Package: guix-patches;
Reported by: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Date: Sat, 20 Apr 2024 23:21:03 UTC
Severity: normal
Tags: patch
Done: Sharlatan Hellseher <sharlatanus <at> gmail.com>
Bug is archived. No further changes may be made.
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andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:21:03 GMT) Full text and rfc822 format available.Sharlatan Hellseher <sharlatanus <at> gmail.com>:andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org.
(Sat, 20 Apr 2024 23:21:04 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: guix-patches <at> gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 00/47] Astronomy 2024/04 updates. Date: Sun, 21 Apr 2024 00:19:37 +0100
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 <at> 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: --8<---------------cut here---------------start------------->8--- ./pre-inst-env guix build cfitsio indi julia-arnoldimethod libxisf parfive psfex python-asdf python-asdf-astropy python-assay python-astroplan python-astropy python-astropy-healpix python-astropy-iers-data python-bayesicfitting python-casa-formats-io python-crds python-exif-read python-gatspy python-ginga python-jwst python-photutils python-pysiaf python-pytest-socket python-rad python-regions python-reproject python-roman-datamodels python-skyfield python-specutils python-stcal python-stdatamodels python-stsci-image python-stsci-imagestats python-stsci-stimage python-sunpy python-supersmoother python-synphot python-tweakwcs scamp stellarium /gnu/store/vdnd125l2g3mmjng502gpn106f0lxp13-stellarium-24.1 /gnu/store/nfncz84xz8qh61s1zgk4bdsd4fzj18ir-scamp-2.10.0 /gnu/store/8blp5lk2wakaxq7gsj5qp3p9viy5d6ph-python-tweakwcs-0.8.7 /gnu/store/563bcym71ymp57kh6y13b0l4ci3836p1-python-synphot-1.4.0 /gnu/store/7243bmnjb129axdf8hl6ncb2izshg42b-python-supersmoother-0.4 /gnu/store/xmqrb8ylglpyxpd4jllrczvvsxssvrmd-python-sunpy-5.1.2 /gnu/store/zbr0cq0ym2gsa18fzgckkwmf6z25dm94-python-stsci-stimage-0.2.8 /gnu/store/iq15ji3g14lbzs4m0ly3xc5fbgm4zz08-python-stsci-imagestats-1.8.2 /gnu/store/jd7bw41528vxxzzcivb5skbky3wiszpl-python-stsci-image-2.3.5 /gnu/store/inp4vi19lch1517ci16qbnm1gwz757bl-python-stdatamodels-1.10.1 /gnu/store/q5p18dlpqy1080agp82qyqjkq41hrrpa-python-stcal-1.7.0 /gnu/store/fvh7f7si5sphwcl1n9pq98nzqhrmjslj-python-specutils-1.14.0 /gnu/store/zpcg7bby7099qhba8b0sxyl1dq83jh07-python-skyfield-1.48 /gnu/store/avdm2a6swr2c3yjf32rfdzyr5gbqdkfk-python-roman-datamodels-0.19.1 /gnu/store/izavyvszb36v6s9i2scza1anxjxpddaa-python-reproject-0.13.1 /gnu/store/7y5k2vh9n48bdd1vb8dri6lkc10r063a-python-regions-0.9 /gnu/store/k4gnfhws4bndjx4np6kmjxx4gapvgc52-python-rad-0.19.2 /gnu/store/wmri5wxmg5bhfva5kb09gx50bw3r1dg7-python-pytest-socket-0.7.0 /gnu/store/3lv3w97y7nm7d2m0q75rbhz994q8759d-python-pysiaf-0.22.0 /gnu/store/8lg6si6056vdp8ld520cyijpcs2pdvyf-python-photutils-1.12 /gnu/store/ca27y6dvrinvd90vhnd35b6pk60vsd1z-python-jwst-1.14.0 /gnu/store/0b1rld810g6qw61zfwxakm00y87hqyn9-python-ginga-5.0.1 /gnu/store/ch54g171q6dldmql8zy563d8rpka4b92-python-gatspy-0.3 /gnu/store/ar89f5lwrfb0jvkyfz50y8liccp84wwx-python-exif-read-3.0.0 /gnu/store/gcmashvb9arz03khxcw89frisvm92r99-python-crds-11.17.20 /gnu/store/iwwll5ma1zp5nma63l669z0j9a8z01yz-python-casa-formats-io-0.3.0 /gnu/store/1kj9s25w82n0rbv8nza3g04hdk5a8b3n-python-bayesicfitting-3.2.1 /gnu/store/j21bfrydd1ps24dv7agdrgjwb1ccxach-python-astropy-iers-data-0.2024.4.15.2.45.49 /gnu/store/gdxnfqryw4vk907jx3c38i6nkjbl4qkb-python-astropy-healpix-1.0.3 /gnu/store/gv5fvf68qdw0vzbcwmpys5y65rd8sjgs-python-astropy-6.0.1 /gnu/store/fdadfm1rgwhaz1na24lw797fchlnp7yf-python-astroplan-0.10 /gnu/store/0cnax1fn7qgp2dklsinfxsp529qymyms-python-assay-0.0.0-0.74617d7 /gnu/store/vsi6cqg75cnj5davswqm3m549gwn2q13-python-asdf-astropy-0.6.1 /gnu/store/scak8mnw103qycklyl6w5hz10yad39fs-python-asdf-3.2.0 /gnu/store/9c6n5zkd3wfchad9i0vaf3is3c56fk0v-psfex-3.24.2 /gnu/store/2c7ni6jxjvhwkrjh7fnvxnfb7k6lcrs1-parfive-2.1.0 /gnu/store/n2pg13iaqz8mwwny285921qlrc0576p0-libxisf-0.2.12 /gnu/store/wa8lgfra92xbwa59xixzpmlyk911k5ni-indi-2.0.7 /gnu/store/w0gnn3301ms307zdjshwpvcp7d0akj5p-cfitsio-4.4.0 --8<---------------cut here---------------end--------------->8--- Dependent build stats: --8<---------------cut here---------------start------------->8--- ./pre-inst-env guix refresh --list-dependent cfitsio indi libxisf parfive psfex python-asdf python-asdf-astropy python-assay python-astroplan python-astropy python-astropy-healpix python-astropy-iers-data python-bayesicfitting python-casa-formats-io python-crds python-exif-read python-gatspy python-ginga python-jwst python-photutils python-pysiaf python-pytest-socket python-rad python-regions python-reproject python-roman-datamodels python-skyfield python-specutils python-stcal python-stdatamodels python-stsci-image python-stsci-imagestats python-stsci-stimage python-sunpy python-supersmoother python-synphot python-tweakwcs scamp stellarium python-tweakwcs scamp stellarium Building the following 28 packages would ensure 86 dependent packages are rebuilt: sextractor <at> 2.28.0 indi <at> 2.0.7 imppg <at> 0.6.5 stellarium <at> 24.1 alfa <at> 2.2 julia-wcs <at> 0.6.2 phd2 <at> 2.6.13 swarp <at> 2.41.5 glnemo2 <at> 1.21.0 gnuastro <at> 0.22 aoflagger <at> 3.4.0 siril <at> 1.2.1 splash <at> 3.10.3 julia-fitsio <at> 0.17.1 gwenview <at> 23.08.5 labplot <at> 2.10.1 python-astroplan <at> 0.10 python-poliastro <at> 0.17.0 python-asdf-compression <at> 0.0.1-0.57cc7e7 python-ginga <at> 5.0.1 ginga-qt5 <at> 5.0.1 python-asdf-zarr <at> 0.0.3 python-aplpy <at> 2.1.0 python-astroalign <at> 2.5.1 scamp <at> 2.10.0 python-radiospectra <at> 0.5.0 python-cesium <at> 0.12.1 python-jwst <at> 1.14.0 /gnu/store/ca27y6dvrinvd90vhnd35b6pk60vsd1z-python-jwst-1.14.0 /gnu/store/53ca7byad86s8b76wf9lf6psdzqfjwr5-python-cesium-0.12.1 /gnu/store/dhyinp5s58zpj6fbl3n1v4wa14nhn229-python-radiospectra-0.5.0 /gnu/store/nfncz84xz8qh61s1zgk4bdsd4fzj18ir-scamp-2.10.0 /gnu/store/cxk4zw7vcqlwm6bk8fkkjhgjb4dfw6lk-python-astroalign-2.5.1 /gnu/store/23iywrrc0nvih9pnbsya1786fxviyidy-python-aplpy-2.1.0 /gnu/store/7920xfflxbdb5316yg56xrf34mgar2y4-python-asdf-zarr-0.0.3 /gnu/store/0jky435fla7hdxj3wqs04zqjrfv9h5m0-ginga-qt5-5.0.1 /gnu/store/0b1rld810g6qw61zfwxakm00y87hqyn9-python-ginga-5.0.1 /gnu/store/ahrjhknayszzxfwc872yg682kp6qm3xl-python-asdf-compression-0.0.1-0.57cc7e7 /gnu/store/dyyqx64jydq5k50rwwg2al5i8z52s0sc-python-poliastro-0.17.0 /gnu/store/fdadfm1rgwhaz1na24lw797fchlnp7yf-python-astroplan-0.10 /gnu/store/bnjhapnqsvynnxsc2zz7zcx4sk0m181z-labplot-2.10.1 /gnu/store/60nzh7pwbm11kkhxrhz6zlgz0qf9qiql-gwenview-23.08.5 /gnu/store/1gr204bg17xav3ncvjxhgqlmyg2q6n8l-julia-fitsio-0.17.1 /gnu/store/gvg3ffdgzkc110dzvsbcwgmzb901pa17-splash-3.10.3 /gnu/store/175jp1zq70h556ffn9166r8z77vy8q14-siril-1.2.1 /gnu/store/s4j9iyz6hi8cs8rx9h6wzxvn6zpicy38-aoflagger-3.4.0 /gnu/store/9fjpdh4facjj1my62hw58syqwns157hs-gnuastro-0.22 /gnu/store/isjd84aik55lpyfay3s7kfaw2c0fx9y4-glnemo2-1.21.0 /gnu/store/diyb7zv44188k8wfm98vlsh4r9fjnm8a-swarp-2.41.5 /gnu/store/qv1wyfwis43gbvkf39rr6mhn150c1939-phd2-2.6.13 /gnu/store/gvkcx2v2cs32rjxjkc2xahdh2aa8kkfa-julia-wcs-0.6.2 /gnu/store/8yp0p9xy59n5ci2xn2zzirwlw825b09w-alfa-2.2 /gnu/store/vdnd125l2g3mmjng502gpn106f0lxp13-stellarium-24.1 /gnu/store/7bkl0yjh3dhrfma5aadg0j5d78vazy5b-imppg-0.6.5 /gnu/store/wa8lgfra92xbwa59xixzpmlyk911k5ni-indi-2.0.7 /gnu/store/palpxpc470pl7vq8qflkv8l1brj61dlf-sextractor-2.28.0 --8<---------------cut here---------------end--------------->8--- 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
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:03 GMT) Full text and rfc822 format available.Message #8 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 02/47] gnu: stellarium: Update to 24.1. Date: Sun, 21 Apr 2024 00:21:51 +0100
* gnu/packages/astronomy.scm (stellarium): Update to 24.1.
Change-Id: I53dea0e03a3b7c4d78b4946a2bbc9a13f9fbec6f
---
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 0aa2efaabc..d82966932d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1345,7 +1345,7 @@ (define-public stackistry
(define-public stellarium
(package
(name "stellarium")
- (version "23.4")
+ (version "24.1")
(source
(origin
(method git-fetch)
@@ -1354,7 +1354,7 @@ (define-public stellarium
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "11l3lql3cxj7s7q7n74qd4rhbjy374b4c0lpm0dr8s85mfrq6fmc"))))
+ (base32 "15r8vg1xb4q8vwy10dfs4543bg6r3463sgrpkqk6fpxx46d8axxp"))))
(build-system cmake-build-system)
;; TODO: Complete documentation build and split into dedicated outputs.
(arguments
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:05 GMT) Full text and rfc822 format available.Message #11 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 01/47] gnu: cfitsio: Update to 4.4.0. Date: Sun, 21 Apr 2024 00:21:50 +0100
* gnu/packages/astronomy.scm (cfitsio): Update to 4.4.0.
Change-Id: Iac79d04b1cfb59038578939266bc4b948fb3c908
---
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 6cd0bb7348..0aa2efaabc 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -451,7 +451,7 @@ (define-public ccfits
(define-public cfitsio
(package
(name "cfitsio")
- (version "4.3.1")
+ (version "4.4.0")
(source
(origin
(method url-fetch)
@@ -459,7 +459,7 @@ (define-public cfitsio
"https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/"
"cfitsio-" version ".tar.gz"))
(sha256
- (base32 "1gk2a07ypmc8rcngakcarprznq7hi3xr9szfv3hy2yv80ppci9s7"))))
+ (base32 "1abb4ky6pjyi9f9ly8qjmkb5h25d5xxqlrxrgjg86q77bbwhr44m"))))
(build-system gnu-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:07 GMT) Full text and rfc822 format available.Message #14 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 03/47] gnu: indi-2.0: Update to 2.0.7. Date: Sun, 21 Apr 2024 00:21:52 +0100
* gnu/packages/astronomy.scm (indi-2.0): Update to 2.0.7.
Change-Id: Ia134449cc18a0c70dcba962b0ea51e2341d34e98
---
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 d82966932d..d8af86b449 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3804,7 +3804,7 @@ (define-public imppg
(define-public indi-2.0
(package
(name "indi")
- (version "2.0.6")
+ (version "2.0.7")
(source
(origin
(method git-fetch)
@@ -3813,7 +3813,7 @@ (define-public indi-2.0
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0j1yr8wz6q6xi4dskv3yyhm0valsyfhcw1n8xpfgzbzbdzc8biyw"))))
+ (base32 "0w3494by88g0sz92adgvy75g7f1609ilsblink9z37n02v83dfxi"))))
(build-system cmake-build-system)
(arguments
;; TODO: fix failing tests on aarch64-system.
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:09 GMT) Full text and rfc822 format available.Message #17 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 04/47] gnu: libxisf: Update to 0.2.12. Date: Sun, 21 Apr 2024 00:21:53 +0100
* gnu/packages/astronomy.scm (libxisf): Update to 0.2.12.
Change-Id: Ide88155581b317cdb74683f49d2ec8b87c6bc5de
---
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 d8af86b449..917b838e7a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3557,7 +3557,7 @@ (define-public libpasastro
(define-public libxisf
(package
(name "libxisf")
- (version "0.2.11")
+ (version "0.2.12")
(source
(origin
(method git-fetch)
@@ -3566,7 +3566,7 @@ (define-public libxisf
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "02lnlsdg7f6pbcfk9amzh2k42wsb19d97yp2jq122lzivx9inwn1"))))
+ (base32 "1bvf3x0xdipkg28c75j6jav3b2llbqvfa6lkwiacxxlzmj0226s2"))))
(build-system cmake-build-system)
(arguments
(list #:configure-flags #~(list "-DUSE_BUNDLED_LIBS=OFF")))
--
2.41.0
lars <at> 6xq.net, marius <at> gnu.org, me <at> bonfacemunyoki.com, sharlatanus <at> gmail.com, tanguy <at> bioneland.org, jgart <at> dismail.de, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:11 GMT) Full text and rfc822 format available.Message #20 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 07/47] gnu: python-exif-read: Update to 3.0.0. Date: Sun, 21 Apr 2024 00:21:56 +0100
* gnu/packages/python-xyz.scm (python-exif-read): Update to 3.0.0.
Change-Id: I19e0a19041aa943a9f3ecf262077328d52ef4d1d
---
gnu/packages/python-xyz.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index bac90b1e07..6011b4137f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5181,13 +5181,13 @@ (define-public python-pyrsistent
(define-public python-exif-read
(package
(name "python-exif-read")
- (version "2.1.2")
+ (version "3.0.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "ExifRead" version))
(sha256
(base32
- "1b90jf6m9vxh9nanhpyvqdq7hmfx5iggw1l8kq10jrs6xgr49qkr"))))
+ "191c7sa0rca8wkspfq8nlfa6davh743mqkzrcayz5gcx2rja7i8a"))))
(build-system python-build-system)
(arguments `(#:tests? #f)) ; no tests
(home-page "https://github.com/ianare/exif-py")
--
2.41.0
lars <at> 6xq.net, marius <at> gnu.org, me <at> bonfacemunyoki.com, sharlatanus <at> gmail.com, tanguy <at> bioneland.org, jgart <at> dismail.de, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:11 GMT) Full text and rfc822 format available.Message #23 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 09/47] gnu: Add python-supersmoother. Date: Sun, 21 Apr 2024 00:21:58 +0100
* gnu/packages/python-science.scm (python-supersmoother): New variable.
Change-Id: I8fb43d746757014e3b773c07458b777b893adb4a
---
gnu/packages/python-science.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 862e101f6a..b39dc5bc5b 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -2449,6 +2449,31 @@ (define-public python-simple-pid
proportional-integral-derivative} controller.")
(license license:expat)))
+(define-public python-supersmoother
+ (package
+ (name "python-supersmoother")
+ (version "0.4")
+ (source
+ (origin
+ (method git-fetch) ; no package in PyPI
+ (uri (git-reference
+ (url "https://github.com/jakevdp/supersmoother")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1lkj8l2mpki6x2pxcwlrplx63lhi8h9v2rzxgjfb0cppsfr8m1wp"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs (list python-numpy))
+ (native-inputs (list python-scipy))
+ (home-page "http://github.com/jakevdp/supersmoother")
+ (synopsis "Python implementation of Friedman's Supersmoother")
+ (description
+ "This package provides an efficient implementation of
+@url{https://www.slac.stanford.edu/pubs/slacpubs/3250/slac-pub-3477.pdf,
+Friedman's SuperSmoother} based in Python. It makes use of numpy for fast
+numerical computation.")
+ (license license:bsd-2)))
+
(define-public python-opt-einsum
(package
(name "python-opt-einsum")
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:12 GMT) Full text and rfc822 format available.Message #26 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 08/47] gnu: Add python-pysiaf. Date: Sun, 21 Apr 2024 00:21:57 +0100
* gnu/packages/astronomy.scm (python-pysiaf): New variable.
Change-Id: Ide732d666bccad885ed3e8c78d62df7e74524b9a
---
gnu/packages/astronomy.scm | 39 ++++++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 917b838e7a..55561c98e7 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4209,6 +4209,45 @@ (define-public python-pyregion
@end itemize")
(license license:expat)))
+(define-public python-pysiaf
+ (package
+ (name "python-pysiaf")
+ (version "0.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pysiaf" version))
+ (sha256
+ (base32 "08wb98k9k4f04455da5ns9rif8pl9r3ih537w1yj393hkjjiyzfz"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "-n" "auto"
+ ;; Disable 2 failing tests, see
+ ;; <https://github.com/spacetelescope/pysiaf/issues/338>
+ "-k" (string-append "not test_write_jwst_siaf_xlsx"
+ " and not test_write_jwst_siaf_xml" ))))
+ (propagated-inputs
+ (list python-astropy
+ python-lxml
+ python-matplotlib
+ python-numpy
+ python-numpydoc
+ python-openpyxl
+ python-requests
+ python-scipy))
+ (native-inputs
+ (list python-pytest python-pytest-xdist))
+ (home-page "https://pysiaf.readthedocs.io/")
+ (synopsis "Handling SIAF for space telescopes")
+ (description
+ "@code{pysiaf} is a python package to access, interpret, maintain, and
+generate @acronym{Handling of Science Instrument Aperture Files, SIAF}, in
+particular for JWST. Tools for applying the frame transformations, plotting,
+comparison, and validation are provided.")
+ (license license:bsd-3)))
+
(define-public python-pysynphot
;; XXX: 2.0.0 was released in 2021 there are a lot of changes since that
;; time and it failed to build with python-astropy 6.0.0, use the latest
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:14 GMT) Full text and rfc822 format available.Message #29 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 10/47] gnu: python-asdf: Update to 3.2.0. Date: Sun, 21 Apr 2024 00:21:59 +0100
* gnu/packages/astronomy.scm (python-asdf): Update to 3.2.0.
[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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 55561c98e7..b06638c49c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4418,13 +4418,13 @@ (define-public python-tweakwcs
(define-public python-asdf
(package
(name "python-asdf")
- (version "3.1.0")
+ (version "3.2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "asdf" version))
(sha256
- (base32 "0fa6y3gmqc0y3nz0h68vq3a84pvx6gc5zp33wg8a4n9b4kipm464"))))
+ (base32 "1wj556g15gwp6ir5hg083l15sifdsf23giqkx0jbn4lgdwjffbgr"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -4432,12 +4432,15 @@ (define-public python-asdf
#~(list "-n" "auto" "-p" "no:legacypath")
#:phases
#~(modify-phases %standard-phases
- ;; ImportError: Error importing plugin " no:legacypath": No module
- ;; named ' no:legacypath'
- (add-before 'check 'fix-tests-setup
+ (add-after 'unpack 'patch-pypojrect-toml
(lambda _
(substitute* "pyproject.toml"
- ((".*:legacypath.*") "")))))))
+ ;; ImportError: Error importing plugin " no:legacypath": No
+ ;; module named ' no:legacypath'
+ ((".*:legacypath.*") "")
+ ;; TypeError: Configuration.__init__() got an unexpected
+ ;; keyword argument 'version_file'
+ (("version_file = \"asdf/_version.py\"") "")))))))
(native-inputs
(list python-fsspec
python-packaging
@@ -4451,7 +4454,6 @@ (define-public python-asdf
(propagated-inputs
(list python-asdf-standard
python-asdf-transform-schemas
- python-asdf-unit-schemas
python-attrs ;; for vendorized jsonschema
python-importlib-metadata
python-jmespath
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:16 GMT) Full text and rfc822 format available.Message #32 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 11/47] gnu: python-asdf-astropy: Update to 0.6.1. Date: Sun, 21 Apr 2024 00:22:00 +0100
* gnu/packages/astronomy.scm (python-asdf-astropy): Update to 0.6.1.
Change-Id: I06f00006fcba1d0e385e6bc3f82f7a85403d94a9
---
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 b06638c49c..749c581571 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4727,13 +4727,13 @@ (define-public python-asdf-zarr
(define-public python-asdf-astropy
(package
(name "python-asdf-astropy")
- (version "0.6.0")
+ (version "0.6.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "asdf-astropy" version))
(sha256
- (base32 "0cxwknkjkgiavwmsz3vzk88c3spdi1cj4kwp62hgj92g2mh5k0zh"))))
+ (base32 "1ipjpjiirycj2npicbp39ka7db61vx45j8dm2iis71g5l1rzkblp"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:17 GMT) Full text and rfc822 format available.Message #35 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 12/47] gnu: python-astropy-iers-data: Update to 0.2024.4.15.2.45.49. Date: Sun, 21 Apr 2024 00:22:01 +0100
* gnu/packages/astronomy.scm (python-astropy-iers-data): Update to 0.2024.4.15.2.45.49.
Change-Id: Iaf902a0f506f149682868d0df0710d400b21f7e6
---
gnu/packages/astronomy.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 749c581571..567cb54685 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1696,13 +1696,13 @@ (define-public python-astropy-iers-data
;; In case of changing the source method git-fetch, consider to check the
;; tag as it's not following the PyPI version, see
;; <https://github.com/astropy/astropy-iers-data/issues/17>.
- (version "0.2024.3.18.0.29.47")
+ (version "0.2024.4.15.2.45.49")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "astropy-iers-data" version))
+ (uri (pypi-uri "astropy_iers_data" version))
(sha256
- (base32 "1mf03iqw09rp6d8hbby33f4jwfjan9gkb1z7xqsjr2jpj7zwpn3y"))))
+ (base32 "15wran1d5bw1mm3xl3ibp6i5aa7icj9p6g1mqcyp596qmdjnm8wp"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:17 GMT) Full text and rfc822 format available.Message #38 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 13/47] gnu: python-astropy: Symplify package. Date: Sun, 21 Apr 2024 00:22:02 +0100
* gnu/packages/astronomy.scm (python-astropy): Simplify package.
[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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 567cb54685..fc3c652132 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1565,9 +1565,20 @@ (define-public python-astropy
;; see https://github.com/astropy/astropy/pull/14311
(with-directory-excursion "cextern"
(for-each delete-file-recursively '("expat" "wcslib")))))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
(list
+ #:test-flags
+ #~(list "--pyargs" "astropy"
+ "-n" "auto"
+ "-k" (string-append
+ ;; Skip tests that need remote data.
+ "not remote_data"
+ ;; E astropy.samp.errors.SAMPProxyError:
+ ;; <SAMPProxyError 1: 'Timeout expired!'>
+ " and not test_main"
+ ;; E ModuleNotFoundError: No module named 'wofz'
+ " and not test_pickle_functional"))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'preparations
@@ -1587,32 +1598,18 @@ (define-public python-astropy
(add-before 'install 'writable-compiler
(lambda _
(make-file-writable "astropy/_compiler.c")))
- (add-before 'check 'prepare-test-environment
- (lambda _
- ;; Some tests require a writable home.
- (setenv "HOME" "/tmp")
- (make-file-writable "astropy/_compiler.c")
- ;; Extensions have to be rebuilt before running the tests.
- (invoke "python" "setup.py" "build_ext" "--inplace"
- "-j" (number->string (parallel-job-count)))))
- ;; TODO: The swap to pyproject-build-system introduced all tests
- ;; failed due to pytest could not load conftest.py, find out how
- ;; to resolve it and migrate completely to pyproject-build-system.
(replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
(when tests?
- (invoke "python" "-m" "pytest" "--pyargs" "astropy"
- ;; with -n : 133.00s
- ;; without -n : 326.14s
- "-n" (number->string (parallel-job-count))
- "-k" (string-append
- ;; Skip tests that need remote data.
- "not remote_data"
- ;; E astropy.samp.errors.SAMPProxyError:
- ;; <SAMPProxyError 1: 'Timeout expired!'>
- " and not test_main"
- ;; E ModuleNotFoundError: No module named 'wofz'
- " and not test_pickle_functional"))))))))
+ (setenv "HOME" "/tmp")
+ (make-file-writable "astropy/_compiler.c")
+ ;; Extensions have to be rebuilt before running the tests.
+ (invoke "python" "setup.py" "build_ext" "--inplace"
+ "-j" (number->string (parallel-job-count)))
+ ;; Step out of the source directory to avoid interference; we
+ ;; want to run the installed code with extensions etc.
+ (with-directory-excursion "/tmp"
+ (apply invoke "pytest" "-v" test-flags))))))))
(native-inputs
(list pkg-config
python-colorlog
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:18 GMT) Full text and rfc822 format available.Message #41 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 15/47] gnu: python-astropy-healpix: Update to 1.0.3. Date: Sun, 21 Apr 2024 00:22:04 +0100
* gnu/packages/astronomy.scm (python-astropy-healpix): Update to 1.0.3.
Change-Id: Iffc1d537bd8b3ec10fbb5ddb7c2fd6251813ccde
---
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 7fcb1a678d..6908be0694 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1654,13 +1654,13 @@ (define-public python-astropy
(define-public python-astropy-healpix
(package
(name "python-astropy-healpix")
- (version "1.0.2")
+ (version "1.0.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "astropy_healpix" version))
(sha256
- (base32 "0fij80ws16xzbph8z9v27w54dnc3vry8fk9p3mvxrglnjgnscvq5"))))
+ (base32 "0ilpwwvdnd4nchivwnbiy1hl07hd2mdg4wb90r2p05kvr5z2lpfy"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:24:20 GMT) Full text and rfc822 format available.Message #44 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 14/47] gnu: python-astropy: Update to 6.0.1. Date: Sun, 21 Apr 2024 00:22:03 +0100
* gnu/packages/astronomy.scm (python-astropy): Update to 6.0.1.
[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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index fc3c652132..7fcb1a678d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1546,13 +1546,13 @@ (define-public celestia-gtk
(define-public python-astropy
(package
(name "python-astropy")
- (version "6.0.0")
+ (version "6.0.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "astropy" version))
(sha256
- (base32 "1nbpqx7ibm8zsyyy17y5rmfjamwz6mv0sy4drlisap9hald81k83"))
+ (base32 "175k2h039c0b8rsf0fdphmxbpjrszd138j8z9zkhh1kd6pg7bac9"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -1574,11 +1574,9 @@ (define-public python-astropy
"-k" (string-append
;; Skip tests that need remote data.
"not remote_data"
- ;; E astropy.samp.errors.SAMPProxyError:
- ;; <SAMPProxyError 1: 'Timeout expired!'>
- " and not test_main"
- ;; E ModuleNotFoundError: No module named 'wofz'
- " and not test_pickle_functional"))
+ ;; ValueError: The truth value of an array with more than
+ ;; one element is ambiguous. Use a.any() or a.all()
+ " and not test_table_comp[t16-t26]"))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'preparations
@@ -1619,7 +1617,6 @@ (define-public python-astropy
python-h5py
python-ipython
python-jplephem
- python-matplotlib
python-objgraph
python-pandas
python-pyarrow
@@ -1629,21 +1626,23 @@ (define-public python-astropy
python-pytest-mpl
python-pytest-xdist
python-scikit-image
- python-scipy
python-setuptools-scm
python-sgp4
python-skyfield
+ python-threadpoolctl
python-timezonefinder))
(inputs
(list expat wcslib))
(propagated-inputs
(list python-astropy-iers-data
python-configobj
+ python-matplotlib
python-numpy
python-packaging
python-ply
python-pyerfa
- python-pyyaml))
+ python-pyyaml
+ python-scipy))
(home-page "https://www.astropy.org/")
(synopsis "Core package for Astronomy in Python")
(description
--
2.41.0
lars <at> 6xq.net, marius <at> gnu.org, me <at> bonfacemunyoki.com, sharlatanus <at> gmail.com, tanguy <at> bioneland.org, jgart <at> dismail.de, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:25:03 GMT) Full text and rfc822 format available.Message #47 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 06/47] gnu: parfive: Update to 2.1.0. Date: Sun, 21 Apr 2024 00:21:55 +0100
* gnu/packages/python-web.scm (parfive): Update to 2.1.0.
Change-Id: I6207150e012c03943d4553854123831d1bba3e55
---
gnu/packages/python-web.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 5a532f8460..fb6abb9d80 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1378,13 +1378,13 @@ (define-public httpie
(define-public parfive
(package
(name "parfive")
- (version "2.0.2")
+ (version "2.1.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "parfive" version))
(sha256
(base32
- "0pf8rzfwxpkn84xzb4v8m1fy3k7kjlh8f9ln4y5xqlnbqpwi30lh"))))
+ "13nw2y7wjzj6w049av6ff4d0zxgbhkrgck0xyh676c114hcv8v6d"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:25:04 GMT) Full text and rfc822 format available.Message #50 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 16/47] gnu: python-jwst: Update to 1.14.0. Date: Sun, 21 Apr 2024 00:22:05 +0100
* gnu/packages/astronomy.scm (python-jwst): Update to 1.14.0.
[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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 6908be0694..374229bcf4 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3969,13 +3969,13 @@ (define-public python-jplephem
(define-public python-jwst
(package
(name "python-jwst")
- (version "1.13.4")
+ (version "1.14.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "jwst" version))
(sha256
(base32
- "0n5cfjayg15kf5p6pns7k2zfcldqz1464ndbldgzanc33fp9wnfz"))))
+ "0knl2x0z3djsln8mi3a4bkxjz49iwmnr1v6wwsk13zvpkfq21vv4"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -3992,19 +3992,21 @@ (define-public python-jwst
(propagated-inputs (list opencv
python-asdf
python-asdf-astropy
- python-asdf-transform-schemas
python-astropy
python-bayesicfitting
python-crds
python-drizzle
python-gwcs
+ python-importlib-metadata
python-jplephem
python-jsonschema
python-numpy
+ python-packaging
python-photutils
python-poppy
python-psutil
python-pyparsing
+ python-pysiaf
python-requests
python-scikit-image
python-scipy
@@ -4014,6 +4016,7 @@ (define-public python-jwst
python-stpipe
python-stsci-image
python-stsci-imagestats
+ python-synphot
python-tweakwcs
python-wiimatch))
(native-inputs (list python-colorama
@@ -4022,6 +4025,7 @@ (define-public python-jwst
python-pytest-doctestplus
python-pytest-openfiles
python-requests-mock
+ ;; python-ruff ; not packed yet in Guix
python-setuptools-scm))
(home-page "https://jwst-pipeline.readthedocs.io/en/latest/")
(synopsis
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:25:05 GMT) Full text and rfc822 format available.Message #53 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 17/47] gnu: python-stcal: Update to 1.7.0. Date: Sun, 21 Apr 2024 00:22:06 +0100
* gnu/packages/astronomy.scm (python-stcal): Update to 1.7.0.
[native-inputs]: Remove python-pytest-openfiles.
Change-Id: Ib33bb72ff73fcf569a2519b3353260461b63c143
---
gnu/packages/astronomy.scm | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 374229bcf4..cb5be9393d 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3229,13 +3229,13 @@ (define-public python-stsci-stimage
(define-public python-stcal
(package
(name "python-stcal")
- (version "1.6.1")
+ (version "1.7.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "stcal" version))
(sha256
- (base32 "1rwvzjpidz0sfp52mqgs25599hbvxyc4gdc1yk0kdm8aynhdwi82"))))
+ (base32 "04ippj90dn2671xg4rvncf7jsbpcflr7dr6jc2h52z7xfd1msb4d"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -3264,7 +3264,6 @@ (define-public python-stcal
python-pytest
python-pytest-cov
python-pytest-doctestplus
- python-pytest-openfiles
python-semantic-version
python-setuptools-scm))
(home-page "https://github.com/spacetelescope/stcal")
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:25:06 GMT) Full text and rfc822 format available.Message #56 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 18/47] gnu: python-stdatamodels: Update to 1.10.1. Date: Sun, 21 Apr 2024 00:22:07 +0100
* gnu/packages/astronomy.scm (python-stdatamodels): Update to 1.10.1.
Change-Id: Ib1626de00fbd060212b125c3a52e116aa126727e
---
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 cb5be9393d..32949d0a13 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3274,13 +3274,13 @@ (define-public python-stcal
(define-public python-stdatamodels
(package
(name "python-stdatamodels")
- (version "1.10.0")
+ (version "1.10.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "stdatamodels" version))
(sha256
- (base32 "00zc7z3f2fjvmms2h7176wnzjb025v0aasc6fiib9055sk34bc94"))))
+ (base32 "1h0imp6j9qrjadhvvqcgrx6dq94qhi0023c8c8r2wddhqrh0h5lg"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:25:08 GMT) Full text and rfc822 format available.Message #59 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 19/47] gnu: python-stsci-imagestats: Update to 1.8.2. Date: Sun, 21 Apr 2024 00:22:08 +0100
* gnu/packages/astronomy.scm (python-stsci-imagestats): Update to 1.8.2.
Change-Id: I13bb6eab789a8aa365f6bf0f0f892d8a17e3cc66
---
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 32949d0a13..b7f7127c24 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3162,13 +3162,13 @@ (define-public python-stsci-image
(define-public python-stsci-imagestats
(package
(name "python-stsci-imagestats")
- (version "1.8.0")
+ (version "1.8.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "stsci.imagestats" version))
(sha256
(base32
- "01jqqrhcna0ghin48bbcza57d12371ny4l4pqws89irwdhd8xr0r"))))
+ "1nmya85bf2747c9ggya6my5b1slk6g2a7bk16rdv8r5a4ah9hda5"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:25:10 GMT) Full text and rfc822 format available.Message #62 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 21/47] gnu: python-synphot: Add custom check phase. Date: Sun, 21 Apr 2024 00:22:10 +0100
* gnu/packages/astronomy.scm (python-synphot): [arguments] <#:phases>:
Remove 'prepare-test-environment phase; add custom 'check phase.
Change-Id: I9cb6d65c226a555ccd62a3a6c08d00868a66f109
---
gnu/packages/astronomy.scm | 21 ++++++++-------------
1 file changed, 8 insertions(+), 13 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 4fea09067c..7ca051aa79 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4348,19 +4348,14 @@ (define-public python-synphot
(list
#:phases
#~(modify-phases %standard-phases
- (add-before 'check 'prepare-test-environment
- (lambda _
- (invoke "python" "setup.py" "build_ext" "--inplace")
- ;; To solve pytest/conftest issue. Pytest tries to load all
- ;; files with word 'test' in them.
- ;;
- ;; ImportError while loading conftest ...
- ;; _pytest.pathlib.ImportPathMismatchError: ...
- ;;
- (call-with-output-file "pytest.ini"
- (lambda (port)
- (format port "[pytest]
-python_files = test_*.py"))))))))
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (when tests?
+ (invoke "python" "setup.py" "build_ext" "--inplace")
+ ;; Step out of the source directory to avoid interference; we
+ ;; want to run the installed code with extensions etc.
+ (with-directory-excursion "/tmp"
+ (apply invoke "pytest" "-v" test-flags))))))))
(propagated-inputs
(list python-astropy
python-dust-extinction
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:25:11 GMT) Full text and rfc822 format available.Message #65 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 22/47] gnu: python-synphot: Update to 1.4.0. Date: Sun, 21 Apr 2024 00:22:11 +0100
* gnu/packages/astronomy.scm (python-synphot): Update to 1.4.0.
Change-Id: I070381de76cfe1bf057d1c8032d2145d5c346fa2
---
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 7ca051aa79..c868cd824e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4336,13 +4336,13 @@ (define-public python-suntime
(define-public python-synphot
(package
(name "python-synphot")
- (version "1.3.0")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "synphot" version))
(sha256
- (base32 "0a54bfrx9aar66040324sw9qdjz5lg67y28sjsxhyv9h3gppc7c0"))))
+ (base32 "0fk860bxaqbamrq15pkqlbvhbf70y50cra2mgvv9r0cxq37isbi6"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:25:12 GMT) Full text and rfc822 format available.Message #68 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 20/47] gnu: python-stsci-image: Refresh package style. Date: Sun, 21 Apr 2024 00:22:09 +0100
* gnu/packages/astronomy.scm (python-stsci-image): Adjust indentation.
[description]: Fix grammar.
Change-Id: I1f4bf751720a3be324644bf417104e36510c62a6
---
gnu/packages/astronomy.scm | 30 +++++++++++++++---------------
1 file changed, 15 insertions(+), 15 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b7f7127c24..4fea09067c 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3135,28 +3135,28 @@ (define-public python-stsci-image
(package
(name "python-stsci-image")
(version "2.3.5")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "stsci.image" version))
- (sha256
- (base32
- "1vnp4256nbdvapa69cmm80sjz11ygxa49abr9nbvssj6nyyp5icb"))))
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "stsci.image" version))
+ (sha256
+ (base32 "1vnp4256nbdvapa69cmm80sjz11ygxa49abr9nbvssj6nyyp5icb"))))
(build-system pyproject-build-system)
(arguments
- (list #:phases #~(modify-phases %standard-phases
- (add-before 'check 'build-extensions
- (lambda _
- ;; Cython extensions have to be built before running
- ;; the tests.
- (invoke "python" "setup.py" "build_ext"
- "--inplace"))))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'check 'build-extensions
+ (lambda _
+ ;; Cython extensions have to be built before running the tests.
+ (invoke "python" "setup.py" "build_ext" "--inplace"))))))
(propagated-inputs (list python-numpy python-scipy))
(native-inputs (list python-pytest python-setuptools-scm))
(home-page "https://github.com/spacetelescope/stsci.image")
(synopsis "Image array manipulation functions")
(description
- "This package provides Python modules of @acronym{STScI, Space Telescope
-Science Institute} image array manipulation functions.")
+ "This package provides a Python module to various @acronym{STScI, Space
+Telescope Science Institute} image array manipulation functions.")
(license license:bsd-3)))
(define-public python-stsci-imagestats
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:25:14 GMT) Full text and rfc822 format available.Message #71 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 23/47] gnu: python-tweakwcs: Adjust indentation. Date: Sun, 21 Apr 2024 00:22:12 +0100
* gnu/packages/astronomy.scm (python-tweakwcs): Adjust indentation.
Change-Id: Ic8c79addbd0253c2364382e6a0e632945eafb05a
---
gnu/packages/astronomy.scm | 40 ++++++++++++++++++++------------------
1 file changed, 21 insertions(+), 19 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index c868cd824e..a43f21f0b1 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4379,26 +4379,28 @@ (define-public python-tweakwcs
(package
(name "python-tweakwcs")
(version "0.8.6")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "tweakwcs" version))
- (sha256
- (base32
- "1j75i02xzd36gp7pf6gks6nmp4ivi9cbphya4l69py5p62iaab99"))))
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "tweakwcs" version))
+ (sha256
+ (base32 "1j75i02xzd36gp7pf6gks6nmp4ivi9cbphya4l69py5p62iaab99"))))
(build-system pyproject-build-system)
- (propagated-inputs (list python-astropy
- python-gwcs
- python-numpy
- python-packaging
- python-spherical-geometry
- python-stsci-imagestats
- python-stsci-stimage))
- (native-inputs (list python-codecov
- python-pytest
- python-pytest-cov
- python-scipy
- python-semantic-version
- python-setuptools-scm))
+ (propagated-inputs
+ (list python-astropy
+ python-gwcs
+ python-numpy
+ python-packaging
+ python-spherical-geometry
+ python-stsci-imagestats
+ python-stsci-stimage))
+ (native-inputs
+ (list python-codecov
+ python-pytest
+ python-pytest-cov
+ python-scipy
+ python-semantic-version
+ python-setuptools-scm))
(home-page "https://tweakwcs.readthedocs.io/en/latest/")
(synopsis
"Algorithms for matching and aligning catalogs and for tweaking the WCS")
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:05 GMT) Full text and rfc822 format available.Message #74 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 27/47] gnu: python-gatspy: Refresh package style. Date: Sun, 21 Apr 2024 00:22:16 +0100
* gnu/packages/astronomy.scm (python-gatspy): Adjust indentetion.
[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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index d183a968ed..bf71843e05 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -675,33 +675,34 @@ (define-public python-gatspy
(package
(name "python-gatspy")
(version "0.3")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "gatspy" version))
- (sha256
- (base32
- "1gw2z6x8nikvnw2gkdl70gr81cwczd1pd7v8ry2kjn6k4kssrfav"))))
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "gatspy" version))
+ (sha256
+ (base32 "1gw2z6x8nikvnw2gkdl70gr81cwczd1pd7v8ry2kjn6k4kssrfav"))))
(build-system pyproject-build-system)
(arguments
(list
- #:phases
- '(modify-phases %standard-phases
- ;; Tests need this
- (add-before 'check 'set-HOME
- (lambda _ (setenv "HOME" "/tmp"))))
#:test-flags
- '(list "-k"
- (string-append
- ;; These tests require internet access
- "not test_download_data.py"
- ;; XXX: we don't have supersmoother
- " and not test_supersmoother.py"))))
- (propagated-inputs (list python-astroml python-numpy python-scipy))
+ ;; These tests require internet access
+ #~(list "-k" "not test_download_data.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; Tests need this
+ (add-before 'check 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp"))))))
+ (propagated-inputs
+ (list python-astroml
+ python-numpy
+ python-scipy
+ python-supersmoother))
(native-inputs (list python-pytest python-nose python-setuptools-scm))
(home-page "https://github.com/astroml/gatspy")
(synopsis "General tools for astronomical time series in Python")
- (description "This package provides general tools for astronomical time
-series in Python.")
+ (description
+ "This package provides general tools for astronomical time series in
+Python.")
(license license:bsd-2)))
(define-public python-ginga
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:06 GMT) Full text and rfc822 format available.Message #77 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 32/47] gnu: python-sunpy: Update to 5.1.2. Date: Sun, 21 Apr 2024 00:22:21 +0100
* gnu/packages/astronomy.scm (python-sunpy): Update to 5.1.2.
Change-Id: I275445d688dfb3c3c3da18a37d7d21d79814f8ef
---
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 dbe589ee1a..0371ed6522 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2806,13 +2806,13 @@ (define-public python-sgp4
(define-public python-sunpy
(package
(name "python-sunpy")
- (version "5.1.1")
+ (version "5.1.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "sunpy" version))
(sha256
- (base32 "07rfdj4v29kcb718sgjfsagazvnl11r01ciqjvazr5x3yadfqrwk"))))
+ (base32 "0h62qh74xanj2drikjch7h0a5g4dsaf3v4qxx38vjazmibc37ynp"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:08 GMT) Full text and rfc822 format available.Message #80 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 33/47] gnu: python-astroplan: Update to 0.10. Date: Sun, 21 Apr 2024 00:22:22 +0100
* gnu/packages/astronomy.scm (python-astroplan): Update to 0.10.
Change-Id: I80a988262e417f8a5501d02db5e16a93b5d037b4
---
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 0371ed6522..52f908611b 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1754,13 +1754,13 @@ (define-public python-astropy-iers-data
(define-public python-astroplan
(package
(name "python-astroplan")
- (version "0.9.1")
+ (version "0.10")
(source
(origin
(method url-fetch)
(uri (pypi-uri "astroplan" version))
(sha256
- (base32 "0jrgii0f11ckxvywinr9kcsljxnpnkh7hv5638wxwcb1iyjmx36r"))))
+ (base32 "0nl7yi0h5nn4id1jifd8hpwzqdarq9z2iq56x0j2kmj3472cjw0n"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:11 GMT) Full text and rfc822 format available.Message #83 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 31/47] gnu: python-skyfield: Enable tests. Date: Sun, 21 Apr 2024 00:22:20 +0100
* gnu/packages/astronomy.scm (python-skyfield): Enable tests.
[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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 15aa313c41..dbe589ee1a 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -5048,15 +5048,27 @@ (define-public python-skyfield
(version "1.48")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "skyfield" version))
+ (method git-fetch) ; PyPI tarball lacks test data
+ (uri (git-reference
+ (url "https://github.com/skyfielders/python-skyfield")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
- (base32 "1qaz0k0lkni3y423r66mkvj99bx08qa9xgqp3cs2df70cmdz30cb"))))
- (build-system python-build-system)
+ (base32 "0l324r4pz7d5w72c7c5akvjx40287hl7sl0qv7swvn2da53vmq0r"))))
+ (build-system pyproject-build-system)
(arguments
- ;; XXX: Tests depend on custom test framework
- ;; https://github.com/brandon-rhodes/assay
- `(#:tests? #f))
+ (list
+ #:test-flags
+ #~(list "-m" "assay" "--batch" "skyfield.tests")
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "ci"
+ (apply invoke "python" test-flags))))))))
+ (native-inputs
+ (list python-assay python-pandas))
(propagated-inputs
(list python-certifi
python-jplephem
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:13 GMT) Full text and rfc822 format available.Message #86 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 34/47] gnu: python-rad: Update to 0.19.2. Date: Sun, 21 Apr 2024 00:22:23 +0100
* gnu/packages/astronomy.scm (python-rad): Update to 0.19.2.
Change-Id: I4de8e8228f6d7ae1ae28cac726fcce5f2058f928
---
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 52f908611b..10eb640e56 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4862,13 +4862,13 @@ (define-public python-gwcs
(define-public python-rad
(package
(name "python-rad")
- (version "0.19.0")
+ (version "0.19.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "rad" version))
(sha256
(base32
- "0cp3nrv1vq3g61zx6dq36vdlxd5i8g52vg4hwpxakmwvqvc8p3gd"))))
+ "08dh9asdjgfmczmqyjplgdvbk3n68qw6akd8h953wq6v3yr4k4rq"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
lars <at> 6xq.net, marius <at> gnu.org, me <at> bonfacemunyoki.com, sharlatanus <at> gmail.com, tanguy <at> bioneland.org, jgart <at> dismail.de, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:15 GMT) Full text and rfc822 format available.Message #89 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 30/47] gnu: Add python-assay. Date: Sun, 21 Apr 2024 00:22:19 +0100
* gnu/packages/python-check.scm (python-assay): New variable.
Change-Id: I0ec910d8c37000ff08119a33e3f42af2269fa494
---
gnu/packages/python-check.scm | 34 +++++++++++++++++++++++++++++++++-
1 file changed, 33 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 777791cb6c..6fdfaad6fb 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -9,7 +9,7 @@
;;; Copyright © 2020 Edouard Klein <edk <at> beaver-labs.com>
;;; Copyright © 2020, 2021 Vinicius Monego <monego <at> posteo.net>
;;; Copyright © 2020 Tanguy Le Carrour <tanguy <at> bioneland.org>
-;;; Copyright © 2021-2023 Sharlatan Hellseher <sharlatanus <at> gmail.com>
+;;; Copyright © 2021-2024 Sharlatan Hellseher <sharlatanus <at> gmail.com>
;;; Copyright © 2021 Brendan Tildesley <mail <at> brendan.scot>
;;; Copyright © 2021, 2022 Guillaume Le Vaillant <glv <at> posteo.net>
;;; Copyright © 2021 Bonface Munyoki Kilyungi <me <at> bonfacemunyoki.com>
@@ -61,6 +61,38 @@ (define-module (gnu packages python-check)
#:use-module (guix packages)
#:use-module (guix utils))
+(define-public python-assay
+ ;; No release yet.
+ (let ((commit "74617d70e77afa09f58b3169cf496679ac5d5621")
+ (revision "0"))
+ (package
+ (name "python-assay")
+ (version (git-version "0.0.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/brandon-rhodes/assay")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1klxmamj88mn0q348r08zksccgsbch8sp0m4b04s3myrqnslp2nd"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags #~(list "-m" "assay.tests")
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (when tests?
+ (apply invoke "python" test-flags)))))))
+ (home-page "https://github.com/brandon-rhodes/assay")
+ (synopsis "Python testing framework")
+ (description
+ "This package provides opiniotated Python test framework prototype.")
+ (license license:expat))))
+
(define-public python-assertpy
(package
(name "python-assertpy")
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:17 GMT) Full text and rfc822 format available.Message #92 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 37/47] gnu: python-casa-formats-io: Update to 0.3.0. Date: Sun, 21 Apr 2024 00:22:26 +0100
* gnu/packages/astronomy.scm (python-casa-formats-io): Update to 0.3.0.
Change-Id: I3f8ca4c981ac31cc955d374b4e4735e53af4c868
---
gnu/packages/astronomy.scm | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 14520b0596..c5243dc6e9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1973,7 +1973,7 @@ (define-public python-bayesicfitting
(define-public python-casa-formats-io
(package
(name "python-casa-formats-io")
- (version "0.2.2")
+ (version "0.3.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "casa-formats-io" version))
--
2.41.0
lars <at> 6xq.net, marius <at> gnu.org, me <at> bonfacemunyoki.com, sharlatanus <at> gmail.com, tanguy <at> bioneland.org, jgart <at> dismail.de, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:18 GMT) Full text and rfc822 format available.Message #95 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 05/47] gnu: python-pytest-socket: Update to 0.7.0. Date: Sun, 21 Apr 2024 00:21:54 +0100
* gnu/packages/python-check.scm (python-pytest-socket): Update to 0.7.0.
Change-Id: I879064eba2f4d93d2e2b519ebdf613685d5b5df9
---
gnu/packages/python-check.scm | 31 +++++++++++++++++++++++--------
1 file changed, 23 insertions(+), 8 deletions(-)
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index b39709d960..777791cb6c 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -420,13 +420,17 @@ (define-public python-vcrpy
(define-public python-pytest-socket
(package
(name "python-pytest-socket")
- (version "0.5.1")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "pytest-socket" version))
- (sha256
- (base32
- "1dkr86nxkxc0ka3rdnpmk335m8gl1zh1sy8i7w4w1jsidbf82jvw"))))
+ (version "0.7.0")
+ (source
+ (origin
+ ;; There are no tests in the PyPI tarball.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/miketheman/pytest-socket")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1m6s07gvljq82hiajzy1v123kpkciziiqdjqfnas169rmzg0bmnp"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -440,7 +444,18 @@ (define-public python-pytest-socket
" and not test_httpx_fails"
" and not test_disabled_urllib_fails"
" and not test_urllib_succeeds_by_default"
- " and not test_enabled_urllib_succeeds"))))
+ " and not test_enabled_urllib_succeeds"
+ " and not test_single_cli_arg_connect_disabled_hostname_resolved"))
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; See <https://github.com/miketheman/pytest-socket/issues/308>
+ (add-after 'unpack 'fix-tests
+ (lambda _
+ (substitute* (list "tests/test_async.py"
+ "tests/test_socket.py"
+ "tests/test_precedence.py")
+ (("from tests.common import assert_socket_blocked")
+ "from common import assert_socket_blocked")))))))
(native-inputs (list python-httpx
python-poetry-core
python-pypa-build
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:20 GMT) Full text and rfc822 format available.Message #98 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 24/47] gnu: python-tweakwcs: Update to 0.8.7. Date: Sun, 21 Apr 2024 00:22:13 +0100
* gnu/packages/astronomy.scm (python-tweakwcs): Update to 0.8.7.
Change-Id: I2ef8f29839a99ec3b40efc34a61f57bc32216c8e
---
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 a43f21f0b1..f57165050f 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4378,13 +4378,13 @@ (define-public python-synphot
(define-public python-tweakwcs
(package
(name "python-tweakwcs")
- (version "0.8.6")
+ (version "0.8.7")
(source
(origin
(method url-fetch)
(uri (pypi-uri "tweakwcs" version))
(sha256
- (base32 "1j75i02xzd36gp7pf6gks6nmp4ivi9cbphya4l69py5p62iaab99"))))
+ (base32 "0cch4z5zmmi1s02n1wdwss8p7qhrzyiajkaik0gga510kgdsvx48"))))
(build-system pyproject-build-system)
(propagated-inputs
(list python-astropy
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:23 GMT) Full text and rfc822 format available.Message #101 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 26/47] gnu: python-ginga: Set HOME for sanity check. Date: Sun, 21 Apr 2024 00:22:15 +0100
* gnu/packages/astronomy.scm (python-ginga) [arguments] <#:phases>: Add
'set-home phase.
Change-Id: I7fc9b043ae8ac465645215dabc9d8643b8e08fe2
---
gnu/packages/astronomy.scm | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 70e3daa501..d183a968ed 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -723,7 +723,13 @@ (define-public python-ginga
(lambda _
(substitute* "setup.cfg"
;; packaging>=23.1
- ((">=23.1") ">=21.3")))))))
+ ((">=23.1") ">=21.3"))))
+ (add-before 'check 'set-home
+ (lambda _
+ ;; Relax matplotlib warning: ... because the default path
+ ;; (/homeless-shelter/.config/matplotlib) is not a writable
+ ;; directory ...
+ (setenv "HOME" "/tmp"))))))
(propagated-inputs
(list opencv
python-astropy
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:24 GMT) Full text and rfc822 format available.Message #104 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 25/47] gnu: python-ginga: Update to 5.0.1. Date: Sun, 21 Apr 2024 00:22:14 +0100
* gnu/packages/astronomy.scm (python-ginga): Update to 5.0.1.
[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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index f57165050f..70e3daa501 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -707,31 +707,45 @@ (define-public python-gatspy
(define-public python-ginga
(package
(name "python-ginga")
- (version "5.0.0")
+ (version "5.0.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ginga" version))
(sha256
- (base32 "1kydi6qqsscgsa55fa2za35vr5j8xjn09lfbnb5ajr8yxdgm4n3y"))))
+ (base32 "1zw93487a0ilkb5w5qjgrdnavxlmdmjp6c2wyc1wp8qahby9c0xa"))))
(build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "setup.cfg"
+ ;; packaging>=23.1
+ ((">=23.1") ">=21.3")))))))
(propagated-inputs
- (list ;;python-exifread ; optional, not packed yet in Guix
+ (list opencv
python-astropy
python-astroquery
python-dateutil
+ python-exif-read
+ python-fitsio
python-magic
python-matplotlib
- python-fitsio
python-numpy
+ python-packaging
python-photutils
python-pillow
+ python-pyyaml
python-qtpy
- python-scipy))
+ python-scipy
+ python-tomli))
(native-inputs
(list python-attrs
python-docutils
python-pytest-astropy
+ python-pytest-astropy-header
python-semantic-version
python-tornado))
(home-page "https://ejeschke.github.io/ginga/")
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:26 GMT) Full text and rfc822 format available.Message #107 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 29/47] gnu: python-bayesicfitting: Update to 3.2.1. Date: Sun, 21 Apr 2024 00:22:18 +0100
* gnu/packages/astronomy.scm (python-bayesicfitting): Update to 3.2.1.
Change-Id: I97bfc44920a3e8f7c2040088f284a38e0a66aa88
---
gnu/packages/astronomy.scm | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 618d0e78bf..15aa313c41 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1933,16 +1933,18 @@ (define-public python-astroscrappy
(define-public python-bayesicfitting
(package
(name "python-bayesicfitting")
- (version "3.2.0")
+ (version "3.2.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/dokester/BayesicFitting")
- (commit (string-append "v" version))))
+ ;; Tag style has been changed, see
+ ;; <https://github.com/dokester/BayesicFitting/issues/23>.
+ (commit (string-append "v." version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0q6v7w9b1xzam0qn5vsl5wrdp1fkfpsn411pzd8wyy9giznpajxi"))))
+ (base32 "0brqvy4r75vh93lj4jwv8wcrc96ka1v44f5ckjvr65y30plnfwg2"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:29 GMT) Full text and rfc822 format available.Message #110 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 36/47] gnu: python-roman-datamodels: Update to 0.19.1. Date: Sun, 21 Apr 2024 00:22:25 +0100
* gnu/packages/astronomy.scm (python-roman-datamodels): Update to 0.19.1.
[propagated-inputs]: Remove python-asdf-standard.
Change-Id: I30e2adef137bb95f37dd7651ebf8c5e6f9e6155f
---
gnu/packages/astronomy.scm | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index fe1bc54157..14520b0596 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -4971,13 +4971,13 @@ (define-public python-radiospectra
(define-public python-roman-datamodels
(package
(name "python-roman-datamodels")
- (version "0.19.0")
+ (version "0.19.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "roman_datamodels" version))
(sha256
(base32
- "1ym06rj637fq9gxncdrn3phplk5djrzdwqghszis0di1dvsrif4j"))))
+ "1fp9rwzm5kzm0hjwwmlx7kym7yriyhxbfg2zr3y625pyvwpnl0a8"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -4990,7 +4990,6 @@ (define-public python-roman-datamodels
(setenv "HOME" "/tmp"))))))
(propagated-inputs (list python-asdf
python-asdf-astropy
- python-asdf-standard
python-astropy
python-gwcs
python-numpy
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:29 GMT) Full text and rfc822 format available.Message #113 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 38/47] gnu: python-specutils: Update to 1.14.0. Date: Sun, 21 Apr 2024 00:22:27 +0100
* gnu/packages/astronomy.scm (python-specutils): Update to 1.14.0.
Change-Id: Ied7078bc28d7b995574fb228797f1d046ea52feb
---
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 c5243dc6e9..ab5ea7394e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3070,13 +3070,13 @@ (define-public python-spectral-cube
(define-public python-specutils
(package
(name "python-specutils")
- (version "1.13.0")
+ (version "1.14.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "specutils" version))
(sha256
- (base32 "0cfsigvsa0i7z2nq9ci9gxccp074kqsgr01xi2npk8xf7cjisrfq"))))
+ (base32 "06l0k8hi4hbfs825cnw948nnkl627g3w48n2pf9rspbvd3vbs2qf"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:30 GMT) Full text and rfc822 format available.Message #116 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 35/47] gnu: python-regions: Update to 0.9. Date: Sun, 21 Apr 2024 00:22:24 +0100
* gnu/packages/astronomy.scm (python-regions): Update to 0.9.
[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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 10eb640e56..fe1bc54157 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2667,13 +2667,13 @@ (define-public python-pyvo
(define-public python-regions
(package
(name "python-regions")
- (version "0.8")
+ (version "0.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "regions" version))
(sha256
- (base32 "09401pz7926zlci7cznd78hmv9947f6jxyy2afqdqc1xaccpzcq2"))))
+ (base32 "0kvfdzqry3vcvphd7ldmppbgn3ab97hbfzwxfrlxls92yi41h3i6"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -2681,14 +2681,21 @@ (define-public python-regions
#~(list "-n" "auto")
#:phases
#~(modify-phases %standard-phases
+ ;; setup.py was removed in 84c80a280431adda00641cda5264c7de18b43b2f
+ ;; for some unknown reason, which caused the package to fail to
+ ;; build. It is being recreated based on that commit.
+ (add-after 'unpack 'create-setup.py
+ (lambda _
+ (call-with-output-file "setup.py"
+ (lambda (port)
+ (format port "from setuptools import setup
+from extension_helpers import get_extensions
+setup(ext_modules=get_extensions())")))))
;; This file is opened in both install and check phases.
- ;; XXX: Check if it is still required.
(add-before 'install 'writable-compiler
(lambda _ (make-file-writable "regions/_compiler.c")))
- (add-before 'check 'prepare-test-environment
+ (add-before 'check 'build-extensions
(lambda _
- (setenv "HOME" "/tmp")
- (make-file-writable "regions/_compiler.c")
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(propagated-inputs
(list python-astropy
@@ -2698,7 +2705,7 @@ (define-public python-regions
python-scipy
python-shapely))
(native-inputs
- (list python-cython
+ (list python-cython-3
python-extension-helpers
python-pytest-arraydiff
python-pytest-astropy
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:32 GMT) Full text and rfc822 format available.Message #119 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 39/47] gnu: python-photutils: Update to 1.12. Date: Sun, 21 Apr 2024 00:22:28 +0100
* gnu/packages/astronomy.scm (python-photutils): Update to 1.12.
[arguments]: <#:phases>: Add 'create-setup.py phase.
Change-Id: I94908eda0eb7741cb23d2d4dc969c91cdbd08fa2
---
gnu/packages/astronomy.scm | 16 ++++++++++++++--
1 file changed, 14 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ab5ea7394e..dd5864a582 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2426,13 +2426,15 @@ (define-public python-ndcube
(define-public python-photutils
(package
(name "python-photutils")
- (version "1.10.0")
+ ;; PyPI version for source archive is missing minor 0, See
+ ;; <https://github.com/astropy/photutils/issues/1727>
+ (version "1.12")
(source
(origin
(method url-fetch)
(uri (pypi-uri "photutils" version))
(sha256
- (base32 "148zhdxhlcgj6dxyzaz78bzxw1q44qa9q9sfdqbfbla0s0w2jaay"))))
+ (base32 "0y4kcj6qjnzwjswc0c2iimh11b0jz6b9ianbh58w4gnb4y71lr6r"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -2440,6 +2442,16 @@ (define-public python-photutils
#~(list "-n" "auto")
#:phases
#~(modify-phases %standard-phases
+ ;; setup.py was removed in 36c3231ce5b80ad470fa78be2e96df859d2daf41
+ ;; for some unknown reason, which caused the package to fail to
+ ;; build. It is being recreated based on that commit.
+ (add-after 'unpack 'create-setup.py
+ (lambda _
+ (call-with-output-file "setup.py"
+ (lambda (port)
+ (format port "from setuptools import setup
+from extension_helpers import get_extensions
+setup(ext_modules=get_extensions())")))))
;; This file is opened in both install and check phases.
(add-before 'install 'writable-compiler
(lambda _ (make-file-writable "photutils/_compiler.c")))
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:34 GMT) Full text and rfc822 format available.Message #122 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 40/47] gnu: python-reproject: Update to 0.13.1. Date: Sun, 21 Apr 2024 00:22:29 +0100
* gnu/packages/astronomy.scm (python-reproject): Update to 0.13.1.
[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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index dd5864a582..32c70b9bdf 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2732,13 +2732,13 @@ (define-public python-regions
(define-public python-reproject
(package
(name "python-reproject")
- (version "0.13.0")
+ (version "0.13.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "reproject" version))
(sha256
- (base32 "1qkjbx8xsawhi1gjzqimais3crvkwgbzy1pr51x6anjjln88rgll"))))
+ (base32 "1xk809h2j3zj37l5lx4l87zanf9zxbxajcrff2b2f2i0jpnmxqv3"))))
(build-system pyproject-build-system)
(arguments
(list
@@ -2754,6 +2754,17 @@ (define-public python-reproject
#:tests? #f
#:phases
#~(modify-phases %standard-phases
+ ;; setup.py was removed in a659a260bdd7635cddc8f33c4ea04a3b6d8c1f84
+ ;; for some unknown reason, which caused the package to fail to
+ ;; build. It is being recreated based on that commit.
+ ;; TODO: Check how to implement it in python-build-system.
+ (add-after 'unpack 'create-setup.py
+ (lambda _
+ (call-with-output-file "setup.py"
+ (lambda (port)
+ (format port "from setuptools import setup
+from extension_helpers import get_extensions
+setup(ext_modules=get_extensions())")))))
(add-before 'install 'writable-compiler
(lambda _
(make-file-writable "reproject/_compiler.c")))
@@ -2778,7 +2789,7 @@ (define-public python-reproject
python-shapely
python-zarr))
(native-inputs
- (list python-cython
+ (list python-cython-3
python-extension-helpers
python-pytest-astropy
python-semantic-version
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:35 GMT) Full text and rfc822 format available.Message #125 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 43/47] gnu: python-crds: Update to 11.17.20. Date: Sun, 21 Apr 2024 00:22:32 +0100
* gnu/packages/astronomy.scm (python-crds): Update to 11.17.20.
Change-Id: I426241c2e216b0261787117a10ceab36197dff12
---
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 5cb62466cb..ee9a35fbc9 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2104,13 +2104,13 @@ (define-public python-cmyt
(define-public python-crds
(package
(name "python-crds")
- (version "11.17.19")
+ (version "11.17.20")
(source (origin
(method url-fetch)
(uri (pypi-uri "crds" version))
(sha256
(base32
- "1x48yw6jnz7dw0myc86ds0qaki6v1anqaihd5qzrxwrrl61kyp6x"))))
+ "0480jjklv2p60fp892dr4qglwv44k86hx29y8q1c967l9k53wc9f"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:35 GMT) Full text and rfc822 format available.Message #128 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 41/47] gnu: python-reproject: Enable tests. Date: Sun, 21 Apr 2024 00:22:30 +0100
* gnu/packages/astronomy.scm (python-reproject): Enable tests.
[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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 32c70b9bdf..58bf607059 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -2742,16 +2742,11 @@ (define-public python-reproject
(build-system pyproject-build-system)
(arguments
(list
- ;; FIXME: Failing tests
- ;;
- ;; reproject/adaptive/core.py:7: in <module>
- ;; from .deforest import map_coordinates
- ;; E ModuleNotFoundError: No module named 'reproject.adaptive.deforest'
- ;;
- ;; Project removed setup.py and there is no alternative to `python
- ;; setup.py build_ext'
- ;; See: https://github.com/pypa/setuptools/discussions/3388
- #:tests? #f
+ #:test-flags
+ #~(list "--arraydiff"
+ "--arraydiff-default-format=fits"
+ "--numprocesses" "auto"
+ "--pyargs" "reproject")
#:phases
#~(modify-phases %standard-phases
;; setup.py was removed in a659a260bdd7635cddc8f33c4ea04a3b6d8c1f84
@@ -2771,9 +2766,11 @@ (define-public python-reproject
(add-before 'check 'writable-compiler
(lambda _
(make-file-writable "reproject/_compiler.c")))
- (add-before 'check 'writable-home
+ (add-before 'check 'prepare-test-environment
(lambda _
- (setenv "HOME" (getcwd)))))))
+ (setenv "HOME" "/tmp")
+ ;; Cython extensions have to be built before running the tests.
+ (invoke "python" "setup.py" "build_ext" "--inplace"))))))
(propagated-inputs
(list python-asdf
python-astropy
@@ -2791,9 +2788,11 @@ (define-public python-reproject
(native-inputs
(list python-cython-3
python-extension-helpers
+ python-pytest
python-pytest-astropy
+ python-pytest-xdist
+ ;; python-sunpy ; circular dependencies, test optional
python-semantic-version
- python-pytest
python-setuptools-scm))
(home-page "https://reproject.readthedocs.io")
(synopsis "Astronomical image reprojection in Python")
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:36 GMT) Full text and rfc822 format available.Message #131 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 44/47] gnu: python-stsci-stimage: Update to 0.2.8. Date: Sun, 21 Apr 2024 00:22:33 +0100
* gnu/packages/astronomy.scm (python-stsci-stimage): Update to 0.2.8.
Change-Id: Ib2f8b9544bc732959d87527d2c55f274dab4393b
---
gnu/packages/astronomy.scm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ee9a35fbc9..b4a82f6353 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3242,13 +3242,13 @@ (define-public python-stsci-imagestats
(define-public python-stsci-stimage
(package
(name "python-stsci-stimage")
- (version "0.2.6")
+ (version "0.2.8")
(source (origin
(method url-fetch)
- (uri (pypi-uri "stsci.stimage" version))
+ (uri (pypi-uri "stsci_stimage" version))
(sha256
(base32
- "0i7xby1gaiplvbqqv8a4f4cw1is8fwj89mix1z3bqrykqi3n24g0"))))
+ "0p188my6djy65a8j6qsc3v0dpr2svqqv90n0pxxzy52vdjiz3w0w"))))
(build-system pyproject-build-system)
(arguments
(list
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:37 GMT) Full text and rfc822 format available.Message #134 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 45/47] gnu: python-stsci-stimage: Adjust test steps. Date: Sun, 21 Apr 2024 00:22:34 +0100
* gnu/packages/astronomy.scm (python-stsci-stimage):
[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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index b4a82f6353..9d82bd4c89 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -3242,6 +3242,8 @@ (define-public python-stsci-imagestats
(define-public python-stsci-stimage
(package
(name "python-stsci-stimage")
+ ;; PyPI version was 0.2.8 but the latest version tag on GiHub was 0.2.7,
+ ;; see <https://github.com/spacetelescope/stsci.stimage/issues/38>
(version "0.2.8")
(source (origin
(method url-fetch)
@@ -3252,27 +3254,26 @@ (define-public python-stsci-stimage
(build-system pyproject-build-system)
(arguments
(list
+ #:test-flags #~(list "test_c")
#:phases
#~(modify-phases %standard-phases
- ;; Test steps are taken from GitHub Actions.
- ;; See https://github.com/spacetelescope/stsci.stimage/issues/27
- (replace 'check
+ ;; Test steps are taken from GitHub Actions, see
+ ;; <https://github.com/spacetelescope/stsci.stimage/issues/27>
+ (add-before 'check 'waf-configure-build
(lambda _
(copy-file (string-append
- #$(this-package-native-input "python-waf") "/bin/waf")
- "waf")
- (invoke "python" "waf" "configure" "build" "do_tests"))))))
- (propagated-inputs (list python-numpy))
+ #$(this-package-native-input "python-waf") "/bin/waf")
+ "waf")
+ (invoke "python" "waf" "configure" "build"))))))
+ (propagated-inputs
+ (list python-numpy))
(native-inputs
- (list python-codecov
- python-pytest
- python-pytest-cov
- python-setuptools-scm
- python-waf))
+ (list python-pytest python-setuptools-scm python-waf))
(home-page "https://stscistimage.readthedocs.io/en/latest/")
(synopsis "STScI image processing")
- (description "This package provides an astronomical Python package with
-image processing functions: @code{xyxymatch}, @code{geomap}.")
+ (description
+ "This package provides an astronomical Python package with image
+processing functions: @code{xyxymatch}, @code{geomap}.")
(license license:bsd-3)))
(define-public python-stcal
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:38 GMT) Full text and rfc822 format available.Message #137 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 47/47] gnu: Add psfex. Date: Sun, 21 Apr 2024 00:22:36 +0100
* gnu/packages/astronomy.scm (psfex): New variable.
Change-Id: I073df933b244811cd09343ea4951f481ad76b075
---
gnu/packages/astronomy.scm | 45 ++++++++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index a9e0583f39..2afcee9aa0 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1131,6 +1131,51 @@ (define-public phd2
from Stark Labs.")
(license license:bsd-3)))
+(define-public psfex
+ (package
+ (name "psfex")
+ (version "3.24.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/astromatic/psfex")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0ykgzyxnxjxqk6b8jng006wjilg4fqaxclpfn8plg6brk1qf39sn"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:configure-flags
+ #~(list "CPPFLAGS=-fcommon"
+ "--enable-openblas"
+ "--enable-plplot"
+ (string-append "--with-fftw-libdir="
+ #$(this-package-input "fftw") "/lib")
+ (string-append "--with-fftw-incdir="
+ #$(this-package-input "fftw") "/include")
+ (string-append "--with-openblas-libdir="
+ #$(this-package-input "openblas") "/lib")
+ (string-append "--with-openblas-incdir="
+ #$(this-package-input "openblas") "/include")
+ (string-append "--with-plplot-libdir="
+ #$(this-package-input "plplot") "/lib")
+ (string-append "--with-plplot-incdir="
+ #$(this-package-input "plplot") "/include"))))
+ (native-inputs
+ (list autoconf automake libtool pkg-config))
+ (inputs
+ (list openblas fftw fftwf plplot))
+ (home-page "https://www.astromatic.net/software/psfex/")
+ (synopsis "Astronomical PSF modelling and quality assessment")
+ (description
+ "@acronym{PSFEx, PSF Extractor} extracts models of the @acronym{PSF,
+Point Spread Function} from FITS images processed with SExtractor, and
+measures the quality of images. The generated PSF models can be used for
+model-fitting photometry or morphological analyses.")
+ (license license:gpl3+)))
+
(define-public sextractor
(package
(name "sextractor")
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:38 GMT) Full text and rfc822 format available.Message #140 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com>, Iliya Tikhonenko <tikhonenko <at> mpe.mpg.de> Subject: [PATCH 42/47] gnu: python-asdf: Adjust inputs. Date: Sun, 21 Apr 2024 00:22:31 +0100
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'
* gnu/packages/astronomy.scm (python-asdf): Adjust inputs.
[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 <at> mpe.mpg.de>
---
gnu/packages/astronomy.scm | 41 +++++++++-----------------------------
1 file changed, 9 insertions(+), 32 deletions(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 58bf607059..5cb62466cb 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -522,8 +522,7 @@ (define-public python-aplpy
python-shapely))
(native-inputs
(list python-pytest-astropy
- python-pytest-mpl
- python-semantic-version))
+ python-pytest-mpl))
(home-page "http://aplpy.github.io")
(synopsis "Astronomical Plotting Library in Python")
(description
@@ -753,7 +752,6 @@ (define-public python-ginga
python-docutils
python-pytest-astropy
python-pytest-astropy-header
- python-semantic-version
python-tornado))
(home-page "https://ejeschke.github.io/ginga/")
(synopsis "Scientific image viewer and toolkit for FITS files")
@@ -2014,8 +2012,7 @@ (define-public python-ccdproc
(build-system pyproject-build-system)
(native-inputs
(list python-memory-profiler
- python-pytest-astropy
- python-semantic-version))
+ python-pytest-astropy))
(propagated-inputs
(list python-astropy
python-astroscrappy
@@ -2138,7 +2135,6 @@ (define-public python-crds
python-nose
python-pylint
python-pytest
- python-semantic-version
python-setuptools-scm))
(home-page "https://hst-crds.stsci.edu")
(synopsis "Calibration Reference Data System for HST and JWST")
@@ -2481,7 +2477,6 @@ (define-public python-photutils
python-extension-helpers
python-pytest-astropy
python-pytest-xdist
- python-semantic-version
python-setuptools-scm))
(home-page "https://github.com/astropy/photutils")
(synopsis "Source detection and photometry")
@@ -2792,7 +2787,6 @@ (define-public python-reproject
python-pytest-astropy
python-pytest-xdist
;; python-sunpy ; circular dependencies, test optional
- python-semantic-version
python-setuptools-scm))
(home-page "https://reproject.readthedocs.io")
(synopsis "Astronomical image reprojection in Python")
@@ -2909,7 +2903,6 @@ (define-public python-sunpy
python-reproject
python-scikit-image
python-scipy
- python-semantic-version
;; python-spiceypy ; Not packed yet in Guix, long jorney.
python-sqlalchemy
python-tqdm
@@ -3069,7 +3062,6 @@ (define-public python-spectral-cube
python-pytest-astropy
python-pytest-xdist
python-regions
- python-semantic-version
python-setuptools-scm))
(home-page "https://spectral-cube.readthedocs.io/en/latest/")
(synopsis "Library for reading and analyzing astrophysical spectral data cubes")
@@ -3124,7 +3116,6 @@ (define-public python-specutils
(native-inputs
(list python-matplotlib
python-pytest-astropy
- python-semantic-version
python-setuptools-scm
python-spectral-cube))
(home-page "https://specutils.readthedocs.io/")
@@ -3322,7 +3313,6 @@ (define-public python-stcal
python-pytest
python-pytest-cov
python-pytest-doctestplus
- python-semantic-version
python-setuptools-scm))
(home-page "https://github.com/spacetelescope/stcal")
(synopsis "STScI tools and algorithms used in calibration pipelines")
@@ -3364,7 +3354,6 @@ (define-public python-stdatamodels
python-pytest-doctestplus
python-pytest-xdist
python-scipy
- python-semantic-version
python-setuptools-scm))
(home-page "https://github.com/spacetelescope/stdatamodels")
(synopsis
@@ -3390,8 +3379,8 @@ (define-public python-stpipe
;; See https://github.com/spacetelescope/stpipe/issues/114
#:test-flags #~(list "-k" "not test_roman_datamodel")))
(build-system pyproject-build-system)
- (propagated-inputs (list python-asdf python-astropy python-crds
- python-semantic-version python-stdatamodels))
+ (propagated-inputs
+ (list python-asdf python-astropy python-crds python-stdatamodels))
(native-inputs (list python-pytest python-pytest-doctestplus
python-pytest-openfiles python-setuptools-scm))
(home-page "https://github.com/spacetelescope/stpipe")
@@ -3429,7 +3418,6 @@ (define-public python-stsynphot
(native-inputs (list python-pytest
python-pytest-astropy
python-pytest-astropy-header
- python-semantic-version
python-setuptools-scm))
(home-page "https://github.com/spacetelescope/stsynphot_refactor")
(synopsis "Synthetic photometry using Astropy for HST and JWST")
@@ -4423,7 +4411,6 @@ (define-public python-synphot
(native-inputs
(list python-pytest
python-pytest-astropy
- python-semantic-version
python-setuptools-scm))
(home-page "https://github.com/spacetelescope/synphot_refactor")
(synopsis "Synthetic photometry using Astropy")
@@ -4457,7 +4444,6 @@ (define-public python-tweakwcs
python-pytest
python-pytest-cov
python-scipy
- python-semantic-version
python-setuptools-scm))
(home-page "https://tweakwcs.readthedocs.io/en/latest/")
(synopsis
@@ -4503,7 +4489,6 @@ (define-public python-asdf
python-pytest-doctestplus
python-pytest-remotedata
python-pytest-xdist
- python-semantic-version
python-setuptools-scm))
(propagated-inputs
(list python-asdf-standard
@@ -4513,7 +4498,8 @@ (define-public python-asdf
python-jmespath
python-lz4
python-numpy
- python-pyyaml))
+ python-pyyaml
+ python-semantic-version))
(home-page "https://github.com/asdf-format/asdf")
(synopsis "Python tools to handle ASDF files")
(description
@@ -4549,7 +4535,6 @@ (define-public python-asdf-compression
(native-inputs
(list python-numpy
python-pytest
- python-semantic-version
python-setuptools-scm))
(propagated-inputs
(list python-asdf
@@ -4648,7 +4633,6 @@ (define python-asdf-coordinates-schemas
(native-inputs
(list python-pytest
python-pytest-xdist
- python-semantic-version
python-setuptools-scm))
(propagated-inputs
(list python-asdf))
@@ -4767,7 +4751,7 @@ (define-public python-asdf-zarr
(propagated-inputs
(list python-asdf python-fsspec python-zarr))
(native-inputs
- (list python-pytest python-semantic-version python-setuptools-scm))
+ (list python-pytest python-setuptools-scm))
(home-page "https://github.com/asdf-format/asdf-zarr")
(synopsis "Asdf extension to support Zarr arrays")
(description
@@ -4802,7 +4786,6 @@ (define-public python-asdf-astropy
python-pandas
python-pytest-astropy
python-scipy
- python-semantic-version
python-setuptools-scm))
(propagated-inputs
(list python-asdf
@@ -4836,7 +4819,6 @@ (define python-asdf-wcs-schemas
(list python-asdf
python-pytest
python-pytest-openfiles
- python-semantic-version
python-setuptools-scm))
(propagated-inputs
(list python-asdf-coordinates-schemas
@@ -4867,7 +4849,6 @@ (define-public python-gwcs
python-pytest
python-pytest-doctestplus
python-pyyaml
- python-semantic-version
python-setuptools-scm))
(propagated-inputs
(list python-asdf
@@ -4905,9 +4886,7 @@ (define-public python-rad
;; python-rad -> python-roman-datamodels -> python-crds -> python-rad
#:test-flags #~(list "--ignore=tests/test_schemas.py")))
(native-inputs
- (list python-pytest
- python-semantic-version
- python-setuptools-scm))
+ (list python-pytest python-setuptools-scm))
(propagated-inputs (list python-asdf python-asdf-astropy))
(home-page "https://github.com/spacetelescope/rad")
(synopsis "Roman Attribute Dictionary")
@@ -5021,7 +5000,6 @@ (define-public python-roman-datamodels
python-pytest-doctestplus
python-pytest-env
python-pytest-xdist
- python-semantic-version
python-setuptools-scm))
(home-page "https://github.com/spacetelescope/roman_datamodels")
(synopsis "Roman Datamodels Support")
@@ -5055,8 +5033,7 @@ (define-public python-astroalign
(list python-astropy
python-ccdproc
python-pillow
- python-pytest
- python-semantic-version))
+ python-pytest))
(propagated-inputs
(list python-bottleneck
python-numpy
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:26:39 GMT) Full text and rfc822 format available.Message #143 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 46/47] gnu: Add scamp. Date: Sun, 21 Apr 2024 00:22:35 +0100
* gnu/packages/astronomy.scm (scamp): New variable.
Change-Id: If32adb281017858b0e7d5816cecb509af3cec835
---
gnu/packages/astronomy.scm | 80 ++++++++++++++++++++++++++++++++++++++
1 file changed, 80 insertions(+)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 9d82bd4c89..a9e0583f39 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -69,6 +69,7 @@ (define-module (gnu packages astronomy)
#:use-module (gnu packages perl)
#:use-module (gnu packages photo)
#:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages plotutils)
#:use-module (gnu packages pretty-print)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
@@ -3771,6 +3772,85 @@ (define-public gpredict
@end itemize")
(license license:gpl2+)))
+(define-public scamp
+ (package
+ (name "scamp")
+ (version "2.10.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/astromatic/scamp")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0qic52mzw9avf1a1fsr85mlh63b7hq6d4wj2d00zgdllmclj5l9q"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:configure-flags
+ #~(list "CPPFLAGS=-fcommon"
+ "--enable-openblas"
+ "--enable-plplot"
+ (string-append "--with-curl-incdir="
+ #$(this-package-input "curl") "/include")
+ (string-append "--with-curl-libdir="
+ #$(this-package-input "curl") "/lib")
+ (string-append "--with-fftw-incdir="
+ #$(this-package-input "fftwf") "/include")
+ (string-append "--with-fftw-libdir="
+ #$(this-package-input "fftwf") "/lib")
+ (string-append "--with-openblas-incdir="
+ #$(this-package-input "openblas") "/include")
+ (string-append "--with-openblas-libdir="
+ #$(this-package-input "openblas") "/lib")
+ (string-append "--with-plplot-incdir="
+ #$(this-package-input "plplot") "/include")
+ (string-append "--with-plplot-libdir="
+ #$(this-package-input "plplot") "/lib"))))
+ (native-inputs
+ (list autoconf
+ automake
+ libtool
+ pkg-config
+ python-astropy
+ python-numpy
+ python-wrapper))
+ (inputs
+ (list curl fftwf openblas plplot))
+ (home-page "https://www.astromatic.net/software/scamp/")
+ (synopsis "Compute astrometric solutions")
+ (description
+ "@acronym{Software for Calibrating AstroMetry and Photometry,SCAMP} is a
+software that computes astrometric projection parameters from source catalogues
+derived from @url{http://fits.gsfc.nasa.gov/,FITS} images. The computed solution
+is expressed according to the
+@url{http://www.atnf.csiro.au/people/mcalabre/WCS/index.html,WCS} standard. The
+main features of SCAMP are:
+
+@itemize
+@item compatibility with @code{SExtractor} FITS or Multi-Extension FITS
+catalogue format in input
+@item generation of WCS-compliant and @code{SWarp}-compatible FITS image headers
+in output
+@item automatic grouping of catalogues on the sky
+@item selectable on-line astrometric reference catalogue
+@item automatic determination of scale, position angle, flipping and coordinate
+shift using fast pattern-matching
+@item various astrometric calibration modes for single detectors and detector
+arrays
+@item combined astrometric solutions for multi-channel/instrument surveys
+@item highly configurable astrometric distortion polynomials
+@item correction for differential chromatic refraction
+@item proper motion measurements
+@item multi-threaded code that takes advantage of multiple processors
+@item @url{http://www.ivoa.net/documents/VOTable,VOTable}-compliant XML output
+of meta-data
+@item @url{http://en.wikipedia.org/wiki/XSLT,XSLT} filter sheet provided for
+convenient access to metadata from a regular web browser
+@end itemize")
+ (license license:gpl3+)))
+
(define-public sgp4
;; Version tag v1.0 is dated to <2021-01-11>, use the lates commit instead.
(let ((commit "6a448b4850e5fbf8c1ca03bb5f6013a9fdc1fd91")
--
2.41.0
andreas <at> enge.fr, bavier <at> posteo.net, sharlatanus <at> gmail.com, guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 20 Apr 2024 23:29:03 GMT) Full text and rfc822 format available.Message #146 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489 <at> debbugs.gnu.org Cc: Sharlatan Hellseher <sharlatanus <at> gmail.com> Subject: [PATCH 28/47] gnu: python-bayesicfitting: Refresh package style. Date: Sun, 21 Apr 2024 00:22:17 +0100
* gnu/packages/astronomy.scm (python-bayesicfitting): Adjust
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(-)
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index bf71843e05..618d0e78bf 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1934,25 +1934,31 @@ (define-public python-bayesicfitting
(package
(name "python-bayesicfitting")
(version "3.2.0")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/dokester/BayesicFitting")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0q6v7w9b1xzam0qn5vsl5wrdp1fkfpsn411pzd8wyy9giznpajxi"))))
- (build-system python-build-system)
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dokester/BayesicFitting")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0q6v7w9b1xzam0qn5vsl5wrdp1fkfpsn411pzd8wyy9giznpajxi"))))
+ (build-system pyproject-build-system)
(arguments
- (list #:phases #~(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "python" "-m" "unittest" "discover"
- "test")))))))
- (propagated-inputs (list python-astropy python-future python-matplotlib
- python-numpy python-scipy))
+ (list
+ #:test-flags #~(list "-m" "unittest" "discover" "test")
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? test-flags #:allow-other-keys)
+ (when tests?
+ (apply invoke "python" test-flags)))))))
+ (propagated-inputs
+ (list python-astropy
+ python-future
+ python-matplotlib
+ python-numpy
+ python-scipy))
(home-page "https://www.bayesicfitting.nl")
(synopsis "Python Toolbox for Astronimical Bayesian fitting")
(description
--
2.41.0
Sharlatan Hellseher <sharlatanus <at> gmail.com>:Sharlatan Hellseher <sharlatanus <at> gmail.com>:Message #151 received at 70489-done <at> debbugs.gnu.org (full text, mbox):
From: Sharlatan Hellseher <sharlatanus <at> gmail.com> To: 70489-done <at> debbugs.gnu.org Subject: [PATCH 00/47] Astronomy 2024/04 updates. Date: Wed, 01 May 2024 08:06:30 +0100
[Message part 1 (text/plain, inline)]
Pushed as 3067eb8d60..147f1f2e0d to master. -- Oleg
[signature.asc (application/pgp-signature, inline)]
guix-patches <at> gnu.org:bug#70489; Package guix-patches.
(Sat, 04 May 2024 04:30:03 GMT) Full text and rfc822 format available.Message #154 received at 70489 <at> debbugs.gnu.org (full text, mbox):
From: Leo Famulari <leo <at> famulari.name> To: 70489 <at> debbugs.gnu.org, sharlatanus <at> gmail.com Subject: Re: bug#70489: [PATCH 00/47] Astronomy 2024/04 updates. Date: Sat, 4 May 2024 00:29:20 -0400
[Message part 1 (text/plain, inline)]
On Wed, May 01, 2024 at 08:06:30AM +0100, Sharlatan Hellseher wrote: > > Pushed as 3067eb8d60..147f1f2e0d to master. Thanks for all the astronomy packages! Great fun in there
[signature.asc (application/pgp-signature, inline)]
Debbugs Internal Request <help-debbugs <at> gnu.org>
to internal_control <at> debbugs.gnu.org.
(Sat, 01 Jun 2024 11:24:18 GMT) Full text and rfc822 format available.
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.