guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit ebf6d0830646ea769aa9b1f0ba9889ad3cfd4331
Author: Nicolas Graves <[email protected]>
AuthorDate: Tue Sep 23 23:54:22 2025 +0200
gnu: python-pymol: Update to 3.1.0.
* gnu/packages/chemistry.scm (python-pymol): Update to 3.1.0.
[build-system]: Switch to pyproject-build-system.
[arguments]<#:tests?>: Disable them.
<#:phases>: Refresh them. Delete 'build phase.
[native-inputs]: Add cmake-minimal, python-pytest, python-setuptools.
[propagated-inputs]: Add python-numpy.
[description]: Improve style.
Change-Id: Ida6105297f294e3fda060d8c8b938fe743faf6e6
Signed-off-by: Sharlatan Hellseher <[email protected]>
---
gnu/packages/chemistry.scm | 99 +++++++++++++++++++++++++---------------------
1 file changed, 53 insertions(+), 46 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 5cbdad2822..bc96da1e0b 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -720,7 +720,7 @@ quantum chemistry (and molecular mechanics) softwares.")
(define-public python-pymol
(package
(name "python-pymol")
- (version "2.5.0")
+ (version "3.1.0")
(source
(origin
(method git-fetch)
@@ -729,54 +729,61 @@ quantum chemistry (and molecular mechanics) softwares.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "08zmfgclkbjkqjpq8xs1mphs1i8rpqj76mcw7m2mrhvma5qj1nr5"))))
- (build-system python-build-system)
+ (base32 "199zhpdljsvfjnvs7h7q17ib7ajnjiwg790rg8xxhaszjd968byq"))))
+ (build-system pyproject-build-system)
(arguments
- '(#:configure-flags
- (list "--glut" "--testing")
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'make-reproducible
- (lambda _
- (substitute* "create_shadertext.py"
- (("time\\.time\\(\\)") "0"))))
- (add-after 'unpack 'add-include-directories
- (lambda* (#:key inputs #:allow-other-keys)
- (setenv "CPLUS_INCLUDE_PATH"
- (string-append (assoc-ref inputs "freetype")
- "/include/freetype2:"
- (assoc-ref inputs "libxml2")
- "/include/libxml2:"
- (getenv "CPLUS_INCLUDE_PATH")))))
- ;; Prevent deleting the leading / in the __init__.py path in the
- ;; launch script.
- (add-after 'unpack 'disable-unchroot
- (lambda _
- (substitute* "setup.py"
- (("self\\.unchroot") ""))))
- ;; The setup.py script does not support one of the Python build
- ;; system's default flags, "--single-version-externally-managed".
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (invoke "python" "setup.py" "install"
- (string-append "--prefix=" (assoc-ref outputs "out"))
- "--root=/"))))))
- (inputs
- (list freetype
- libpng
- freeglut
- glew
- libxml2
- mmtf-cpp
- python-pyqt
- glm
- netcdf))
- (native-inputs (list catch2))
+ (list
+ ;; XXX: Most tests fail with import errors.
+ #:tests? #f
+ #:configure-flags
+ #~(list "--glut" "--testing")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'make-reproducible
+ (lambda _
+ (substitute* "create_shadertext.py"
+ (("time\\.time\\(\\)")
+ "0"))))
+ (add-after 'unpack 'add-include-directories
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (list
+ (search-input-directory inputs "/include/freetype2")
+ (search-input-directory inputs "/include/libxml2")
+ (getenv "CPLUS_INCLUDE_PATH"))
+ ":"))))
+ ;; Prevent deleting the leading / in the __init__.py path in the
+ ;; launch script.
+ (add-after 'unpack 'disable-unchroot
+ (lambda _
+ (substitute* "setup.py"
+ (("self\\.unchroot")
+ ""))))
+ ;; The setup.py script does not support one of the Python build
+ ;; system's default flags, "--single-version-externally-managed".
+ (delete 'build)
+ (replace 'install
+ (lambda _
+ (invoke "python" "setup.py" "install"
+ (string-append "--prefix=" #$output) "--root=/"))))))
+ (inputs (list freetype
+ libpng
+ freeglut
+ glew
+ libxml2
+ mmtf-cpp
+ python-pyqt
+ glm
+ netcdf))
+ (native-inputs (list cmake-minimal catch2 python-pytest python-setuptools))
+ (propagated-inputs (list python-numpy))
(home-page "https://pymol.org";)
(synopsis "Molecular visualization system")
- (description "PyMOL is a capable molecular viewer and renderer. It can be
-used to prepare publication-quality figures, to share interactive results with
-your colleagues, or to generate pre-rendered animations.")
+ (description
+ "PyMOL is a capable molecular viewer and renderer. It can be used to
+prepare publication-quality figures, to share interactive results with your
+colleagues, or to generate pre-rendered animations.")
(license license:bsd-3)))
(define-public python-pyscf
