[bug#63136] [PATCH 00/14]: python-astropy: Update to 5.2.2, fix build.

[bug#63136] [PATCH 00/14]: python-astropy: Update to 5.2.2, fix build.

[Sharlatan Hellseher]

Hi Guix!

Here is the first portion of patches fixing failed to build graph of some
astronomical software where python-astropy plays important role. I tried to
bump to the latest buildable version and clean up packages where possible.

Package h3 needs some extra attention to check the license (it is Uber's
project with Apache-2 license as seen on front page).

h3 comes as C library with few language bindings, maybe, rest of them would be
included to Guix :) but for now it's only python-h3 and lower version
python-h3-3 to build python-timezonefinder.

> guix build --rounds=2 python-pytest-doctestplus python-pytest-filter-subpackage python-pytest-astropy python-extension-helpers python-jplephem python-skyfield python-pytest-remotedata python-pytest-arraydiff python-pytest-mpl python-astropy
> /gnu/store/1rgqf2szj1lsxpblb2wcb6hj1vykbpaf-python-astropy-5.2.2
> /gnu/store/xrkmzpaazaydhfchrl9dii522fsd4qir-python-pytest-mpl-0.16.1
> /gnu/store/4kx2im5j5pgydmhfflqzbipqwf2vx1xq-python-pytest-arraydiff-0.5.0
> /gnu/store/gr3sqfqyck4mmvqx735c8qrj3bhy7ni7-python-pytest-remotedata-0.4.0
> /gnu/store/fdp92xqqkiv4pggfsycxpkbz5pwk8g8p-python-skyfield-1.46
> /gnu/store/8j6hkls1jnadcnbn7nc4qjw3jd1wzhyc-python-jplephem-2.18
> /gnu/store/f43gcwsh51qnzx87gwm2xlrhry925nrm-python-extension-helpers-1.0.0
> /gnu/store/jqq065pc1g8z1822crpk8854pwi194hj-python-pytest-astropy-0.10.0
> /gnu/store/b3bpzjzklx0xklp10xnwscia7c7hx1pj-python-pytest-filter-subpackage-0.1.2
> /gnu/store/rwzqivchng64qwv4r5v29khn10bs53qz-python-pytest-doctestplus-0.12.1

Astropy has a lot of tests and 97.207% passed!
> = 23768 passed, 420 skipped, 139 deselected, 124 xfailed in 281.98s (0:04:41) ==
> phase `check' succeeded after 287.3 seconds
> starting phase `sanity-check'
> validating 'astropy' /gnu/store/1rgqf2szj1lsxpblb2wcb6hj1vykbpaf-python-astropy-5.2.2/lib/python3.10/site-packages
> ...checking requirements: OK
> ...trying to load module astropy: OK
> ...trying to load endpoint console_scripts fits2bitmap: OK
> ...trying to load endpoint console_scripts fitscheck: OK
> ...trying to load endpoint console_scripts fitsdiff: OK
> ...trying to load endpoint console_scripts fitsheader: OK
> ...trying to load endpoint console_scripts fitsinfo: OK
> ...trying to load endpoint console_scripts samp_hub: OK
> ...trying to load endpoint console_scripts showtable: OK
> ...trying to load endpoint console_scripts volint: OK
> ...trying to load endpoint console_scripts wcslint: OK

I could not list dependent packages due to internal faileur:
> ./pre-inst-env guix refresh python-astropy -l
> Backtrace:
> In ice-9/boot-9.scm:
>   1752:10 16 (with-exception-handler _ _ #:unwind? _ # _)
> In unknown file:
>           15 (apply-smob/0 #<thunk 7f1409d012e0>)
> In ice-9/boot-9.scm:
>     724:2 14 (call-with-prompt _ _ #<procedure default-prompt-handle…>)
> In ice-9/eval.scm:
>     619:8 13 (_ #(#(#<directory (guile-user) 7f1409d06c80>)))
> In guix/ui.scm:
>    2300:7 12 (run-guix . _)
>   2263:10 11 (run-guix-command _ . _)
> In ice-9/boot-9.scm:
>   1752:10 10 (with-exception-handler _ _ #:unwind? _ # _)
>   1752:10  9 (with-exception-handler _ _ #:unwind? _ # _)
> In guix/store.scm:
>    659:37  8 (thunk)
>   2168:25  7 (run-with-store #<store-connection 256.99 7f1409c26410> …)
> In guix/scripts/refresh.scm:
>    494:47  6 (_ _)
> In guix/packages.scm:
>   1405:32  5 (package-closure _ #:system _)
>   1592:16  4 (package->bag _ _ _ #:graft? _)
>   1693:48  3 (thunk)
> In gnu/packages/polkit.scm:
>    165:22  2 (inputs #<package xfce4-session@4.18.2 gnu/packages/xfc…>)
> In ice-9/boot-9.scm:
>   1685:16  1 (raise-exception _ #:continuable? _)
>   1685:16  0 (raise-exception _ #:continuable? _)
> 
> ice-9/boot-9.scm:1685:16: In procedure raise-exception:
> error: polkit-for-system: unbound variable

Thanks!

Sharlatan Hellseher (14):
  gnu: python-pytest-doctestplus: Update to 0.12.1.
  gnu: Add h3.
  gnu: Sort use-module alphabetically in (gnu packages geo).
  gnu: Add python-h3.
  gnu: Add python-timezonefinder.
  gnu: pytest-filter-subpackage: Update to 0.1.2.
  gnu: python-pytest-astropy: Simplify package.
  gnu: python-extension-helpers: Update to 1.0.0.
  gnu: python-jplephem: Update to 2.18.
  gnu: python-skyfield: Update to 1.46.
  gnu: python-pytest-remotedata: Update to 0.4.0.
  gnu: python-pytest-arraydiff: Update to 0.5.0.
  gnu: python-pytest-mpl: Update to 0.16.1.
  gnu: python-astropy: Update to 5.2.2, fix build.

 gnu/packages/astronomy.scm    |  29 +++++---
 gnu/packages/geo.scm          | 127 ++++++++++++++++++++++++++++++++--
 gnu/packages/python-check.scm | 116 ++++++++++++-------------------
 gnu/packages/python-xyz.scm   |  25 ++++---
 gnu/packages/time.scm         |  37 ++++++++++
 5 files changed, 238 insertions(+), 96 deletions(-)


base-commit: b8b3af93da5340eecab77fa7b12c7ce364bf11cf
-- 
2.39.2

[bug#63136] [PATCH 01/14] gnu: python-pytest-doctestplus: Update to 0.12.1.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-pytest-doctestplus): Update to
0.12.1.
[build-system]: Use pyproject-build-system.
[arguments]<phases>: Remove modify-phases and add test-flags option
instead.
[native-inputs]: Add python-numpy.
---
 gnu/packages/python-check.scm | 31 ++++++++++++-------------------
 1 file changed, 12 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index c42cd426b1..dd0600a2fc 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -577,32 +577,25 @@ (define-public python-pytest-arraydiff
 (define-public python-pytest-doctestplus
   (package
     (name "python-pytest-doctestplus")
-    (version "0.11.2")
+    (version "0.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-doctestplus" version))
        (sha256
-        (base32 "0j1lvlj3ps975q9hmg8i6rpqm0313j3r18bc3l8mz6khb7vav4zk"))))
-    (build-system python-build-system)
+        (base32 "10ciqylgziihxwxryxvxgmkqgws51pqcarn0gbh1d4cxx55rx5vs"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             ;; Make the installed plugin discoverable by Pytest.
-             (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest" "-k"
-                       (string-append   ; skip tests that require remote data
-                        "not test_remote_data_url"
-                        " and not test_remote_data_float_cmp"
-                        " and not test_remote_data_ignore_whitespace"
-                        " and not test_remote_data_ellipsis"
-                        " and not test_remote_data_requires"
-                        " and not test_remote_data_ignore_warnings"))))))))
+     (list #:test-flags
+           #~(list "-k" (string-append
+                         "not test_remote_data_url"
+                         " and not test_remote_data_float_cmp"
+                         " and not test_remote_data_ignore_whitespace"
+                         " and not test_remote_data_ellipsis"
+                         " and not test_remote_data_requires"
+                         " and not test_remote_data_ignore_warnings"))))
     (native-inputs
-     (list python-pytest python-setuptools-scm))
+     (list python-numpy python-pytest python-setuptools-scm))
     (home-page "https://github.com/astropy/pytest-doctestplus")
     (synopsis "Pytest plugin with advanced doctest features")
     (description
-- 
2.39.2

[bug#63136] [PATCH 02/14] gnu: Add h3.

[Sharlatan Hellseher]

* gnu/packages/geo.scm (h3): New variable.
---
 gnu/packages/geo.scm | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index cd56f50bf0..7b327a930d 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -14,7 +14,7 @@
 ;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020 Christopher Baines <mail@cbaines.net>
 ;;; Copyright © 2020, 2021, 2022, 2023 Felix Gruber <felgru@posteo.net>
-;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021, 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021, 2023 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2021, 2022 Nikolay Korotkiy <sikmir@disroot.org>
@@ -227,6 +227,30 @@ (define-public cdo
 than 600 operators available.")
     (license license:bsd-3)))
 
+(define-public h3
+  (package
+    (name "h3")
+    (version "4.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/uber/h3")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0x764xzna8ka6yhgv2y4hb158a61y3g9a6835qckqp7wfkpqvb7f"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")))
+    (home-page "https://h3geo.org/")
+    (synopsis "Hexagonal hierarchical geospatial indexing system")
+    (description "H3 is a geospatial indexing system using a hexagonal grid
+that can be (approximately) subdivided into finer and finer hexagonal grids,
+combining the benefits of a hexagonal grid with S2's hierarchical
+subdivisions.")
+    (license license:asl2.0)))
+
 (define-public memphis
   (package
     (name "memphis")
-- 
2.39.2

[bug#63136] [PATCH 03/14] gnu: Sort use-module alphabetically in (gnu packages geo).

[Sharlatan Hellseher]

* gnu/packages/geo.scm: Sort use-module alphabetically to ease
maintenance.
---
 gnu/packages/geo.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 7b327a930d..b49b74a949 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -38,6 +38,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages geo)
+  #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system ant)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system glib-or-gtk)
@@ -47,12 +48,11 @@ (define-module (gnu packages geo)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
-  #:use-module (guix gexp)
   #:use-module (guix download)
+  #:use-module (guix gexp)
   #:use-module (guix git-download)
-  #:use-module (guix svn-download)
-  #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
+  #:use-module (guix svn-download)
   #:use-module (guix utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
@@ -89,9 +89,9 @@ (define-module (gnu packages geo)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages haskell-apps)
   #:use-module (gnu packages haskell-xyz)
+  #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
   #:use-module (gnu packages image-processing)
-  #:use-module (gnu packages icu4c)
   #:use-module (gnu packages java)
   #:use-module (gnu packages kde)
   #:use-module (gnu packages libusb)
@@ -118,8 +118,8 @@ (define-module (gnu packages geo)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages speech)
-  #:use-module (gnu packages swig)
   #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages swig)
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
-- 
2.39.2

[bug#63136] [PATCH 04/14] gnu: Add python-h3.

[Sharlatan Hellseher]

* gnu/packages/geo.scm (python-h3): New variable.
---
 gnu/packages/geo.scm | 54 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index b49b74a949..a5a2567d83 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -251,6 +251,60 @@ (define-public h3
 subdivisions.")
     (license license:asl2.0)))
 
+(define-public python-h3
+  (package
+    (name "python-h3")
+    (version "4.0.0b2")
+    (source
+     (origin
+       (method git-fetch) ; no tests data in PyPi package
+       (uri (git-reference
+             (url "https://github.com/uber/h3-py")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1k1n256hhlh05gjcj64pqh08zlaz6962jkb6nk1aazsgg8p41zs0"))
+       (modules '((guix build utils)))
+       ;; Remove bundeled H3 lib.
+       (snippet #~(begin (delete-file-recursively "src/h3lib")))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; FIXME: Check why these tests are failing.
+      ;; test_versions - assert (4, 1) == (4, 0)
+      ;; test_resolution - h3._cy.error_system.H3Failed
+      #:test-flags #~(list "-k" (string-append
+                                 "not test_versions"
+                                 " and not test_resolution"))
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; Use packaged in Guix h3 source.
+          (add-after 'unpack 'patch-cmakelists
+            (lambda _
+              (substitute* "CMakeLists.txt"
+                (("add_subdirectory\\(src/h3lib\\)")
+                 (string-append
+                  "include_directories(" #$(this-package-input "h3")
+                  "/include/h3)\n"
+                  "link_directories(" #$(this-package-input "h3")
+                  "/lib)\n"))
+                ((".*CMAKE_CURRENT_BINARY_DIR.*")
+                 (string-append #$(this-package-input "h3")
+                                "/include/h3/h3api.h\n"))))))))
+    (native-inputs
+     (list cmake
+           python-cython
+           python-numpy
+           python-pytest
+           python-scikit-build
+           python-setuptools-scm))
+    (inputs (list h3))
+    (home-page "https://uber.github.io/h3-py")
+    (synopsis "Python bindings for H3")
+    (description "This package provides a Python bindings for H3, a
+hierarchical hexagonal geospatial indexing system")
+    (license license:asl2.0)))
+
 (define-public memphis
   (package
     (name "memphis")
-- 
2.39.2

[bug#63136] [PATCH 05/14] gnu: Add python-timezonefinder.

[Sharlatan Hellseher]

* gnu/packages/time.scm (python-timezonefinder): New variable.
* gnu/packages/geo.scm (h3-3, python-h3-3): New variables. The latest
compatible versions to build python-timezonefinder.
---
 gnu/packages/geo.scm  | 37 +++++++++++++++++++++++++++++++++++++
 gnu/packages/time.scm | 37 +++++++++++++++++++++++++++++++++++++
 2 files changed, 74 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index a5a2567d83..907eb2cc93 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -251,6 +251,23 @@ (define-public h3
 subdivisions.")
     (license license:asl2.0)))
 
+;; For python-timezonefinder, remove it when it starts supporting newer
+;; version.
+(define-public h3-3
+  (package
+    (inherit h3)
+    (name "h3")
+    (version "3.7.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/uber/h3")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0bvsljfxmjvl23v9gxykc4aynjzh5xfy3wg02bxad7cknr1amx9j"))))))
+
 (define-public python-h3
   (package
     (name "python-h3")
@@ -305,6 +322,26 @@ (define-public python-h3
 hierarchical hexagonal geospatial indexing system")
     (license license:asl2.0)))
 
+;; For python-timezonefinder, remove it when it starts supporting newer
+;; version.
+(define-public python-h3-3
+  (package
+    (inherit python-h3)
+    (name "python-h3")
+    (version "3.7.6")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/uber/h3-py")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16gxa1sivghxw179rik87r918mjasars2qkzidlwq83qfa4axn20"))))
+    (inputs
+     (modify-inputs (package-inputs python-h3)
+       (replace "h3" h3-3)))))
+
 (define-public memphis
   (package
     (name "memphis")
diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index c0bcb848b3..36b561b041 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -21,6 +21,7 @@
 ;;; Copyright © 2021 Ryan Prior <rprior@protonmail.com>
 ;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
 ;;; Copyright © 2022 Pradana AUMARS <paumars@courrier.dev>
+;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -40,7 +41,9 @@
 (define-module (gnu packages time)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages geo)
   #:use-module (gnu packages golang)
+  #:use-module (gnu packages libffi)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
@@ -50,8 +53,10 @@ (define-module (gnu packages time)
   #:use-module (gnu packages)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix download)
+  #:use-module (guix gexp)
   #:use-module (guix git-download)
   #:use-module (guix licenses)
   #:use-module (guix packages))
@@ -278,6 +283,38 @@ (define-public python-ciso8601
 Python datetime objects.")
     (license expat)))
 
+(define-public python-timezonefinder
+  (package
+    (name "python-timezonefinder")
+    (version "6.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       ;; The PyPi distribution doesn't include the tests.
+       (uri (git-reference
+             (url "https://github.com/jannikmi/timezonefinder")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0qv9rh6j8c1cqwh4sxrfl1m1ah4aqrf0w2kyrf5cgrpfxi6xr94z"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; TODO: Guix has lower python-pytz than required in the latest
+      ;; version:  pytz.exceptions.UnknownTimeZoneError:
+      ;; 'America/Ciudad_Juarez'
+      ;; It's optional, remove this constrain where python-pytz is updated.
+      #:test-flags #~(list "-k" "not test_with_pytz")))
+    (native-inputs
+     (list python-poetry-core python-pytest))
+    (propagated-inputs
+     (list python-cffi python-h3-3 python-numba python-numpy python-pytz))
+    (home-page "https://timezonefinder.michelfe.it/gui")
+    (synopsis "Finding the timezone of any coordinates on Earth offline")
+    (description "This is a python package for looking up the corresponding
+timezone for given coordinates on earth entirely offline.")
+    (license expat)))
+
 (define-public python-tzlocal
   (package
     (name "python-tzlocal")
-- 
2.39.2

[bug#63136] [PATCH 06/14] gnu: pytest-filter-subpackage: Update to 0.1.2.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (pytest-filter-subpackage): Update to
0.1.2.
[build-system]: Use pyproject-build-system.
[arguments]: Drop no more required phases.
[native-inputs]: Add python-setuptools-scm.
---
 gnu/packages/python-check.scm | 22 +++++++---------------
 1 file changed, 7 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index dd0600a2fc..3be8920e3c 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -633,27 +633,19 @@ (define-public python-pytest-exploratory
 (define-public python-pytest-filter-subpackage
   (package
     (name "python-pytest-filter-subpackage")
-    (version "0.1.1")
+    (version "0.1.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-filter-subpackage" version))
        (sha256
-        (base32 "1s4s2kd31yc65rfvl4xhy8xx806xhy59kc7668h6b6wq88xgrn5p"))))
-    (build-system python-build-system)
-    (arguments
-     '(;; One test is failing. There's an issue reported upstream. See
-       ;; https://github.com/astropy/pytest-filter-subpackage/issues/3.
-       ;; Disable it for now.
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Make the installed plugin discoverable by Pytest.
-             (add-installed-pythonpath inputs outputs)
-             (invoke "pytest" "-vv" "-k" "not test_with_rst"))))))
+        (base32 "10hpl3f7g2bm29lakmp8492b7lr0dp90khfni12m4gl02xks7bhz"))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest python-pytest-cov python-pytest-doctestplus))
+     (list python-pytest
+           python-pytest-cov
+           python-pytest-doctestplus
+           python-setuptools-scm))
     (home-page "https://github.com/astropy/pytest-filter-subpackage")
     (synopsis "Pytest plugin for filtering based on sub-packages")
     (description
-- 
2.39.2

[bug#63136] [PATCH 07/14] gnu: python-pytest-astropy: Simplify package.

[Sharlatan Hellseher]

* gnu/package/python-check.scm (python-pytest-astropy): Simplify package.
[arguments]<phases>: Remove remove-requirement phase.
---
 gnu/packages/python-check.scm | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 3be8920e3c..b5a68143f3 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -518,16 +518,7 @@ (define-public python-pytest-astropy
        (sha256
         (base32 "04g2rh261s3s6ym8mwi4iv2a6anbgwvwzcvkyilfck6yxrncdqw5"))))
     (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; there are no tests
-       #:phases
-       (modify-phases %standard-phases
-         ;; There is a bug somewhere that makes pytest-filter-subpackage appear
-         ;; as version 0.0.0 to setup.py.  Remove it from the requirements.
-         (add-after 'unpack 'remove-requirement
-           (lambda _
-             (substitute* "setup.cfg"
-               ((".*pytest-filter-subpackage.*") "")))))))
+    (arguments (list #:tests? #f)) ; there are no tests
     (native-inputs
      (list python-attrs python-pytest-mock python-setuptools-scm))
     (propagated-inputs
-- 
2.39.2

[bug#63136] [PATCH 08/14] gnu: python-extension-helpers: Update to 1.0.0.

[Sharlatan Hellseher]

* gnu/packages/python-xyz.scm (python-extension-helpers): Update to
1.0.0.
[build-system]: Use pyproject-build-system.
[arguments]<tests>: Disable them, as pytest can't load the test suite.
[native-inputs]: Add python-setuptools-scm.
[home-page]: Re-point to actual project home page.
[synopsis]: Adjust it to cover actual project.
[description]: ... as above.
---
 gnu/packages/python-xyz.scm | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e2d082091f..162c6c4e57 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3569,23 +3569,30 @@ (define-public python-exceptiongroup
 (define-public python-extension-helpers
 (package
   (name "python-extension-helpers")
-  (version "0.1")
+  (version "1.0.0")
   (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "extension-helpers" version))
       (sha256
-        (base32 "10iqjzmya2h4sk765dlm1pbqypwlqyh8rw59a5m9i63d3klnz2mc"))))
-  (build-system python-build-system)
+        (base32 "1rjha07ds633fb81hn3i2yzk3v2flbi6qa091ix4mkvrgk3gl6ya"))))
+  (build-system pyproject-build-system)
+  ;; FIXME: pytest failed to load test suit, find out why.
+  ;;  - _pytest.pathlib.ImportPathMismatchError: ('extension_helpers.conftes
+  (arguments (list #:tests? #f))
   (native-inputs
-    (list python-coverage python-pytest-astropy python-pytest-cov
+    (list python-coverage
+          python-pytest
+          python-pytest-astropy
+          python-pytest-cov
           python-setuptools-scm))
-  (home-page "https://github.com/astropy/astropy-helpers")
-  (synopsis
-   "Utilities for building and installing packages in the Astropy ecosystem")
+  (home-page "https://extension-helpers.readthedocs.io")
+  (synopsis "Astropy ecosystem utilities for building and installing packages")
   (description
-    "The extension-helpers package includes many build, installation, and
-documentation-related tools used by the Astropy project.")
+    "The extension-helpers package includes convenience helpers to assist with
+building Python packages with compiled C/Cython extensions.  It is developed by
+the Astropy project but is intended to be general and usable by any Python
+package.")
   (license license:bsd-3)))
 
 (define-public python-extras
-- 
2.39.2

[bug#63136] [PATCH 09/14] gnu: python-jplephem: Update to 2.18.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-jplephem): Update to 2.18.
---
 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 888e5bb1d7..3344f87e63 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2474,13 +2474,13 @@ (define-public sunclock
 (define-public python-jplephem
   (package
     (name "python-jplephem")
-    (version "2.17")
+    (version "2.18")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "jplephem" version))
        (sha256
-        (base32 "09xaibxnwbzzs3x9g3ibqa2la17z3r6in93321glh02dbibfbip1"))))
+        (base32 "1rgswy52ismij0bkmfqwbml5zikzvzzs1f833dwk0y64lkl12aa9"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
2.39.2

[bug#63136] [PATCH 10/14] gnu: python-skyfield: Update to 1.46.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-skyfield): Update to 1.46.
---
 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 3344f87e63..bd7fb22a31 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3017,13 +3017,13 @@ (define-public python-astroalign
 (define-public python-skyfield
   (package
     (name "python-skyfield")
-    (version "1.39")
+    (version "1.46")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "skyfield" version))
        (sha256
-        (base32 "1qh3k7g9dm6idppk87hnwxpx9a22xx98vav0zk31p6291drak3as"))))
+        (base32 "1r4kpsh1pa4h3diyxy3gyapp0rykfjdqmn5w348a2ck2qkdlx997"))))
     (build-system python-build-system)
     (arguments
      ;; NOTE: (Sharlatan-20210207T163305+0000): tests depend on custom test
-- 
2.39.2

[bug#63136] [PATCH 11/14] gnu: python-pytest-remotedata: Update to 0.4.0.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-pytest-remotedata): Update to
0.4.0.
[build-system]: Use pyproject-build-system.
[arguments]<phases>: Simplify by removing not required phase
modification and use <test-flags> instead.
[native-inputs]: Add python-setuptools-scm.
[propagated-inputs]: Delete python-six, add python-packaging.
---
 gnu/packages/python-check.scm | 25 +++++++++----------------
 1 file changed, 9 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index b5a68143f3..71bbf59d49 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -735,30 +735,23 @@ (define-public python-pytest-openfiles
 (define-public python-pytest-remotedata
   (package
     (name "python-pytest-remotedata")
-    (version "0.3.2")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-remotedata" version))
        (sha256
-        (base32 "1h6g6shib6z07azf12rnsa053470ggbd7hy3bnbw8nf3nza5h372"))))
-    (build-system python-build-system)
+        (base32 "1j5106j331cfdyfcwzrbs3yby84mq1b0kddfysq12z2dwdcca8dy"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Make the installed plugin discoverable by Pytest.
-             (add-installed-pythonpath inputs outputs)
-             (invoke "pytest" "-vv" "-k"
-                     (string-append
-                      ;; These tests require internet access. Disable them.
-                      "not test_default_behavior"
-                      " and not test_strict_with_decorator")))))))
+     (list
+      #:test-flags #~(list "-k" (string-append
+                                 "not test_default_behavior"
+                                 " and not test_strict_with_decorator"))))
     (native-inputs
-     (list python-pytest))
+     (list python-pytest python-setuptools-scm))
     (propagated-inputs
-     (list python-six))
+     (list python-packaging))
     (home-page "https://github.com/astropy/pytest-remotedata")
     (synopsis "Pytest plugin for controlling remote data access")
     (description
-- 
2.39.2

[bug#63136] [PATCH 12/14] gnu: python-pytest-arraydiff: Update to 0.5.0.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-pytest-arraydiff): Update to
0.5.0.
[native-inputs]: Add python-setuptools-scm.
[propagated-inputs]: Remove python-six.
---
 gnu/packages/python-check.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 71bbf59d49..9a61f59d56 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -541,22 +541,22 @@ (define-public python-pytest-astropy
 (define-public python-pytest-arraydiff
   (package
     (name "python-pytest-arraydiff")
-    (version "0.3")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-arraydiff" version))
        (sha256
-        (base32 "05bcvhh2ycxa35znl8b3l9vkcmx7vwm5c3fpakbpw46c7vsn4bfy"))))
+        (base32 "1livzfbi7ag17hskd5845dh1kdir24f7jrbw8y2s1pyhzyz4jhbi"))))
     (build-system python-build-system)
     (arguments
      ;; Tests require python-astropy, which itself requires this package.
      ;; Disable tests to avoid the circular dependency problem.
      '(#:tests? #f))
     (native-inputs
-     (list python-pytest)) ; for sanity-check
+     (list python-pytest python-setuptools-scm)) ; for sanity-check
     (propagated-inputs
-     (list python-numpy python-six))
+     (list python-numpy))
     (home-page "https://github.com/astropy/pytest-arraydiff")
     (synopsis "Pytest plugin to help with comparing array output from tests")
     (description
-- 
2.39.2

[bug#63136] [PATCH 13/14] gnu: python-pytest-mpl: Update to 0.16.1.

[Sharlatan Hellseher]

* gnu/packages/python-check.scm (python-pytest-mpl): Update to 0.16.1.
[build-system]: Use pyproject-build-system.
[arguments]<phases>: Simplify phases by removing redundant modification
and use <test-flags> instead.
[propagated-inputs]: Add python-jinja2, python-packaging.
---
 gnu/packages/python-check.scm | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 9a61f59d56..d939ade03b 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -831,24 +831,25 @@ (define-public python-pytest-mockito
 (define-public python-pytest-mpl
   (package
     (name "python-pytest-mpl")
-    (version "0.11")
+    (version "0.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-mpl" version))
        (sha256
-        (base32 "1km202c1s5kcn52fx0266p06qb34va3warcby594dh6vixxa9i96"))))
-    (build-system python-build-system)
+        (base32 "0sa4229xkkah3fdg9wnqnvb9j13xsd3x1h5rwbsgb3sf2a0icmrd"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (invoke "pytest" "-vv"))))))
+     (list
+      #:test-flags #~(list "-m" "mpl_image_compare")))
     (native-inputs
      (list python-pytest))
     (propagated-inputs
-     (list python-matplotlib python-nose python-pillow))
+     (list python-jinja2
+           python-matplotlib
+           python-nose
+           python-packaging
+           python-pillow))
     (home-page "https://github.com/matplotlib/pytest-mpl")
     (synopsis "Pytest plugin to help with testing figures output from Matplotlib")
     (description
-- 
2.39.2

[bug#63136] [PATCH 14/14] gnu: python-astropy: Update to 5.2.2, fix build.

[Sharlatan Hellseher]

* gnu/packages/astronomy.scm (python-astropy): Update to 5.2.2.
[arguments]<phases>{check}: Skip 2 more failing tests.
[native-inputs]: Add python-colorlog, python-h5py, python-pandas,
python-pyarrow, python-pytest-astropy-header, python-scikit-image,
python-scipy, python-timezonefinder.
---
 gnu/packages/astronomy.scm | 21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index bd7fb22a31..355f09fa57 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -41,6 +41,7 @@ (define-module (gnu packages astronomy)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages geo)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages glib)
@@ -1131,13 +1132,13 @@ (define-public celestia-gtk
 (define-public python-astropy
   (package
     (name "python-astropy")
-    (version "5.2.1")
+    (version "5.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "astropy" version))
        (sha256
-        (base32 "08xc6brs7xwiqchhsjq8l10p6qc5p68cfxps7s889spqfyh2gbpn"))
+        (base32 "170ddflli35mvhf6pla7aizfw8a7ckq66g1mi1br99dx2r3y7ag6"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -1187,21 +1188,33 @@ (define-public python-astropy
                (invoke "python" "setup.py" "build_ext" "--inplace")
                (invoke "python" "-m" "pytest" "--pyargs" "astropy"
                        ;; Skip tests that need remote data.
-                       "-m" "not remote_data")))))))
+                       "-k" (string-append
+                             "not remote_data"
+                             ;; XXX: Check why this tests failing.
+                             " and not test_ignore_sigint"
+                             " and not test_parquet_filter"))))))))
     (native-inputs
      (list pkg-config
+           python-colorlog
            python-coverage
            python-cython
            python-extension-helpers
+           python-h5py
            python-ipython
            python-jplephem
            python-objgraph
+           python-pandas
+           python-pyarrow
            python-pytest
            python-pytest-astropy
+           python-pytest-astropy-header
            python-pytest-xdist
+           python-scikit-image
+           python-scipy
            python-setuptools-scm
            python-sgp4
-           python-skyfield))
+           python-skyfield
+           python-timezonefinder))
     (inputs
      (list cfitsio expat wcslib))
     (propagated-inputs
-- 
2.39.2

[bug#63136]

[Sharlatan Hellseher]

[-- Attachment #1: Type: text/plain, Size: 96 bytes --]

Hi,

A gentle ping for review. Please let me know if I need to update patch set.

Regards,
Oleg

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bug#63136:

[Efraim Flashner]

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On Tue, May 02, 2023 at 03:51:28PM +0100, Sharlatan Hellseher wrote:
> Hi,
> 
> A gentle ping for review. Please let me know if I need to update patch set.
> 
> Regards,
> Oleg

Everything looks good. I've gone ahead and pushed the patches.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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