[PATCH 00/47] Astronomy 2024/04 updates.

Hi Guix!

Mid spring update of astronomical software is ready to be reviewed. This time

I've concentrated on fixing build and check phases of some Python projects

which are become complicated to pack with, even so powerful,

pyproject-build-system (no setup.py, dependencies to higher version of other

packages, requirement to build extension, ... the subject for guix dev mailing

list indeed).

Main highlights:

- CFITSIO is updated to the latest 4.4.0 version and all dependent packages

were checked.

- Stellarium is updated to the latest 24.1 version.

- A long chain of pended packages depending on plplot now started.

- Fixed issue with python-semantic-version on runtime, reported by Iliya

Tikhonenko <tikhonenko@mpe.mpg.de>.

- added [5/5]

- [X] psfex :: Astronomical PSF modelling and quality assessment

- [X] python-assay :: Python testing framework

- [X] python-pysiaf :: Handling SIAF for space telescopes

- [X] python-supersmoother :: Python implementation of Friedman's Supersmoother

- [X] scamp :: Compute astrometric solutions

- updated [30/30]

- [X] cfitsio 4.3.1 -> 4.4.0

- [X] indi 2.0.6 -> 2.0.7

- [X] libxisf 0.2.11 -> 0.2.12

- [X] parfive 2.0.2 -> 2.1.0

- [X] python-asdf 3.1.0 -> 3.2.0

- [X] python-asdf-astropy 0.6.0 -> 0.6.1

- [X] python-astroplan 0.9.1 -> 0.10

- [X] python-astropy 6.0.0 -> 6.0.1

- [X] python-astropy-healpix 1.0.2 -> 1.0.3

- [X] python-astropy-iers-data 0.2024.3.18.0.29.47 -> 0.2024.4.15.2.45.49

- [X] python-bayesicfitting 3.2.0 -> 3.2.1

- [X] python-casa-formats-io 0.2.2 -> 0.3.0

- [X] python-crds 11.17.19 -> 11.17.20

- [X] python-ginga 5.0.0 -> 5.0.1

- [X] python-jwst 1.13.4 -> 1.14.0

- [X] python-photutils 1.10.0 -> 1.12.0

- [X] python-rad 0.19.0 -> 0.19.2

- [X] python-regions 0.8 -> 0.9

- [X] python-reproject 0.13.0 -> 0.13.1

- [X] python-roman-datamodels 0.19.0 -> 0.19.1

- [X] python-specutils 1.13.0 -> 1.14.0

- [X] python-stcal 1.6.1 -> 1.7.0

- [X] python-stdatamodels 1.10.0 -> 1.10.1

- [X] python-stsci-imagestats 1.8.0 -> 1.8.2

- [X] python-stsci-stimage 0.2.6 -> 0.2.8

- [X] python-sunpy 5.1.1 -> 5.1.2

- [X] python-synphot 1.3.0 -> 1.4.0

- [X] python-tweakwcs 0.8.6 -> 0.8.7

- [X] stellarium 23.4 -> 24.1

Plan for the next month to continue with packaging Astropy affiliated packages from the list

available at https://www.astropy.org/affiliated/registry.json,bring more foundation packages like

HELPix, which allow to start a new chain of dependent packages, check what is left to bring

python-yt.

Build stats:

Dependent build stats:

Sharlatan Hellseher (47):

gnu: cfitsio: Update to 4.4.0.

gnu: stellarium: Update to 24.1.

gnu: indi-2.0: Update to 2.0.7.

gnu: libxisf: Update to 0.2.12.

gnu: python-pytest-socket: Update to 0.7.0.

gnu: parfive: Update to 2.1.0.

gnu: python-exif-read: Update to 3.0.0.

gnu: Add python-pysiaf.

gnu: Add python-supersmoother.

gnu: python-asdf: Update to 3.2.0.

gnu: python-asdf-astropy: Update to 0.6.1.

gnu: python-astropy-iers-data: Update to 0.2024.4.15.2.45.49.

gnu: python-astropy: Symplify package.

gnu: python-astropy: Update to 6.0.1.

gnu: python-astropy-healpix: Update to 1.0.3.

gnu: python-jwst: Update to 1.14.0.

gnu: python-stcal: Update to 1.7.0.

gnu: python-stdatamodels: Update to 1.10.1.

gnu: python-stsci-imagestats: Update to 1.8.2.

gnu: python-stsci-image: Refresh package style.

gnu: python-synphot: Add custom check phase.

gnu: python-synphot: Update to 1.4.0.

gnu: python-tweakwcs: Adjust indentation.

gnu: python-tweakwcs: Update to 0.8.7.

gnu: python-ginga: Update to 5.0.1.

gnu: python-ginga: Set HOME for sanity check.

gnu: python-gatspy: Refresh package style.

gnu: python-bayesicfitting: Refresh package style.

gnu: python-bayesicfitting: Update to 3.2.1.

gnu: Add python-assay.

gnu: python-skyfield: Enable tests.

gnu: python-sunpy: Update to 5.1.2.

gnu: python-astroplan: Update to 0.10.

gnu: python-rad: Update to 0.19.2.

gnu: python-regions: Update to 0.9.

gnu: python-roman-datamodels: Update to 0.19.1.

gnu: python-casa-formats-io: Update to 0.3.0.

gnu: python-specutils: Update to 1.14.0.

gnu: python-photutils: Update to 1.12.

gnu: python-reproject: Update to 0.13.1.

gnu: python-reproject: Enable tests.

gnu: python-asdf: Adjust inputs.

gnu: python-crds: Update to 11.17.20.

gnu: python-stsci-stimage: Update to 0.2.8.

gnu: python-stsci-stimage: Adjust test steps.

gnu: Add scamp.

gnu: Add psfex.

gnu/packages/astronomy.scm | 709 +++++++++++++++++++++-----------

gnu/packages/python-check.scm | 65 ++-

gnu/packages/python-science.scm | 25 ++

gnu/packages/python-web.scm | 4 +-

gnu/packages/python-xyz.scm | 4 +-

5 files changed, 544 insertions(+), 263 deletions(-)

base-commit: 43a4215cad8c6da357f895569c0cedf5e854cee0

--

2.41.0

Change-Id: I53dea0e03a3b7c4d78b4946a2bbc9a13f9fbec6f

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Change-Id: Iac79d04b1cfb59038578939266bc4b948fb3c908

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Change-Id: Ia134449cc18a0c70dcba962b0ea51e2341d34e98

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Change-Id: Ide88155581b317cdb74683f49d2ec8b87c6bc5de

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Change-Id: I19e0a19041aa943a9f3ecf262077328d52ef4d1d

---

gnu/packages/python-xyz.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Change-Id: I8fb43d746757014e3b773c07458b777b893adb4a

---

gnu/packages/python-science.scm | 25 +++++++++++++++++++++++++

1 file changed, 25 insertions(+)

Change-Id: Ide732d666bccad885ed3e8c78d62df7e74524b9a

---

gnu/packages/astronomy.scm | 39 ++++++++++++++++++++++++++++++++++++++

1 file changed, 39 insertions(+)

[arguments] <#:phases>: Replace 'fix-tests-setup with

'patch-pyprojectct-toml phase and add one more substitution rule.

[propagated-inputs]: Remove python-asdf-unit-schemas.

Change-Id: I9e7a0282ed0a9eb82a20988762792e10ae33496b

---

gnu/packages/astronomy.scm | 16 +++++++++-------

1 file changed, 9 insertions(+), 7 deletions(-)

Change-Id: I06f00006fcba1d0e385e6bc3f82f7a85403d94a9

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Change-Id: Iaf902a0f506f149682868d0df0710d400b21f7e6

---

gnu/packages/astronomy.scm | 6 +++---

1 file changed, 3 insertions(+), 3 deletions(-)

[build-system]: Swap to pyproject-build-system.

[arguments] <#:phases>: Merge 'prepare-test-environment into custom

'check phase and move test arguments to <#:test-arguments>.

Change-Id: I80098c3eb4e9d95ef2c651d5416196165be3f7c0

---

gnu/packages/astronomy.scm | 47 ++++++++++++++++++--------------------

1 file changed, 22 insertions(+), 25 deletions(-)

Change-Id: Iffc1d537bd8b3ec10fbb5ddb7c2fd6251813ccde

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

[arguments]: <#:test-flags>: Enable recently failing tests; disable some

new one.

[propagated-inputs]: Add python-matplotlib and python-scipy.

[native-inputs]: Remove python-matplotlib and python-scipy; add

python-threadpoolctl.

Change-Id: Iaa48c84565d11c944444ecd1fd77291f4b3c8c3c

---

gnu/packages/astronomy.scm | 19 +++++++++----------

1 file changed, 9 insertions(+), 10 deletions(-)

Change-Id: I6207150e012c03943d4553854123831d1bba3e55

---

gnu/packages/python-web.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

[propagated-inputs]: Remove python-asdf-transform-schemas; add

python-importlib-metadata, python-packaging, python-pysiaf, and

python-synphot.

Change-Id: I0310e0680457a7851d07fa14406edf079000fcd5

---

gnu/packages/astronomy.scm | 10 +++++++---

1 file changed, 7 insertions(+), 3 deletions(-)

[native-inputs]: Remove python-pytest-openfiles.

Change-Id: Ib33bb72ff73fcf569a2519b3353260461b63c143

---

gnu/packages/astronomy.scm | 5 ++---

1 file changed, 2 insertions(+), 3 deletions(-)

Change-Id: Ib1626de00fbd060212b125c3a52e116aa126727e

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Change-Id: I13bb6eab789a8aa365f6bf0f0f892d8a17e3cc66

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Remove 'prepare-test-environment phase; add custom 'check phase.

Change-Id: I9cb6d65c226a555ccd62a3a6c08d00868a66f109

---

gnu/packages/astronomy.scm | 21 ++++++++-------------

1 file changed, 8 insertions(+), 13 deletions(-)

Change-Id: I070381de76cfe1bf057d1c8032d2145d5c346fa2

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

[description]: Fix grammar.

Change-Id: I1f4bf751720a3be324644bf417104e36510c62a6

---

gnu/packages/astronomy.scm | 30 +++++++++++++++---------------

1 file changed, 15 insertions(+), 15 deletions(-)

Change-Id: Ic8c79addbd0253c2364382e6a0e632945eafb05a

---

gnu/packages/astronomy.scm | 40 ++++++++++++++++++++------------------

1 file changed, 21 insertions(+), 19 deletions(-)

[arguments]: Use #~ qutation style.

<#:test-flags>: Activate tests for supersmoother.

[propagated-inputs]: Add python-supersmoother.

Change-Id: Ibbaae0f87693f5f4aa6e3f92d567881ad58dbfba

---

gnu/packages/astronomy.scm | 41 +++++++++++++++++++-------------------

1 file changed, 21 insertions(+), 20 deletions(-)

Change-Id: I275445d688dfb3c3c3da18a37d7d21d79814f8ef

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Change-Id: I80a988262e417f8a5501d02db5e16a93b5d037b4

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

[source]: Swap to git checkout containing test data.

[build-system]: Swap to pyproject-build-system.

[native-inputs]: Add python-assay and python-pandas.

Change-Id: Ia4604ab2e44860dcf1294688639d3c54881f8d8c

---

gnu/packages/astronomy.scm | 26 +++++++++++++++++++-------

1 file changed, 19 insertions(+), 7 deletions(-)

Change-Id: I4de8e8228f6d7ae1ae28cac726fcce5f2058f928

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Change-Id: I0ec910d8c37000ff08119a33e3f42af2269fa494

---

gnu/packages/python-check.scm | 34 +++++++++++++++++++++++++++++++++-

1 file changed, 33 insertions(+), 1 deletion(-)

Change-Id: I3f8ca4c981ac31cc955d374b4e4735e53af4c868

---

gnu/packages/astronomy.scm | 2 +-

1 file changed, 1 insertion(+), 1 deletion(-)

Change-Id: I879064eba2f4d93d2e2b519ebdf613685d5b5df9

---

gnu/packages/python-check.scm | 31 +++++++++++++++++++++++--------

1 file changed, 23 insertions(+), 8 deletions(-)

Change-Id: I2ef8f29839a99ec3b40efc34a61f57bc32216c8e

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

'set-home phase.

Change-Id: I7fc9b043ae8ac465645215dabc9d8643b8e08fe2

---

gnu/packages/astronomy.scm | 8 +++++++-

1 file changed, 7 insertions(+), 1 deletion(-)

[arguments] <#:phases>: Add 'relax-requirements phase.

[propagated-inputs]: Add opencv, python-exif-read python-packaging,

python-pyyaml, and python-tomli.

[native-inputs]: Add python-pytest-astropy-header.

Change-Id: I314bbd9a037b134a03f5a4a174ab878e9523e4b6

---

gnu/packages/astronomy.scm | 24 +++++++++++++++++++-----

1 file changed, 19 insertions(+), 5 deletions(-)

Change-Id: I97bfc44920a3e8f7c2040088f284a38e0a66aa88

---

gnu/packages/astronomy.scm | 8 +++++---

1 file changed, 5 insertions(+), 3 deletions(-)

[propagated-inputs]: Remove python-asdf-standard.

Change-Id: I30e2adef137bb95f37dd7651ebf8c5e6f9e6155f

---

gnu/packages/astronomy.scm | 5 ++---

1 file changed, 2 insertions(+), 3 deletions(-)

Change-Id: Ied7078bc28d7b995574fb228797f1d046ea52feb

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

[arguments] <#:phases>: Add 'create-setup.py phase, rename

'prepare-test-environment to 'build-extensions to reflect purpose.

[native-inputs]: Remove python-cython; add python-cython-3.

Change-Id: Ia634f93336eb7658c4eaeeb7ddb6539c2e0adee3

---

gnu/packages/astronomy.scm | 21 ++++++++++++++-------

1 file changed, 14 insertions(+), 7 deletions(-)

[arguments]: <#:phases>: Add 'create-setup.py phase.

Change-Id: I94908eda0eb7741cb23d2d4dc969c91cdbd08fa2

---

gnu/packages/astronomy.scm | 16 ++++++++++++++--

1 file changed, 14 insertions(+), 2 deletions(-)

[arguments]: <#:phases>: Add 'create-setup.py phase.

[native-inputs]: Remove python-cython; add python-cython-3.

Change-Id: I77845fa1a9748901bc08235ba95060d39b64e467

---

gnu/packages/astronomy.scm | 17 ++++++++++++++---

1 file changed, 14 insertions(+), 3 deletions(-)

Change-Id: I426241c2e216b0261787117a10ceab36197dff12

---

gnu/packages/astronomy.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

[arguments]: <#:tests-flags>: Add them as seen in tox.ini.

<#:phases>: Rename 'writable-home to 'prepare-test-environment to reflect

purpose and build extension before tests.

[native-inputs]: Add python-xdist.

Change-Id: I7a5454e3ce241b7a54626f8aba27602b4965c25b

---

gnu/packages/astronomy.scm | 25 ++++++++++++-------------

1 file changed, 12 insertions(+), 13 deletions(-)

Change-Id: Ib2f8b9544bc732959d87527d2c55f274dab4393b

---

gnu/packages/astronomy.scm | 6 +++---

1 file changed, 3 insertions(+), 3 deletions(-)

[arguments]: <#:test-flags>: Add them. <#:phases>: Fail over to default

'check phase and add 'waf-configure-build phase before check.

[native-inputs]: Remove python-codecov and, python-pytest-cov.

[description]: Fix indentation.

Change-Id: I350c4ced2cb4afaff72d4d4941d198932cd888f5

---

gnu/packages/astronomy.scm | 29 +++++++++++++++--------------

1 file changed, 15 insertions(+), 14 deletions(-)

Change-Id: I073df933b244811cd09343ea4951f481ad76b075

---

gnu/packages/astronomy.scm | 45 ++++++++++++++++++++++++++++++++++++++

1 file changed, 45 insertions(+)

python-asdf requires python-semantic-version during runtime which may be

reproduced by:

guix shell python-asdf python -- python3 -c 'import asdf'

<...>

ModuleNotFoundError: No module named 'semantic_version'

[native-inputs]: Remove python-semantic-version.

[propagated-inputs]: Add python-semantic-version.

(python-asdf-astropy, python-asdf-compression, python-asdf-coordinates-schemas,

python-asdf-wcs-schemas, python-asdf-zarr, python-astroalignn, python-ccdproc,

python-crds, python-ginga, python-gwcs, python-photutils, python-rad,

python-reproject, python-roman-datamodels, python-spectral-cube,

python-specutils, python-stcal, python-stdatamodels, python-stpipe,

python-stsynphot, python-sunpy, python-synphot, python-tweakwcs): Remove

python-semantic-version from native or propagated inputs.

Change-Id: I96bf57f77c327f4ff208e0b173e84bcdd4c287da

Reported-by: Iliya Tikhonenko <tikhonenko@mpe.mpg.de>

---

gnu/packages/astronomy.scm | 41 +++++++++-----------------------------

1 file changed, 9 insertions(+), 32 deletions(-)

Change-Id: If32adb281017858b0e7d5816cecb509af3cec835

---

gnu/packages/astronomy.scm | 80 ++++++++++++++++++++++++++++++++++++++

1 file changed, 80 insertions(+)

indentation.

[build-system]: Swap to pyproject-build-system.

[arguments] <#:test-flags>: Add them.

<#:phases>: Use test flags in 'check phase.

Change-Id: Iffc8591199bbaf2a0da95b6b22476e34121dbe79

---

gnu/packages/astronomy.scm | 42 ++++++++++++++++++++++----------------

1 file changed, 24 insertions(+), 18 deletions(-)

Pushed as 3067eb8d60..147f1f2e0d to master.

--

Oleg