guix_mirror_bot pushed a commit to branch astro-updates in repository guix.
commit ccb7b148d1c3c8f6286b5dd586b2a9a0c0109950 Author: Sharlatan Hellseher <[email protected]> AuthorDate: Wed Nov 19 22:13:25 2025 +0000 gnu: Add python-pypeit. * gnu/packages/astronomy.scm (python-pypeit, python-pypeit-minimal): New variables. Change-Id: I735665845a9a6497661e89b1337923c8f425e1c2 --- gnu/packages/astronomy.scm | 116 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 116 insertions(+) diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index b9be8fd866..75bad765c1 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -6975,6 +6975,122 @@ N-Chilada and RAMSES AMR outputs.") (sha256 (base32 "0rl9ais4yc6kdijq1il4vi3mplp7z6bcih4x55axhan5n3n7riwi")))))) +(define-public python-pypeit + (package + (name "python-pypeit") + (version "1.17.4") ;XXX: Newer versions need to be built with NumPy 2+ + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pypeit/PypeIt";) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "16y4vkjmd29zrjhhv2fyv9rksjblri3zf6m81mhmhys5sy09xmfz")))) + (build-system pyproject-build-system) + (arguments + (list + ;; tests: 242 passed, 10 skipped, 5 deselected, 120 warnings + #:test-flags + ;; Tests still try to download test data even it's available in + ;; "pypeit/data". + #~(list "--deselect=pypeit/tests/test_install.py::test_install_telluric" + #$@(map (lambda (test) (string-append "--deselect=pypeit/" + "tests/test_pkgdata.py::" + test)) + (list "test_cloud_url" + "test_fetch_github_files" + "test_github_contents" + "test_cache_to_pkg"))) + #:phases + #~(modify-phases %standard-phases + ;; XXX: See: <https://github.com/pypeit/PypeIt/issues/1786>. + (add-after 'unpack 'remove-missing-scripts-entry-points + (lambda _ + (substitute* "setup.cfg" + ((".*pypeit_install_ql_calibs.*") "") + ((".*pypeit_ql_multislit.*") "")))) + (add-after 'unpack 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))) + (add-after 'install 'include-package-data + ;; XXX: PyPI archive provides pypeit/data but during build from + ;; Git it's ignored for some reason, add it manually. + (lambda* (#:key inputs outputs #:allow-other-keys) + (copy-recursively "pypeit/data" + (string-append (site-packages inputs outputs) + "/pypeit/data")))) + (add-before 'check 'pre-check + (lambda _ + (system "Xvfb &") + (setenv "DISPLAY" ":0") + (setenv "HOME" "/tmp") + (setenv "MPLBACKEND" "agg"))) + (add-before 'check 'post-check + (lambda _ + (for-each delete-file-recursively + (find-files #$output "__pycache__" #:directories? #t))))))) + (native-inputs + (list nss-certs-for-test + python-cython + python-pygit2 + python-pytest + python-scikit-image + python-setuptools + python-setuptools-scm + python-shapely + python-specutils + xorg-server-for-tests)) + (propagated-inputs + (list python-astropy-6 + python-bottleneck + python-configobj + python-extension-helpers + python-fast-histogram + python-ginga + python-ipython + python-linetools + python-matplotlib + python-numpy + python-packaging + python-pyerfa + python-pygithub + python-pyqt-6 + python-pyyaml + python-qtpy + python-scikit-learn + python-scipy)) + (home-page "https://github.com/pypeit/PypeIt";) + (synopsis "Spectroscopic Data Reduction Pipeline") + (description + "PypeIt is a Python package for semi-automated reduction of astronomical +spectroscopic data. Its algorithms build on decades-long development of +previous data reduction pipelines by the developers. + +It is designed to be used by both advanced spectroscopists with prior data +reduction expertise and astronomers with no prior experience of data +reduction. It is highly configurable and designed to be applied to any +standard slit-imaging spectrograph, including long-slit, multi-slit, as well +as cross-dispersed echelle spectra.") + (license license:bsd-3))) + +;; A bare minimal package, mainly to use in tests and reduce closure +;; size. Tests are left out in the main package to slim down native-inputs. +(define-public python-pypeit-minimal + (package/inherit python-pypeit + (name "python-pypeit-minimal") + (arguments + (substitute-keyword-arguments + (package-arguments python-pypeit) + ((#:tests? _ #t) #f) + ((#:phases phases '%standard-phases) + #~(modify-phases #$phases + (delete 'pre-check))))) + (native-inputs + (list python-setuptools + python-setuptools-scm)))) + (define-public python-pyregion (package (name "python-pyregion")
