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

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3 participants
  • Efraim Flashner
  • Vinicius Monego
  • Sharlatan Hellseher
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Submitted by
Sharlatan Hellseher
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Debbugs page

Sharlatan Hellseher wrote 2 years ago
(address . guix-patches@gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
cover.1684276664.git.sharlatanus@gmail.com
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.

Toggle quote (9 lines)
> ./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
Sharlatan Hellseher wrote 2 years ago
[PATCH 02/19] gnu: python-asdf-wcs-schemas: Symplify.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
a0a9c89e9a7f5b19ed3705d4aab099e68eaa247f.1684276664.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (28 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 01/19] gnu: python-asdf-astropy: Update to 0.4.0.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
4968969990fa74d2686acda178e0d71ed4c41478.1684276664.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (34 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 03/19] gnu: python-gwcs: Update to 0.18.3.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
5868ae85ed4005fcfba904eb70b1043fc0c097c9.1684276664.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-gwcs): Update to 0.18.3.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 05/19] gnu: python-spherical-geometry: Add update note.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
f33f3fa545c970961edf28d92b40bc3b5df12f9d.1684276664.git.sharlatanus@gmail.com
* 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(+)

Toggle diff (15 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 04/19] gnu: python-sunpy: Update to 4.1.5.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
a67c96261594703c5d6d673402418503906ecee5.1684276664.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (73 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 07/19] gnu: python-ccdproc: Enable tests.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
851a6c2bac6f45e6776435d442ecc50425b7f286.1684276664.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-ccdproc): Enable tests.
---
gnu/packages/astronomy.scm | 5 -----
1 file changed, 5 deletions(-)

Toggle diff (18 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 06/19] gnu: python-sgp4: Update to 2.22.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
43d72aa153d2fd8b06eb0071862eb4c8a62126e1.1684276664.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-sgp4): Update to 2.22.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 08/19] gnu: python-reproject: Update to 0.10.0.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
9527807b60e2fd7134ab149708466c4d83fc397d.1684276665.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-reproject): Update to 0.10.0.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 09/19] gnu: python-pyvo: Update to 1.4.1.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
bcc2defcc24298e8d7f82ca7c99f3667430245eb.1684276665.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (38 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 19/19] gnu: python-asdf-coordinates-schemas: Update to 0.2.0.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
295e95158f62347910501a7ec632fe9ccb2265c5.1684276665.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (37 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 10/19] gnu: python-fitsio: Use Gexp.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
ced40e21dc0810e7f07ed249cda4b37c13259963.1684276665.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-fitsio): Adjust package style by
using Gexp.
---
gnu/packages/astronomy.scm | 39 +++++++++++++++++++-------------------
1 file changed, 20 insertions(+), 19 deletions(-)

Toggle diff (54 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 11/19] gnu: python-astropy-healpix: Use Gexp.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
e4a7c21503c86b35fb9da3d906acfe34fe9ada18.1684276665.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (42 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 12/19] gnu: python-astroquery: Use Gexp.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
a0f6e692504ec5f3edd8dee52b39d963395084ab.1684276665.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-astroquery): Use Gexp to simplify
package style.
---
gnu/packages/astronomy.scm | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)

Toggle diff (26 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 13/19] gnu: python-pynbody: Update to 1.3.1, simplify.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
60d6982378d94467982a1ba02100ceb57ccedd2b.1684276665.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (96 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 14/19] gnu: python-astral: Update to 3.2.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
b878905b7b246f66041a0b6900ec14ffe0b3b78e.1684276665.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (90 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 15/19] gnu: python-poppy: Update to 1.1.1.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
e326f700441fc3b7a525a99b489ab40c079d06da.1684276665.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-poppy): Update to 1.1.1.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 16/19] gnu: python-photutils: Update to 1.7.0.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
f957ab9c0ebe76dcb459b828734ffd20644e96a7.1684276665.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-photutils): Update to 1.7.0.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 17/19] gnu: python-ephem: Update to 4.1.4.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
6ce1d7cddc8d0bff6b9ebc6c85be74c82cd95373.1684276665.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-ephem): Update t 4.1.4.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH 18/19] gnu: python-asdf: Update to 2.15.0.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
aa705cda9188b139b95887f93a3b1df8b4846988.1684276665.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (40 lines)
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
Sharlatan Hellseher wrote 2 years ago
(address . 63542@debbugs.gnu.org)(address . efraim@flashner.co.il)
CAO+9K5p0MxFD98tb4SvMsCXMO7GMVAvFZmskXKvRwscRDmvRpQ@mail.gmail.com
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: file
Vinicius Monego wrote 2 years ago
8fce5f3160c4808c81f7c1c565b94c3e8351cde1.camel@posteo.net
Em qua, 2023-05-17 às 00:23 +0100, Sharlatan Hellseher escreveu:
Toggle quote (78 lines)
> * 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.

Toggle quote (9 lines)
>      (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.

Toggle quote (4 lines)
>             python-pandas
>             python-reproject
>             python-scikit-image

[...]

Vinicius
Vinicius Monego wrote 2 years ago
Re: [bug#63542] [PATCH 12/19] gnu: python-astroquery: Use Gexp.
c8823651198075729e90b82abacaa091c009bfde.camel@posteo.net
Em qua, 2023-05-17 às 00:23 +0100, Sharlatan Hellseher escreveu:
Toggle quote (17 lines)
> * 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?

Toggle quote (20 lines)
>      (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
Vinicius Monego wrote 2 years ago
Re: [bug#63542] [PATCH 14/19] gnu: python-astral: Update to 3.2.
b8c58dcda2fbfca1af09015b07bc4e9632aad09c.camel@posteo.net
Em qua, 2023-05-17 às 00:23 +0100, Sharlatan Hellseher escreveu:
Toggle quote (12 lines)
> * 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(-)
>
>

[...]

Toggle quote (6 lines)
> +                    " 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.

Toggle quote (24 lines)
> +                    " 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
Vinicius Monego wrote 2 years ago
Re: [bug#63542] [PATCH 18/19] gnu: python-asdf: Update to 2.15.0.
b5164bc6cdce5bcd8377a3e468a52040019efee9.camel@posteo.net
Em qua, 2023-05-17 às 00:23 +0100, Sharlatan Hellseher escreveu:
Toggle quote (43 lines)
> * 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
Vinicius Monego wrote 2 years ago
Re: [bug#63542]
e85dea6e28d4fed38f82dd3c5a4c386547c446a2.camel@posteo.net
Em ter, 2023-05-23 às 19:33 +0100, Sharlatan Hellseher escreveu:
Toggle quote (14 lines)
> 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
Efraim Flashner wrote 2 years ago
Re: Astronomy May updates
(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
ZG200dTOAFdNUrQY@3900XT
On Tue, May 23, 2023 at 07:33:22PM +0100, Sharlatan Hellseher wrote:
Toggle quote (5 lines)
> 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.

Toggle quote (3 lines)
> 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
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Sharlatan Hellseher wrote 2 years ago
[PATCH v2 00/20]: Cover review points.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
cover.1684964119.git.sharlatanus@gmail.com
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 01/20] gnu: python-asdf-astropy: Update to 0.4.0.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
4968969990fa74d2686acda178e0d71ed4c41478.1684964119.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (34 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 02/20] gnu: python-asdf-wcs-schemas: Symplify.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
a0a9c89e9a7f5b19ed3705d4aab099e68eaa247f.1684964119.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (28 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 03/20] gnu: python-gwcs: Update to 0.18.3.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
5868ae85ed4005fcfba904eb70b1043fc0c097c9.1684964119.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-gwcs): Update to 0.18.3.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 05/20] gnu: python-spherical-geometry: Add update note.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
e7537ca67b8660368015afb56b7c950c10afea0c.1684964119.git.sharlatanus@gmail.com
* 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(+)

Toggle diff (15 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 07/20] gnu: python-ccdproc: Enable tests.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
412f92b8f4d6229154dfe9542f9c9cd932519a77.1684964119.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-ccdproc): Enable tests.
---
gnu/packages/astronomy.scm | 5 -----
1 file changed, 5 deletions(-)

Toggle diff (18 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 06/20] gnu: python-sgp4: Update to 2.22.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
c632eaf2fae5dad2a9f36cc8a6ef84d48ca29974.1684964119.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-sgp4): Update to 2.22.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 04/20] gnu: python-sunpy: Update to 4.1.5.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
7dbe28c6339c8473cd1ec5d9551f6a64c288270c.1684964119.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (68 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 08/20] gnu: python-reproject: Update to 0.10.0.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
ad8477bee08865caef67306da11fc924a8caf2d2.1684964119.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-reproject): Update to 0.10.0.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 09/20] gnu: python-pyvo: Update to 1.4.1.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
c56c467f08469138001cc80a8de77e3f6a2aab8a.1684964119.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (38 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 10/20] gnu: python-fitsio: Use Gexp.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
1f31f3b01dd3424205f7c5416131022feba1fd97.1684964119.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-fitsio): Adjust package style by
using Gexp.
---
gnu/packages/astronomy.scm | 39 +++++++++++++++++++-------------------
1 file changed, 20 insertions(+), 19 deletions(-)

Toggle diff (54 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 11/20] gnu: python-astropy-healpix: Use Gexp.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
b9e41c78789fad8a826a6665391ff32a21c1c2fe.1684964119.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (42 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 12/20] gnu: python-astroquery: Use Gexp.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
1241553e15bd7bdbb61d7bda6d67820da8e33972.1684964119.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-astroquery): Use Gexp to simplify
package style.
---
gnu/packages/astronomy.scm | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)

Toggle diff (26 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 13/20] gnu: python-pynbody: Update to 1.3.1, simplify.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
7666bf908c80b9669128a73eadbd87a59ae735b6.1684964119.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (96 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 14/20] gnu: python-astral: Update to 3.2.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
185fa2ab4f22978c998bba45550981ed6677940c.1684964119.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (73 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 15/20] gnu: python-poppy: Update to 1.1.1.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
e7172d950c6f3bbcfef8998329e8523bdc9ee1c5.1684964119.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-poppy): Update to 1.1.1.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 16/20] gnu: python-photutils: Update to 1.7.0.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
ed2d88eaf43b29e7fd9dd999d04d407e2cf5163f.1684964119.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-photutils): Update to 1.7.0.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 17/20] gnu: python-ephem: Update to 4.1.4.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
32d3e68b5bf30598948f4529324e6b19fe5a6e2f.1684964119.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-ephem): Update t 4.1.4.
---
gnu/packages/astronomy.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 18/20] gnu: python-asdf: Update to 2.15.0.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
8135bdd48b7eef6b61fb2d47ff7afb13dd06d8f3.1684964119.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (30 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 20/20] gnu: python-asdf: Enable tests.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
45d483550c53b7eff76c0461cb292a1f4ab5c6b5.1684964119.git.sharlatanus@gmail.com
* gnu/packages/astronomy.scm (python-asdf): Enable the most tests.
---
gnu/packages/astronomy.scm | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)

Toggle diff (26 lines)
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
Sharlatan Hellseher wrote 2 years ago
[PATCH v2 19/20] gnu: python-asdf-coordinates-schemas: Update to 0.2.0.
(address . 63542@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
f1265fb7bb39521c0aa76d4ac372769f968afedb.1684964119.git.sharlatanus@gmail.com
* 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(-)

Toggle diff (37 lines)
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
Vinicius Monego wrote 2 years ago
Re: [bug#63542] [PATCH v2 00/20]: Cover review points.
929fd5b85e9b3eb3d2f96c0abc6477df44442f08.camel@posteo.net
Em qua, 2023-05-24 às 22:51 +0100, Sharlatan Hellseher escreveu:


[...]

Toggle quote (29 lines)
> 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
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