[PATCH]: gnu: Add python-gwcs

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3 participants
  • Vinicius Monego
  • Mathieu Othacehe
  • Sharlatan Hellseher
Owner
unassigned
Submitted by
Sharlatan Hellseher
Severity
normal
S
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Sharlatan Hellseher wrote on 11 Nov 2021 14:17
(address . guix-patches@gnu.org)
CAO+9K5ppbo8uz8xn1uD6G5x30MHbu4afGGg7HU8eGLOmMo3K9w@mail.gmail.com
successfully built
/gnu/store/w870dhpqfq5ycggj9510kj1y54wqgz7v-python-gwcs-0.16.1.drv
--
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From 5504205f6fcff3741c86bc8e9d203ea5da2ab431 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Thu, 11 Nov 2021 13:14:41 +0000
Subject: [PATCH] gnu: Add python-gwcs

* gnu/packages/astronomy.scm: (python-gwcs): New variable.
---
gnu/packages/astronomy.scm | 43 ++++++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)

Toggle diff (56 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index fc8959faad..59708e8e6b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -708,6 +708,49 @@ (define-public python-astropy
astronomy and astrophysics.")
(license license:bsd-3)))
+(define-public python-gwcs
+ (package
+ (name "python-gwcs")
+ (version "0.16.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "gwcs" version))
+ (sha256
+ (base32 "0xjmv0v8bdzhpq61gvp76bx17pbcvxs8vp2gmn0rgs01zkrg8csk"))))
+ (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" "--pyargs" "gwcs")))))))
+ (native-inputs
+ `(("python-jsonschema" ,python-jsonschema)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-doctestplus" ,python-pytest-doctestplus)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-semantic-version" ,python-semantic-version)
+ ("python-setuptools-scm" ,python-setuptools-scm)))
+ (propagated-inputs
+ `(("python-asdf" ,python-asdf)
+ ("python-astropy" ,python-astropy)
+ ("python-numpy" ,python-numpy)
+ ("python-scipy" ,python-scipy)))
+ (home-page "https://gwcs.readthedocs.io/en/latest/")
+ (synopsis "Generalized World Coordinate System")
+ (description
+ "Generalized World Coordinate System (GWCS) is an Astropy affiliated package
+providing tools for managing the World Coordinate System of astronomical data.
+
+GWCS takes a general approach to the problem of expressing transformations
+between pixel and world coordinates. It supports a data model which includes the
+entire transformation pipeline from input coordinates (detector by default) to
+world coordinates. It is tightly integrated with Astropy.")
+ (license license:bsd-3)))
+
(define-public libnova
(package
(name "libnova")
--
2.33.1
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Sharlatan Hellseher wrote on 26 Dec 2021 20:01
(address . 51765@debbugs.gnu.org)
CAO+9K5ozMHChdvtONnWeA5HK9iW7xqpZxGvPKJQLpoTexQvsvQ@mail.gmail.com
Hi Guix team!
Just a gentle ping for this patch, thanks.
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Mathieu Othacehe wrote on 26 Dec 2021 20:55
(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)(address . 51765@debbugs.gnu.org)
87r19znnsv.fsf@gnu.org
Hello,

Toggle quote (2 lines)
> /gnu/store/w870dhpqfq5ycggj9510kj1y54wqgz7v-python-gwcs-0.16.1.drv

Sorry for the delay! Looks like the 0.18.0 release is out there. The
build dependency python-pytest-arraydiff also fails to build. Could you
please have a look?

Thanks,

Mathieu
S
S
Sharlatan Hellseher wrote on 26 Dec 2021 21:47
(name . Mathieu Othacehe)(address . othacehe@gnu.org)(address . 51765@debbugs.gnu.org)
CAO+9K5ptu4adJ6KTqPPcX2iA=P9Z6TRj=yu9UtPAemQr6J+ToQ@mail.gmail.com
Hi,

As it depends on astropy and it's failing right now, this patch list
may be reviewed first:


I'll update gwcs to the 0.18.0 when this issue is resovled:

phase `check' succeeded after 0.0 seconds
starting phase `sanity-check'
validating 'pytest-arraydiff'
/gnu/store/hcg67xxfvlgg2kga73f026bzs9ck97lh-python-pytest-arraydiff-0.3/lib/python3.9/site-packages
...checking requirements: ERROR: pytest-arraydiff==0.3 The 'pytest'
distribution was not found and is required by pytest-arraydiff
error: in phase 'sanity-check': uncaught exception:
%exception #<&invoke-error program: "python" arguments:
("/gnu/store/nwwr89v2vyg1hs48i49m083vhczsgh3m-sanity-check.py"
"/gnu/store/hcg67xxfvlgg2kga73f026bzs9ck97lh-python-pytest-arraydiff-0.3/lib/python3.9/site-packages")
exit-status: 1 term-signal: #f stop-signal: #f>
phase `sanity-check' failed after 0.1 seconds
command "python"
"/gnu/store/nwwr89v2vyg1hs48i49m083vhczsgh3m-sanity-check.py"
"/gnu/store/hcg67xxfvlgg2kga73f026bzs9ck97lh-python-pytest-arraydiff-0.3/lib/python3.9/site-packages"
failed with status 1
builder for `/gnu/store/aa1hlq988yfk816xf0mk6d8lkp0hrmzh-python-pytest-arraydiff-0.3.drv'
failed with exit code 1
build of /gnu/store/aa1hlq988yfk816xf0mk6d8lkp0hrmzh-python-pytest-arraydiff-0.3.drv
failed
View build log at
'/var/log/guix/drvs/aa/1hlq988yfk816xf0mk6d8lkp0hrmzh-python-pytest-arraydiff-0.3.drv.bz2'.
guix build: error: build of
`/gnu/store/aa1hlq988yfk816xf0mk6d8lkp0hrmzh-python-pytest-arraydiff-0.3.drv'
failed

On Sun, 26 Dec 2021 at 19:55, Mathieu Othacehe <othacehe@gnu.org> wrote:
Toggle quote (16 lines)
>
>
> Hello,
>
> > /gnu/store/w870dhpqfq5ycggj9510kj1y54wqgz7v-python-gwcs-0.16.1.drv
>
> Sorry for the delay! Looks like the 0.18.0 release is out there. The
> build dependency python-pytest-arraydiff also fails to build. Could you
> please have a look?
>
> Thanks,
>
> Mathieu



--

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M
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Mathieu Othacehe wrote on 26 Dec 2021 21:55
(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)(address . 51765@debbugs.gnu.org)
87mtknnl1s.fsf@gnu.org
Hey,

Toggle quote (2 lines)
> I'll update gwcs to the 0.18.0 when this issue is resovled:

Nicolas just took care of it :).

Thanks,

Mathieu
S
S
Sharlatan Hellseher wrote on 2 Jan 2022 23:48
(address . 51765@debbugs.gnu.org)(name . Mathieu Othacehe)(address . othacehe@gnu.org)
CAO+9K5pDfaVRvv98ObZfxJnA=N9-gaG7JN5zajjE9Hq9Ngk7mg@mail.gmail.com
Hi Guix team and Happy New 2022 Year!
The update took more time then I expected, but eventually it's
finished with some extra modification and new patch list.
Sharlatan Hellseher (6):
gnu: python-asdf: Update to 2.8.3
gnu: Add asdf-transform-schemas
gnu: Add asdf-coordinates-schemas
gnu: Add asdf-astropy
gnu: Add asdf-wcs-schemas
gnu: Add gwcs
gnu/packages/astronomy.scm | 209 +++++++++++++++++++++++++++++++++----
1 file changed, 191 insertions(+), 18 deletions(-)
base-commit: 01ec5efff7cf95cae69493bd4ccfdd21a38770ae
On Sun, 26 Dec 2021 at 20:55, Mathieu Othacehe <othacehe@gnu.org> wrote:
Toggle quote (11 lines)
>
>
> Hey,
>
> > I'll update gwcs to the 0.18.0 when this issue is resovled:
>
> Nicolas just took care of it :).
>
> Thanks,
>
> Mathieu
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Sharlatan Hellseher wrote on 2 Jan 2022 23:48
(address . 51765@debbugs.gnu.org)
CAO+9K5qUM1G9vnh_hsPVkPhDm5EWN41t6anEZsxrcmSiPkoQgw@mail.gmail.com
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From 051573892c1db5679f20155583eb50e7d2be5100 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Sun, 2 Jan 2022 20:24:03 +0000
Subject: [PATCH 1/6] gnu: python-asdf: Update to 2.8.3

* gnu/packages/astronomy.scm: (python-asdf): Update to 2.8.3
Refactor package style.
[inputs]->[propagated-inputs]: To satisfy sanity checks of other
packages depended on python-asdf. Add new input python-jmespath
---
gnu/packages/astronomy.scm | 37 +++++++++++++++++++------------------
1 file changed, 19 insertions(+), 18 deletions(-)

Toggle diff (60 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 1f9eca9a44..5b5887fb2e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1238,34 +1238,35 @@ (define-public python-sep
(define-public python-asdf
(package
(name "python-asdf")
- (version "2.7.4")
+ (version "2.8.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "asdf" version))
(sha256
- (base32 "1mj52l2m8pbhiqacgjakjpvqi8kyx470yw151lcsswbq5wp0rsc6"))))
+ (base32 "0i4vq1hsympjgb1yvn4ql0gm8j1mki9ggmj03533kmg0nbzp03yy"))))
(build-system python-build-system)
(arguments
- ;; TODO: (Sharlatan-20210207T165820+0000): Tests depend on astropy, astropy
- ;; depends on asdf. Disable circular dependence.
- `(#:tests? #f))
+ ;; NOTE: (Sharlatan-20211229T201059+0000): Tests depend on astropy and
+ ;; gwcs, astropy gwcs depend on asdf. Disable circular dependence.
+ (list #:tests? #f))
(native-inputs
- `(("packaging" ,python-packaging)
- ("semantic-version" ,python-semantic-version)
- ("setuptools-scm" ,python-setuptools-scm)))
- (inputs
- `(("importlib-resources" ,python-importlib-resources)
- ("jsonschema" ,python-jsonschema)
- ("numpy" ,python-numpy)
- ("pyyaml" ,python-pyyaml)))
- (home-page "https://github.com/asdf-format/asdf")
- (synopsis "Python tools to handle ASDF files")
- (description
- "The Advanced Scientific Data Format (ASDF) is a next-generation
+ (list python-setuptools-scm
+ python-semantic-version
+ python-packaging))
+ (propagated-inputs
+ (list python-importlib-resources
+ python-jsonschema
+ python-jmespath
+ python-numpy
+ python-pyyaml))
+ (home-page "https://github.com/asdf-format/asdf")
+ (synopsis "Python tools to handle ASDF files")
+ (description
+ "The Advanced Scientific Data Format (ASDF) is a next-generation
interchange format for scientific data. This package contains the Python
implementation of the ASDF Standard.")
- (license license:bsd-3)))
+ (license license:bsd-3)))
(define-public python-astroalign
(package
--
2.34.0
S
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Sharlatan Hellseher wrote on 2 Jan 2022 23:48
(address . 51765@debbugs.gnu.org)
CAO+9K5pAJOaLoJ_c0eF3hRUO+BcLM1=AXTBq_QzAAX6zwcxN0Q@mail.gmail.com
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From b1ec99ee7222751e7b7393b3ea2ce32e6131a0d3 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Sun, 2 Jan 2022 21:10:12 +0000
Subject: [PATCH 2/6] gnu: Add asdf-transform-schemas

* gnu/packages/astronomy.scm: (python-asdf-transform-schemas): New variable.
---
gnu/packages/astronomy.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)

Toggle diff (44 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 5b5887fb2e..8d08c5421d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1268,6 +1268,37 @@ (define-public python-asdf
implementation of the ASDF Standard.")
(license license:bsd-3)))
+(define-public python-asdf-transform-schemas
+ (package
+ (name "python-asdf-transform-schemas")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "asdf_transform_schemas" version))
+ (sha256
+ (base32 "1gmzd81hw4ppsvzrc91wcbjpcw9hhv9gavllv7nyi7qjb54c837g"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ ;; FIXME: (Sharlatan-20211229T160902+0000): tests run via tox
+ #:tests? #f))
+ (native-inputs
+ (list python-semantic-version
+ python-setuptools-scm))
+ (propagated-inputs
+ (list python-asdf))
+ (home-page "https://github.com/asdf-format/asdf-transform-schemas")
+ (synopsis "ASDF schemas for transforms")
+ (description
+ "This package provides ASDF schemas for validating transform tags. Users
+should not need to install this directly; instead, install an implementation
+package such as asdf-astropy, which includes asdf-transform-schemas as a
+dependency.")
+ ;; Copyright (C) 2021 Association of Universities for Research in Astronomy (AURA)
+ ;; https://github.com/asdf-format/asdf-transform-schemas/blob/master/LICENSE
+ (license license:bsd-3)))
+
(define-public python-astroalign
(package
(name "python-astroalign")
--
2.34.0
S
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Sharlatan Hellseher wrote on 2 Jan 2022 23:48
(address . 51765@debbugs.gnu.org)
CAO+9K5o5m38pqtLVbCJB=VSyuP6oV_oPL0PNb7qmnRD_75zBJw@mail.gmail.com
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From 241525ef2ed98cfb0cbc63c22a8d5658fad5e4d7 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Sun, 2 Jan 2022 21:12:17 +0000
Subject: [PATCH 3/6] gnu: Add asdf-coordinates-schemas

* gnu/packages/astronomy.scm: (python-asdf-coordinates-schemas): New variable.
---
gnu/packages/astronomy.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)

Toggle diff (38 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 8d08c5421d..e775d342ae 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1299,6 +1299,31 @@ (define-public python-asdf-transform-schemas
;; https://github.com/asdf-format/asdf-transform-schemas/blob/master/LICENSE
(license license:bsd-3)))
+(define-public python-asdf-coordinates-schemas
+ (package
+ (name "python-asdf-coordinates-schemas")
+ (version "0.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "asdf_coordinates_schemas" version))
+ (sha256
+ (base32 "0ahwhsz5jzljnpkfd2kvspirg823lnj5ip9sfkd9cx09z1nlz8jg"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ ;; NOTE: (Sharlatan-20211229T161056+0000): tests require tox
+ #:tests? #f))
+ (native-inputs
+ (list python-semantic-version
+ python-setuptools-scm))
+ (propagated-inputs
+ (list python-asdf))
+ (home-page "https://github.com/asdf-format/asdf-coordinates-schemas")
+ (synopsis "ASDF coordinates schemas")
+ (description "ASDF coordinates schemas")
+ (license license:bsd-3)))
+
(define-public python-astroalign
(package
(name "python-astroalign")
--
2.34.0
S
S
Sharlatan Hellseher wrote on 2 Jan 2022 23:49
(address . 51765@debbugs.gnu.org)
CAO+9K5pJP7-7_qQ8MhYRMzwj2tGLxfx8fhXP0QkOhZ+kno_1xA@mail.gmail.com
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From 17071312c2498ef2169f7b5d3e15af46fe47c7a3 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Sun, 2 Jan 2022 21:14:11 +0000
Subject: [PATCH 4/6] gnu: Add asdf-astropy

* gnu/packages/astronomy.scm: (python-asdf-astropy): New variable.
---
gnu/packages/astronomy.scm | 35 +++++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)

Toggle diff (48 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e775d342ae..0bd0c05afa 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1324,6 +1324,41 @@ (define-public python-asdf-coordinates-schemas
(description "ASDF coordinates schemas")
(license license:bsd-3)))
+(define-public python-asdf-astropy
+ (package
+ (name "python-asdf-astropy")
+ (version "0.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "asdf_astropy" version))
+ (sha256
+ (base32 "0bzgah7gskvnz6jcrzipvzixv8k2jzjkskqwxngzwp4nxgjbcvi4"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ ;; NOTE: (Sharlatan-20211229T161056+0000): tests require tox and failing
+ ;; after not finding setuptools_scm when enabled.
+ #:tests? #f))
+ (native-inputs
+ (list python-coverage
+ python-pytest-astropy
+ python-semantic-version
+ python-setuptools-scm
+ python-tox))
+ (propagated-inputs
+ (list python-asdf
+ python-asdf-coordinates-schemas
+ python-asdf-transform-schemas
+ python-astropy
+ python-numpy
+ python-packaging))
+ (home-page "https://github.com/astropy/asdf-astropy")
+ (synopsis "ASDF serialization support for astropy")
+ (description "ASDF serialization support for astropy")
+ ;; Copyright (C) 2021 Association of Universities for Research in Astronomy (AURA)
+ (license license:bsd-3)))
+
(define-public python-astroalign
(package
(name "python-astroalign")
--
2.34.0
S
S
Sharlatan Hellseher wrote on 2 Jan 2022 23:49
(address . 51765@debbugs.gnu.org)
CAO+9K5o2WeOBZSt9mRsGBQjxaDSGXtGTSwJVV7Ln5QmqumHPyA@mail.gmail.com
--
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From 67f8f900a7cc904bd06085b6c3eed5fb7f68fb38 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Sun, 2 Jan 2022 22:34:19 +0000
Subject: [PATCH 5/6] gnu: Add asdf-wcs-schemas

* gnu/packages/astronomy.scm: (python-asdf-wcs-schemas): New variable.
---
gnu/packages/astronomy.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)

Toggle diff (43 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 0bd0c05afa..e3c7495ed4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1324,6 +1324,36 @@ (define-public python-asdf-coordinates-schemas
(description "ASDF coordinates schemas")
(license license:bsd-3)))
+(define-public python-asdf-wcs-schemas
+ (package
+ (name "python-asdf-wcs-schemas")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "asdf_wcs_schemas" version))
+ (sha256
+ (base32 "0khyab9mnf2lv755as8kwhk3lqqpd3f4291ny3b9yp3ik86fzhz1"))))
+ (build-system python-build-system)
+ (arguments
+ ;; FIXME: (Sharlatan-20211229T155217+0000): tox can't find setuptools,
+ ;; check if running tests with tox is still required.
+ (list #:tests? #f))
+ (native-inputs
+ (list python-semantic-version
+ python-setuptools-scm
+ python-tox))
+ (inputs
+ (list python-asdf))
+ (home-page "https://github.com/asdf-format/asdf-wcs-schemas")
+ (synopsis "ASDF WCS Schemas")
+ (description "World Coordinate System (WCS) as the Advanced Scientific Data
+Format (ASDF) schemas")
+ ;; FIXME: (Sharlatan-20220102T211658+0000): Check the lisense type
+ ;; Copyright (C) 2021 Association of Universities for Research in Astronomy (AURA)
+ ;; https://github.com/asdf-format/asdf-wcs-schemas/blob/main/LICENSE
+ (license license:bsd-3)))
+
(define-public python-asdf-astropy
(package
(name "python-asdf-astropy")
--
2.34.0
S
S
Sharlatan Hellseher wrote on 2 Jan 2022 23:49
(address . 51765@debbugs.gnu.org)
CAO+9K5pXWUVa5cP+xvsJKBP-Rq49J4C_OBxeZm6TOeD-BVHcDw@mail.gmail.com
--
… ??? ????? - ???????????? ?????????????? ?????? ??????? ????????
????? ????? ????? ? ??? ??????, ??????????? ????? ???????, ??
?????????? ?? ? ????????? ??????? ????? ? ?????????????????.
From e252c2cd52cc91526923ac43f714f7bab767bf93 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Sun, 2 Jan 2022 22:43:17 +0000
Subject: [PATCH 6/6] gnu: Add gwcs

* gnu/packages/astronomy.scm: (python-gwcs): New variable.
---
gnu/packages/astronomy.scm | 51 ++++++++++++++++++++++++++++++++++++++
1 file changed, 51 insertions(+)

Toggle diff (68 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e3c7495ed4..77f8cfa024 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -66,6 +66,7 @@ (define-module (gnu packages astronomy)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
+ #:use-module (guix gexp)
#:use-module (ice-9 match)
#:use-module (srfi srfi-1))
@@ -1438,3 +1439,53 @@ (define-public python-skyfield
"Skyfield computes positions for the stars, planets, and satellites in
orbit around the Earth.")
(license license:expat)))
+
+(define-public python-gwcs
+ (package
+ (name "python-gwcs")
+ (version "0.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "gwcs" version))
+ (sha256
+ (base32 "194j49m8xjjzv9pp8cnj06igz8sdxb0nphyybcc7mhigw0f0kr30"))))
+ (build-system python-build-system)
+ (arguments
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ ;; NOTE: (Sharlatan-20211229T163203+0000): Check if tests
+ ;; need to be run via tox
+ (invoke "python" "-m" "pytest" "--pyargs" "gwcs")))))))
+ (native-inputs
+ (list python-jsonschema
+ python-jmespath
+ python-pytest
+ python-pytest-doctestplus
+ python-pyyaml
+ python-semantic-version
+ python-setuptools-scm))
+ (inputs
+ (list python-asdf
+ python-asdf-astropy
+ python-astropy
+ python-asdf-wcs-schemas
+ python-numpy
+ python-scipy))
+ (home-page "https://gwcs.readthedocs.io/en/latest/")
+ (synopsis "Generalized World Coordinate System")
+ (description
+ "Generalized World Coordinate System (GWCS) is an Astropy affiliated package
+providing tools for managing the World Coordinate System of astronomical data.
+
+GWCS takes a general approach to the problem of expressing transformations
+between pixel and world coordinates. It supports a data model which includes the
+entire transformation pipeline from input coordinates (detector by default) to
+world coordinates. It is tightly integrated with Astropy.")
+ ;; NOTE: (Sharlatan-20211229T210517+0000): There is no reference to any
+ ;; license in source.
+ (license #f)))
--
2.34.0
V
V
Vinicius Monego wrote on 4 Jan 2022 03:41
b97bedbd76523e9917b4dc82099289d19090b0b4.camel@posteo.net
Hi Sharlatan,

I am commenting on the second patch and will comment on the others in
this same message.

Toggle quote (5 lines)
> + (arguments
> + (list
> + ;; FIXME: (Sharlatan-20211229T160902+0000): tests run via tox
> + #:tests? #f))

The procedure is more or less the same for all Astropy related
packages. They use tox as an abstraction for pytest. You can run tests
by overriding the check phase:

Toggle quote (9 lines)
> (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")))))))

I also had to add a few more native inputs:

Toggle quote (8 lines)
> (native-inputs
> (list python-jsonschema
> python-numpy
> python-pytest
> python-pyyaml
> python-semantic-version
> python-setuptools-scm))

It should work all the same for the remaining packages in the series.

There's no need to add a comment about the copyright holder:

Toggle quote (5 lines)
> + ;; Copyright (C) 2021 Association of Universities for Research
> in Astronomy (AURA)
> + ;;
> https://github.com/asdf-format/asdf-transform-schemas/blob/master/LICENSE

Some of the other patches like 3 and 4 do not follow description
standards like missing full sentences and full stop. You can run `guix
lint` in the packages to catch some linting errors.

In patch 6, gexp is being used without ungexp. In that case it
shouldn't be used. `(arguments (list ...))` should be `(arguments `())`
when gexp isn't being used, same for the other patches too. gwcs
license is bsd-3 according to copyright headers and the LICENSE file in
the license/ directory. Inputs in patches 5 and 6 may also have to be
propagated if they are libraries.
S
S
Sharlatan Hellseher wrote on 4 Jan 2022 22:39
(address . 51765@debbugs.gnu.org)(name . Vinicius Monego)(address . monego@posteo.net)
CAO+9K5p1RGRZb=m5xpDBg7A1_R43T=wkavxbb_h=7DMKdM+CiA@mail.gmail.com
Hi!

Thank you for fead back @Vinicius Monego !

I've added aditional changes to all mentioned patches but I've not
created patch list from scratch. Let me know if would be easy to merge
patches first.

Sharlatan Hellseher (5):
gnu: asdf-transform-schemas: Enable tests
gnu: asdf-coordinates-schemas: Enable tests
gnu: asdf-astropy: Enable tests
gnu: asdf-wcs-schemas: Enable tests
gnu: gwcs: Refactor package

gnu/packages/astronomy.scm | 101 +++++++++++++++++++++----------------
1 file changed, 57 insertions(+), 44 deletions(-)


base-commit: 4c812db049d5c9f2c438748e180f9486ad221b0a
prerequisite-patch-id: 56820d9ea09a7a53f0c576466db455e706707db2
prerequisite-patch-id: ad03d8286b6789e5c16216f66766ffa403ba2e87
prerequisite-patch-id: 7ada40e42ec009357b74914aa3ed3e31bc0924aa
prerequisite-patch-id: 18f6a0a2503f7359d051f10cfe01e421a3c20511
prerequisite-patch-id: dabf500576aec3742492c67f9a80fabf56872502
prerequisite-patch-id: ee0536ce1c726c3c7cea82067b7bc983d785139c


On Tue, 4 Jan 2022 at 02:41, Vinicius Monego <monego@posteo.net> wrote:
Toggle quote (56 lines)
>
> Hi Sharlatan,
>
> I am commenting on the second patch and will comment on the others in
> this same message.
>
> > + (arguments
> > + (list
> > + ;; FIXME: (Sharlatan-20211229T160902+0000): tests run via tox
> > + #:tests? #f))
>
> The procedure is more or less the same for all Astropy related
> packages. They use tox as an abstraction for pytest. You can run tests
> by overriding the check phase:
>
> > (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")))))))
>
> I also had to add a few more native inputs:
>
> > (native-inputs
> > (list python-jsonschema
> > python-numpy
> > python-pytest
> > python-pyyaml
> > python-semantic-version
> > python-setuptools-scm))
>
> It should work all the same for the remaining packages in the series.
>
> There's no need to add a comment about the copyright holder:
>
> > + ;; Copyright (C) 2021 Association of Universities for Research
> > in Astronomy (AURA)
> > + ;;
> > https://github.com/asdf-format/asdf-transform-schemas/blob/master/LICENSE
>
> Some of the other patches like 3 and 4 do not follow description
> standards like missing full sentences and full stop. You can run `guix
> lint` in the packages to catch some linting errors.
>
> In patch 6, gexp is being used without ungexp. In that case it
> shouldn't be used. `(arguments (list ...))` should be `(arguments `())`
> when gexp isn't being used, same for the other patches too. gwcs
> license is bsd-3 according to copyright headers and the LICENSE file in
> the license/ directory. Inputs in patches 5 and 6 may also have to be
> propagated if they are libraries.
>


--

… ??? ????? - ???????????? ?????????????? ?????? ??????? ????????
????? ????? ????? ? ??? ??????, ??????????? ????? ???????, ??
?????????? ?? ? ????????? ??????? ????? ? ?????????????????.
S
S
Sharlatan Hellseher wrote on 4 Jan 2022 22:39
(address . 51765@debbugs.gnu.org)
CAO+9K5pMXGuoGyRNHkU6yygfPKy8kqkPn5UoKbCLy6t3Rh_RRQ@mail.gmail.com
--
… ??? ????? - ???????????? ?????????????? ?????? ??????? ????????
????? ????? ????? ? ??? ??????, ??????????? ????? ???????, ??
?????????? ?? ? ????????? ??????? ????? ? ?????????????????.
From 14e610532921448bb56332de502819b3607a18bf Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Tue, 4 Jan 2022 20:44:50 +0000
Subject: [PATCH 1/5] gnu: asdf-transform-schemas: Enable tests

* gnu/packages/astronomy.scm: (asdf-transform-schemas): Enable tests.
[native-inputs]: Add python-pytest
---
gnu/packages/astronomy.scm | 15 +++++++++------
1 file changed, 9 insertions(+), 6 deletions(-)

Toggle diff (36 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 77f8cfa024..e7c1d6fbf6 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1281,11 +1281,16 @@ (define-public python-asdf-transform-schemas
(base32 "1gmzd81hw4ppsvzrc91wcbjpcw9hhv9gavllv7nyi7qjb54c837g"))))
(build-system python-build-system)
(arguments
- (list
- ;; FIXME: (Sharlatan-20211229T160902+0000): tests run via tox
- #:tests? #f))
+ `(#: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")))))))
(native-inputs
- (list python-semantic-version
+ (list python-pytest
+ python-semantic-version
python-setuptools-scm))
(propagated-inputs
(list python-asdf))
@@ -1296,8 +1301,6 @@ (define-public python-asdf-transform-schemas
should not need to install this directly; instead, install an implementation
package such as asdf-astropy, which includes asdf-transform-schemas as a
dependency.")
- ;; Copyright (C) 2021 Association of Universities for Research in Astronomy (AURA)
- ;; https://github.com/asdf-format/asdf-transform-schemas/blob/master/LICENSE
(license license:bsd-3)))
(define-public python-asdf-coordinates-schemas
--
2.34.0
S
S
Sharlatan Hellseher wrote on 4 Jan 2022 22:40
(address . 51765@debbugs.gnu.org)
CAO+9K5oK-aiw14zQEoV2hddrHqvNtwO62PiVtwqjxxCcL_31kQ@mail.gmail.com
--
… ??? ????? - ???????????? ?????????????? ?????? ??????? ????????
????? ????? ????? ? ??? ??????, ??????????? ????? ???????, ??
?????????? ?? ? ????????? ??????? ????? ? ?????????????????.
From 7cac0fa900b92da2ad81cf0c4f02e63c3c992e47 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Tue, 4 Jan 2022 20:47:17 +0000
Subject: [PATCH 2/5] gnu: asdf-coordinates-schemas: Enable tests

* gnu/packages/astronomy.scm: (python-asdf-coordinates-schemas): Enable tests.
[native-inputs]: Add python-pytest.
[description]: Extand description string.
---
gnu/packages/astronomy.scm | 16 +++++++++++-----
1 file changed, 11 insertions(+), 5 deletions(-)

Toggle diff (35 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e7c1d6fbf6..b3d6a85240 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1315,17 +1315,23 @@ (define-public python-asdf-coordinates-schemas
(base32 "0ahwhsz5jzljnpkfd2kvspirg823lnj5ip9sfkd9cx09z1nlz8jg"))))
(build-system python-build-system)
(arguments
- (list
- ;; NOTE: (Sharlatan-20211229T161056+0000): tests require tox
- #:tests? #f))
+ `(#: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")))))))
(native-inputs
- (list python-semantic-version
+ (list python-pytest
+ python-semantic-version
python-setuptools-scm))
(propagated-inputs
(list python-asdf))
(home-page "https://github.com/asdf-format/asdf-coordinates-schemas")
(synopsis "ASDF coordinates schemas")
- (description "ASDF coordinates schemas")
+ (description
+ "This package provides ASDF schemas for validating coordinates tags.")
(license license:bsd-3)))
(define-public python-asdf-wcs-schemas
--
2.34.0
S
S
Sharlatan Hellseher wrote on 4 Jan 2022 22:40
(address . 51765@debbugs.gnu.org)
CAO+9K5rVqFiT77zAYUanqRDumBtp9LDZAuX4ycjUpoJ9dHU9Ww@mail.gmail.com
--
… ??? ????? - ???????????? ?????????????? ?????? ??????? ????????
????? ????? ????? ? ??? ??????, ??????????? ????? ???????, ??
?????????? ?? ? ????????? ??????? ????? ? ?????????????????.
From 31ec5424f918fd0fef27181b3ce9e5772ae8e303 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Tue, 4 Jan 2022 20:50:08 +0000
Subject: [PATCH 3/5] gnu: asdf-astropy: Enable tests

* gnu/packages/astronomy.scm: (python-asdf-astropy): Enable tests.
[native-inputs]: Add python-h5py, python-matplotlib, python-pandas,
python-scipy. Remove python-tox.
[description]: Extand description string.
---
gnu/packages/astronomy.scm | 23 +++++++++++++++--------
1 file changed, 15 insertions(+), 8 deletions(-)

Toggle diff (47 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b3d6a85240..dc3a6accb6 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1376,16 +1376,22 @@ (define-public python-asdf-astropy
(base32 "0bzgah7gskvnz6jcrzipvzixv8k2jzjkskqwxngzwp4nxgjbcvi4"))))
(build-system python-build-system)
(arguments
- (list
- ;; NOTE: (Sharlatan-20211229T161056+0000): tests require tox and failing
- ;; after not finding setuptools_scm when enabled.
- #:tests? #f))
+ `(#: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")))))))
(native-inputs
(list python-coverage
+ python-h5py
+ python-matplotlib
+ python-pandas
python-pytest-astropy
+ python-scipy
python-semantic-version
- python-setuptools-scm
- python-tox))
+ python-setuptools-scm))
(propagated-inputs
(list python-asdf
python-asdf-coordinates-schemas
@@ -1395,8 +1401,9 @@ (define-public python-asdf-astropy
python-packaging))
(home-page "https://github.com/astropy/asdf-astropy")
(synopsis "ASDF serialization support for astropy")
- (description "ASDF serialization support for astropy")
- ;; Copyright (C) 2021 Association of Universities for Research in Astronomy (AURA)
+ (description
+ "This package includes plugins that provide ASDF serialization support for
+astropy objects.")
(license license:bsd-3)))
(define-public python-astroalign
--
2.34.0
S
S
Sharlatan Hellseher wrote on 4 Jan 2022 22:40
(address . 51765@debbugs.gnu.org)
CAO+9K5ppuXudxk3WD7as99+q8AC06CGJY6v_VHLzYkGtkVh1iw@mail.gmail.com
--
… ??? ????? - ???????????? ?????????????? ?????? ??????? ????????
????? ????? ????? ? ??? ??????, ??????????? ????? ???????, ??
?????????? ?? ? ????????? ??????? ????? ? ?????????????????.
From 8ab774217a93cf0d4cc1995ee97f1485e168a2b6 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Tue, 4 Jan 2022 21:10:55 +0000
Subject: [PATCH 4/5] gnu: asdf-wcs-schemas: Enable tests

* gnu/packages/astronomy.scm: (python-asdf-wcs-schemas): Enable tests.
[native-inputs]: Add python-pytest.
[inputs]->[propagated-inputs]: To allow this package to be used as
library input.
---
gnu/packages/astronomy.scm | 24 +++++++++++++-----------
1 file changed, 13 insertions(+), 11 deletions(-)

Toggle diff (42 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index dc3a6accb6..5538f77f16 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1346,22 +1346,24 @@ (define-public python-asdf-wcs-schemas
(base32 "0khyab9mnf2lv755as8kwhk3lqqpd3f4291ny3b9yp3ik86fzhz1"))))
(build-system python-build-system)
(arguments
- ;; FIXME: (Sharlatan-20211229T155217+0000): tox can't find setuptools,
- ;; check if running tests with tox is still required.
- (list #:tests? #f))
+ `(#: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")))))))
(native-inputs
- (list python-semantic-version
+ (list python-pytest
python-setuptools-scm
- python-tox))
- (inputs
+ python-semantic-version))
+ (propagated-inputs
(list python-asdf))
(home-page "https://github.com/asdf-format/asdf-wcs-schemas")
(synopsis "ASDF WCS Schemas")
- (description "World Coordinate System (WCS) as the Advanced Scientific Data
-Format (ASDF) schemas")
- ;; FIXME: (Sharlatan-20220102T211658+0000): Check the lisense type
- ;; Copyright (C) 2021 Association of Universities for Research in Astronomy (AURA)
- ;; https://github.com/asdf-format/asdf-wcs-schemas/blob/main/LICENSE
+ (description
+ "This package provides ASDF schemas for validating World Coordinate
+System (WCS) tags.")
(license license:bsd-3)))
(define-public python-asdf-astropy
--
2.34.0
S
S
Sharlatan Hellseher wrote on 4 Jan 2022 22:40
(address . 51765@debbugs.gnu.org)
CAO+9K5rvbz3p-SGShC_4cR6SqA6k5LNOL2QjjrJ40SEKQ_w2=g@mail.gmail.com
--
… ??? ????? - ???????????? ?????????????? ?????? ??????? ????????
????? ????? ????? ? ??? ??????, ??????????? ????? ???????, ??
?????????? ?? ? ????????? ??????? ????? ? ?????????????????.
From 6c7c70d12685dab78cc1687f003f3cdc18d359f4 Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Tue, 4 Jan 2022 21:21:31 +0000
Subject: [PATCH 5/5] gnu: gwcs: Refactor package

* gnu/packages/astronomy.scm: (python-gwcs): Refactor package.
[arguments]: Drop using gexp
[inputs]->[propagated-inputs]: To allow using package as in input library.
[lisense]: Add BSD-3 lisense
---
gnu/packages/astronomy.scm | 23 +++++++++--------------
1 file changed, 9 insertions(+), 14 deletions(-)

Toggle diff (54 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 5538f77f16..5c8bffdd57 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -66,7 +66,6 @@ (define-module (gnu packages astronomy)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
- #:use-module (guix gexp)
#:use-module (ice-9 match)
#:use-module (srfi srfi-1))
@@ -1470,15 +1469,13 @@ (define-public python-gwcs
(base32 "194j49m8xjjzv9pp8cnj06igz8sdxb0nphyybcc7mhigw0f0kr30"))))
(build-system python-build-system)
(arguments
- (list #:phases
- #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- ;; NOTE: (Sharlatan-20211229T163203+0000): Check if tests
- ;; need to be run via tox
- (invoke "python" "-m" "pytest" "--pyargs" "gwcs")))))))
+ `(#: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")))))))
(native-inputs
(list python-jsonschema
python-jmespath
@@ -1487,7 +1484,7 @@ (define-public python-gwcs
python-pyyaml
python-semantic-version
python-setuptools-scm))
- (inputs
+ (propagated-inputs
(list python-asdf
python-asdf-astropy
python-astropy
@@ -1504,6 +1501,4 @@ (define-public python-gwcs
between pixel and world coordinates. It supports a data model which includes the
entire transformation pipeline from input coordinates (detector by default) to
world coordinates. It is tightly integrated with Astropy.")
- ;; NOTE: (Sharlatan-20211229T210517+0000): There is no reference to any
- ;; license in source.
- (license #f)))
+ (license license:bsd-3)))
--
2.34.0
V
V
Vinicius Monego wrote on 5 Jan 2022 00:01
c3991c3a9db8f8fb2d904baccd7e0f2c181ae82b.camel@posteo.net
Em ter, 2022-01-04 às 21:39 +0000, Sharlatan Hellseher escreveu:
Toggle quote (10 lines)
> Hi!
>
> Thank you for fead back @Vinicius Monego !
>
> I've added aditional changes to all mentioned patches but I've not
> created patch list from scratch. Let me know if would be easy to
> merge
> patches first.
>

The best way is to rebase to and amend the commits in the series and
send it from scratch again formatted with v2, v3, etc using --reroll-
count=2 in git format-patch.

You can also submit the patches using `git send-email --
to="NNN@debbugs.gnu.org" <patches>` where NNN is the ID of the issue,
here 51765. Check [1] to see how to configure it.

If you can merge them somehow it is preferable.

S
S
Sharlatan Hellseher wrote on 15 Jan 2022 00:40
(address . 51765@debbugs.gnu.org)(name . Vinicius Monego)(address . monego@posteo.net)
CAO+9K5oE5oNz1h-iqSYV_cSoWyxnB7rd9ikohaxARq44QQeH8Q@mail.gmail.com
Hi Guix team!

I've setup git send-email (finally!) but strugled with rebase and
amend my old commit into new ones.
I've pul lates changes from upstream add combined changes per commit:

Sharlatan Hellseher (6):
gnu: python-asdf: Update to 2.8.3
gnu: Add asdf-transform-schemas
gnu: Add asdf-coordinates-schemas
gnu: Add asdf-astropy
gnu: Add asdf-wcs-schemas
gnu: Add gwcs

gnu/packages/astronomy.scm | 222 ++++++++++++++++++++++++++++++++++---
1 file changed, 204 insertions(+), 18 deletions(-)


base-commit: 056935506b8b5550ebeb3acfc1d0c3b4f11b6a2e

On Tue, 4 Jan 2022 at 23:01, Vinicius Monego <monego@posteo.net> wrote:
Toggle quote (27 lines)
>
> Em ter, 2022-01-04 às 21:39 +0000, Sharlatan Hellseher escreveu:
> > Hi!
> >
> > Thank you for fead back @Vinicius Monego !
> >
> > I've added aditional changes to all mentioned patches but I've not
> > created patch list from scratch. Let me know if would be easy to
> > merge
> > patches first.
> >
>
> The best way is to rebase to and amend the commits in the series and
> send it from scratch again formatted with v2, v3, etc using --reroll-
> count=2 in git format-patch.
>
> You can also submit the patches using `git send-email --
> to="NNN@debbugs.gnu.org" <patches>` where NNN is the ID of the issue,
> here 51765. Check [1] to see how to configure it.
>
> If you can merge them somehow it is preferable.
>
> [1] https://git-send-email.io/
>
>


--

… ??? ????? - ???????????? ?????????????? ?????? ??????? ????????
????? ????? ????? ? ??? ??????, ??????????? ????? ???????, ??
?????????? ?? ? ????????? ??????? ????? ? ?????????????????.
S
S
Sharlatan Hellseher wrote on 15 Jan 2022 00:40
[PATCH 2/6] gnu: Add asdf-transform-schemas
(address . 51765@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
20220114234025.18817-2-sharlatanus@gmail.com
* gnu/packages/astronomy.scm: (python-asdf-transform-schemas): New variable.
---
gnu/packages/astronomy.scm | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)

Toggle diff (47 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index f1392c55e3..957f4d9a88 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1299,6 +1299,40 @@ (define-public python-asdf
implementation of the ASDF Standard.")
(license license:bsd-3)))
+(define-public python-asdf-transform-schemas
+ (package
+ (name "python-asdf-transform-schemas")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "asdf_transform_schemas" version))
+ (sha256
+ (base32 "1gmzd81hw4ppsvzrc91wcbjpcw9hhv9gavllv7nyi7qjb54c837g"))))
+ (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")))))))
+ (native-inputs
+ (list python-pytest
+ python-semantic-version
+ python-setuptools-scm))
+ (propagated-inputs
+ (list python-asdf))
+ (home-page "https://github.com/asdf-format/asdf-transform-schemas")
+ (synopsis "ASDF schemas for transforms")
+ (description
+ "This package provides ASDF schemas for validating transform tags. Users
+should not need to install this directly; instead, install an implementation
+package such as asdf-astropy, which includes asdf-transform-schemas as a
+dependency.")
+ (license license:bsd-3)))
+
(define-public python-astroalign
(package
(name "python-astroalign")
--
2.34.0
S
S
Sharlatan Hellseher wrote on 15 Jan 2022 00:40
[PATCH 3/6] gnu: Add asdf-coordinates-schemas
(address . 51765@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
20220114234025.18817-3-sharlatanus@gmail.com
* gnu/packages/astronomy.scm: (python-asdf-coordinates-schemas): New variable.
---
gnu/packages/astronomy.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)

Toggle diff (44 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 957f4d9a88..e3b81cbad2 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1333,6 +1333,37 @@ (define-public python-asdf-transform-schemas
dependency.")
(license license:bsd-3)))
+(define-public python-asdf-coordinates-schemas
+ (package
+ (name "python-asdf-coordinates-schemas")
+ (version "0.1.0")
+ (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")))))))
+ (native-inputs
+ (list python-pytest
+ python-semantic-version
+ python-setuptools-scm))
+ (propagated-inputs
+ (list python-asdf))
+ (home-page "https://github.com/asdf-format/asdf-coordinates-schemas")
+ (synopsis "ASDF coordinates schemas")
+ (description
+ "This package provides ASDF schemas for validating coordinates tags.")
+ (license license:bsd-3)))
+
(define-public python-astroalign
(package
(name "python-astroalign")
--
2.34.0
S
S
Sharlatan Hellseher wrote on 15 Jan 2022 00:40
[PATCH 1/6] gnu: python-asdf: Update to 2.8.3
(address . 51765@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
20220114234025.18817-1-sharlatanus@gmail.com
* gnu/packages/astronomy.scm: (python-asdf): Update to 2.8.3
Refactor package style.
[inputs]->[propagated-inputs]: To satisfy sanity checks of other
packages depended on python-asdf. Add new input python-jmespath
---
gnu/packages/astronomy.scm | 37 +++++++++++++++++++------------------
1 file changed, 19 insertions(+), 18 deletions(-)

Toggle diff (60 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a7a07fa3a8..f1392c55e3 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1269,34 +1269,35 @@ (define-public python-sep
(define-public python-asdf
(package
(name "python-asdf")
- (version "2.7.4")
+ (version "2.8.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "asdf" version))
(sha256
- (base32 "1mj52l2m8pbhiqacgjakjpvqi8kyx470yw151lcsswbq5wp0rsc6"))))
+ (base32 "0i4vq1hsympjgb1yvn4ql0gm8j1mki9ggmj03533kmg0nbzp03yy"))))
(build-system python-build-system)
(arguments
- ;; TODO: (Sharlatan-20210207T165820+0000): Tests depend on astropy, astropy
- ;; depends on asdf. Disable circular dependence.
- `(#:tests? #f))
+ ;; NOTE: (Sharlatan-20211229T201059+0000): Tests depend on astropy and
+ ;; gwcs, astropy gwcs depend on asdf. Disable circular dependence.
+ (list #:tests? #f))
(native-inputs
- `(("packaging" ,python-packaging)
- ("semantic-version" ,python-semantic-version)
- ("setuptools-scm" ,python-setuptools-scm)))
- (inputs
- `(("importlib-resources" ,python-importlib-resources)
- ("jsonschema" ,python-jsonschema)
- ("numpy" ,python-numpy)
- ("pyyaml" ,python-pyyaml)))
- (home-page "https://github.com/asdf-format/asdf")
- (synopsis "Python tools to handle ASDF files")
- (description
- "The Advanced Scientific Data Format (ASDF) is a next-generation
+ (list python-setuptools-scm
+ python-semantic-version
+ python-packaging))
+ (propagated-inputs
+ (list python-importlib-resources
+ python-jsonschema
+ python-jmespath
+ python-numpy
+ python-pyyaml))
+ (home-page "https://github.com/asdf-format/asdf")
+ (synopsis "Python tools to handle ASDF files")
+ (description
+ "The Advanced Scientific Data Format (ASDF) is a next-generation
interchange format for scientific data. This package contains the Python
implementation of the ASDF Standard.")
- (license license:bsd-3)))
+ (license license:bsd-3)))
(define-public python-astroalign
(package
--
2.34.0
S
S
Sharlatan Hellseher wrote on 15 Jan 2022 00:40
[PATCH 4/6] gnu: Add asdf-astropy
(address . 51765@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
20220114234025.18817-4-sharlatanus@gmail.com
* gnu/packages/astronomy.scm: (python-asdf-astropy): New variable.
---
gnu/packages/astronomy.scm | 42 ++++++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)

Toggle diff (55 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index e3b81cbad2..64a643b977 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1364,6 +1364,48 @@ (define-public python-asdf-coordinates-schemas
"This package provides ASDF schemas for validating coordinates tags.")
(license license:bsd-3)))
+(define-public python-asdf-astropy
+ (package
+ (name "python-asdf-astropy")
+ (version "0.1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "asdf_astropy" version))
+ (sha256
+ (base32 "0bzgah7gskvnz6jcrzipvzixv8k2jzjkskqwxngzwp4nxgjbcvi4"))))
+ (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")))))))
+ (native-inputs
+ (list python-coverage
+ python-h5py
+ python-matplotlib
+ python-pandas
+ python-pytest-astropy
+ python-scipy
+ python-semantic-version
+ python-setuptools-scm))
+ (propagated-inputs
+ (list python-asdf
+ python-asdf-coordinates-schemas
+ python-asdf-transform-schemas
+ python-astropy
+ python-numpy
+ python-packaging))
+ (home-page "https://github.com/astropy/asdf-astropy")
+ (synopsis "ASDF serialization support for astropy")
+ (description
+ "This package includes plugins that provide ASDF serialization support for
+astropy objects.")
+ (license license:bsd-3)))
+
(define-public python-astroalign
(package
(name "python-astroalign")
--
2.34.0
S
S
Sharlatan Hellseher wrote on 15 Jan 2022 00:40
[PATCH 5/6] gnu: Add asdf-wcs-schemas
(address . 51765@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
20220114234025.18817-5-sharlatanus@gmail.com
* gnu/packages/astronomy.scm: (python-asdf-wcs-schemas): New variable.
---
gnu/packages/astronomy.scm | 32 ++++++++++++++++++++++++++++++++
1 file changed, 32 insertions(+)

Toggle diff (45 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 64a643b977..b025b86736 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1406,6 +1406,38 @@ (define-public python-asdf-astropy
astropy objects.")
(license license:bsd-3)))
+(define-public python-asdf-wcs-schemas
+ (package
+ (name "python-asdf-wcs-schemas")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (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")))))))
+ (native-inputs
+ (list python-pytest
+ python-setuptools-scm
+ python-semantic-version))
+ (propagated-inputs
+ (list python-asdf))
+ (home-page "https://github.com/asdf-format/asdf-wcs-schemas")
+ (synopsis "ASDF WCS Schemas")
+ (description
+ "This package provides ASDF schemas for validating World Coordinate
+System (WCS) tags.")
+ (license license:bsd-3)))
+
(define-public python-astroalign
(package
(name "python-astroalign")
--
2.34.0
S
S
Sharlatan Hellseher wrote on 15 Jan 2022 00:40
[PATCH 6/6] gnu: Add gwcs
(address . 51765@debbugs.gnu.org)(name . Sharlatan Hellseher)(address . sharlatanus@gmail.com)
20220114234025.18817-6-sharlatanus@gmail.com
* gnu/packages/astronomy.scm: (python-gwcs): New variable.
---
gnu/packages/astronomy.scm | 46 ++++++++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)

Toggle diff (56 lines)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b025b86736..60dd968838 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1487,3 +1487,49 @@ (define-public python-skyfield
"Skyfield computes positions for the stars, planets, and satellites in
orbit around the Earth.")
(license license:expat)))
+
+(define-public python-gwcs
+ (package
+ (name "python-gwcs")
+ (version "0.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "gwcs" version))
+ (sha256
+ (base32 "194j49m8xjjzv9pp8cnj06igz8sdxb0nphyybcc7mhigw0f0kr30"))))
+ (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")))))))
+ (native-inputs
+ (list python-jsonschema
+ python-jmespath
+ python-pytest
+ python-pytest-doctestplus
+ python-pyyaml
+ python-semantic-version
+ python-setuptools-scm))
+ (propagated-inputs
+ (list python-asdf
+ python-asdf-astropy
+ python-astropy
+ python-asdf-wcs-schemas
+ python-numpy
+ python-scipy))
+ (home-page "https://gwcs.readthedocs.io/en/latest/")
+ (synopsis "Generalized World Coordinate System")
+ (description
+ "Generalized World Coordinate System (GWCS) is an Astropy affiliated package
+providing tools for managing the World Coordinate System of astronomical data.
+
+GWCS takes a general approach to the problem of expressing transformations
+between pixel and world coordinates. It supports a data model which includes the
+entire transformation pipeline from input coordinates (detector by default) to
+world coordinates. It is tightly integrated with Astropy.")
+ (license license:bsd-3)))
--
2.34.0
V
V
Vinicius Monego wrote on 30 Jan 2022 16:07
Re: [PATCH 1/6] gnu: python-asdf: Update to 2.8.3
f2a172323b8c62f39bcf880d890b0b52a2c8a3bd.camel@posteo.net
Hi,

Em sex, 2022-01-14 às 23:40 +0000, Sharlatan Hellseher escreveu:
Toggle quote (76 lines)
> * gnu/packages/astronomy.scm: (python-asdf): Update to 2.8.3
>   Refactor package style.
>   [inputs]->[propagated-inputs]: To satisfy sanity checks of other
>   packages depended on python-asdf. Add new input python-jmespath
> ---
>  gnu/packages/astronomy.scm | 37 +++++++++++++++++++-----------------
> -
>  1 file changed, 19 insertions(+), 18 deletions(-)
>
> diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
> index a7a07fa3a8..f1392c55e3 100644
> --- a/gnu/packages/astronomy.scm
> +++ b/gnu/packages/astronomy.scm
> @@ -1269,34 +1269,35 @@ (define-public python-sep
>  (define-public python-asdf
>    (package
>      (name "python-asdf")
> -    (version "2.7.4")
> +    (version "2.8.3")
>      (source
>       (origin
>         (method url-fetch)
>         (uri (pypi-uri "asdf" version))
>         (sha256
> -        (base32
> "1mj52l2m8pbhiqacgjakjpvqi8kyx470yw151lcsswbq5wp0rsc6"))))
> +        (base32
> "0i4vq1hsympjgb1yvn4ql0gm8j1mki9ggmj03533kmg0nbzp03yy"))))
>      (build-system python-build-system)
>      (arguments
> -     ;; TODO: (Sharlatan-20210207T165820+0000): Tests depend on
> astropy, astropy
> -     ;; depends on asdf. Disable circular dependence.
> -     `(#:tests? #f))
> +     ;; NOTE: (Sharlatan-20211229T201059+0000): Tests depend on
> astropy and
> +     ;; gwcs, astropy gwcs depend on asdf. Disable circular
> dependence.
> +     (list #:tests? #f))
>      (native-inputs
> -     `(("packaging" ,python-packaging)
> -       ("semantic-version" ,python-semantic-version)
> -       ("setuptools-scm" ,python-setuptools-scm)))
> -     (inputs
> -      `(("importlib-resources" ,python-importlib-resources)
> -        ("jsonschema" ,python-jsonschema)
> -        ("numpy" ,python-numpy)
> -        ("pyyaml" ,python-pyyaml)))
> -     (home-page "https://github.com/asdf-format/asdf")
> -     (synopsis "Python tools to handle ASDF files")
> -     (description
> -      "The Advanced Scientific Data Format (ASDF) is a next-
> generation
> +     (list python-setuptools-scm
> +           python-semantic-version
> +           python-packaging))
> +    (propagated-inputs
> +     (list python-importlib-resources
> +           python-jsonschema
> +           python-jmespath
> +           python-numpy
> +           python-pyyaml))
> +    (home-page "https://github.com/asdf-format/asdf")
> +    (synopsis "Python tools to handle ASDF files")
> +    (description
> +     "The Advanced Scientific Data Format (ASDF) is a next-
> generation
>  interchange format for scientific data.  This package contains the
> Python
>  implementation of the ASDF Standard.")
> -     (license license:bsd-3)))
> +    (license license:bsd-3)))
>  
>  (define-public python-astroalign
>    (package

Ideally this change should be in two separate commits: one to propagate
inputs and another to update, but I'm going to leave this one as is for
this time.

I also made the following changes:

- Adjusted commit messages
- Set schema variables as non-public
- Changed descriptions
- Moved gwcs definition closer to the other variables
- Updated your copyright line
and pushed the whole series, thanks!
Closed
?