $2}')
> /gnu/store/da3yv8v7gxcar4abmhkg1vlh6nrizqq6-python-sunpy-4.1.5
> /gnu/store/adg4dm7x0m7jcc9l85b85q2hpsyl0rvg-python-astroalign-2.4.2
> /gnu/store/16mdzw3xfqcd0x4nbs648way1z6psky6-python-poliastro-0.17.0
> /gnu/store/h709xxp1zn0mdv9p23g1c7r80k5vsg38-python-spherical-geometry-1.2.22
> /gnu/store/ksmy9f2n633f52qp929wldhlisms8jfg-python-poppy-1.1.1
> /gnu/store/r12mnqg0yx1gy0zrmbr95gy719rxj4w1-python-regions-0.7
> /gnu/store/493halkqfx3dz8jrc51211n3yfxswxm3-python-photutils-1.7.0

Sharlatan Hellseher (19):
  gnu: python-asdf-astropy: Update to 0.4.0.
  gnu: python-asdf-wcs-schemas: Symplify.
  gnu: python-gwcs: Update to 0.18.3.
  gnu: python-sunpy: Update to 4.1.5.
  gnu: python-spherical-geometry: Add update note.
  gnu: python-sgp4: Update to 2.22.
  gnu: python-ccdproc: Enable tests.
  gnu: python-reproject: Update to 0.10.0.
  gnu: python-pyvo: Update to 1.4.1.
  gnu: python-fitsio: Use Gexp.
  gnu: python-astropy-healpix: Use Gexp.
  gnu: python-astroquery: Use Gexp.
  gnu: python-pynbody: Update to 1.3.1, simplify.
  gnu: python-astral: Update to 3.2.
  gnu: python-poppy: Update to 1.1.1.
  gnu: python-photutils: Update to 1.7.0.
  gnu: python-ephem: Update to 4.1.4.
  gnu: python-asdf: Update to 2.15.0.
  gnu: python-asdf-coordinates-schemas: Update to 0.2.0.

 gnu/packages/astronomy.scm | 366 ++++++++++++++++++-------------------
 1 file changed, 182 insertions(+), 184 deletions(-)


base-commit: 242cc93438d67f5b35602d5add02e230850b0b43
-- 
2.39.2

[bug#63542] [PATCH 01/19] gnu: python-asdf-astropy: Update to 0.4.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.4.0.
[arguments]: Add pre check phase.
[native-inputs]: Remove python-matplotlib.
---
 gnu/packages/astronomy.scm | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9bc790ef4b..e180a2f81a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2974,18 +2974,23 @@ (define python-asdf-unit-schemas
 (define-public python-asdf-astropy
   (package
     (name "python-asdf-astropy")
-    (version "0.3.0")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "asdf_astropy" version))
+       (uri (pypi-uri "asdf-astropy" version))
        (sha256
-        (base32 "1gp5iav0a9g9q0zb22vhzi3v9vwk5wn2nxvr3mvi3bsdcdj3h23v"))))
+        (base32 "1difb2y1hlalbhrw8znwmmc0vzgg44zfsay98lpllb7y0536fas6"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'set-home-env
+            (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-coverage
            python-h5py
-           python-matplotlib
            python-pandas
            python-pytest-astropy
            python-scipy
-- 
2.39.2

[bug#63542] [PATCH 02/19] gnu: python-asdf-wcs-schemas: Symplify.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-wcs-schemas): Symplify package.
[build-system]: Use pyproject-build-system.
---
 gnu/packages/astronomy.scm | 14 ++------------
 1 file changed, 2 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e180a2f81a..0d0e45a3b1 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3020,19 +3020,9 @@ (define python-asdf-wcs-schemas
        (uri (pypi-uri "asdf_wcs_schemas" version))
        (sha256
         (base32 "0khyab9mnf2lv755as8kwhk3lqqpd3f4291ny3b9yp3ik86fzhz1"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest")))))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest
-           python-setuptools-scm
-           python-semantic-version))
+     (list python-pytest python-setuptools-scm python-semantic-version))
     (propagated-inputs
      (list python-asdf))
     (home-page "https://github.com/asdf-format/asdf-wcs-schemas")
-- 
2.39.2

[bug#63542] [PATCH 03/19] gnu: python-gwcs: Update to 0.18.3.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-gwcs): Update to 0.18.3.
---
 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 0d0e45a3b1..5c07ff2c8d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3036,13 +3036,13 @@ (define python-asdf-wcs-schemas
 (define-public python-gwcs
   (package
     (name "python-gwcs")
-    (version "0.18.2")
+    (version "0.18.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "gwcs" version))
        (sha256
-        (base32 "0v9qcq6zl74d6s882s6xmas144jfalvll6va8rvrxmvpx4vqjzhg"))))
+        (base32 "0mgyk5mgmj242g8nl7glcj689vry3ncwf04b8q3hasjcc9bs0rm4"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-jsonschema
-- 
2.39.2

[bug#63542] [PATCH 04/19] gnu: python-sunpy: Update to 4.1.5.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sunpy): Update to 4.1.5, simplify
package.
[arguments]{test-flags}: Disable 2 failing tests.
[arguments]{phases}: Simplify prepare-test-environment by remove
redundant substitution.
[inputs]: Add opencv for OpenCV-Pyton support.
---
 gnu/packages/astronomy.scm | 31 ++++++++++---------------------
 1 file changed, 10 insertions(+), 21 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 5c07ff2c8d..10c435b00e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1885,16 +1885,21 @@ (define-public python-sgp4
 (define-public python-sunpy
   (package
     (name "python-sunpy")
-    (version "4.1.1")
+    (version "4.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sunpy" version))
        (sha256
-        (base32 "1h8dnsic96bxm5l278vk6jj5h4bh1b143fghsvv5rhigk137vysp"))))
+        (base32 "1j5g0ivsrc5ji9s7jc3kcbi2injfs3y31pm3priycljwcsxspkpm"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~(list "-k" (string-append
+                    ;; XXX: Failed: DID NOT RAISE <class 'ModuleNotFoundError'>
+                    "not test_main_nonexisting_module"
+                    " and not test_main_stdlib_module"))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'install 'writable-compiler
@@ -1902,24 +1907,7 @@ (define-public python-sunpy
               (make-file-writable "sunpy/_compiler.c")))
           (add-before 'check 'prepare-test-environment
             (lambda _
-              (setenv "HOME" "/tmp")
-              (make-file-writable "sunpy/_compiler.c")
-              ;; TODO: (Sharlatan-20221106T115800+0000): Review failing tests
-              (substitute* "sunpy/image/tests/test_transform.py"
-                (("def test_clipping") "def __off_test_clipping")
-                (("def test_nans") "def __off_test_nans")
-                (("def test_endian") "def __off_test_endian"))
-              (substitute* "sunpy/map/tests/test_mapbase.py"
-                (("def test_derotating_nonpurerotation_pcij")
-                 "def __off_test_derotating_nonpurerotation_pcij"))
-              (substitute* "sunpy/map/sources/tests/test_mdi_source.py"
-                (("def test_synoptic_source")
-                 "def __off_test_synoptic_source"))
-              (substitute* "sunpy/tests/tests/test_self_test.py"
-                (("def test_main_nonexisting_module")
-                 "def __off_test_main_nonexisting_module")
-                (("def test_main_stdlib_module")
-                 "def __off_test_main_stdlib_module")))))))
+              (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-aiohttp
            python-extension-helpers
@@ -1932,6 +1920,8 @@ (define-public python-sunpy
            python-pytest-mpl
            python-pytest-xdist
            python-setuptools-scm))
+    (inputs
+     (list opencv)) ; Includes OpenCV-Python
     (propagated-inputs
      (list parfive
            python-asdf
@@ -1950,7 +1940,6 @@ (define-public python-sunpy
            python-matplotlib
            python-mpl-animators
            python-numpy
-           ;; python-opencv-python ; not packed yet
            python-pandas
            python-reproject
            python-scikit-image
-- 
2.39.2

[bug#63542] [PATCH 04/19] gnu: python-sunpy: Update to 4.1.5.

[Vinicius Monego]

Em qua, 2023-05-17 às 00:23 +0100, Sharlatan Hellseher escreveu:
> * gnu/packages/astronomy.scm (python-sunpy): Update to 4.1.5,
> simplify
> package.
> [arguments]{test-flags}: Disable 2 failing tests.
> [arguments]{phases}: Simplify prepare-test-environment by remove
> redundant substitution.
> [inputs]: Add opencv for OpenCV-Pyton support.
> ---
>  gnu/packages/astronomy.scm | 31 ++++++++++---------------------
>  1 file changed, 10 insertions(+), 21 deletions(-)
> 
> diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
> index 5c07ff2c8d..10c435b00e 100644
> --- a/gnu/packages/astronomy.scm
> +++ b/gnu/packages/astronomy.scm
> @@ -1885,16 +1885,21 @@ (define-public python-sgp4
>  (define-public python-sunpy
>    (package
>      (name "python-sunpy")
> -    (version "4.1.1")
> +    (version "4.1.5")
>      (source
>       (origin
>         (method url-fetch)
>         (uri (pypi-uri "sunpy" version))
>         (sha256
> -        (base32
> "1h8dnsic96bxm5l278vk6jj5h4bh1b143fghsvv5rhigk137vysp"))))
> +        (base32
> "1j5g0ivsrc5ji9s7jc3kcbi2injfs3y31pm3priycljwcsxspkpm"))))
>      (build-system pyproject-build-system)
>      (arguments
>       (list
> +      #:test-flags
> +      #~(list "-k" (string-append
> +                    ;; XXX: Failed: DID NOT RAISE <class
> 'ModuleNotFoundError'>
> +                    "not test_main_nonexisting_module"
> +                    " and not test_main_stdlib_module"))
>        #:phases
>        #~(modify-phases %standard-phases
>            (add-before 'install 'writable-compiler
> @@ -1902,24 +1907,7 @@ (define-public python-sunpy
>                (make-file-writable "sunpy/_compiler.c")))
>            (add-before 'check 'prepare-test-environment
>              (lambda _
> -              (setenv "HOME" "/tmp")
> -              (make-file-writable "sunpy/_compiler.c")
> -              ;; TODO: (Sharlatan-20221106T115800+0000): Review
> failing tests
> -              (substitute* "sunpy/image/tests/test_transform.py"
> -                (("def test_clipping") "def __off_test_clipping")
> -                (("def test_nans") "def __off_test_nans")
> -                (("def test_endian") "def __off_test_endian"))
> -              (substitute* "sunpy/map/tests/test_mapbase.py"
> -                (("def test_derotating_nonpurerotation_pcij")
> -                 "def __off_test_derotating_nonpurerotation_pcij"))
> -              (substitute*
> "sunpy/map/sources/tests/test_mdi_source.py"
> -                (("def test_synoptic_source")
> -                 "def __off_test_synoptic_source"))
> -              (substitute* "sunpy/tests/tests/test_self_test.py"
> -                (("def test_main_nonexisting_module")
> -                 "def __off_test_main_nonexisting_module")
> -                (("def test_main_stdlib_module")
> -                 "def __off_test_main_stdlib_module")))))))
> +              (setenv "HOME" "/tmp"))))))
>      (native-inputs
>       (list python-aiohttp
>             python-extension-helpers
> @@ -1932,6 +1920,8 @@ (define-public python-sunpy
>             python-pytest-mpl
>             python-pytest-xdist
>             python-setuptools-scm))
> +    (inputs
> +     (list opencv)) ; Includes OpenCV-Python
> 

Judging from the SunPy source code on GitHub, OpenCV is only used for
one function (cv2_filter2d), a faster implementation of scipy's
convolve2d. In setup.cfg it is listed a test and docs dependency only.
To reduce size and breakage, IMO it shouldn't be an input. It seems to
be used only at runtime so it could be installed separately.

>      (propagated-inputs
>       (list parfive
>             python-asdf
> @@ -1950,7 +1940,6 @@ (define-public python-sunpy
>             python-matplotlib
>             python-mpl-animators
>             python-numpy
> -           ;; python-opencv-python ; not packed yet

The opencv package builds opencv-python (cv2 namespace), as mentioned
in the (inputs) comment, although it doesn't ship with the python-
prefix.

>             python-pandas
>             python-reproject
>             python-scikit-image

[...]

Vinicius

[bug#63542] [PATCH 05/19] gnu: python-spherical-geometry: Add update note.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-spherical-geometry): Package can't
be updated to the latest version due to an open issue in upstream where
system qb library is in use.
---
 gnu/packages/astronomy.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 10c435b00e..6288de3d19 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1988,6 +1988,8 @@ (define-public python-astral
 (define-public python-spherical-geometry
   (package
     (name "python-spherical-geometry")
+    ;; XXX: Can't be updated to the latest see:
+    ;; https://github.com/spacetelescope/spherical_geometry/issues/227
     (version "1.2.22")
     (source
      (origin
-- 
2.39.2

[bug#63542] [PATCH 06/19] gnu: python-sgp4: Update to 2.22.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sgp4): Update to 2.22.
---
 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 6288de3d19..6adf7c990e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1856,13 +1856,13 @@ (define-public python-reproject
 (define-public python-sgp4
   (package
     (name "python-sgp4")
-    (version "2.21")
+    (version "2.22")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sgp4" version))
        (sha256
-        (base32 "1vzcrlrlzmhbycdz16m8v241l8zx49vsy81wcd0yjxs80isvhyb1"))))
+        (base32 "1yc6gcbhz80i875j0wf6ikx7rzs0m7m1qp72dmdhdjidmpma5w0p"))))
     (build-system python-build-system)
     (propagated-inputs
      (list python-numpy))
-- 
2.39.2

[bug#63542] [PATCH 07/19] gnu: python-ccdproc: Enable tests.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ccdproc): Enable tests.
---
 gnu/packages/astronomy.scm | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6adf7c990e..b283cce222 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1370,11 +1370,6 @@ (define-public python-ccdproc
        (sha256
         (base32 "0fy1sni87cr05dkljd8wb7vgh7z9agh8wv5kiagxcpbcf8l06jv1"))))
     (build-system pyproject-build-system)
-    (arguments
-     ;; FIXME: Test failed a lot with: DeprecationWarning: distutils Version
-     ;; classes are deprecated. Use packaging.version instead (see:
-     ;; https://github.com/astropy/ccdproc/issues/805).
-     (list #:tests? #f))
     (native-inputs (list python-memory-profiler python-pytest-astropy))
     (propagated-inputs
      (list python-astropy
-- 
2.39.2

[bug#63542] [PATCH 08/19] gnu: python-reproject: Update to 0.10.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-reproject): Update to 0.10.0.
---
 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 b283cce222..4a53b29eab 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1795,13 +1795,13 @@ (define-public python-regions
 (define-public python-reproject
   (package
     (name "python-reproject")
-    (version "0.9.1")
+    (version "0.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "reproject" version))
        (sha256
-        (base32 "1msysqbhkfi3bmw29wipk250a008bnng7din56md9ipbwiar8x55"))))
+        (base32 "1ha0a1ja7k09ysd05adffgsapfwzc6m6az34a0av2mhmlwy4zb1q"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.39.2

[bug#63542] [PATCH 09/19] gnu: python-pyvo: Update to 1.4.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pyvo): Update to 1.4.1.
[build-system]: Switch to use pyproject-build-system.
[arguments]: Stop modifying standard phases.
[native-inputs]: Add python-setuptools-scm.
---
 gnu/packages/astronomy.scm | 19 ++++---------------
 1 file changed, 4 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 4a53b29eab..afde394708 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1723,27 +1723,16 @@ (define-public python-poppy
 (define-public python-pyvo
   (package
     (name "python-pyvo")
-    (version "1.2.1")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyvo" version))
        (sha256
-        (base32 "1ri5yp6903386lkn79mdcmlax7zsfrrrjbcvb91wxydcc9yasc1n"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "python" "-m" "pytest" "--pyargs" "pyvo" "-k"
-                       (string-append   ; these tests use the network
-                        "not test_access_with_string"
-                        " and not test_access_with_list"
-                        " and not test_access_with_expansion"))))))))
+        (base32 "17acv1yhz1jrsx9f35nr1vg276ibaivh4i243qkmp6abzvfyg907"))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest-astropy python-requests-mock))
+     (list python-pytest-astropy python-requests-mock python-setuptools-scm))
     (propagated-inputs
      (list python-astropy python-mimeparse python-pillow python-requests))
     (home-page "https://github.com/astropy/pyvo")
-- 
2.39.2

[bug#63542] [PATCH 10/19] gnu: python-fitsio: Use Gexp.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-fitsio): Adjust package style by
using Gexp.
---
 gnu/packages/astronomy.scm | 39 +++++++++++++++++++-------------------
 1 file changed, 20 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index afde394708..25b372b06d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -476,27 +476,28 @@ (define-public python-fitsio
        (modules '((guix build utils)))
        (snippet
         ;; Remove the bundled cfitsio
-        `(begin
-           (delete-file-recursively "cfitsio3490")
-           (substitute* "MANIFEST.in"
-             (("recursive-include cfitsio3490.*$\n") ""))))))
+        #~(begin
+            (delete-file-recursively "cfitsio3490")
+            (substitute* "MANIFEST.in"
+              (("recursive-include cfitsio3490.*$\n") ""))))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'unbundle-cfitsio
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let* ((cfitsio (assoc-ref inputs "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))))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'unbundle-cfitsio
+            (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))))))))
     (inputs (list curl))
     (propagated-inputs
      (list python-numpy cfitsio))
-- 
2.39.2

[bug#63542] [PATCH 11/19] gnu: python-astropy-healpix: Use Gexp.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy-healpix): Simplify package
by using Gexp.
[build-system]: Shift to pyproject-build-system.
[arguments]{phases}: Shift to use standard check phase.
---
 gnu/packages/astronomy.scm | 28 ++++++++++++----------------
 1 file changed, 12 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 25b372b06d..be4961b49e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1243,23 +1243,19 @@ (define-public python-astropy-healpix
        (uri (pypi-uri "astropy_healpix" version))
        (sha256
         (base32 "1n1svmd41iv944zf4anbnsigd47zr4dfjf49vrc7m6928gmq9hw8"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; This file is opened in both install and check phases.
-         (add-before 'install 'writable-compiler
-           (lambda _ (make-file-writable "astropy_healpix/_compiler.c")))
-         (add-before 'check 'writable-compiler
-           (lambda _ (make-file-writable "astropy_healpix/_compiler.c")))
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               ;; Extensions have to be rebuilt before running the tests.
-               (invoke "python" "setup.py" "build_ext" "--inplace")
-               (invoke "python" "-m" "pytest"
-                       "--pyargs" "astropy_healpix")))))))
+     (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 "astropy_healpix/_compiler.c")))
+          (add-before 'check 'prepare-test-environment
+            (lambda _
+              ;; Extensions have to be rebuilt before running the tests.
+              (invoke "python" "setup.py" "build_ext" "--inplace")
+              (make-file-writable "astropy_healpix/_compiler.c"))))))
     (native-inputs
      (list python-extension-helpers
            python-hypothesis
-- 
2.39.2

[bug#63542] [PATCH 12/19] gnu: python-astroquery: Use Gexp.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroquery): Use Gexp to simplify
package style.
---
 gnu/packages/astronomy.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index be4961b49e..5f5de193d0 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1280,15 +1280,15 @@ (define-public python-astroquery
         (base32 "1vhkzsqlgn3ji5by2rdf2gwklhbyzvpzb1iglalhqjkkrdaaaz1h"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
+     (list
+      #:phases
+       #~(modify-phases %standard-phases
          (add-before 'check 'writable-home
            (lambda _                    ; some tests need a writable home
              (setenv "HOME" (getcwd))))
          (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+           (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
-               (add-installed-pythonpath inputs outputs)
                (invoke "python" "-m" "pytest" "--pyargs" "astroquery"
                        ;; Skip tests that require online data.
                        "-m" "not remote_data")))))))
-- 
2.39.2

[bug#63542] [PATCH 12/19] gnu: python-astroquery: Use Gexp.

[Vinicius Monego]

Em qua, 2023-05-17 às 00:23 +0100, Sharlatan Hellseher escreveu:
> * gnu/packages/astronomy.scm (python-astroquery): Use Gexp to
> simplify
> package style.
> ---
>  gnu/packages/astronomy.scm | 8 ++++----
>  1 file changed, 4 insertions(+), 4 deletions(-)
> 
> diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
> index be4961b49e..5f5de193d0 100644
> --- a/gnu/packages/astronomy.scm
> +++ b/gnu/packages/astronomy.scm
> @@ -1280,15 +1280,15 @@ (define-public python-astroquery
>          (base32
> "1vhkzsqlgn3ji5by2rdf2gwklhbyzvpzb1iglalhqjkkrdaaaz1h"))))
>      (build-system python-build-system)
> 

Astroquery contains pyproject.toml in its source code, did you attempt
to switch to pyproject-build-system here?

>      (arguments
> -     `(#:phases
> -       (modify-phases %standard-phases
> +     (list
> +      #:phases
> +       #~(modify-phases %standard-phases
>           (add-before 'check 'writable-home
>             (lambda _                    ; some tests need a writable
> home
>               (setenv "HOME" (getcwd))))
>           (replace 'check
> -           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
> +           (lambda* (#:key tests? #:allow-other-keys)
>               (when tests?
> -               (add-installed-pythonpath inputs outputs)
>                 (invoke "python" "-m" "pytest" "--pyargs"
> "astroquery"
>                         ;; Skip tests that require online data.
>                         "-m" "not remote_data")))))))

[...]

Vinicius

[bug#63542] [PATCH 13/19] gnu: python-pynbody: Update to 1.3.1, simplify.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pynbody): Update to 1.3.1, simplify
package.
[build-system]: Shift to pyproject-build-system.
[arguments]: Do not modify standard phases, use #:test-flags instead.
---
 gnu/packages/astronomy.scm | 77 +++++++++++++++++---------------------
 1 file changed, 34 insertions(+), 43 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 5f5de193d0..058d3a6dcc 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2603,55 +2603,46 @@ (define-public python-pyerfa
 (define-public python-pynbody
   (package
     (name "python-pynbody")
-    (version "1.2.3")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pynbody" version))
        (sha256
-        (base32 "1jxwk2s4qz1znvyak2lj7ld01kl1jh87xp81ki7a8dz1gcy93fkx"))))
-    (build-system python-build-system)
+        (base32 "1yp7ja66zqmbnh7bbwbyimxq1nkrmjrcif2rzfm1hswm0fp2fbga"))))
+    (build-system pyproject-build-system)
     (arguments
-     (list #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'unpack 'disable-tests-require-testdata
-                 (lambda _
-                   ;; Disable tests which need to download additional 1.0GiB+
-                   ;; of test data archive from
-                   ;; http://star.ucl.ac.uk/~app/testdata.tar.gz
-                   ;;    https://github.com/pynbody/pynbody/blob/ \
-                   ;;    f4bd482dc47532831b3ec115c7cb07149d61bfc5/ \
-                   ;;    .github/workflows/build-test.yaml#L41
-                   (with-directory-excursion "tests"
-                     (for-each delete-file
-                               '("gravity_test.py"
-                                 "adaptahop_test.py"
-                                 "ahf_halos_test.py"
-                                 "array_test.py"
-                                 "bridge_test.py"
-                                 "family_test.py"
-                                 "partial_tipsy_test.py"
-                                 "snapshot_test.py"
-                                 "test_profile.py"
-                                 "gadget_test.py"
-                                 "gadgethdf_test.py"
-                                 "grafic_test.py"
-                                 "halotools_test.py"
-                                 "nchilada_test.py"
-                                 "ramses_new_ptcl_format_test.py"
-                                 "ramses_test.py"
-                                 "rockstar_test.py"
-                                 "sph_image_test.py"
-                                 "sph_smooth_test.py"
-                                 "subfind_test.py"
-                                 "subfindhdf_gadget4_test.py"
-                                 "tipsy_test.py")))))
-               (replace 'check
-                 (lambda* (#:key tests? inputs outputs #:allow-other-keys)
-                   (when tests?
-                     (add-installed-pythonpath inputs outputs)
-                     (setenv "HOME" "/tmp")
-                     (invoke "pytest" "-vv")))))))
+     (list
+      #:test-flags
+      #~(list
+         ;; Disable tests which need to download additional 1.0GiB+
+         ;; of test data archive from
+         ;; http://star.ucl.ac.uk/~app/testdata.tar.gz
+         ;;    https://github.com/pynbody/pynbody/blob/ \
+         ;;    f4bd482dc47532831b3ec115c7cb07149d61bfc5/ \
+         ;;    .github/workflows/build-test.yaml#L41
+         "--ignore=tests/gravity_test.py"
+         "--ignore=tests/adaptahop_test.py"
+         "--ignore=tests/ahf_halos_test.py"
+         "--ignore=tests/array_test.py"
+         "--ignore=tests/bridge_test.py"
+         "--ignore=tests/family_test.py"
+         "--ignore=tests/partial_tipsy_test.py"
+         "--ignore=tests/snapshot_test.py"
+         "--ignore=tests/test_profile.py"
+         "--ignore=tests/gadget_test.py"
+         "--ignore=tests/gadgethdf_test.py"
+         "--ignore=tests/grafic_test.py"
+         "--ignore=tests/halotools_test.py"
+         "--ignore=tests/nchilada_test.py"
+         "--ignore=tests/ramses_new_ptcl_format_test.py"
+         "--ignore=tests/ramses_test.py"
+         "--ignore=tests/rockstar_test.py"
+         "--ignore=tests/sph_image_test.py"
+         "--ignore=tests/sph_smooth_test.py"
+         "--ignore=tests/subfind_test.py"
+         "--ignore=tests/subfindhdf_gadget4_test.py"
+         "--ignore=tests/tipsy_test.py")))
     (native-inputs
      (list python-cython
            python-pandas
-- 
2.39.2

[bug#63542] [PATCH 14/19] gnu: python-astral: Update to 3.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astral): Update to 3.2.
[build-system]: Shift to pyproject-build-system.
[arguments]: Use Gexps. Do not modify staged phases, use #:test-flags
instead and partly enable tests (128 of 334).
[native-inputs]: Add python-poetry-core.
---
 gnu/packages/astronomy.scm | 70 ++++++++++++++++++++++++++++++++------
 1 file changed, 59 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 058d3a6dcc..ab539efcfe 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1939,24 +1939,72 @@ (define-public python-sunpy
 (define-public python-astral
   (package
     (name "python-astral")
-    (version "2.2")
+    (version "3.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astral" version))
        (sha256
-        (base32 "1gkggdibccmdy9glymw3kbrkzm6svvsg0lk56hhy92y4smkrj7g4"))))
-    (build-system python-build-system)
+        (base32 "121xag65rmv6pszbi3d206yz3jfwmpkf0jxjrxrd2scy5r0knz4v"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest")))))))
+     (list
+      #:test-flags
+      ;; XXX: Disable tests which require newer version of python-pytz.
+      ;; No time zone found with key Pacific/Auckland
+      #~(list "-k" (string-append
+                    "not test_TimezoneLookup"
+                    " and not test_Sun"
+                    " and not test_Dawn"
+                    " and not test_Sunrise"
+                    " and not test_SolarNoon"
+                    " and not test_Dusk"
+                    " and not test_Sunset"
+                    " and not test_SolarElevation"
+                    " and not test_SolarAzimuth"
+                    " and not test_TimeAtAltitude"
+                    " and not test_MoonNoDate"
+                    " and not test_lookup"
+                    " and not test_tzinfo"
+                    " and not test_australia"
+                    " and not test_adak"
+                    " and not test_australia"
+                    " and not test_Elevation_NonNaive"
+                    " and not test_Wellington"
+                    " and not test_Sun_Local_tzinfo[day0-dawn0]"
+                    " and not test_Sun_Local_tzinfo[day1-dawn1]"
+                    " and not test_Sun_Local_tzinfo[day2-dawn2]"
+                    " and not test_Sun_Local_tzinfo[day3-dawn3]"
+                    " and not test_Sun_Local_tzinfo[day4-dawn4]"
+                    " and not test_Sun_Local_str[day0-dawn0]"
+                    " and not test_Sun_Local_str[day1-dawn1]"
+                    " and not test_Sun_Local_str[day2-dawn2]"
+                    " and not test_Sun_Local_str[day3-dawn3]"
+                    " and not test_Sun_Local_str[day4-dawn4]"
+                    " and not test_SolarZenith_London[dt0-102.6]"
+                    " and not test_SolarZenith_London[dt1-93.3]"
+                    " and not test_SolarZenith_London[dt2-87.8]"
+                    " and not test_SolarZenith_London[dt3-46]"
+                    " and not test_SolarZenith_London[dt4-71]"
+                    " and not test_SolarZenith_Riyadh[dt0-32]"
+                    " and not test_SolarZenith_Riyadh[dt1-126]"
+                    " and not test_moonrise_utc[date_0-risetime0]"
+                    " and not test_moonrise_utc[date_1-risetime1]"
+                    " and not test_moonrise_utc[date_2-risetime2]"
+                    " and not test_moonrise_wellington[date_0-risetime0]"
+                    " and not test_moonrise_wellington[date_1-risetime1]"
+                    " and not test_moonset_wellington[date_0-settime0]"
+                    " and not test_moonset_wellington[date_1-settime1]"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'prepare-test-environment
+            (lambda _
+              (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-freezegun python-setuptools-scm))
+     (list python-freezegun
+           python-poetry-core
+           python-pytest
+           python-setuptools-scm))
     (propagated-inputs
      (list python-dataclasses python-pytest python-pytz))
     (home-page "https://github.com/sffjunkie/astral")
-- 
2.39.2

[bug#63542] [PATCH 14/19] gnu: python-astral: Update to 3.2.

[Vinicius Monego]

Em qua, 2023-05-17 às 00:23 +0100, Sharlatan Hellseher escreveu:
> * gnu/packages/astronomy.scm (python-astral): Update to 3.2.
> [build-system]: Shift to pyproject-build-system.
> [arguments]: Use Gexps. Do not modify staged phases, use #:test-flags
> instead and partly enable tests (128 of 334).
> [native-inputs]: Add python-poetry-core.
> ---
>  gnu/packages/astronomy.scm | 70 ++++++++++++++++++++++++++++++++----
> --
>  1 file changed, 59 insertions(+), 11 deletions(-)
> 
> 

[...]

> +                    " and not test_Sun_Local_tzinfo[day0-dawn0]"
> +                    " and not test_Sun_Local_tzinfo[day1-dawn1]"
> +                    " and not test_Sun_Local_tzinfo[day2-dawn2]"
> +                    " and not test_Sun_Local_tzinfo[day3-dawn3]"
> +                    " and not test_Sun_Local_tzinfo[day4-dawn4]"

AFAIK we don't skip each test by argument individually. If it fails
with every argument, the test can be skipped by name.

> +                    " and not test_Sun_Local_str[day0-dawn0]"
> +                    " and not test_Sun_Local_str[day1-dawn1]"
> +                    " and not test_Sun_Local_str[day2-dawn2]"
> +                    " and not test_Sun_Local_str[day3-dawn3]"
> +                    " and not test_Sun_Local_str[day4-dawn4]"
> +                    " and not test_SolarZenith_London[dt0-102.6]"
> +                    " and not test_SolarZenith_London[dt1-93.3]"
> +                    " and not test_SolarZenith_London[dt2-87.8]"
> +                    " and not test_SolarZenith_London[dt3-46]"
> +                    " and not test_SolarZenith_London[dt4-71]"
> +                    " and not test_SolarZenith_Riyadh[dt0-32]"
> +                    " and not test_SolarZenith_Riyadh[dt1-126]"
> +                    " and not test_moonrise_utc[date_0-risetime0]"
> +                    " and not test_moonrise_utc[date_1-risetime1]"
> +                    " and not test_moonrise_utc[date_2-risetime2]"
> +                    " and not test_moonrise_wellington[date_0-
> risetime0]"
> +                    " and not test_moonrise_wellington[date_1-
> risetime1]"
> +                    " and not test_moonset_wellington[date_0-
> settime0]"
> +                    " and not test_moonset_wellington[date_1-
> settime1]"))

[...]

Vinicius

[bug#63542] [PATCH 15/19] gnu: python-poppy: Update to 1.1.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-poppy): Update to 1.1.1.
---
 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 ab539efcfe..f289ebdcab 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1676,13 +1676,13 @@ (define-public python-poliastro
 (define-public python-poppy
   (package
     (name "python-poppy")
-    (version "1.0.3")
+    (version "1.1.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "poppy" version))
               (sha256
                (base32
-                "050cn6aabd1dxbi7zihbqnkl79hz6q6d5n6g25zmrpvc4sii171m"))))
+                "0s8rb61q8dz66s8d3qg44kb6bb5gi40zl41ik9wyccgb4kyf3brp"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      ;; XXX: With python-synphot (marked as optional) package added to the list
-- 
2.39.2

[bug#63542] [PATCH 16/19] gnu: python-photutils: Update to 1.7.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-photutils): Update to 1.7.0.
---
 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 f289ebdcab..5630b65185 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1567,13 +1567,13 @@ (define-public python-mpl-animators
 (define-public python-photutils
   (package
     (name "python-photutils")
-    (version "1.6.0")
+    (version "1.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "photutils" version))
        (sha256
-        (base32 "0w4kxl6aqjp2wv396krw30kwg6cmmska8gvgpihm2i2zxyzz39vd"))))
+        (base32 "1bq4ma402lpa5d6l85awlc23kasxf40nq8hgi3iyrilnfikan0jz"))))
     (build-system python-build-system)
     (arguments
      `(#:test-target "pytest"
-- 
2.39.2

[bug#63542] [PATCH 17/19] gnu: python-ephem: Update to 4.1.4.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ephem): Update t 4.1.4.
---
 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 5630b65185..ce8c313185 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1497,13 +1497,13 @@ (define-public python-drms
 (define-public python-ephem
   (package
     (name "python-ephem")
-    (version "4.1.3")
+    (version "4.1.4")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ephem" version))
               (sha256
                (base32
-                "0smmm3l8csnw9rrimh8mpyjrm80jaafjl184spnji98vk22qd8bz"))))
+                "0q67z79lgwdylxagbsjm42xvsmk5jmgvghy36m2n5lb2446rz9bk"))))
     (build-system python-build-system)
     (native-inputs (list tzdata))
     (home-page "https://rhodesmill.org/pyephem/")
-- 
2.39.2

[bug#63542] [PATCH 18/19] gnu: python-asdf: Update to 2.15.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf): Update to 2.15.0.
[arguments]: Use Gexps and enable the most of the tests.
[native-inputs]: Add python-fsspec.
---
 gnu/packages/astronomy.scm | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ce8c313185..ed787665ea 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2747,23 +2747,25 @@ (define-public python-suntime
 (define-public python-asdf
   (package
     (name "python-asdf")
-    (version "2.13.0")
+    (version "2.15.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf" version))
        (sha256
-        (base32 "1zixzv4n2fryaszsfchqh2nvp0gzvarhz03fc721yw6iafdadqij"))))
+        (base32 "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8"))))
     (build-system pyproject-build-system)
     (arguments
-     ;; FIXME: Tests fail a lot with
-     ;;
-     ;; ERROR  - _pytest.pathlib.ImportPathMismatchError:
-     ;; ('asdf.conftest', '/gnu/sto...
-     ;;
-     `(#:tests? #f))
+     (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
            python-packaging
            python-psutil
            python-pytest
-- 
2.39.2

[bug#63542] [PATCH 18/19] gnu: python-asdf: Update to 2.15.0.

[Vinicius Monego]

Em qua, 2023-05-17 às 00:23 +0100, Sharlatan Hellseher escreveu:
> * gnu/packages/astronomy.scm (python-asdf): Update to 2.15.0.
> [arguments]: Use Gexps and enable the most of the tests.
> [native-inputs]: Add python-fsspec.
> ---
>  gnu/packages/astronomy.scm | 18 ++++++++++--------
>  1 file changed, 10 insertions(+), 8 deletions(-)
> 
> diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
> index ce8c313185..ed787665ea 100644
> --- a/gnu/packages/astronomy.scm
> +++ b/gnu/packages/astronomy.scm
> @@ -2747,23 +2747,25 @@ (define-public python-suntime
>  (define-public python-asdf
>    (package
>      (name "python-asdf")
> -    (version "2.13.0")
> +    (version "2.15.0")
>      (source
>       (origin
>         (method url-fetch)
>         (uri (pypi-uri "asdf" version))
>         (sha256
> -        (base32
> "1zixzv4n2fryaszsfchqh2nvp0gzvarhz03fc721yw6iafdadqij"))))
> +        (base32
> "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8"))))
>      (build-system pyproject-build-system)
>      (arguments
> -     ;; FIXME: Tests fail a lot with
> -     ;;
> -     ;; ERROR  - _pytest.pathlib.ImportPathMismatchError:
> -     ;; ('asdf.conftest', '/gnu/sto...
> -     ;;
> -     `(#:tests? #f))
> +     (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"))))

Usually, updating and enabling tests are done in separate commits.

Vinicius

[bug#63542] [PATCH 19/19] gnu: python-asdf-coordinates-schemas: Update to 0.2.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-coordinates-schemas): Update
to 0.2.0.
[build-system]: Shift to python-build-system.
[arguments]: Do not modify standard phases.
---
 gnu/packages/astronomy.scm | 18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ed787665ea..eaa947d360 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2861,26 +2861,16 @@ (define python-asdf-transform-schemas
 (define python-asdf-coordinates-schemas
   (package
     (name "python-asdf-coordinates-schemas")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf_coordinates_schemas" version))
        (sha256
-        (base32 "0ahwhsz5jzljnpkfd2kvspirg823lnj5ip9sfkd9cx09z1nlz8jg"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest")))))))
+        (base32 "1x6mipg76c6qldq8s2p2wpsq0cpr9b5krp62xskljdz1f84abyg3"))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest
-           python-semantic-version
-           python-setuptools-scm))
+     (list python-pytest python-semantic-version python-setuptools-scm))
     (propagated-inputs
      (list python-asdf))
     (home-page "https://github.com/asdf-format/asdf-coordinates-schemas")
-- 
2.39.2

[bug#63542]

[Sharlatan Hellseher]

[-- Attachment #1: Type: text/plain, Size: 255 bytes --]

Hi Guix!

A gentle ping on this issue.
Please let me know if it requires any adjustments.

I would like bring python-jwst (James Webb Space Telescope) to Guix, hoping
it would bring more attention to the project from astronomical community.

Thanks,
Oleg

[-- Attachment #2: Type: text/html, Size: 906 bytes --]

[bug#63542]

[Vinicius Monego]

Em ter, 2023-05-23 às 19:33 +0100, Sharlatan Hellseher escreveu:
> Hi Guix!
> 
> A gentle ping on this issue.
> Please let me know if it requires any adjustments.
> 
> I would like bring python-jwst (James Webb Space Telescope) to Guix,
> hoping it would bring more attention to the project from astronomical
> community.
> 
> Thanks,
> Oleg
> 
> 

Hi Sharlatan,

I requested adjustments on patches 4, 12, 14 and 18. Could you send a
v2 with the changes?

Vinicius

[bug#63542] Astronomy May updates

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 721 bytes --]

On Tue, May 23, 2023 at 07:33:22PM +0100, Sharlatan Hellseher wrote:
> Hi Guix!
> 
> A gentle ping on this issue.
> Please let me know if it requires any adjustments.

I see that Vinicius Monego is looking for a v2 on patches 4, 12, 14 and
18 to address a couple of issues. Can you take a look at those? Thanks.

> I would like bring python-jwst (James Webb Space Telescope) to Guix, hoping
> it would bring more attention to the project from astronomical community.

That would be really cool.

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

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 833 bytes --]

[bug#63542] [PATCH v2 00/20]: Cover review points.

[Sharlatan Hellseher]

Hi Vinicius and Efraim!

Thank you for the review and here is my v2 of patch set.

* 04 gnu: python-sunpy: Update to 4.1.5: opencv moved to native-inputs to
let tests pass but do not propagate it to user's profile.

* 12 gnu: python-astroquery: Use Gexp: My attempt to use pyproject-build-system
was unsuccessful and caused build to fail, I might come back to it later as
with python-build-system the package passed all phased just fine.

* 14 gnu: python-astral: Update to 3.2: I've skipped tests directly without
arguments.

* 18 gnu: python-asdf: Update to 2.15.0: Only update is present and the
enabling test commit is moved to new 20.

Sharlatan Hellseher (20):
  gnu: python-asdf-astropy: Update to 0.4.0.
  gnu: python-asdf-wcs-schemas: Symplify.
  gnu: python-gwcs: Update to 0.18.3.
  gnu: python-sunpy: Update to 4.1.5.
  gnu: python-spherical-geometry: Add update note.
  gnu: python-sgp4: Update to 2.22.
  gnu: python-ccdproc: Enable tests.
  gnu: python-reproject: Update to 0.10.0.
  gnu: python-pyvo: Update to 1.4.1.
  gnu: python-fitsio: Use Gexp.
  gnu: python-astropy-healpix: Use Gexp.
  gnu: python-astroquery: Use Gexp.
  gnu: python-pynbody: Update to 1.3.1, simplify.
  gnu: python-astral: Update to 3.2.
  gnu: python-poppy: Update to 1.1.1.
  gnu: python-photutils: Update to 1.7.0.
  gnu: python-ephem: Update to 4.1.4.
  gnu: python-asdf: Update to 2.15.0.
  gnu: python-asdf-coordinates-schemas: Update to 0.2.0.
  gnu: python-asdf: Enable tests.

 gnu/packages/astronomy.scm | 350 +++++++++++++++++--------------------
 1 file changed, 165 insertions(+), 185 deletions(-)


base-commit: 242cc93438d67f5b35602d5add02e230850b0b43
-- 
2.39.2

[bug#63542] [PATCH v2 01/20] gnu: python-asdf-astropy: Update to 0.4.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.4.0.
[arguments]: Add pre check phase.
[native-inputs]: Remove python-matplotlib.
---
 gnu/packages/astronomy.scm | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9bc790ef4b..e180a2f81a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2974,18 +2974,23 @@ (define python-asdf-unit-schemas
 (define-public python-asdf-astropy
   (package
     (name "python-asdf-astropy")
-    (version "0.3.0")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "asdf_astropy" version))
+       (uri (pypi-uri "asdf-astropy" version))
        (sha256
-        (base32 "1gp5iav0a9g9q0zb22vhzi3v9vwk5wn2nxvr3mvi3bsdcdj3h23v"))))
+        (base32 "1difb2y1hlalbhrw8znwmmc0vzgg44zfsay98lpllb7y0536fas6"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'set-home-env
+            (lambda _ (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-coverage
            python-h5py
-           python-matplotlib
            python-pandas
            python-pytest-astropy
            python-scipy
-- 
2.39.2

[bug#63542] [PATCH v2 02/20] gnu: python-asdf-wcs-schemas: Symplify.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-wcs-schemas): Symplify package.
[build-system]: Use pyproject-build-system.
---
 gnu/packages/astronomy.scm | 14 ++------------
 1 file changed, 2 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e180a2f81a..0d0e45a3b1 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3020,19 +3020,9 @@ (define python-asdf-wcs-schemas
        (uri (pypi-uri "asdf_wcs_schemas" version))
        (sha256
         (base32 "0khyab9mnf2lv755as8kwhk3lqqpd3f4291ny3b9yp3ik86fzhz1"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest")))))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest
-           python-setuptools-scm
-           python-semantic-version))
+     (list python-pytest python-setuptools-scm python-semantic-version))
     (propagated-inputs
      (list python-asdf))
     (home-page "https://github.com/asdf-format/asdf-wcs-schemas")
-- 
2.39.2

[bug#63542] [PATCH v2 03/20] gnu: python-gwcs: Update to 0.18.3.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-gwcs): Update to 0.18.3.
---
 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 0d0e45a3b1..5c07ff2c8d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3036,13 +3036,13 @@ (define python-asdf-wcs-schemas
 (define-public python-gwcs
   (package
     (name "python-gwcs")
-    (version "0.18.2")
+    (version "0.18.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "gwcs" version))
        (sha256
-        (base32 "0v9qcq6zl74d6s882s6xmas144jfalvll6va8rvrxmvpx4vqjzhg"))))
+        (base32 "0mgyk5mgmj242g8nl7glcj689vry3ncwf04b8q3hasjcc9bs0rm4"))))
     (build-system pyproject-build-system)
     (native-inputs
      (list python-jsonschema
-- 
2.39.2

[bug#63542] [PATCH v2 04/20] gnu: python-sunpy: Update to 4.1.5.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sunpy): Update to 4.1.5, simplify
package.
[arguments]{test-flags}: Disable 2 failing tests.
[arguments]{phases}: Simplify prepare-test-environment by remove
redundant substitution.
[inputs]: Add opencv for OpenCV-Pyton support.
---
 gnu/packages/astronomy.scm | 32 ++++++++++----------------------
 1 file changed, 10 insertions(+), 22 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 5c07ff2c8d..196aeba0e3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1885,16 +1885,21 @@ (define-public python-sgp4
 (define-public python-sunpy
   (package
     (name "python-sunpy")
-    (version "4.1.1")
+    (version "4.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sunpy" version))
        (sha256
-        (base32 "1h8dnsic96bxm5l278vk6jj5h4bh1b143fghsvv5rhigk137vysp"))))
+        (base32 "1j5g0ivsrc5ji9s7jc3kcbi2injfs3y31pm3priycljwcsxspkpm"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~(list "-k" (string-append
+                    ;; XXX: Failed: DID NOT RAISE <class 'ModuleNotFoundError'>
+                    "not test_main_nonexisting_module"
+                    " and not test_main_stdlib_module"))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'install 'writable-compiler
@@ -1902,26 +1907,10 @@ (define-public python-sunpy
               (make-file-writable "sunpy/_compiler.c")))
           (add-before 'check 'prepare-test-environment
             (lambda _
-              (setenv "HOME" "/tmp")
-              (make-file-writable "sunpy/_compiler.c")
-              ;; TODO: (Sharlatan-20221106T115800+0000): Review failing tests
-              (substitute* "sunpy/image/tests/test_transform.py"
-                (("def test_clipping") "def __off_test_clipping")
-                (("def test_nans") "def __off_test_nans")
-                (("def test_endian") "def __off_test_endian"))
-              (substitute* "sunpy/map/tests/test_mapbase.py"
-                (("def test_derotating_nonpurerotation_pcij")
-                 "def __off_test_derotating_nonpurerotation_pcij"))
-              (substitute* "sunpy/map/sources/tests/test_mdi_source.py"
-                (("def test_synoptic_source")
-                 "def __off_test_synoptic_source"))
-              (substitute* "sunpy/tests/tests/test_self_test.py"
-                (("def test_main_nonexisting_module")
-                 "def __off_test_main_nonexisting_module")
-                (("def test_main_stdlib_module")
-                 "def __off_test_main_stdlib_module")))))))
+              (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-aiohttp
+     (list opencv ; For tests, includes OpenCV-Python
+           python-aiohttp
            python-extension-helpers
            python-hvpy
            python-packaging
@@ -1950,7 +1939,6 @@ (define-public python-sunpy
            python-matplotlib
            python-mpl-animators
            python-numpy
-           ;; python-opencv-python ; not packed yet
            python-pandas
            python-reproject
            python-scikit-image
-- 
2.39.2

[bug#63542] [PATCH v2 05/20] gnu: python-spherical-geometry: Add update note.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-spherical-geometry): Package can't
be updated to the latest version due to an open issue in upstream where
system qb library is in use.
---
 gnu/packages/astronomy.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 196aeba0e3..04a1895662 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1987,6 +1987,8 @@ (define-public python-astral
 (define-public python-spherical-geometry
   (package
     (name "python-spherical-geometry")
+    ;; XXX: Can't be updated to the latest see:
+    ;; https://github.com/spacetelescope/spherical_geometry/issues/227
     (version "1.2.22")
     (source
      (origin
-- 
2.39.2

[bug#63542] [PATCH v2 06/20] gnu: python-sgp4: Update to 2.22.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-sgp4): Update to 2.22.
---
 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 04a1895662..a7fb5b3290 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1856,13 +1856,13 @@ (define-public python-reproject
 (define-public python-sgp4
   (package
     (name "python-sgp4")
-    (version "2.21")
+    (version "2.22")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sgp4" version))
        (sha256
-        (base32 "1vzcrlrlzmhbycdz16m8v241l8zx49vsy81wcd0yjxs80isvhyb1"))))
+        (base32 "1yc6gcbhz80i875j0wf6ikx7rzs0m7m1qp72dmdhdjidmpma5w0p"))))
     (build-system python-build-system)
     (propagated-inputs
      (list python-numpy))
-- 
2.39.2

[bug#63542] [PATCH v2 07/20] gnu: python-ccdproc: Enable tests.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ccdproc): Enable tests.
---
 gnu/packages/astronomy.scm | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a7fb5b3290..8f1078df02 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1370,11 +1370,6 @@ (define-public python-ccdproc
        (sha256
         (base32 "0fy1sni87cr05dkljd8wb7vgh7z9agh8wv5kiagxcpbcf8l06jv1"))))
     (build-system pyproject-build-system)
-    (arguments
-     ;; FIXME: Test failed a lot with: DeprecationWarning: distutils Version
-     ;; classes are deprecated. Use packaging.version instead (see:
-     ;; https://github.com/astropy/ccdproc/issues/805).
-     (list #:tests? #f))
     (native-inputs (list python-memory-profiler python-pytest-astropy))
     (propagated-inputs
      (list python-astropy
-- 
2.39.2

[bug#63542] [PATCH v2 08/20] gnu: python-reproject: Update to 0.10.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-reproject): Update to 0.10.0.
---
 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 8f1078df02..9e3a36e1d1 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1795,13 +1795,13 @@ (define-public python-regions
 (define-public python-reproject
   (package
     (name "python-reproject")
-    (version "0.9.1")
+    (version "0.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "reproject" version))
        (sha256
-        (base32 "1msysqbhkfi3bmw29wipk250a008bnng7din56md9ipbwiar8x55"))))
+        (base32 "1ha0a1ja7k09ysd05adffgsapfwzc6m6az34a0av2mhmlwy4zb1q"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.39.2

[bug#63542] [PATCH v2 09/20] gnu: python-pyvo: Update to 1.4.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pyvo): Update to 1.4.1.
[build-system]: Switch to use pyproject-build-system.
[arguments]: Stop modifying standard phases.
[native-inputs]: Add python-setuptools-scm.
---
 gnu/packages/astronomy.scm | 19 ++++---------------
 1 file changed, 4 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9e3a36e1d1..29bc60ae98 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1723,27 +1723,16 @@ (define-public python-poppy
 (define-public python-pyvo
   (package
     (name "python-pyvo")
-    (version "1.2.1")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyvo" version))
        (sha256
-        (base32 "1ri5yp6903386lkn79mdcmlax7zsfrrrjbcvb91wxydcc9yasc1n"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "python" "-m" "pytest" "--pyargs" "pyvo" "-k"
-                       (string-append   ; these tests use the network
-                        "not test_access_with_string"
-                        " and not test_access_with_list"
-                        " and not test_access_with_expansion"))))))))
+        (base32 "17acv1yhz1jrsx9f35nr1vg276ibaivh4i243qkmp6abzvfyg907"))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest-astropy python-requests-mock))
+     (list python-pytest-astropy python-requests-mock python-setuptools-scm))
     (propagated-inputs
      (list python-astropy python-mimeparse python-pillow python-requests))
     (home-page "https://github.com/astropy/pyvo")
-- 
2.39.2

[bug#63542] [PATCH v2 10/20] gnu: python-fitsio: Use Gexp.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-fitsio): Adjust package style by
using Gexp.
---
 gnu/packages/astronomy.scm | 39 +++++++++++++++++++-------------------
 1 file changed, 20 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 29bc60ae98..c72be7b30b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -476,27 +476,28 @@ (define-public python-fitsio
        (modules '((guix build utils)))
        (snippet
         ;; Remove the bundled cfitsio
-        `(begin
-           (delete-file-recursively "cfitsio3490")
-           (substitute* "MANIFEST.in"
-             (("recursive-include cfitsio3490.*$\n") ""))))))
+        #~(begin
+            (delete-file-recursively "cfitsio3490")
+            (substitute* "MANIFEST.in"
+              (("recursive-include cfitsio3490.*$\n") ""))))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'unbundle-cfitsio
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let* ((cfitsio (assoc-ref inputs "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))))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'unbundle-cfitsio
+            (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))))))))
     (inputs (list curl))
     (propagated-inputs
      (list python-numpy cfitsio))
-- 
2.39.2

[bug#63542] [PATCH v2 11/20] gnu: python-astropy-healpix: Use Gexp.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy-healpix): Simplify package
by using Gexp.
[build-system]: Shift to pyproject-build-system.
[arguments]{phases}: Shift to use standard check phase.
---
 gnu/packages/astronomy.scm | 28 ++++++++++++----------------
 1 file changed, 12 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c72be7b30b..c8f3a8e965 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1243,23 +1243,19 @@ (define-public python-astropy-healpix
        (uri (pypi-uri "astropy_healpix" version))
        (sha256
         (base32 "1n1svmd41iv944zf4anbnsigd47zr4dfjf49vrc7m6928gmq9hw8"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; This file is opened in both install and check phases.
-         (add-before 'install 'writable-compiler
-           (lambda _ (make-file-writable "astropy_healpix/_compiler.c")))
-         (add-before 'check 'writable-compiler
-           (lambda _ (make-file-writable "astropy_healpix/_compiler.c")))
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               ;; Extensions have to be rebuilt before running the tests.
-               (invoke "python" "setup.py" "build_ext" "--inplace")
-               (invoke "python" "-m" "pytest"
-                       "--pyargs" "astropy_healpix")))))))
+     (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 "astropy_healpix/_compiler.c")))
+          (add-before 'check 'prepare-test-environment
+            (lambda _
+              ;; Extensions have to be rebuilt before running the tests.
+              (invoke "python" "setup.py" "build_ext" "--inplace")
+              (make-file-writable "astropy_healpix/_compiler.c"))))))
     (native-inputs
      (list python-extension-helpers
            python-hypothesis
-- 
2.39.2

[bug#63542] [PATCH v2 12/20] gnu: python-astroquery: Use Gexp.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astroquery): Use Gexp to simplify
package style.
---
 gnu/packages/astronomy.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c8f3a8e965..c74867948f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1280,15 +1280,15 @@ (define-public python-astroquery
         (base32 "1vhkzsqlgn3ji5by2rdf2gwklhbyzvpzb1iglalhqjkkrdaaaz1h"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
+     (list
+      #:phases
+       #~(modify-phases %standard-phases
          (add-before 'check 'writable-home
            (lambda _                    ; some tests need a writable home
              (setenv "HOME" (getcwd))))
          (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+           (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
-               (add-installed-pythonpath inputs outputs)
                (invoke "python" "-m" "pytest" "--pyargs" "astroquery"
                        ;; Skip tests that require online data.
                        "-m" "not remote_data")))))))
-- 
2.39.2

[bug#63542] [PATCH v2 13/20] gnu: python-pynbody: Update to 1.3.1, simplify.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-pynbody): Update to 1.3.1, simplify
package.
[build-system]: Shift to pyproject-build-system.
[arguments]: Do not modify standard phases, use #:test-flags instead.
---
 gnu/packages/astronomy.scm | 77 +++++++++++++++++---------------------
 1 file changed, 34 insertions(+), 43 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c74867948f..011e1374fc 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2602,55 +2602,46 @@ (define-public python-pyerfa
 (define-public python-pynbody
   (package
     (name "python-pynbody")
-    (version "1.2.3")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pynbody" version))
        (sha256
-        (base32 "1jxwk2s4qz1znvyak2lj7ld01kl1jh87xp81ki7a8dz1gcy93fkx"))))
-    (build-system python-build-system)
+        (base32 "1yp7ja66zqmbnh7bbwbyimxq1nkrmjrcif2rzfm1hswm0fp2fbga"))))
+    (build-system pyproject-build-system)
     (arguments
-     (list #:phases
-           #~(modify-phases %standard-phases
-               (add-after 'unpack 'disable-tests-require-testdata
-                 (lambda _
-                   ;; Disable tests which need to download additional 1.0GiB+
-                   ;; of test data archive from
-                   ;; http://star.ucl.ac.uk/~app/testdata.tar.gz
-                   ;;    https://github.com/pynbody/pynbody/blob/ \
-                   ;;    f4bd482dc47532831b3ec115c7cb07149d61bfc5/ \
-                   ;;    .github/workflows/build-test.yaml#L41
-                   (with-directory-excursion "tests"
-                     (for-each delete-file
-                               '("gravity_test.py"
-                                 "adaptahop_test.py"
-                                 "ahf_halos_test.py"
-                                 "array_test.py"
-                                 "bridge_test.py"
-                                 "family_test.py"
-                                 "partial_tipsy_test.py"
-                                 "snapshot_test.py"
-                                 "test_profile.py"
-                                 "gadget_test.py"
-                                 "gadgethdf_test.py"
-                                 "grafic_test.py"
-                                 "halotools_test.py"
-                                 "nchilada_test.py"
-                                 "ramses_new_ptcl_format_test.py"
-                                 "ramses_test.py"
-                                 "rockstar_test.py"
-                                 "sph_image_test.py"
-                                 "sph_smooth_test.py"
-                                 "subfind_test.py"
-                                 "subfindhdf_gadget4_test.py"
-                                 "tipsy_test.py")))))
-               (replace 'check
-                 (lambda* (#:key tests? inputs outputs #:allow-other-keys)
-                   (when tests?
-                     (add-installed-pythonpath inputs outputs)
-                     (setenv "HOME" "/tmp")
-                     (invoke "pytest" "-vv")))))))
+     (list
+      #:test-flags
+      #~(list
+         ;; Disable tests which need to download additional 1.0GiB+
+         ;; of test data archive from
+         ;; http://star.ucl.ac.uk/~app/testdata.tar.gz
+         ;;    https://github.com/pynbody/pynbody/blob/ \
+         ;;    f4bd482dc47532831b3ec115c7cb07149d61bfc5/ \
+         ;;    .github/workflows/build-test.yaml#L41
+         "--ignore=tests/gravity_test.py"
+         "--ignore=tests/adaptahop_test.py"
+         "--ignore=tests/ahf_halos_test.py"
+         "--ignore=tests/array_test.py"
+         "--ignore=tests/bridge_test.py"
+         "--ignore=tests/family_test.py"
+         "--ignore=tests/partial_tipsy_test.py"
+         "--ignore=tests/snapshot_test.py"
+         "--ignore=tests/test_profile.py"
+         "--ignore=tests/gadget_test.py"
+         "--ignore=tests/gadgethdf_test.py"
+         "--ignore=tests/grafic_test.py"
+         "--ignore=tests/halotools_test.py"
+         "--ignore=tests/nchilada_test.py"
+         "--ignore=tests/ramses_new_ptcl_format_test.py"
+         "--ignore=tests/ramses_test.py"
+         "--ignore=tests/rockstar_test.py"
+         "--ignore=tests/sph_image_test.py"
+         "--ignore=tests/sph_smooth_test.py"
+         "--ignore=tests/subfind_test.py"
+         "--ignore=tests/subfindhdf_gadget4_test.py"
+         "--ignore=tests/tipsy_test.py")))
     (native-inputs
      (list python-cython
            python-pandas
-- 
2.39.2

[bug#63542] [PATCH v2 14/20] gnu: python-astral: Update to 3.2.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astral): Update to 3.2.
[build-system]: Shift to pyproject-build-system.
[arguments]: Use Gexps. Do not modify staged phases, use #:test-flags
instead and partly enable tests (128 of 334).
[native-inputs]: Add python-poetry-core.
---
 gnu/packages/astronomy.scm | 53 ++++++++++++++++++++++++++++++--------
 1 file changed, 42 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 011e1374fc..7883919203 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1938,24 +1938,55 @@ (define-public python-sunpy
 (define-public python-astral
   (package
     (name "python-astral")
-    (version "2.2")
+    (version "3.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astral" version))
        (sha256
-        (base32 "1gkggdibccmdy9glymw3kbrkzm6svvsg0lk56hhy92y4smkrj7g4"))))
-    (build-system python-build-system)
+        (base32 "121xag65rmv6pszbi3d206yz3jfwmpkf0jxjrxrd2scy5r0knz4v"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest")))))))
+     (list
+      #:test-flags
+      ;; XXX: Disable tests which require newer version of python-pytz.
+      ;; No time zone found with key Pacific/Auckland
+      #~(list "-k" (string-append
+                    "not test_TimezoneLookup"
+                    " and not test_Sun"
+                    " and not test_Dawn"
+                    " and not test_Sunrise"
+                    " and not test_SolarNoon"
+                    " and not test_Dusk"
+                    " and not test_Sunset"
+                    " and not test_SolarElevation"
+                    " and not test_SolarAzimuth"
+                    " and not test_TimeAtAltitude"
+                    " and not test_MoonNoDate"
+                    " and not test_lookup"
+                    " and not test_tzinfo"
+                    " and not test_australia"
+                    " and not test_adak"
+                    " and not test_australia"
+                    " and not test_Elevation_NonNaive"
+                    " and not test_Wellington"
+                    " and not test_Sun_Local_tzinfo"
+                    " and not test_Sun_Local_str"
+                    " and not test_SolarZenith_London"
+                    " and not test_SolarZenith_Riyadh"
+                    " and not test_moonrise_utc"
+                    " and not test_moonrise_wellington"
+                    " and not test_moonset_wellington"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'prepare-test-environment
+            (lambda _
+              (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list python-freezegun python-setuptools-scm))
+     (list python-freezegun
+           python-poetry-core
+           python-pytest
+           python-setuptools-scm))
     (propagated-inputs
      (list python-dataclasses python-pytest python-pytz))
     (home-page "https://github.com/sffjunkie/astral")
-- 
2.39.2

[bug#63542] [PATCH v2 15/20] gnu: python-poppy: Update to 1.1.1.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-poppy): Update to 1.1.1.
---
 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 7883919203..c606eabf5b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1676,13 +1676,13 @@ (define-public python-poliastro
 (define-public python-poppy
   (package
     (name "python-poppy")
-    (version "1.0.3")
+    (version "1.1.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "poppy" version))
               (sha256
                (base32
-                "050cn6aabd1dxbi7zihbqnkl79hz6q6d5n6g25zmrpvc4sii171m"))))
+                "0s8rb61q8dz66s8d3qg44kb6bb5gi40zl41ik9wyccgb4kyf3brp"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      ;; XXX: With python-synphot (marked as optional) package added to the list
-- 
2.39.2

[bug#63542] [PATCH v2 16/20] gnu: python-photutils: Update to 1.7.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-photutils): Update to 1.7.0.
---
 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 c606eabf5b..f7997fd358 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1567,13 +1567,13 @@ (define-public python-mpl-animators
 (define-public python-photutils
   (package
     (name "python-photutils")
-    (version "1.6.0")
+    (version "1.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "photutils" version))
        (sha256
-        (base32 "0w4kxl6aqjp2wv396krw30kwg6cmmska8gvgpihm2i2zxyzz39vd"))))
+        (base32 "1bq4ma402lpa5d6l85awlc23kasxf40nq8hgi3iyrilnfikan0jz"))))
     (build-system python-build-system)
     (arguments
      `(#:test-target "pytest"
-- 
2.39.2

[bug#63542] [PATCH v2 17/20] gnu: python-ephem: Update to 4.1.4.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-ephem): Update t 4.1.4.
---
 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 f7997fd358..b9fbb9d829 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1497,13 +1497,13 @@ (define-public python-drms
 (define-public python-ephem
   (package
     (name "python-ephem")
-    (version "4.1.3")
+    (version "4.1.4")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ephem" version))
               (sha256
                (base32
-                "0smmm3l8csnw9rrimh8mpyjrm80jaafjl184spnji98vk22qd8bz"))))
+                "0q67z79lgwdylxagbsjm42xvsmk5jmgvghy36m2n5lb2446rz9bk"))))
     (build-system python-build-system)
     (native-inputs (list tzdata))
     (home-page "https://rhodesmill.org/pyephem/")
-- 
2.39.2

[bug#63542] [PATCH v2 18/20] gnu: python-asdf: Update to 2.15.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf): Update to 2.15.0.
[native-inputs]: Add python-fsspec.
---
 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 b9fbb9d829..8c5d0455bc 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2729,13 +2729,13 @@ (define-public python-suntime
 (define-public python-asdf
   (package
     (name "python-asdf")
-    (version "2.13.0")
+    (version "2.15.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf" version))
        (sha256
-        (base32 "1zixzv4n2fryaszsfchqh2nvp0gzvarhz03fc721yw6iafdadqij"))))
+        (base32 "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8"))))
     (build-system pyproject-build-system)
     (arguments
      ;; FIXME: Tests fail a lot with
@@ -2746,6 +2746,7 @@ (define-public python-asdf
      `(#:tests? #f))
     (native-inputs
      (list python-astropy
+           python-fsspec
            python-packaging
            python-psutil
            python-pytest
-- 
2.39.2

[bug#63542] [PATCH v2 19/20] gnu: python-asdf-coordinates-schemas: Update to 0.2.0.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf-coordinates-schemas): Update
to 0.2.0.
[build-system]: Shift to python-build-system.
[arguments]: Do not modify standard phases.
---
 gnu/packages/astronomy.scm | 18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 8c5d0455bc..e3ebaee8b4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2842,26 +2842,16 @@ (define python-asdf-transform-schemas
 (define python-asdf-coordinates-schemas
   (package
     (name "python-asdf-coordinates-schemas")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asdf_coordinates_schemas" version))
        (sha256
-        (base32 "0ahwhsz5jzljnpkfd2kvspirg823lnj5ip9sfkd9cx09z1nlz8jg"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest")))))))
+        (base32 "1x6mipg76c6qldq8s2p2wpsq0cpr9b5krp62xskljdz1f84abyg3"))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest
-           python-semantic-version
-           python-setuptools-scm))
+     (list python-pytest python-semantic-version python-setuptools-scm))
     (propagated-inputs
      (list python-asdf))
     (home-page "https://github.com/asdf-format/asdf-coordinates-schemas")
-- 
2.39.2

[bug#63542] [PATCH v2 20/20] gnu: python-asdf: Enable tests.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-asdf): Enable the most tests.
---
 gnu/packages/astronomy.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e3ebaee8b4..67b5a601e3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2738,12 +2738,13 @@ (define-public python-asdf
         (base32 "11s56797l5330kkhppkyz0bsvms016knmyswj4gx91zrxf8iqvv8"))))
     (build-system pyproject-build-system)
     (arguments
-     ;; FIXME: Tests fail a lot with
-     ;;
-     ;; ERROR  - _pytest.pathlib.ImportPathMismatchError:
-     ;; ('asdf.conftest', '/gnu/sto...
-     ;;
-     `(#:tests? #f))
+     (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
-- 
2.39.2

bug#63542: [PATCH v2 00/20]: Cover review points.

[Vinicius Monego]

Em qua, 2023-05-24 às 22:51 +0100, Sharlatan Hellseher escreveu:


[...]

> Sharlatan Hellseher (20):
>   gnu: python-asdf-astropy: Update to 0.4.0.
>   gnu: python-asdf-wcs-schemas: Symplify.
>   gnu: python-gwcs: Update to 0.18.3.
>   gnu: python-sunpy: Update to 4.1.5.
>   gnu: python-spherical-geometry: Add update note.
>   gnu: python-sgp4: Update to 2.22.
>   gnu: python-ccdproc: Enable tests.
>   gnu: python-reproject: Update to 0.10.0.
>   gnu: python-pyvo: Update to 1.4.1.
>   gnu: python-fitsio: Use Gexp.
>   gnu: python-astropy-healpix: Use Gexp.
>   gnu: python-astroquery: Use Gexp.
>   gnu: python-pynbody: Update to 1.3.1, simplify.
>   gnu: python-astral: Update to 3.2.
>   gnu: python-poppy: Update to 1.1.1.
>   gnu: python-photutils: Update to 1.7.0.
>   gnu: python-ephem: Update to 4.1.4.
>   gnu: python-asdf: Update to 2.15.0.
>   gnu: python-asdf-coordinates-schemas: Update to 0.2.0.
>   gnu: python-asdf: Enable tests.
> 
>  gnu/packages/astronomy.scm | 350 +++++++++++++++++------------------
> --
>  1 file changed, 165 insertions(+), 185 deletions(-)
> 
> 
> base-commit: 242cc93438d67f5b35602d5add02e230850b0b43

I reworded the commit messages, made some styles changes to save a few
lines and pushed, thanks!

Vinicius