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[bug#56729] [RFC PATCH v3 31/32] gnu: Add python-sagemath-standard.
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From: |
vicvbcun |
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Subject: |
[bug#56729] [RFC PATCH v3 31/32] gnu: Add python-sagemath-standard. |
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Date: |
Mon, 29 May 2023 22:38:40 +0200 |
* gnu/packages/sagemath.scm (python-sagemath-standard): New variable.
---
Notes:
sage currently uses python's `sys.prefix' as
`SAGE_VENV' (i.e. `/gnu/store/…-python-…' instead of
`/gnu/store/…-sagemath-…'), causing a warning to be printed when running as
notebook.
`sage' unsets the `SAGE_VENV' environment variable and later tests if it is
set and if this predictably is not the case uses `sage-venv-config' to
determine `SAGE_VENV'. `sage-venv-config' itself uses `sys.prefix'
unconditionally as `SAGE_VENV'.
Therefore, wrapping `sage' with a the appropriate value for `SAGE_VENV' does
not work and would need patching.
gnu/packages/sagemath.scm | 199 +++++++++++++++++++++++++++++++++++++-
1 file changed, 198 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index dfe5874ed3..4f23a7b7a0 100644
--- a/gnu/packages/sagemath.scm
+++ b/gnu/packages/sagemath.scm
@@ -4,6 +4,7 @@
;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2021 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2023 vicvbcun <guix@ikherbers.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -25,6 +26,7 @@ (define-module (gnu packages sagemath)
#:use-module (guix build-system copy)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
+ #:use-module (guix build-system pyproject)
#:use-module (guix build-system trivial)
#:use-module (guix download)
#:use-module (guix gexp)
@@ -38,13 +40,22 @@ (define-module (gnu packages sagemath)
#:use-module (gnu packages bdw-gc)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages freedesktop)
+ #:use-module (gnu packages gd)
+ #:use-module (gnu packages graph)
+ #:use-module (gnu packages graphics)
+ #:use-module (gnu packages guile)
#:use-module (gnu packages image)
#:use-module (gnu packages lisp)
+ #:use-module (gnu packages m4)
+ #:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages python)
- #:use-module (gnu packages python-xyz))
+ #:use-module (gnu packages python-science)
+ #:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages sqlite))
(define-public python-cypari2
@@ -493,3 +504,189 @@ (define-public sagemath-data-polytopes-db
(synopsis "Lists of 2- and 3-dimensional reflexive polytopes")
(description synopsis)
(license #f)))
+
+(define-public python-sagemath-standard
+ (package
+ (name "python-sagemath-standard")
+ (version "10.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/sagemath/sage";)
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "01nfpp3zh43kil7pqyrdvxyawmny0sc656kbg833c2l1y6iwppyc"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f ; tests are run in the `sagemath' package
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'prepare-build
+ (lambda _
+ (setenv "SAGE_NUM_THREADS"
+ (number->string (parallel-job-count)))
+ (setenv "SAGE_VENV" #$output)
+
+ (setenv "PYTHONPATH" (string-append (getcwd)
"/pkgs/sage-setup"))
+
+ ;; broken symlink we don't need
+ (delete-file "pkgs/sage-conf/bin/sage-env-config")
+ (delete-file "pkgs/sage-conf_pypi/sage_root/configure")
+
+ ;; Run this before 'ensure-no-mtimes-pre-1980 so that there
+ ;; are no broken symlinks
+ (with-directory-excursion "build/pkgs/sagelib"
+ (let
+ ((original-path (getenv "PATH")))
+ (setenv "PATH" (string-append original-path
":../../bin"))
+ (invoke "sh" "./bootstrap")
+ (setenv "PATH" original-path)))))
+ (add-before 'build 'cd-to-src
+ (lambda _
+ (chdir "pkgs/sagemath-standard")))
+ ;; `setuptools' replaces shebangs that match `#!.*python.*' by
+ ;; the intepreter running it. Unfortunately this also matches
+ ;; `sage-python'. But using `sage-python' prevents a weird bug
+ ;; where python's `multiprocessing.resource_tracker' would
+ ;; execute `sage-runtests' instead of `python'.
+ (add-after 'install 'fix-shebangs
+ (lambda _
+ (let*
+ ((bin (string-append #$output "/bin"))
+ (sage-python (string-append bin "/sage-python")))
+ (substitute* (find-files bin
+ ;; don't touch these to prevent
cycles
+ ;; sage-num-threads.py ->
sage-env -> sage
+ ;; sage-venv-config ->
sage-python -> sage
+ (negate
+ (file-name-predicate
(string-join '("^sage-coverage$"
+
"^sage-num-threads\\.py$"
+
"^sage-venv-config$")
+
"|"))))
+ ;; be careful that we don't substitute the newline
+ ;; character
+ (("^#!.*python-toolchain[^\n]*") (string-append "#!"
sage-python))))))
+ (add-after 'install 'remove-unnecessary-scripts
+ (lambda _
+ (for-each
+ delete-file
+ (find-files (string-append #$output "/bin")
"^sage-rebase"))))
+ (replace 'wrap
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let*
+ ((python-path (search-path-as-string->list (getenv
"GUIX_PYTHONPATH")))
+ (python (dirname (search-input-file inputs
"/bin/python3")))
+ (coreutils (dirname (search-input-file inputs
"/bin/readlink")))
+ (sed (dirname (search-input-file inputs "/bin/sed")))
+ (xdg-open (dirname (search-input-file inputs
"/bin/xdg-open")))
+ (maxima-version #$(package-version (this-package-input
"maxima")))
+ (maxima-fas (search-input-file inputs
+ (string-append
"/lib/maxima/"
+
maxima-version
+
"/binary-ecl/maxima.fas")))
+ (combinatorial-design (search-input-directory inputs
"/share/combinatorial_designs"))
+ (conway-polynomials (search-input-directory inputs
"/share/conway_polynomials"))
+ (ellcurve (search-input-directory inputs
"/share/ellcurves"))
+ (cremona-mini (search-input-directory inputs
"/share/cremona"))
+ (graphs (search-input-directory inputs
"/share/graphs"))
+ (polytope (search-input-directory inputs
"/share/reflexive_polytopes"))
+ (gap-lib (search-input-directory inputs "/lib/gap"))
+ (gap-share (search-input-directory inputs
"/share/gap")))
+ ;; wrap everything possible, all things with shebang
+ ;; #!*/sage-* are still covered, as sage-* itself will be
+ ;; wrapped
+ (for-each
+ (lambda (file)
+ (false-if-exception
+ (wrap-script file
+ `("GUIX_PYTHONPATH" = ,python-path)
+ `("PATH" prefix (,(string-append #$output "/bin")
,coreutils ,python ,sed ,xdg-open))
+ `("MAXIMA_FAS" = (,maxima-fas))
+ `("COMBINATORIAL_DESIGN_DATA_DIR" =
(,combinatorial-design))
+ `("CONWAY_POLYNOMIALS_DATA_DIR" =
(,conway-polynomials))
+ `("ELLCURVE_DATA_DIR" = (,ellcurve))
+ `("CREMONA_MINI_DATA_DIR" = (,cremona-mini))
+ `("GRAPHS_DATA_DIR" = (,graphs))
+ `("POLYTOPE_DATA_DIR" = (,polytope))
+ `("GAP_LIB_DIR" = (,gap-lib))
+ `("GAP_SHARE_DIR" = (,gap-share)))))
+ (find-files (string-append #$output "/bin")))))))))
+ (inputs (list arb
+ boost
+ brial
+ cliquer
+ coreutils
+ edge-addition-planarity-suite
+ gd
+ givaro
+ glpk
+ gmp
+ guile-3.0 ; for wrap-script
+ iml
+ libbraiding
+ libhomfly
+ linbox
+ m4ri
+ m4rie
+ mpc
+ mpfi
+ python-cypari2
+ python-gmpy2
+ python-jinja2
+ python-jupyter-core
+ python-memory-allocator
+ python-numpy
+ python-pplpy
+ rw
+ sagemath-data-combinatorial-designs
+ sagemath-data-conway-polynomials
+ sagemath-data-elliptic-curves
+ sagemath-data-graphs
+ sagemath-data-polytopes-db
+ sed
+ symmetrica
+ xdg-utils
+ zlib))
+ (native-inputs (list m4 pkg-config python-cython))
+ (propagated-inputs (list cddlib
+ ecl ; also buildtime
+ eclib ; also buildtime
+ flint ; also buildtime
+ gap ; also buildtime
+ gfan
+ giac ; also buildtime
+ gmp-ecm ; also buildtime
+ gsl ; also buildtime
+ lcalc ; also buildtime
+ maxima
+ mpfr
+ nauty
+ ntl ; also buildtime
+ openblas ; also buildtime
+ palp
+ pari-gp ; also buildtime
+ pkg-config ; also buildtime (native)
+ python-fpylll
+ python-ipython
+ python-ipywidgets
+ python-lrcalc
+ python-networkx
+ python-pkgconfig
+ python-primecountpy
+ python-scipy
+ python-sympy
+ singular ; also buildtime
+ sqlite
+ sympow
+ tachyon))
+ (home-page "https://www.sagemath.org";)
+ (synopsis "Python-based computer algebra system")
+ (description
+ "SageMath is a free open-source mathematics software system licensed
+under the GPL. It builds on top of many existing open-source packages: NumPy,
+SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their
+combined power through a common, Python-based language or directly via
+interfaces or wrappers.")
+ (license license:gpl3)))
--
2.40.1
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