From 58b6dc4d55ac61d60331bfc01cfd41f3205550c1 Mon Sep 17 00:00:00 2001 From: Janneke Nieuwenhuizen Date: Thu, 25 Sep 2025 09:00:38 +0200 Subject: [PATCH 01/41] gnu: guile-emacs: Fix build with gcc-14. * gnu/packages/guile.scm (guile-for-guile-emacs)[arguments]: Replace emacs-minimal's CFLAGS in #:configure-flags with specific and extra flags to relax gcc-14's strictness. Change-Id: I6b3f871695eb25fbf84a2334525e1d0e15e36b92 --- gnu/packages/emacs.scm | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index de1564b1e30..776c11a350f 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -744,7 +744,12 @@ Started in 2014 as a GSOC project, Guile-Emacs was resurrected in 2024.") (substitute-keyword-arguments `(#:strip-binaries? #f ,@(package-arguments emacs)) ((#:configure-flags flags ''()) - #~`("CFLAGS=-Og -ggdb3" + #~`(#$(string-append "CFLAGS=-Og -ggdb3" + " -Wno-error=implicit-function-declaration" + " -Wno-error=implicit-int" + " -Wno-error=incompatible-pointer-types" + " -Wno-error=int-conversion" + " -Wno-error=shift-count-negative") "--with-native-compilation=no" "--without-modules" "--without-threads" @@ -752,9 +757,11 @@ Started in 2014 as a GSOC project, Guile-Emacs was resurrected in 2024.") "--without-cairo" "--without-tree-sitter" "--with-imagemagick" - ,@(fold delete #$flags '("--with-cairo" - "--with-modules" - "--with-native-compilation=aot")))) + ,@(fold delete #$flags + '("CFLAGS=-g -O2 -Wno-error=incompatible-pointer-types" + "--with-cairo" + "--with-modules" + "--with-native-compilation=aot")))) ((#:make-flags flags #~'()) #~(list "V=1")) ((#:phases phases) From 29d364498ee87e134cb53ee15350001417eaedc6 Mon Sep 17 00:00:00 2001 From: Baptiste Strazzulla Date: Wed, 20 Aug 2025 18:33:19 +0200 Subject: [PATCH 02/41] gnu: git-lfs: Fix build. This change is to bypass combination of go-build-system and custom make targets where the import path is set manually, see discussion in guix/guix#2133. * gnu/packages/version-control.scm (git-lfs): Rename binary and home page Change-Id: Ic87627412f715ebed07cf79ddd298e777746975f Reviewed-by: Nicolas Graves Reviewed-by: Maxim Cournoyer Signed-off-by: Sharlatan Hellseher --- gnu/packages/version-control.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index f03994406e7..b870f7396d2 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -4224,7 +4224,11 @@ will reconstruct the object along its delta-base chain and return it.") (install-file manpage (string-append #$output "/share/man/man1"))) (find-files "." "^git-lfs.*\\.1$")))))) - #~())))) + #~()) + (add-after 'install 'rename-binary + (lambda _ + (with-directory-excursion (string-append #$output "/bin") + (rename-file "v3" "git-lfs"))))))) (native-inputs (append (list git-minimal go-github-com-avast-retry-go @@ -4251,7 +4255,7 @@ will reconstruct the object along its delta-base chain and return it.") (if (supported-package? ruby-asciidoctor/minimal) (list ronn-ng ruby-asciidoctor/minimal) '()))) - (home-page "https://git-lfs.github.com/") + (home-page "https://git-lfs.com/") (synopsis "Git extension for versioning large files") (description "Git Large File Storage (LFS) replaces large files such as audio samples, From ace78713a9ee7abfdd19e2f009c3fb606b797160 Mon Sep 17 00:00:00 2001 From: jgart Date: Thu, 25 Sep 2025 10:55:39 -0500 Subject: [PATCH 03/41] gnu: trealla: Update to 2.83.8. * gnu/packages/prolog.scm (trealla): Update to 2.83.8. Change-Id: I190612b48e6a69e31384bb12d81465a668f2de59 --- gnu/packages/prolog.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/prolog.scm b/gnu/packages/prolog.scm index 62299065f0a..c6d5f42aa5b 100644 --- a/gnu/packages/prolog.scm +++ b/gnu/packages/prolog.scm @@ -185,7 +185,7 @@ it.") (define-public trealla (package (name "trealla") - (version "2.83.5") + (version "2.83.8") (source (origin (method git-fetch) @@ -194,7 +194,7 @@ it.") (url "https://github.com/trealla-prolog/trealla") (commit (string-append "v" version)))) (sha256 - (base32 "04d1h8331dsb1gbrp28h2sqkwqh3cfzbdlziczwqk2kyyp9sf9f8")) + (base32 "1bpfzrwsgbmjl1maiaw5b8ixkgh548gw1lkiznsjgkjm7dxr4ns4")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (native-inputs From d460e33a1151742f4b0dbe5e8ec9c7a46be171ea Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 13:11:07 +0100 Subject: [PATCH 04/41] gnu: Add python-pytest-asdf-plugin. * gnu/packages/python-check.scm (python-pytest-asdf-plugin): New variable. Change-Id: I2de8c8ef9ddd6cc4b764079d6461996d01d1a21c --- gnu/packages/python-check.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index c95596dd4d6..1f66fd5b037 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -1777,6 +1777,31 @@ data arrays produced during tests, in particular in cases where the arrays are too large to conveniently hard-code them in the tests.") (license license:bsd-3))) +(define-public python-pytest-asdf-plugin + (package + (name "python-pytest-asdf-plugin") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pytest_asdf_plugin" version)) + (sha256 + (base32 "0bcfl1s7yrnr2rlpr3hswcg9jyq6gnj0ppmpzppw9xgj796ycfb5")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f ;to avoid import astronomy module + #:phases + #~(modify-phases %standard-phases + (delete 'sanity-check)))) + (native-inputs + (list python-setuptools-next + python-setuptools-scm-next)) + (home-page "https://github.com/asdf-format/pytest-asdf-plugin") + (synopsis "Pytest plugin for testing ASDF schemas") + (description + "This package provides a Pytest plugin for testing ASDF schemas.") + (license license:bsd-3))) + (define-public python-pytest-astropy (package (name "python-pytest-astropy") From 90f6bdb48f4480e98f1c53216eff1f280da5c864 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 13:11:32 +0100 Subject: [PATCH 05/41] gnu: python-asdf-bootstrap: Adjust native inputs. * gnu/packages/astronomy.scm (python-asdf-bootstrap)[native-inputs]: Remove python-wheel; add python-setuptools-scm. Change-Id: I64bf50dac3c40f22754120e3f8b0658ca907909c --- 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 4e67b747ed9..0bb228909bb 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2074,7 +2074,7 @@ Astropy objects.") (delete 'sanity-check)))) (native-inputs (list python-setuptools - python-wheel)) + python-setuptools-scm)) (propagated-inputs (list python-importlib-metadata python-numpy From 243e375b74539653853f928461e1d4d29eef5a33 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 13:12:12 +0100 Subject: [PATCH 06/41] gnu: python-asdf-standard: Update to 1.4.0. * gnu/packages/astronomy.scm (python-asdf-standard): Update to 1.4.0. [native-inputs]: Remove python-astropy-minimal, python-jsonschema, python-pypa-build, and python-wheel; add python-pytest-asdf-plugin, and python-pyyaml. Change-Id: I37840d6c17630ce69312ebf2a755fb9a97edfe15 --- gnu/packages/astronomy.scm | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 0bb228909bb..3b2d3267618 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2161,26 +2161,23 @@ implementation package such as asdf-astropy.") (define-public python-asdf-standard (package (name "python-asdf-standard") - (version "1.3.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf_standard" version)) (sha256 - (base32 - "0r7dxbiwngpwwjdbs2vqk94v1vjsgyilswkq180d5slx74grcn2r")))) + (base32 "1p7x5j8ym70c2cmgnv0113i4q465jbrqg8311mwbfz5q1lfi4pqc")))) (build-system pyproject-build-system) (native-inputs (list python-asdf-bootstrap python-asdf-transform-schemas-bootstrap - python-astropy-minimal - python-jsonschema - python-pypa-build - python-pytest python-packaging + python-pytest + python-pytest-asdf-plugin + python-pyyaml python-setuptools-next - python-setuptools-scm - python-wheel)) + python-setuptools-scm)) (home-page "https://asdf-standard.readthedocs.io/") (synopsis "ASDF standard schemas") (description From 6b2218669398a1a00339bab384fd8b48ee6d7f23 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 13:27:42 +0100 Subject: [PATCH 07/41] gnu: python-asdf: Update to 5.0.0. * gnu/packages/astronomy.scm (python-asdf): Update to 5.0.0. [native-inputs]: Remove python-pytest-doctestplus, and python-wheel. Change-Id: I45e2315744846358aa51c3853ae529283be68dcf --- gnu/packages/astronomy.scm | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 3b2d3267618..0daa49e2d94 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1958,13 +1958,13 @@ Main features: (define-public python-asdf (package (name "python-asdf") - (version "4.4.0") + (version "5.0.0") (source (origin (method url-fetch) (uri (pypi-uri "asdf" version)) (sha256 - (base32 "0gincjs1vn6wxryazbkgmxy45cn1azb2yphj7nwg05yjwccn257p")))) + (base32 "1405fmv0f8dxr949njfw368bkm7w8cnqr5w6nqlxr68vvc1pghx7")))) (build-system pyproject-build-system) (arguments (list @@ -1973,24 +1973,23 @@ Main features: (native-inputs (list python-psutil python-pytest - python-pytest-doctestplus python-pytest-remotedata python-pytest-xdist python-setuptools - python-setuptools-scm - python-wheel)) + python-setuptools-scm)) (propagated-inputs (list python-asdf-standard python-asdf-transform-schemas python-attrs ;; for vendorized jsonschema - python-fsspec python-importlib-metadata python-jmespath - python-lz4 python-numpy python-packaging python-pyyaml - python-semantic-version)) + python-semantic-version + ;; [optional] + python-fsspec + python-lz4)) (home-page "https://github.com/asdf-format/asdf") (synopsis "Python tools to handle ASDF files") (description From 05c74f0da5faf9840436780470d169d43cfb63d1 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 21:05:11 +0100 Subject: [PATCH 08/41] gnu: Add python-asdf-4. * gnu/packages/astronomy.scm (python-asdf-4): New variable. Change-Id: Ia2a9fcb07684724168760cd3ab188ed0c5160a41 --- gnu/packages/astronomy.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 0daa49e2d94..c6d24ce8c1f 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2009,6 +2009,17 @@ implementation of the ASDF Standard.") (sha256 (base32 "0scnw5y4x5k3vyfylq0w612b662xlccx3gsscaw082zlv2yxfyh4")))))) +(define-public python-asdf-4 + (package + (inherit python-asdf) + (version "4.5.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asdf" version)) + (sha256 + (base32 "1h9dvnxdcd7cmjddpfnjsn6a1acav8gm5307gf7kpifacf99fdqz")))))) + (define-public python-asdf-astropy (package (name "python-asdf-astropy") From 293eb05468322b2f04439784dcab7d96cc29b0ac Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 10 Sep 2025 16:56:44 +0100 Subject: [PATCH 09/41] gnu: python-astropy-iers-data: Update to 0.2025.9.15.0.37.0. * gnu/packages/astronomy.scm (python-astropy-iers-data): Update to 0.2025.9.15.0.37.0. Change-Id: Ieac1455b9256a431fea430c771b8d62ae62f9cbb --- 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 c6d24ce8c1f..a3917c70eb8 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2853,13 +2853,13 @@ astronomy and astrophysics.") (define-public python-astropy-iers-data (package (name "python-astropy-iers-data") - (version "0.2025.8.18.0.40.14") + (version "0.2025.9.15.0.37.0") (source (origin (method url-fetch) (uri (pypi-uri "astropy_iers_data" version)) (sha256 - (base32 "1srqhva7snjaygfji4947q4lxhdqph1l97lxjvk4s8ls5w32yrhc")))) + (base32 "1n4i60fni2l6bph2kj2smy9rzcjhl3s79ihw9v1sgdf1zpf17r9k")))) (build-system pyproject-build-system) (arguments (list #:tests? #f)) ; no tests From 12629b999672773bb4f502e81ed15911f8a595ef Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 13:45:45 +0100 Subject: [PATCH 10/41] gnu: python-asdf-astropy: Adjust native inputs. * gnu/packages/astronomy.scm (python-asdf-astropy)[native-inputs]: Remove python-wheel; add python-pytest-asdf-plugin. Change-Id: I8d23eb286c80c4b87527f6a5d66f4dc130556a7c --- 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 a3917c70eb8..16a3ab10cc2 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2054,12 +2054,12 @@ implementation of the ASDF Standard.") (lambda _ (setenv "HOME" "/tmp")))))) (native-inputs (list python-pytest + python-pytest-asdf-plugin python-pytest-astropy python-pytest-xdist python-scipy python-setuptools - python-setuptools-scm - python-wheel)) + python-setuptools-scm)) (propagated-inputs (list python-asdf python-asdf-coordinates-schemas From 2de2d2ea4b27db6da5292719f6e09a06c0da331e Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 10 Sep 2025 17:15:24 +0100 Subject: [PATCH 11/41] gnu: python-astropy-healpix: Remove relax-requirements phase. * gnu/packages/astronomy.scm (python-astropy-healpix) [arguments] : Remove 'relax-requirements. Change-Id: Ie5cb8b3b266c80079d631ba89eb5be50fb6ea0e1 --- gnu/packages/astronomy.scm | 5 ----- 1 file changed, 5 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 16a3ab10cc2..ee29bfa1f9f 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2826,11 +2826,6 @@ astronomy and astrophysics.") (list #:phases #~(modify-phases %standard-phases - (add-after 'unpack 'relax-requirements - (lambda _ - (substitute* "setup.cfg" - ;; numpy>=1.25 - ((">=1.25") ">=1.24")))) (replace 'check (lambda* (#:key tests? test-flags #:allow-other-keys) (when tests? From 91eb624d873f34c6ed7537f84abe72f5d1e0422f Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 14:50:48 +0100 Subject: [PATCH 12/41] gnu: python-specutils: Adjust native inputs. * gnu/packages/astronomy.scm (python-specutils)[native-inputs]: Add python-pytest-asdf-plugin. Change-Id: If1ceacc589d586b1b576eae3e16e6bcca6f8d392 --- gnu/packages/astronomy.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index ee29bfa1f9f..61f869aa8e2 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -7804,6 +7804,7 @@ of axis order, spatial projections, and spectral units that exist in the wild. (setenv "HOME" "/tmp")))))) (native-inputs (list python-matplotlib + python-pytest-asdf-plugin python-pytest-astropy python-setuptools python-setuptools-scm From 73f6f25b3370971e1d409d5ac71e3161f46d4857 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 13:50:46 +0100 Subject: [PATCH 13/41] gnu: python-rad: Adjust native inputs. * gnu/packages/astronomy.scm (python-rad)[native-inputs]: Add python-pytest-asdf-plugin. Change-Id: I9390af5200c17c96f31489d365570f5b4448b780 --- gnu/packages/astronomy.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 61f869aa8e2..37ac9a342b7 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -6727,7 +6727,7 @@ end products of specific X-ray observatories.") (build-system pyproject-build-system) (arguments (list - ;; 1131 passed, 1 skipped + ;; tests: 1253 passed, 1 skipped #:test-flags ;; Ignore tests requiring python-crds to break cycle: ;; python-rad -> python-roman-datamodels -> python-crds -> python-rad @@ -6739,6 +6739,7 @@ end products of specific X-ray observatories.") "--ignore=tests/test_latest.py"))) (native-inputs (list python-pytest + python-pytest-asdf-plugin python-pytest-doctestplus python-semantic-version python-setuptools-next From 0abf9e40cddb38afbfe28c3724a4e79eeeea5e3d Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 16:53:00 +0100 Subject: [PATCH 14/41] gnu: python-photutils: Update to 2.3.0. * gnu/packages/astronomy.scm (python-photutils): Update to 2.3.0. [native-inputs]: Remove python-setuptools and python-setuptools-scm; add python-setuptools-next and python-setuptools-scm-next. Change-Id: Ic2a6bd2b7b89249f57cae95812c597a255e3ed2d --- gnu/packages/astronomy.scm | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 37ac9a342b7..6b4d42cbef7 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -5683,16 +5683,17 @@ photometry, segmentations, Petrosian profiling, and Sérsic fitting.") (define-public python-photutils (package (name "python-photutils") - (version "2.2.0") + (version "2.3.0") (source (origin (method url-fetch) (uri (pypi-uri "photutils" version)) (sha256 - (base32 "1h1bf8694pf9qdv9gf0934v6dk08d3ybrj858salqnfz6prnfnzb")))) + (base32 "1xyrnf0ynh8l3dad8s93dyqk3m9gvmxgvrji1nb9yillfzvjfxcl")))) (build-system pyproject-build-system) (arguments (list + ;; tests: 1843 passed, 22 skipped #:test-flags #~(list "--pyargs" "photutils" "--numprocesses" (number->string (min 8 (parallel-job-count)))) @@ -5703,6 +5704,13 @@ photometry, segmentations, Petrosian profiling, and Sérsic fitting.") (when tests? (with-directory-excursion "/tmp" (apply invoke "pytest" "-vv" test-flags)))))))) + (native-inputs + (list python-cython-3 + python-extension-helpers + python-pytest-astropy + python-pytest-xdist + python-setuptools-next + python-setuptools-scm-next)) (propagated-inputs (list python-astropy python-bottleneck @@ -5715,17 +5723,11 @@ photometry, segmentations, Petrosian profiling, and Sérsic fitting.") python-scipy python-shapely python-tqdm)) - (native-inputs - (list python-cython-3 - python-extension-helpers - python-pytest-astropy - python-pytest-xdist - python-setuptools - python-setuptools-scm)) (home-page "https://github.com/astropy/photutils") (synopsis "Source detection and photometry") - (description "Photutils is an Astropy package for detection and photometry -of astronomical sources.") + (description + "Photutils is an Astropy package for detection and photometry of +astronomical sources.") (license license:bsd-3))) (define-public python-pint-pulsar From 3fdac3c5edf430024847f14f66157995f61d4d44 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 14:50:47 +0100 Subject: [PATCH 15/41] gnu: python-crds: Update to 13.0.4. * gnu/packages/astronomy.scm (python-crds): Update to 13.0.4. [propagated-inputs]: Remove python-boto3 and python-pysynphot. [native-inputs]: Remove python-stsynphot and python-wheel. Change-Id: I275d5d8eee1fa24bd3f6ffde7c107f258347dc94 --- gnu/packages/astronomy.scm | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 6b4d42cbef7..ced57355eb0 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -3637,13 +3637,13 @@ Spectrograph}.") (define-public python-crds (package (name "python-crds") - (version "12.1.11") + (version "13.0.4") (source (origin (method url-fetch) (uri (pypi-uri "crds" version)) (sha256 - (base32 "1h4n5wyv23pa1fld2nfqph6app8zxb8zkzv5p1w6dm11n7zbnxih")))) + (base32 "02901rqzvgd8ssw1rv3skinqbxp0nycwx75k7n3bn3fjyfn2g2zc")))) (build-system pyproject-build-system) (arguments (list @@ -3683,19 +3683,18 @@ Spectrograph}.") python-pytest-astropy python-pytest-doctestplus python-setuptools - python-setuptools-scm - python-stsynphot - python-wheel)) + python-setuptools-scm)) (propagated-inputs - (list python-asdf - python-astropy - python-beautifulsoup4 - python-boto3 - python-filelock + (list python-astropy python-numpy - python-parsley - python-pysynphot + python-filelock + python-asdf python-requests + python-parsley + ;; [optional] + python-beautifulsoup4 + ;; python-crds -> python-ci-watson -> python-jwst -> python-crds + ;; python-jwst python-roman-datamodels python-stsynphot)) (home-page "https://hst-crds.stsci.edu") From e23647e38ba76d188a36281f700182d2296c4a6f Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 21:05:13 +0100 Subject: [PATCH 16/41] gnu: python-stdatamodels: Adjust inputs. * gnu/packages/astronomy.scm (python-stdatamodels)[propagated-inputs]: Remove python-asdf; add python-asdf-4. [native-inputs]: Add python-pytest-asdf-plugin. Change-Id: I01923c7e830e4214733f71226d1c22fbd903113e --- gnu/packages/astronomy.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index ced57355eb0..8250dc8304e 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -8094,6 +8094,7 @@ and CAS statistics), as well as fitting 2D Sérsic profiles.") python-crds python-psutil python-pytest + python-pytest-asdf-plugin python-pytest-doctestplus python-pytest-xdist python-scipy @@ -8101,7 +8102,7 @@ and CAS statistics), as well as fitting 2D Sérsic profiles.") python-setuptools-scm python-wheel)) (propagated-inputs - (list python-asdf + (list python-asdf-4 python-asdf-astropy python-astropy python-numpy)) From 600844bb07e0c50e4db4d887de46fb07ddadf580 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 15:17:19 +0100 Subject: [PATCH 17/41] gnu: python-pixell: Update to 0.30.0. * gnu/packages/astronomy.scm (python-pixell): Update to 0.30.0. [arguments] : Add 'relax-requirements. [propagated-inputs]: Remove python-coveralls and python-cython. Change-Id: Ife73368e5de635dc76818a6c249039483557b6c3 --- gnu/packages/astronomy.scm | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 8250dc8304e..37ff2dcdbbc 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -5857,14 +5857,26 @@ and the use of a modern programming language, techniques, and libraries (define-public python-pixell (package (name "python-pixell") - (version "0.29.0") + (version "0.30.0") (source (origin (method url-fetch) (uri (pypi-uri "pixell" version)) (sha256 - (base32 "17ivl01j2a6j6frzxdmzb4bdbs94n8rkipz2lh3zhhkx17djlbfh")))) + (base32 "0ncqqwvpg47yihlplzmhn8za8y7wab5k71n87nz8bcvzj8gnmpvw")))) (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + ;; XXX: To prevent sanity check faileur in dependent + ;; packages, Cython, Coveralls and Pytests are not required + ;; during runtime. + (lambda _ + (substitute* "pyproject.toml" + ((" 'cython',") "") + ((" 'coveralls>=1.5',") "") + ((" 'pytest>=4.6',") ""))))))) (native-inputs (list gfortran meson-python @@ -5874,8 +5886,6 @@ and the use of a modern programming language, techniques, and libraries python-pytest)) (propagated-inputs (list python-astropy - python-coveralls - python-cython ; check why it needs in installation python-dateutil python-ducc0 python-h5py From 250b9dbf196867a1dff1085bd947b6e2e10ab37d Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 12:52:33 +0100 Subject: [PATCH 18/41] gnu: indi: Update to 2.1.5.1. * gnu/packages/astronomy.scm (indi): Update to 2.1.5.1. Change-Id: I0352d87cd021b837b771f3aac79373126f8fac5b --- 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 37ff2dcdbbc..5d9ee53c095 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1244,7 +1244,7 @@ floating-point (no compression, LZW- or ZIP-compressed), FITS 8-bit, 16-bit, (define-public indi (package (name "indi") - (version "2.1.5") + (version "2.1.5.1") (source (origin (method git-fetch) @@ -1253,7 +1253,7 @@ floating-point (no compression, LZW- or ZIP-compressed), FITS 8-bit, 16-bit, (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "03qr5kvjr9dy8pwppn74mblkjxvm1nksbw2d9xinva8x4lxv8pry")))) + (base32 "1wak0wnd05grc357wa4snyx3f7nc8ymbpfndialhywfi6a43gdlr")))) (build-system cmake-build-system) (arguments (list From 6d22d8a0f01a0038a294cd2dbcec79fafee11738 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Sat, 20 Sep 2025 22:00:59 +0100 Subject: [PATCH 19/41] gnu: python-astrocut: Update to 1.1.0. * gnu/packages/astronomy.scm (python-astrocut): Update to 1.1.0. [arguments] : Skip one more test. Change-Id: I6a88a8b1ef9c4426061d2da42e3332acacd235a1 --- gnu/packages/astronomy.scm | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 5d9ee53c095..4c31a9ec1b4 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -2406,13 +2406,13 @@ astronomical images, especially when there is no WCS information available.") (define-public python-astrocut (package (name "python-astrocut") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "astrocut" version)) (sha256 - (base32 "14m713y90zj3v5hhlmq79cslqlr8dz8y3zyk454qda01fkcj6za7")))) + (base32 "1i8cpghk31cds9ipgap2ffws7jqy0smgk6w6kihxwpcw34jkr8h4")))) (build-system pyproject-build-system) (arguments (list @@ -2437,7 +2437,12 @@ astronomical images, especially when there is no WCS information available.") "test_tess_footprint_cutout_write_as_tpf" ;; Some NumPy compatability errors during tests. "test_get_cutout_limits" - "test_get_cutout_wcs") + "test_get_cutout_wcs" + ;; botocore.exceptions.EndpointConnectionError: + ;; Could not connect to the endpoint URL: + ;; "https://stpubdata.s3.amazonaws.com/tess/public/\ + ;; footprints/tess_ffi_footprint_cache.json" + "test_tess_footprint_cutout") " and not ")) #:phases #~(modify-phases %standard-phases From 599f6e9799404876f2e013db6cf215ef42b41ed9 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 19:24:34 +0100 Subject: [PATCH 20/41] gnu: python-pysm3: Update to 3.4.2. * gnu/packages/astronomy.scm (python-pysm3): Update to 3.4.2. [arguments] : Rework the list of skipped test. [propagated-inputs]: Add python-h5py, python-numpy, and python-scipy. [native-inputs]: Add python-nbval. Change-Id: Ifd661013923eab089c3a952b70f1ce45e2cca53f --- gnu/packages/astronomy.scm | 38 +++++++++++++++++++++++++------------- 1 file changed, 25 insertions(+), 13 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 4c31a9ec1b4..682770e40f3 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -6554,16 +6554,16 @@ natively in Siril.") (define-public python-pysm3 (package (name "python-pysm3") - (version "3.4.1a1") + (version "3.4.2") (source (origin (method git-fetch) ; no tests data in the PyPI tarball (uri (git-reference - (url "https://github.com/galsci/pysm") - (commit version))) + (url "https://github.com/galsci/pysm") + (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0rp22d1ckln9j490ga5snk0xb28qal1i10m4kqmhg7sfkw7dnnzs")))) + (base32 "0r8njxss389hqz1nxixamhclays6blyrq7qnrzs2776w9c0cv6vb")))) (build-system pyproject-build-system) (arguments (list @@ -6572,36 +6572,44 @@ natively in Siril.") ;; ;; #~(list "-k" (string-join - (list "not test_model" + (list "not test_bandpass_unit_conversion" "test_bandpass_unit_conversion_CMB2MJysr" "test_bandpass_unit_conversion_MJysr2KRJ" "test_cmb_lensed" + "test_cmb_lensed_delens" + "test_cmb_lensed_l01" + "test_cmb_lensed_no_delens" + "test_cmb_lensed_with_patch_object" "test_cmb_map" "test_cmb_map_bandpass" "test_co" "test_co_model" - "test_dust_model" - "test_model_d12" "test_d10_vs_d11" + "test_dust_model" "test_dust_model_353" "test_gnilc_857" + "test_healpix_output_nside" "test_highfreq_dust_model" + "test_model" + "test_model_d12" "test_presmoothed" - "test_sky_max_nside" - "test_sky_max_nside_highres" "test_read_map_unit" "test_read_map_unit_dimensionless" - "test_healpix_output_nside" + "test_s6_vs_s5" + "test_sky_max_nside" + "test_sky_max_nside_highres" "test_smoothing_healpix" "test_smoothing_healpix_beamwindow" - "test_s6_vs_s5" "test_synch_44" "test_synch_model_noscaling" "test_synch_model_s7_44" "test_synch_model_s7_noscaling" "test_synchrotron_model" - "test_bandpass_unit_conversion") - " and not ")) + ;; RuntimeError: This function has been removed. Use + ;; reproject.healpix2map(...method='harm'). + "test_car_nosmoothing") + " and not ") + "tests") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'set-version @@ -6611,6 +6619,7 @@ natively in Siril.") (list nss-certs-for-test python-hatch-vcs python-hatchling + python-nbval python-netcdf4 python-pixell python-psutil @@ -6620,8 +6629,11 @@ natively in Siril.") python-xarray)) (propagated-inputs (list python-astropy + python-h5py python-healpy python-numba + python-numpy + python-scipy python-toml)) (home-page "https://pysm3.readthedocs.io/") (synopsis "Sky emission simulations for Cosmic Microwave Background experiments") From f16195a2750385747441534a7978706667ef82ea Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 15:28:21 +0100 Subject: [PATCH 21/41] gnu: python-sunraster: Update to 0.6.2. * gnu/packages/astronomy.scm (python-sunraster): Update to 0.6.2. Change-Id: I526a946a58f6709e9e4df009c20b9ad48c756045 --- 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 682770e40f3..327011b4860 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -9021,13 +9021,13 @@ to the SolarSoft data analysis environment.") (define-public python-sunraster (package (name "python-sunraster") - (version "0.6.1") + (version "0.6.2") (source (origin (method url-fetch) (uri (pypi-uri "sunraster" version)) (sha256 - (base32 "0a1w7958n4m1qm59x6y00a0p45b5drnj1ippwl7gvszbwamhr2gr")))) + (base32 "0rpxarw108igdgxvdz1g63yhyam6mgkpp7l1kkcxqyqv9najnrh4")))) (build-system pyproject-build-system) (arguments (list From 28ec37413184eb525e64c043e340d4210ff7e363 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 16:49:44 +0100 Subject: [PATCH 22/41] gnu: python-jwst: Update to 1.19.2. * gnu/packages/astronomy.scm (python-jwst): Update to 1.19.2. [phases]{relax-requirements}: Adjust the list of versions. [propagated-inputs]: Remove python-asdf; add python-asdf-4. Change-Id: Ib72d1514d054389adc8487fb49e74adc9071fad1 --- 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 327011b4860..ca55996db7f 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -4926,13 +4926,13 @@ milliarcsecond).") (define-public python-jwst (package (name "python-jwst") - (version "1.19.1") + (version "1.19.2") (source (origin (method url-fetch) (uri (pypi-uri "jwst" version)) (sha256 - (base32 "1bds1a8bgyac19bwr7kf6wcknkmmchji23svhr8mpciga8gm27gv")) + (base32 "08c6wm7nchdq3cha9267h0i49s81yq0rz5y6nsbmganx0i9sg2aq")) (modules '((guix build utils))) (snippet #~(begin @@ -4957,6 +4957,8 @@ milliarcsecond).") (add-before 'build 'relax-requirements (lambda _ (substitute* "pyproject.toml" + ;; asdf>=4.0,<5 + ((">=4.0,<5") ">=4.0") ;; drizzle>=2.0.1,<2.1.0 ((">=2.0.1,<2.1.0") ">=2.0.1") ;; stcal>=1.14.1,<1.15.0 @@ -4984,7 +4986,7 @@ milliarcsecond).") (propagated-inputs ;; opencv provides OpenCV-Python which is Listed as install requirement. (list opencv - python-asdf + python-asdf-4 python-asdf-astropy python-astropy python-bayesicfitting From 9d6d92d1dd6ebc27bfcc05d6f6bbdf9308e55782 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 15:07:39 +0100 Subject: [PATCH 23/41] gnu: python-dkist: Adjust native inputs. * gnu/packages/astronomy.scm (python-dkist)[native-inputs]: Add python-pytest-asdf-plugin. Change-Id: Iae4d236eeee4aa708cd4158380d73ba8e1cb2eb0 --- gnu/packages/astronomy.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index ca55996db7f..2323dafb225 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -3785,6 +3785,7 @@ Cesium.") (list python-pydot python-pytest python-pytest-cov + python-pytest-asdf-plugin python-pytest-doctestplus python-pytest-filter-subpackage python-pytest-httpserver From fcbb8d4397d274dabf09e14cd7a93d009fa32f2b Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 16:24:52 +0100 Subject: [PATCH 24/41] gnu: aocommon: Update to 0.0.0-3.1444d66. * gnu/packages/astronomy.scm (aocommon): Update to 0.0.0-3.1444d66. [arguments] : Install CMake directory. Change-Id: I7f86569cd8049c308b6a2867dea95e86b8f56360 --- gnu/packages/astronomy.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 2323dafb225..ca467a9f381 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -190,8 +190,8 @@ randomly altered. (license license:gpl3))) (define-public aocommon - (let ((commit "9272ea36693a7ce7aa3524a9e212a60a509c3b8a") - (revision "2")) + (let ((commit "1444d66a59e757e7a0c74447e9f8d7a69c5e102d") + (revision "3")) (package (name "aocommon") (version (git-version "0.0.0" revision commit)) @@ -199,15 +199,16 @@ randomly altered. (origin (method git-fetch) (uri (git-reference - (url "https://gitlab.com/aroffringa/aocommon") - (commit commit))) + (url "https://gitlab.com/aroffringa/aocommon") + (commit commit))) (sha256 - (base32 "0klcrrlkc4sjpr83m2gnwb65lg798rydyvrlpangf7np1qg4zbk5")) + (base32 "06kdkkarx4bmp9808bwlx35vnp6g0vfzaxx1ijvzwgsjgg8yi5cp")) (file-name (git-file-name name version)))) (build-system copy-build-system) (arguments (list #:install-plan - #~'(("include/aocommon" "include/aocommon")))) + #~'(("include/aocommon" "include/aocommon") + ("CMake" "CMake")))) (home-page "https://gitlab.com/aroffringa/aocommon") (synopsis "Collection of functionality that is reused in astronomical applications") (description From c3bea11624a08cc249df7500f7ef872b06904994 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 16:37:59 +0100 Subject: [PATCH 25/41] gnu: aoflagger: Update to 3.4.0-0.b3a459d. * gnu/packages/astronomy.scm (aoflagger): Update to 3.4.0-0.b3a459d. [source] : Remove it as no longer required. * gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Deregister patch. Change-Id: I54535150959c5c7ef2c11c1b1541c287b935ed90 --- gnu/local.mk | 1 - gnu/packages/astronomy.scm | 114 +++++++++--------- ...flagger-use-system-provided-pybind11.patch | 38 ------ 3 files changed, 58 insertions(+), 95 deletions(-) delete mode 100644 gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch diff --git a/gnu/local.mk b/gnu/local.mk index 1ef437c3a80..0e083bec7a2 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -991,7 +991,6 @@ dist_patch_DATA = \ %D%/packages/patches/antiword-CVE-2014-8123.patch \ %D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch \ %D%/packages/patches/antlr3-3_3-fix-java8-compilation.patch \ - %D%/packages/patches/aoflagger-use-system-provided-pybind11.patch \ %D%/packages/patches/apr-fix-atomics.patch \ %D%/packages/patches/apr-skip-getservbyname-test.patch \ %D%/packages/patches/aria-maestosa-scons-python3.patch \ diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index ca467a9f381..1158fd17939 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -218,65 +218,67 @@ reused in several astronomical applications, such as @code{wsclean}, (license license:gpl3+)))) (define-public aoflagger - (package - (name "aoflagger") - (version "3.4.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://gitlab.com/aroffringa/aoflagger") - (commit (string-append "v" version)))) - (sha256 - (base32 "0dxmcy04cayhs4s2z41wls1dnmg9hkffvlqcmc660idqziffvv1g")) - (patches - (search-patches "aoflagger-use-system-provided-pybind11.patch")) - (file-name (git-file-name name version)))) - (build-system cmake-build-system) - (arguments - (list - ;; Tests require external files download from - ;; https://www.astron.nl/citt/ci_data/aoflagger/ - #:tests? #f - #:configure-flags - #~(list (string-append "-DCASACORE_ROOT_DIR=" - #$(this-package-input "casacore"))) - #:phases - #~(modify-phases %standard-phases - ;; aocommon and pybind11 are expected to be found as git submodules, - ;; link them before build. - (add-after 'unpack 'link-submodule-package - (lambda _ - (rmdir "external/aocommon") - (symlink #$(this-package-native-input "aocommon") - (string-append (getcwd) "/external/aocommon"))))))) - (native-inputs - (list aocommon - boost - pkg-config - python - pybind11)) - (inputs - (list casacore - cfitsio - fftw - gsl - gtkmm-3 - hdf5 - libpng - libsigc++ - libxml2 - lua - openblas - zlib)) - (home-page "https://gitlab.com/aroffringa/aoflagger") - (synopsis "Astronomical tool that can find and remove radio-frequency interference") - (description - "AOFlagger is a tool that can find and remove radio-frequency + ;; 3.4.0 was released in 2023, there are a lot of changes and compatibility + ;; for EveryBeam. + (let ((commit "b3a459df54b35ec18821ae0a392eeef1ca92cdba") + (revision "0")) + (package + (name "aoflagger") + (version (git-version "3.4.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/aroffringa/aoflagger") + (commit commit))) + (sha256 + (base32 "0fgm2svdw52m348hi28pnknxsdy54dkfd7y388b14hwf9z5ransa")) + (file-name (git-file-name name version)))) + (build-system cmake-build-system) + (arguments + (list + ;; Tests require external files download from + ;; https://www.astron.nl/citt/ci_data/aoflagger/ + #:tests? #f + #:configure-flags + #~(list (string-append "-DCASACORE_ROOT_DIR=" + #$(this-package-input "casacore"))) + #:phases + #~(modify-phases %standard-phases + ;; aocommon and pybind11 are expected to be found as git submodules, + ;; link them before build. + (add-after 'unpack 'link-submodule-package + (lambda _ + (rmdir "external/aocommon") + (symlink #$(this-package-native-input "aocommon") + (string-append (getcwd) "/external/aocommon"))))))) + (native-inputs + (list aocommon + boost + pkg-config + python + pybind11)) + (inputs + (list casacore + cfitsio + fftw + gsl + gtkmm-3 + hdf5 + libpng + libsigc++ + libxml2 + lua + openblas + zlib)) + (home-page "https://gitlab.com/aroffringa/aoflagger") + (synopsis "Astronomical tool that can find and remove radio-frequency interference") + (description + "AOFlagger is a tool that can find and remove radio-frequency interference (RFI) in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible, and the tools are applicable to a wide set of telescopes.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public astroterm (package diff --git a/gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch b/gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch deleted file mode 100644 index 76bc52a4bae..00000000000 --- a/gnu/packages/patches/aoflagger-use-system-provided-pybind11.patch +++ /dev/null @@ -1,38 +0,0 @@ -This patch was borrowed from Debian's package: -https://salsa.debian.org/debian-astro-team/aoflagger/-/blob/0484ef75a663e3e07738550cdade46f433a53dac/debian/patches/Use-system-provided-pybind11.patch -Description: Use system provided pybind11 -Author: Ole Streicher -Origin: Debian -Last-Update: Mon, 30 Aug 2021 11:05:37 +0200 ---- - CMakeLists.txt | 10 +++++----- - 1 file changed, 5 insertions(+), 5 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 655ea5e..824ee2a 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -62,11 +62,6 @@ foreach(ExternalSubmodule IN LISTS ExternalSubmoduleDirectories) - endif() - endforeach() - --# Include aocommon/pybind11 headers --include_directories("${CMAKE_SOURCE_DIR}/external/aocommon/include") --add_subdirectory("${CMAKE_SOURCE_DIR}/external/pybind11") --include_directories(SYSTEM ${pybind11_INCLUDE_DIR}) -- - find_package( - HDF5 - COMPONENTS C CXX -@@ -101,6 +96,11 @@ find_package(PythonInterp REQUIRED) - message(STATUS "Using python version ${PYTHON_VERSION_STRING}") - include_directories(SYSTEM ${PYTHON_INCLUDE_DIRS}) - -+# Include pybind11 headers -+find_package(pybind11 REQUIRED) -+include_directories("${CMAKE_SOURCE_DIR}/external/aocommon/include") -+include_directories(${pybind11_INCLUDE_DIR}) -+ - # boost::alignment requires Boost 1.56 - find_package(Boost 1.56.0 REQUIRED COMPONENTS date_time filesystem system - unit_test_framework) From 666f8a29170179c41ab269b692f4956fdcf6361c Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 12:52:34 +0100 Subject: [PATCH 26/41] gnu: phd2: Update to 2.6.13-1.4353f6b. * gnu/packages/astronomy.scm (phd2): Update to 2.6.13-1.4353f6b. Change-Id: I12107e14051a0b99497b0be74b7880e6c997ca03 --- 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 1158fd17939..a30ef7e7ba8 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1686,8 +1686,8 @@ R. Seaman's protocol} (define-public phd2 ;; The tag 2.6.13 was placed in 2023, but there are a lot of changes, fixes ;; and compatability with indi@2, use the latest commit from master branch. - (let ((commit "cc00236e79810da48e691e6a4785eb7e10b794ac") - (revision "0")) + (let ((commit "4353f6b2a1438caea44a9c2fb4d639a96478e697") + (revision "1")) (package (name "phd2") (version (git-version "2.6.13" revision commit)) @@ -1699,7 +1699,7 @@ R. Seaman's protocol} (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1b6fzniy5w9bx4627761nd4laargy728zvhw4k69dinwdwdi8jjw")) + (base32 "1bb8bmclgkpcqdx5jqag1raa4jviczkwyckbhph3xlg7zjbckik2")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-26))) From 7be28fb16d3fbb980fdbc432e3abdfb33d45b14f Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 16:46:10 +0100 Subject: [PATCH 27/41] gnu: python-aiapy: Update to 0.10.2. * gnu/packages/astronomy.scm (python-aiapy): Update to 0.10.2. Change-Id: I1c31db6e8e63cd03c17d0145160e9df51f6193a4 --- 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 a30ef7e7ba8..88721e981b9 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1854,13 +1854,13 @@ model-fitting photometry or morphological analyses.") (define-public python-aiapy (package (name "python-aiapy") - (version "0.10.1") + (version "0.10.2") (source (origin (method url-fetch) (uri (pypi-uri "aiapy" version)) (sha256 - (base32 "009zj20jcqlw2i8llx0pnxyz8416h4ng9avpqjrqszlhcq9xavrn")))) + (base32 "0lr8v2bakqxqn516fr45905lcql72kac3q6rdzn24rn95f812n27")))) (build-system pyproject-build-system) (arguments (list From 908087dc2748fa123daf52a3ffacd82a323bf655 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 13:45:58 +0100 Subject: [PATCH 28/41] gnu: python-camb: Update to 1.6.4. * gnu/packages/astronomy.scm (python-camb): Update to 1.6.4. [native-inputs]: Remove python-wheel. Change-Id: Ie5c7219ac4208336700c204bd7cccb0b0cb0e410 --- 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 88721e981b9..175520d949c 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -3129,13 +3129,13 @@ Origins Spectrograph}.") (define-public python-camb (package (name "python-camb") - (version "1.6.2") + (version "1.6.4") (source (origin (method url-fetch) (uri (pypi-uri "camb" version)) (sha256 - (base32 "1h9zdfsk14vx8hwpsvgs351cid1waggd47hj0yhy69djz935rgq5")))) + (base32 "1l9c8s263i3zgs50sn000yw0vyhrk56rvfcv18pwxs1zbq8bw0si")))) (build-system pyproject-build-system) (arguments (list @@ -3151,7 +3151,6 @@ Origins Spectrograph}.") (list gfortran python-packaging python-setuptools - python-wheel which)) ; for fortran/Makefile (propagated-inputs (list python-numpy From 1de82e9abc6c96ff7a24ae2650ffa14b5099ea2a Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 16:47:13 +0100 Subject: [PATCH 29/41] gnu: python-fitsio: Update to 1.2.8. * gnu/packages/astronomy.scm (python-fitsio): Update to 1.2.8. [native-inputs]: Remove python-setuptools and python-wheel; add python-setuptools-next. Change-Id: Ief3f63918b39beb42980d93958553ed6032ac27d --- gnu/packages/astronomy.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 175520d949c..b3a917a4892 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -4169,13 +4169,13 @@ all the input image headers.") (define-public python-fitsio (package (name "python-fitsio") - (version "1.2.6") + (version "1.2.8") (source (origin (method url-fetch) (uri (pypi-uri "fitsio" version)) (sha256 - (base32 "1brkkfqgfwbnl1si7hppripcixmsfjs5lpbn18yrwxziafycvc1k")) + (base32 "1cbynx6lyf38863njqyg1gnpcdp69bxywmi0ckhzgf9wicxf31nk")) (modules '((guix build utils))) (snippet ;; Remove the bundled cfitsio. When update the package check the @@ -4202,8 +4202,7 @@ all the input image headers.") #$(this-package-input "cfitsio") "/lib"))))))) (native-inputs (list python-pytest - python-setuptools - python-wheel)) + python-setuptools-next)) (inputs (list curl cfitsio From 91208ff17e6f320df7a7b7ed96caf18f31ce6ddf Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 15:07:41 +0100 Subject: [PATCH 30/41] gnu: python-irispy-lmsal: Update to 0.4.0. * gnu/packages/astronomy.scm (python-irispy-lmsal): Update to 0.4.0. [arguments] : Skip one more test. Change-Id: Iebc28295f2de58d928ad17c8d51fd19289a162bb --- gnu/packages/astronomy.scm | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index b3a917a4892..0a3e3dec631 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -4813,23 +4813,32 @@ observationally-derived galaxy merger catalogs.") (define-public python-irispy-lmsal (package (name "python-irispy-lmsal") - (version "0.3.1") + (version "0.4.0") (source (origin (method url-fetch) (uri (pypi-uri "irispy_lmsal" version)) (sha256 - (base32 "037ip97kb5sq98shgw4d1c5x7lpbzksampfw7d97x59zbvbmvwhn")))) + (base32 "1al7nyw2d2175gbij7ab2q0ks3wsf4b7n6g89ic2mpg4v1ybyxw5")))) (build-system pyproject-build-system) (arguments (list + ;; tests: 68 passed, 1 skipped, 9 deselected, 2 warnings #:test-flags ;; See: . ;; Expected: ;; np.float64(0.33) ;; Got: ;; 0.33 - #~(list "--deselect=irispy/obsid.py::irispy.obsid.ObsID") + #~(list "--deselect=irispy/obsid.py::irispy.obsid.ObsID" + ;; TODO: Report upstram. + ;; Arrays are not almost equal to 4 decimals + ;; Mismatched elements: 42 / 3601 (1.17%) + ;; Max absolute difference: 0.34272391 + ;; Max relative difference: 0.00491848 + ;; x: array([0., 0., 0., ..., 0., 0., 0.]) + ;; y: array([0., 0., 0., ..., 0., 0., 0.], dtype='>f4') + "-k" "not test_get_latest_response_to_idl") #:phases #~(modify-phases %standard-phases ;; XXX: It fails to check SunPy's optional inputs versions. From 76be5dc586ef1f1caaedc0b8b10bc57b8546660c Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 15:24:18 +0100 Subject: [PATCH 31/41] gnu: python-space-dolphin: Update to 1.2.0. * gnu/packages/astronomy.scm (python-space-dolphin): Update to 1.2.0. [native-inputs]: Remove python-wheel. Change-Id: I32cfc5455cf413b4129da476d584b3a820f2899f --- gnu/packages/astronomy.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 0a3e3dec631..535bc25959b 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -7542,13 +7542,13 @@ but has evolved to support other missions as well.") (define-public python-space-dolphin (package (name "python-space-dolphin") - (version "1.1.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (pypi-uri "space_dolphin" version)) (sha256 - (base32 "0qsdaqbdf51ai54w4d483bf9kxjjcsr5fiqs861z7k7s7zrjms0r")))) + (base32 "162899av6mp0wkjbas07xkqjr70qbvirgnnch7hb501gz0rb50bh")))) (build-system pyproject-build-system) (arguments (list @@ -7562,8 +7562,7 @@ but has evolved to support other missions as well.") (setenv "NUMBA_CACHE_DIR" "/tmp")))))) (native-inputs (list ;; python-pytest - python-setuptools - python-wheel)) + python-setuptools)) (propagated-inputs (list python-astropy python-corner From 14389a53f66d3f5f0ec07af2998ceb36d2372cef Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 10 Sep 2025 16:43:16 +0100 Subject: [PATCH 32/41] gnu: splash: Update to 3.11.5. * gnu/packages/astronomy.scm (splash): Update to 3.11.5. Change-Id: I21b9aba416869158e0dbcba2aa947f69e9e5fcaf --- 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 535bc25959b..af3f67327eb 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -9815,7 +9815,7 @@ astronomical fields. SkyMaker is part of the (define-public splash (package (name "splash") - (version "3.11.4") + (version "3.11.5") (source (origin (method git-fetch) @@ -9824,7 +9824,7 @@ astronomical fields. SkyMaker is part of the (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "13p4hjdpr0yacgh8v3lf5vy1d0hdh5axbwpgi91wafm0xx6zpgkv")))) + (base32 "1sdfgn2rh1gq3n1ya55qhv9j8bf700f2lhp2k9avy1aix903ry36")))) (build-system gnu-build-system) (arguments ;; FIXME: Tests failed From 371572e80c9bcaf92d65748330dcf2fffc7008e2 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 17:10:15 +0100 Subject: [PATCH 33/41] gnu: uraniborg: Update to 0.0.12. * gnu/packages/astronomy.scm (uraniborg): Update to 0.0.12. Change-Id: I21c6a0ce5d93350c807bda47a6044d0f6d970701 --- 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 af3f67327eb..07747b79bac 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -10274,7 +10274,7 @@ n-body file formats (nemo, Gadget binaries 1 and 2, Gadget hdf5, Ramses).") (define-public uraniborg (package (name "uraniborg") - (version "0.0.10") + (version "0.0.12") (source (origin (method git-fetch) @@ -10283,7 +10283,7 @@ n-body file formats (nemo, Gadget binaries 1 and 2, Gadget hdf5, Ramses).") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0bz2k2x06nyvhr9v4z6f21cf29pqsj9m4qyn8sdbl421wsqj31wg")))) + (base32 "1n24c7ihz49piry36sfvig9qag948k4wkn9a7b5v7c1yax5ab4ap")))) (build-system go-build-system) (arguments (list From 4be030e62f051ae9038fd8be81bf072a954ed0fb Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 11:02:33 +0100 Subject: [PATCH 34/41] gnu: Add celestia-content. * gnu/packages/astronomy.scm (celestia-content): New variable. Change-Id: Id5eb5c666dc4171960273c8553b02f72b225907f --- gnu/packages/astronomy.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 07747b79bac..ab78d8710ac 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -602,6 +602,40 @@ time. The position and movement of solar system objects is calculated accurately in real time at any rate desired.") (license license:gpl2+))) +(define-public celestia-content + ;; No rleases or version tags. + (let ((commit "10bd43b0e8925f6ee9bb9687522708a95338d664") + (revision "0")) + (package + (name "celestia-content") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/CelestiaProject/CelestiaContent") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1gah823hdf0lhyql6ln6cmivfl9d8dr7yp3mrc1rcw7bm4hbb2qq")))) + (build-system cmake-build-system) + (arguments + (list + #:tests? #f)) ;no tests were found + (native-inputs + (list gettext-minimal + imagemagick)) + (home-page "https://celestia.space/") + (synopsis "Data files for Celestia space simulator") + (description + "This package provides data content for Celestia. +@itemize +@item Scientific Data Base +@item Texture maps +@item 3D Models +@end itemize") + (license license:gpl2+)))) + (define-public celestia-gtk (deprecated-package "celestia-gtk" celestia)) From 6f0c59665884b8eb7f5e48f6da2528f4a148bd09 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 11:02:35 +0100 Subject: [PATCH 35/41] gnu: celestia: Update to 1.6.4-0.d3f4040. This is a follow-up to 51640e48200a0b8c5234be62683e89439de1be64. Celestia is built from the latest commit providing Qt6 support and many other new features. * gnu/packages/astronomy.scm (celestia): Update to 1.6.4-0.d3f4040. [buld-system]: Switch to cmake-build-system. [arguments] : Adjust it for the build. : Remove 'patch-lua-version; add 'install-content. [inputs]: Remove freeglut and libtheora; add eigen, ffmpeg, fmt, freetype, gperf, libavif, libepoxy, qtbase, and qtwayland. [propagated-inputs]: Add perl. [native-inputs]: Remove autoconf, automake, libgit2, libtool, and perl; add boost and celestia-content. Change-Id: Ida03597bd9c2d5de31322b3aae88baa6b007889c --- gnu/packages/astronomy.scm | 121 ++++++++++++++++++++----------------- 1 file changed, 65 insertions(+), 56 deletions(-) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index ab78d8710ac..9efb6244537 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -78,12 +78,14 @@ #:use-module (gnu packages golang) #:use-module (gnu packages golang-maths) #:use-module (gnu packages golang-xyz) + #:use-module (gnu packages gperf) #:use-module (gnu packages gps) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) #:use-module (gnu packages gtk) #:use-module (gnu packages image) #:use-module (gnu packages image-processing) + #:use-module (gnu packages imagemagick) #:use-module (gnu packages jupyter) #:use-module (gnu packages libevent) #:use-module (gnu packages libusb) @@ -540,67 +542,74 @@ Library with namespaces, exception handling, and member template functions.") "See License.txt in the distribution.")))) (define-public celestia - (package - (name "celestia") - (version "1.6.4") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/celestiaproject/celestia") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0nz9k5nd2zmrbwj1qhsfwmvqymqk8c4yjxpybck44isrild2ah9j")))) - (build-system gnu-build-system) - (arguments - (list - #:modules - `((guix build gnu-build-system) - (guix build utils) - (srfi srfi-1) - (srfi srfi-71)) - #:configure-flags - #~(list "--with-glut" - (string-append "--with-lua=" #$(this-package-input "lua"))) - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'patch-lua-version - (lambda _ - (let* ((_ version (package-name->name+version - #$(this-package-input "lua"))) - (components (string-split version #\.)) - (major+minor (string-join (take components 2) "."))) - (substitute* "configure.ac" - (("lua5.3") - (string-append "lua-" major+minor))))))))) - (native-inputs - (list autoconf - automake - gettext-minimal - libgit2 - libtool - perl - pkg-config)) - (inputs - (list freeglut - glu - libjpeg-turbo - libpng - libtheora - mesa)) - (propagated-inputs - (list lua)) - (home-page "https://celestia.space/") - (synopsis "Real-time 3D visualization of space") - (description - "This simulation program lets you explore our universe in three + ;; 1.6.4 was placed in 2023 while master migrated to Qt6, use the lates + ;; commit for now. + (let ((commit "d3f4040401f5f71bcca79e55d53be75c05b867ef") + (revision "0")) + (package + (name "celestia") + (version (git-version "1.6.4" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/celestiaproject/celestia") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0rqkzxyf8gfjprhj1c19d7chhc3b94wlq2119wz0c344rx7hnh9l")))) + (build-system cmake-build-system) + (arguments + (list + #:tests? #f ;no tests were found + #:configure-flags + #~(list "-DENABLE_FFMPEG=ON" + "-DENABLE_GLES=ON" + "-DENABLE_LIBAVIF=ON" + "-DENABLE_QT6=ON" + "-DENABLE_TOOLS=ON" + "-DUSE_QT6=ON") + #:phases + #~(modify-phases %standard-phases + ;; TODO: Wrap celestia-content instead of copping it, if posible. + (add-after 'install 'install-content + (lambda _ + (copy-recursively + (string-append #$(this-package-native-input "celestia-content") + "/share") + (string-append #$output "/share"))))))) + (native-inputs + (list boost + celestia-content + gettext-minimal + pkg-config)) + (inputs + (list eigen + ffmpeg + fmt + freetype + glu + gperf + libavif + libepoxy + libjpeg-turbo + libpng + mesa + qtbase + qtwayland)) + (propagated-inputs + (list lua + perl)) + (home-page "https://celestia.space/") + (synopsis "Real-time 3D visualization of space") + (description + "This simulation program lets you explore our universe in three dimensions. Celestia simulates many different types of celestial objects. From planets and moons to star clusters and galaxies, you can visit every object in the expandable database and view it from any point in space and time. The position and movement of solar system objects is calculated accurately in real time at any rate desired.") - (license license:gpl2+))) + (license license:gpl2+)))) (define-public celestia-content ;; No rleases or version tags. From a3296214cc33f509c27e9bb3afb17e83fdac2671 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 17 Sep 2025 23:18:34 +0100 Subject: [PATCH 36/41] gnu: Add fitsverify. * gnu/packages/astronomy.scm (fitsverify): New variable. Change-Id: I07e72835d1cf481d785c652d6fa5861b236764a9 --- gnu/packages/astronomy.scm | 53 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 9efb6244537..79558fec908 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -919,6 +919,59 @@ applications of EyE include adaptive filtering, feature detection and cosmetic corrections.") (license license:cecill))) +(define-public fitsverify + (package + (name "fitsverify") + (version "4.22") + (source + (origin + (method url-fetch) + (uri (string-append "https://heasarc.gsfc.nasa.gov/docs/software/ftools/" + name "/" name "-" version ".tar.gz")) + (sha256 + (base32 "1d0qvgmrpv09qm4vi4n26frx4qb3mrdn261rs6vvrvg0lw1yhibc")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ;no tests + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; no configure + (replace 'build + (lambda* _ + ;; Build steps are taken from Debian's package definition. + (invoke #$(cc-for-target) "-o" #$name + "ftverify.c" + "fvrf_data.c" + "fvrf_file.c" + "fvrf_head.c" + "fvrf_key.c" + "fvrf_misc.c" + "-DSTANDALONE" + "-lcfitsio" + "-lm"))) + (replace 'install + (lambda _ + (install-file #$name (string-append #$output "/bin"))))))) + (inputs + (list cfitsio)) + (home-page "https://heasarc.gsfc.nasa.gov/docs/software/ftools/fitsverify/index.html") + (synopsis "FITS File Format-Verification Tool") + (description + "Fitsverify is a computer program that rigorously checks whether a +@acronym{FITS, Flexible Image Transport System} data file conforms to the +requirements defined in Version 3.0 of the +@url{http://fits.gsfc.nasa.gov/fits_documentation.html, FITS Standard +document}.") + (properties + '((release-monitoring-url . + "https://heasarc.gsfc.nasa.gov/docs/software/ftools/fitsverify/"))) + ;; The license is the same as for CFITSIO, see + ;; URL: + ;; File: + (license (license:non-copyleft "file://License.txt" + "See License.txt in the distribution.")))) + (define-public ginga (package (name "ginga") From d0262fabecc74310693c26817af9320d73be51b8 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 15:37:21 +0100 Subject: [PATCH 37/41] gnu: Add python-corsikaio. * gnu/packages/astronomy.scm (python-corsikaio): New variable. Change-Id: Ia01b9a117681978d8d5e968e447e805dea3385ec --- gnu/packages/astronomy.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 79558fec908..2c22fed0f1f 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -3680,6 +3680,42 @@ JSON template file alongside Python routines for visualizing and comparing lens models possibly obtained from different modeling codes.") (license license:gpl3))) +(define-public python-corsikaio + (package + (name "python-corsikaio") + (version "0.5.0") + (source + (origin + (method git-fetch) ; no tests in the PyPI tarball + (uri (git-reference + (url "https://github.com/cta-observatory/pycorsikaio") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1afv7jra31fi2g85z8jzmjr6w1wk9xs4v2cg06df2zffqfgfjnjj")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'set-env-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))))) + (native-inputs + (list python-pytest + python-scipy + python-setuptools-next + python-setuptools-scm)) + (propagated-inputs + (list python-numpy)) + (home-page "https://github.com/cta-observatory/pycorsikaio") + (synopsis "Reader for CORSIKA binary output files") + (description + "This package implements a reader for +@url{https://www.iap.kit.edu/corsika/, @acronym{CORSIKA, COsmic Ray +SImulations for KAscade}} binary output files using NumPy.") + (license license:expat))) + (define-public python-cosmopy (package (name "python-cosmopy") From 818aa007dde867ed49b9b30a3e90c8f6d07eceb1 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 15:39:49 +0100 Subject: [PATCH 38/41] gnu: Add python-eventio. * gnu/packages/astronomy.scm (python-eventio): New variable. Change-Id: I1ed9191e9433778090f725faaf12cfb343869e41 --- gnu/packages/astronomy.scm | 45 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 2c22fed0f1f..e6aa04827ac 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -4237,6 +4237,51 @@ numerical python, statistics, and file input/output. Includes specialized tools for astronomers.") (license license:gpl2+))) +(define-public python-eventio + (package + (name "python-eventio") + (version "1.16.1") + (source + (origin + (method git-fetch) ; no test data in the PyPI tarball + (uri (git-reference + (url "https://github.com/cta-observatory/pyeventio") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jg2zgs0z5jfkdkbgxiiclxkyxrz4zhb57x1ji0c5pd2vsrn4g92")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-env-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))) + (add-before 'build 'relax-gcc-14-strictness + (lambda _ + (setenv "CFLAGS" (string-join + (list "-g" "-O2" + "-Wno-error=implicit-function-declaration" + "-Wno-error=int-conversion") + " "))))))) + (native-inputs + (list python-cython + python-numpy + python-pytest + python-setuptools-next + python-setuptools-scm-next)) + (propagated-inputs + (list python-corsikaio + python-matplotlib + python-numpy + python-zstandard)) + (home-page "https://github.com/cta-observatory/pyeventio") + (synopsis "Python read-only implementation of the EventIO file format") + (description + "Python read-only implementation of the @code{EventIO} file format.") + (license license:expat))) + (define-public python-extinction (package (name "python-extinction") From 47ebec0a488bb9d5c65a07b34f8d4a0edcf88ddb Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 15:32:32 +0100 Subject: [PATCH 39/41] gnu: Add python-pydl. * gnu/packages/astronomy.scm (python-pydl): New variable. Change-Id: If6ef2787bc72fdfcbddaf27b5dd115126914850b --- gnu/packages/astronomy.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index e6aa04827ac..15930d32118 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -6334,6 +6334,35 @@ Pipeline Library, CPL} toolkit, including the CPL plugin interface.") (properties '((upstream-name . "pycpl"))) (license license:bsd-3))) +(define-public python-pydl + (package + (name "python-pydl") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pydl" version)) + (sha256 + (base32 "0z08c05qf0ix4h348n0hhxixn1wipdm55g9z6qys24z41ywf69jh")))) + (build-system pyproject-build-system) + (native-inputs + (list python-pytest-astropy + python-pytest-mock + python-setuptools-next + python-setuptools-scm)) + (propagated-inputs + (list python-astropy + python-scipy)) + (home-page "https://github.com/weaverba137/pydl") + (synopsis "IDL astronomy routines converted to Python") + (description + "This package consists of Python replacements for functions that are part +of the @url{https://www.nv5geospatialsoftware.com/Products/IDL, IDL} built-in +library or part of astronomical IDL libraries. The emphasis is on reproducing +results of the astronomical library functions. Only the bare minimum of IDL +built-in functions are implemented to support this.") + (license license:bsd-3))) + (define-public python-pyerfa (package (name "python-pyerfa") From c03d2f343802f3d2e19350880f95c157ba35a51b Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Thu, 18 Sep 2025 15:30:33 +0100 Subject: [PATCH 40/41] gnu: Add python-raccoon. * gnu/packages/astronomy.scm (python-raccoon): New variable. Change-Id: Iad8afa0f86b28ff2558588c6e99f317afb7b367d --- gnu/packages/astronomy.scm | 43 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 15930d32118..d7c8c971489 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -6961,6 +6961,49 @@ export the simulated X-ray events to other software packages to simulate the end products of specific X-ray observatories.") (license license:bsd-3))) +(define-public python-raccoon + (package + (name "python-raccoon") + (version "1.0.0") + (source + (origin + ;; PyPi tarball lacks tests. + (method git-fetch) + (uri (git-reference + (url "https://github.com/ajshajib/raccoon") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1hn8g7zxga47yhk4y9nrbnz0n7apflczlaszr79h4lg6b4v4h9f4")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "-k" (string-join + ;; Three tests fail with error: AttributeError: module + ;; 'numpy' has no attribute 'trapezoid'. + (list "not test_clean_cube" + "test_clean_cube_with_min_n_amplitude_and_min_n_f" + "test_clean_cube_with_wiggle_detection_thresholds") + " and not ")))) + (native-inputs + (list python-pytest + python-setuptools-next)) + (propagated-inputs + (list python-astropy + python-matplotlib + python-numpy + python-scipy + python-statsmodels + python-tqdm)) + (home-page "https://github.com/ajshajib/raccoon") + (synopsis "Clean modulation due to resampling noise in the JWST/NIRSpec IFS spectra") + (description + "Package Raccoon cleans the \"wiggles\" (i.e., low-frequency sinusoidal +artifacts) in the JWST-NIRSpec IFS (integral field spectroscopy) data. These +wiggles are caused by resampling noise or aliasing artifacts.") + (license license:bsd-3))) + (define-public python-rad (package (name "python-rad") From 19cd5a7a71f273c4ca339e68480c50446e06150b Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Wed, 17 Sep 2025 23:14:28 +0100 Subject: [PATCH 41/41] gnu: Add tenmon. * gnu/packages/astronomy.scm (tenmon, libxisf-for-tenmon): New variables. Change-Id: I0398fe657aa944883d1160265fe0113a0ae24ab0 --- gnu/packages/astronomy.scm | 93 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index d7c8c971489..ff891311ec8 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -1742,6 +1742,25 @@ PixInsight}. It implements 1.0 specification}.") (license license:gpl3+))) +(define-public libxisf-for-tenmon + ;; This is an exact commit required for tenmon git submodule. + (let ((commit "556bb22d2675ee6072c6224fef3da0fb5d93db41") + (revision "0")) + (hidden-package + (package + (inherit libxisf) + (name "libxisf") + (version (git-version "0.2.13" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitea.nouspiro.space/nou/libXISF") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "037dijy0ql1mwm8nddwawlf3ms6w30kxdlkrjjprfsss80ssn30k")))))))) + (define-public missfits (package (name "missfits") @@ -10485,6 +10504,80 @@ See related paper @url{https://ui.adsabs.harvard.edu/abs/2006MNRAS.369..655H/abstract}.") (license license:gpl3+))) +(define-public tenmon + (package + (name "tenmon") + (version "20250915") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitea.nouspiro.space/nou/tenmon") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ay95kdsmv4xli25l7khga4ldwy4irrfc15649s3mgqcd5gl3pfw")))) + (build-system cmake-build-system) + (arguments + (list + #:tests? #f ;no test target + #:configure-flags + #~(list "-DCMAKE_C_FLAGS=-Wno-error=implicit-function-declaration") + #:phases + #~(modify-phases %standard-phases + ;; libxisf is expected to be found as git submodule, link it before + ;; build. + (add-after 'unpack 'link-libxisf + (lambda _ + (rmdir "libXISF") + (symlink #+(package-source (this-package-native-input "libxisf")) + (string-append (getcwd) "/libXISF"))))))) + (native-inputs + (list git-minimal/pinned + libxisf-for-tenmon + pkg-config )) + (inputs + (list cfitsio + glu + gsl + libexif + libraw + qtbase + qtcharts + qtdeclarative + wcslib + zstd + (list zstd "lib"))) + (home-page "https://nouspiro.space/?page_id=206") + (synopsis "FITS and XISF image viewer, converter and indexer") + (description + "FITS/XISF image viewer with multithreaded image loading. It is intended +primarily for viewing astro photos and images with support of following +formats: + +@itemize +@item FITS 8, 16 bit integer and 32 bit float +@item XISF 8, 16 bit integer and 32 bit float +@item RAW CR2, DNG, NEF +@item JPEG, PNG, BMP, GIF, PBM, PGM, PPM and SVG images +@end itemize + +Features: +@itemize +@item using same stretch function as PixInsight +@item OpenGL accelerated drawing +@item index and search FITS XISF header data +@item quick mark images and then copy/move marked files +@item convert FITS <-> XISF +@item convert FITS/XISF -> JPEG/PNG +@item image statistics mean, media, min, max +@item support for WCS +@item thumbnails +@item convert CFA images to colour - debayer +@item color space aware +@end itemize") + (license license:gpl3+))) + (define-public unsio ;; There is no versioned tag, use the latest commit. (let ((commit "ac48210ec24432ec3ad330c4203e7eb21876a921")