GNU bug report logs - #75032
[PATCH 00/13] Add more SageMath packages

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 00/13] Add more SageMath packages
Date: Sun, 22 Dec 2024 17:25:21 +0000

Some of the patches have been rebased and updated from https://issues.guix.gnu.org/56729

Others have been chosen from https://doc.sagemath.org/html/en/reference/spkg/

After this series is merged, these will be the missing non-optional packages from the above page:

 - elliptic-curves
 - gnumake-tokenpool (v0.0.7+ needs Python 3.11+)
 - jmol
 - jupyter-jsmol
 - jupyter-lsp (depends on newer webcolors package)
 - jupyterlab (depends on newer webcolors package)
 - jupyterlab-mathjax2 (depends on jupyterlab)
 - pari-seadata-small
 - pplpy-doc
 - sage-conf
 - sage-docbuild
 - sage-setup
 - sagenb-export
 - sagetex
 - threejs

I think we can start to package sagelib after elliptic-curves and pari-seadata-small are packaged.

Vinicius Monego (6):
  gnu: Add sagemath-data-conway-polynomials.
  gnu: Add python-pytz-deprecation-shim.
  gnu: Add python-lrcalc.
  gnu: Add sympow.
  gnu: Add gfan.
  gnu: Add python-sphinx-inline-tabs.

vicvbcun (7):
  gnu: Add sagemath-data-polytopes-db.
  gnu: Add sagemath-data-graphs.
  gnu: Add sagemath-data-combinatorial-designs.
  gnu: Add palp.
  gnu: Add tachyon.
  gnu: pari-gp: Use G-Expressions.
  gnu: pari-gp: Install galdata.

 gnu/packages/algebra.scm  |  63 ++++++++++++++++++-----
 gnu/packages/graphics.scm |  59 +++++++++++++++++++++
 gnu/packages/maths.scm    | 105 +++++++++++++++++++++++++++++++++++++-
 gnu/packages/sagemath.scm |  95 ++++++++++++++++++++++++++++++++++
 gnu/packages/sphinx.scm   |  23 ++++++++-
 gnu/packages/time.scm     |  26 ++++++++++
 6 files changed, 356 insertions(+), 15 deletions(-)


base-commit: da94cd1ea69559a80d291c6a574b0f23e30c64f2
--
2.39.5

Message #8 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 01/13] gnu: Add sagemath-data-conway-polynomials.
Date: Sun, 22 Dec 2024 17:26:45 +0000

* gnu/packages/sagemath.scm (sagemath-data-conway-polynomials): New variable.

Change-Id: Ia3a087b19a0ade5d927422bd365283d209df0863
---
 gnu/packages/sagemath.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 008f54a5e7..734aabf739 100644
--- a/gnu/packages/sagemath.scm
+++ b/gnu/packages/sagemath.scm
@@ -381,3 +381,24 @@ (define-public zn-poly
 coefficients of which are modular integers.")
     (license (list license:gpl2 license:gpl3)) ; dual licensed
     (home-page "https://gitlab.com/sagemath/zn_poly")))
+
+(define-public sagemath-data-conway-polynomials
+  (package
+    (name "sagemath-data-conway-polynomials")
+    (version "0.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "conway_polynomials" version))
+       (sha256
+        (base32 "1wz03a08kwlswx1pcr5d99ppmhpfzs2a5i969rnb2ghsz1j9yqag"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-pytest python-setuptools python-wheel))
+    (home-page "https://github.com/sagemath/conway-polynomials")
+    (synopsis "Python interface to Frank Lübeck's Conway polynomial database")
+    (description "This package provides a Python interface to Frank Lübeck's
+Conway polynomial database.  These are used in several computer algebra
+systems such as GAP and SageMath to provide quick access to those Conway
+polynomials.  The aim of this package is to make them available through a
+generic Python interface.")
+    (license license:gpl3+)))
-- 
2.39.5

Message #11 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: vicvbcun <guix <at> ikherbers.com>
Subject: [PATCH 02/13] gnu: Add sagemath-data-polytopes-db.
Date: Sun, 22 Dec 2024 17:26:46 +0000

From: vicvbcun <guix <at> ikherbers.com>

* gnu/packages/sagemath.scm (sagemath-data-polytopes-db): New variable.

Change-Id: I8dd6cbd0b71a01d817486882bec8f126dece7e36
Co-authored by: Vinicius Monego <monego <at> posteo.net>

Change-Id: Iada71a7939e5deadf6888af6c21621e5458622d1
---
 gnu/packages/sagemath.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 734aabf739..1fefb26e36 100644
--- a/gnu/packages/sagemath.scm
+++ b/gnu/packages/sagemath.scm
@@ -23,6 +23,7 @@
 
 (define-module (gnu packages sagemath)
   #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
@@ -402,3 +403,25 @@ (define-public sagemath-data-conway-polynomials
 polynomials.  The aim of this package is to make them available through a
 generic Python interface.")
     (license license:gpl3+)))
+
+(define-public sagemath-data-polytopes-db
+  (package
+    (name "sagemath-data-polytopes-db")
+    (version "20170220")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://mirrors.mit.edu/sage/spkg/upstream/polytopes_db"
+                    "/polytopes_db-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "1q0cd811ilhax4dsj9y5p7z8prlalqr7k9mzq178c03frbgqny6b"))))
+    (build-system copy-build-system)
+    (arguments '(#:install-plan '(("." "share/reflexive_polytopes"))))
+    (home-page "https://www.sagemath.org")
+    (synopsis "Lists of 2- and 3-dimensional reflexive polytopes")
+    (description
+     "This package contains data for 2- and 3-dimensional reflexive polytopes
+to be used by SageMath.")
+    ;; Debian says GPLv2+.
+    (license license:gpl2+)))
-- 
2.39.5

Message #14 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: vicvbcun <guix <at> ikherbers.com>
Subject: [PATCH 03/13] gnu: Add sagemath-data-graphs.
Date: Sun, 22 Dec 2024 17:26:47 +0000

From: vicvbcun <guix <at> ikherbers.com>

* gnu/packages/sagemath.scm (sagemath-data-graphs): New variable.

Change-Id: I7c537aac21f43a8712fd6d542551f78c3ebaec68
Co-authored by: Vinicius Monego <monego <at> posteo.net>

Change-Id: I88f35ccf94cfe0d866ef57cb893844c8285d5138
---
 gnu/packages/sagemath.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 1fefb26e36..514af19da8 100644
--- a/gnu/packages/sagemath.scm
+++ b/gnu/packages/sagemath.scm
@@ -425,3 +425,27 @@ (define-public sagemath-data-polytopes-db
 to be used by SageMath.")
     ;; Debian says GPLv2+.
     (license license:gpl2+)))
+
+(define-public sagemath-data-graphs
+  (package
+    (name "sagemath-data-graphs")
+    (version "20210214")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://mirrors.mit.edu/sage/spkg/upstream/"
+                    "graphs/graphs-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "0h9p5wrxips51x6vpfiiaqzp9j004nwppzc9qc2iaqakk06pq8q7"))))
+    (build-system copy-build-system)
+    (arguments
+     '(#:install-plan '(("." "share/graphs"))))
+    (home-page "https://www.sagemath.org")
+    (synopsis "Database of graphs")
+    (description
+     "This package contains databases of graphs.  It also includes the
+@acronym{ISGCI, Information System on Graph Classes and their Inclusions}
+database.")
+    ;; Debian says GPLv2+.
+    (license license:gpl2+)))
-- 
2.39.5

Message #17 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: vicvbcun <guix <at> ikherbers.com>
Subject: [PATCH 04/13] gnu: Add sagemath-data-combinatorial-designs.
Date: Sun, 22 Dec 2024 17:26:48 +0000

From: vicvbcun <guix <at> ikherbers.com>

* gnu/packages/sagemath.scm (sagemath-data-combinatorial-designs): New
variable.

Change-Id: Ib1ad3675256be1958427cd37a76bb5bdbf16fd12
Co-authored by: Vinicius Monego <monego <at> posteo.net>

Change-Id: I758e22fabcc11ca0583ab899acc0c653a35c7f43
---
 gnu/packages/sagemath.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 514af19da8..d1cba8dcdb 100644
--- a/gnu/packages/sagemath.scm
+++ b/gnu/packages/sagemath.scm
@@ -449,3 +449,30 @@ (define-public sagemath-data-graphs
 database.")
     ;; Debian says GPLv2+.
     (license license:gpl2+)))
+
+(define-public sagemath-data-combinatorial-designs
+  (package
+    (name "sagemath-data-combinatorial-designs")
+    (version "20140630")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://mirrors.mit.edu/sage/spkg/upstream/"
+                    "combinatorial_designs/combinatorial_designs-"
+                    version ".tar.bz2"))
+              (sha256
+               (base32
+                "0bj8ngiq59hipa6izi6g5ph5akmy4cbk0vlsb0wa67f7grnnqj69"))))
+    (build-system copy-build-system)
+    (arguments
+     '(#:install-plan '(("." "share/combinatorial_designs/"))))
+    (home-page "https://www.sagemath.org")
+    (synopsis "Data for Combinatorial Designs")
+    (description
+     "This package data for combinatorial designs.  It currently contains:
+
+@itemize
+@item The table of @acronym{MOLS, Mutually orthogonal Latin squares} from the
+Handbook of Combinatorial Designs, 2ed.
+@end itemize")
+    (license license:public-domain)))
-- 
2.39.5

Message #20 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 05/13] gnu: Add python-pytz-deprecation-shim.
Date: Sun, 22 Dec 2024 17:26:49 +0000

* gnu/packages/time.scm (python-pytz-deprecation-shim): New variable.

Change-Id: I481ea9818444d9a14efcf7b11d44c68a5f2fec3f
---
 gnu/packages/time.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm
index f1aeae7340..0d84dee178 100644
--- a/gnu/packages/time.scm
+++ b/gnu/packages/time.scm
@@ -25,6 +25,7 @@
 ;;; Copyright © 2024 Liliana Marie Prikler <liliana.prikler <at> gmail.com>
 ;;; Copyright © 2024 Sharlatan Hellseher <sharlatanus <at> gmail.com>
 ;;; Copyright © 2024 Zheng Junjie <873216071 <at> qq.com>
+;;; Copyright © 2024 Vinicius Monego <monego <at> posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -169,6 +170,31 @@ (define-public python-tzdata
     (description "This package provides a thin Python wrapper around tzdata.")
     (license asl2.0)))
 
+(define-public python-pytz-deprecation-shim
+  (package
+    (name "python-pytz-deprecation-shim")
+    (version "0.1.0.post0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytz_deprecation_shim" version))
+       (sha256
+        (base32 "17d58msbi18dc4lk29hcrgylvrv9vhniwi24axfdwvb13fp7n2dg"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-dateutil python-tzdata))
+    (native-inputs (list python-pytest
+                         python-pytz
+                         python-setuptools
+                         python-wheel))
+    (home-page "https://github.com/pganssle/pytz-deprecation-shim")
+    (synopsis "Shims to make deprecation of pytz easier")
+    (description
+     "This package aims to make the transition away from @code{pytz} easier.
+It is intended for temporary usage only, and should allow you to drop your
+dependency on @code{pytz} while also giving your users notice that eventually
+you will remove support for the pytz-specific interface.")
+    (license asl2.0)))
+
 (define-public python-pytz
   (package
     (name "python-pytz")
-- 
2.39.5

Message #23 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 07/13] gnu: Add sympow.
Date: Sun, 22 Dec 2024 17:26:51 +0000

* gnu/packages/maths.scm (sympow): New variable.

Change-Id: Iaeaea352f0a3a65a877b2845ecdc18856ded6d3c
---
 gnu/packages/maths.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index f3265423b4..1ca0144bfd 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -158,6 +158,7 @@ (define-module (gnu packages maths)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages m4)
+  #:use-module (gnu packages man)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
@@ -898,6 +899,40 @@ (define-public 4ti2
 integer programming problems and computes Markov bases for statistics.")
     (license license:gpl2+)))
 
+(define-public sympow
+  (package
+    (name "sympow")
+    (version "2.023.7")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+         (url "https://gitlab.com/rezozer/forks/sympow")
+         (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0ilnxygkj4g5arjiyd16k00cvnjlqs0cpc8hk64kbqhl877mm5i9"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:tests? #f ; no tests
+           #:phases #~(modify-phases %standard-phases
+                        (replace 'configure
+                          (lambda* (#:key inputs #:allow-other-keys)
+                            (substitute* "Configure"
+                              (("/bin/sh") (search-input-file inputs "/bin/bash")))
+                            (setenv "PREFIX" #$output)
+                            (setenv "VARPREFIX" #$output)
+                            (invoke "bash" "./Configure"))))))
+    (native-inputs (list bash-minimal coreutils help2man pari-gp which))
+    (home-page "https://gitlab.com/rezozer/forks/sympow")
+    (synopsis "Symmetric power elliptic curve L-functions")
+    (description "SYMPOW is a mathematical program to compute special values
+of symmetric power elliptic curve L-functions; it can compute up to about 64
+digits of precision.")
+    (license (license:non-copyleft "file://COPYING"
+                                   "See COPYING in the distribution."))))
+
 (define-public cddlib
   (package
     (name "cddlib")
-- 
2.39.5

Message #26 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 06/13] gnu: Add python-lrcalc.
Date: Sun, 22 Dec 2024 17:26:50 +0000

* gnu/packages/algebra.scm (python-lrcalc): New variable.

Change-Id: Id174ecfa092786ca16fbde2be68e12af0b2d9af3
---
 gnu/packages/algebra.scm | 28 ++++++++++++++++++++++++++--
 1 file changed, 26 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 3f73d9295d..4d7b4001cd 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -59,6 +59,7 @@ (define-module (gnu packages algebra)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages ruby)
@@ -72,6 +73,7 @@ (define-module (gnu packages algebra)
   #:use-module (guix build-system ant)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix build-system r)
   #:use-module (guix download)
@@ -1623,6 +1625,28 @@ (define-public lrcalc
     (license license:gpl2+)
     (home-page "https://sites.math.rutgers.edu/~asbuch/lrcalc/")))
 
+(define-public python-lrcalc
+  (package
+    (name "python-lrcalc")
+    (version "2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "lrcalc" version))
+       (sha256
+        (base32 "1adassfjalsdsngy01c37835qsx3gj0jx9cinc9b91x4xnd51873"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f)) ; there are no tests
+    (native-inputs (list python-cython python-setuptools python-wheel))
+    (inputs (list lrcalc))
+    (home-page "https://math.rutgers.edu/~asbuch/lrcalc")
+    (synopsis "Python bindings for the Littlewood-Richardson Calculator")
+    (description
+     "This package provides Python bindings for the Littlewood-Richardson
+Calculator.")
+    (license license:gpl3+)))
+
 (define-public iml
   (package
     (name "iml")
@@ -1638,8 +1662,8 @@ (define-public iml
     (build-system gnu-build-system)
     (inputs
      `(("gmp" ,gmp)
-       ("cblas" ,openblas))) ; or any other BLAS library; the documentation
-                             ; mentions ATLAS in particular
+       ("cblas" ,openblas)))    ; or any other BLAS library; the documentation
+                                        ; mentions ATLAS in particular
     (arguments
      `(#:configure-flags
        (list
-- 
2.39.5

Message #29 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 08/13] gnu: Add gfan.
Date: Sun, 22 Dec 2024 17:26:52 +0000

* gnu/packages/maths.scm (gfan): New variable.

Change-Id: I3b4952ddfcaecac17ab29bb3cd2f56fc125ab763
---
 gnu/packages/maths.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 1ca0144bfd..35de236ba2 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -871,6 +871,41 @@ (define-public linasm
 and much more.")
     (license license:lgpl3+)))
 
+(define-public gfan
+  (package
+    (name "gfan")
+    (version "0.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://users-math.au.dk/jensen/software"
+                           "/gfan/gfan" version ".tar.gz"))
+       (sha256
+        (base32 "17lqripnsdb5hn7nnhgn4siajgh1jh9nkaplca3akm74w5bkg0xb"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:make-flags #~(list (string-append "PREFIX=" #$output)
+                           (string-append "CC=" #$(cc-for-target))
+                           (string-append "CXX=" #$(cxx-for-target)))
+      #:phases #~(modify-phases %standard-phases
+                   (delete 'configure)
+                   ;; cddlib is distributed with the 'cddlib' header name,
+                   ;; but gfan expects it to be named 'cdd'.  Substitute
+                   ;; the include headers to make gfan find it.
+                   (add-after 'unpack 'fix-cdd-reference
+                     (lambda _
+                       (substitute* '("src/lp_cdd.cpp"
+                                      "src/gfanlib_zcone.cpp"
+                                      "src/app_librarytest.cpp")
+                         (("#include \"cdd") "#include \"cddlib")))))))
+    (inputs (list cddlib gmp))
+    (home-page "https://users-math.au.dk/jensen/software/gfan/gfan.html")
+    (synopsis "Compute Gröbner fans and tropical varieties")
+    (description "Gfan is a software package for computing Gröbner fans and
+tropical varieties.")
+    (license license:gpl2)))
+
 (define-public 4ti2
   (package
     (name "4ti2")
-- 
2.39.5

Message #32 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: vicvbcun <guix <at> ikherbers.com>
Subject: [PATCH 09/13] gnu: Add palp.
Date: Sun, 22 Dec 2024 17:26:53 +0000

From: vicvbcun <guix <at> ikherbers.com>

* gnu/packages/maths.scm (palp): New variable.

Change-Id: I37ee870858fef505999dfdc02d1955673366d718
Co-authored by: Vinicius Monego <monego <at> posteo.net>

Change-Id: I853cbccca5c34355d9df74a3cbbd5f818a21ebb5
---
 gnu/packages/maths.scm | 35 +++++++++++++++++++++++++++++++++--
 1 file changed, 33 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 35de236ba2..e89c17a2c0 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5573,6 +5573,37 @@ (define-public libblastrampoline
 library.")
     (license license:expat)))
 
+(define-public palp
+  (package
+    (name "palp")
+    (version "2.21")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/palp-"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "1myxjv0jxgr9acchwnjh9g5l61wxwiva3q6c1d6892lr37r7njky"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:make-flags #~(list (string-append "CC=" #$(cc-for-target)))
+           #:tests? #f ; no tests
+           #:phases #~(modify-phases %standard-phases
+                        (delete 'configure)
+                        (replace 'install
+                          (lambda _
+                            (for-each
+                             (lambda (name)
+                               (install-file name (string-append #$output "/bin")))
+                             '("class.x" "cws.x" "mori.x" "nef.x" "poly.x")))))))
+    (home-page "http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html")
+    (synopsis "Package for Analyzing Lattice Polytopes")
+    (description
+     "PALP is a set of programs for calculations with lattice polytopes and
+applications to toric geometry.")
+    (license license:gpl3)))
+
 (define-public blis
   (package
     (name "blis")
@@ -5600,9 +5631,9 @@ (define-public blis
       #~(modify-phases %standard-phases
           (replace 'configure
             (lambda* (#:key outputs target system (configure-flags '())
-                      #:allow-other-keys)
+                            #:allow-other-keys)
               ;; This is a home-made 'configure' script.
-              (let* (;; Guix-specific support for choosing the configuration
+              (let* ( ;; Guix-specific support for choosing the configuration
                      ;; via #:configure-flags: see below for details.
                      (config-flag-prefix "--blis-config=")
                      (maybe-config-flag (find
-- 
2.39.5

Message #35 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: vicvbcun <guix <at> ikherbers.com>
Subject: [PATCH 10/13] gnu: Add tachyon.
Date: Sun, 22 Dec 2024 17:26:54 +0000

From: vicvbcun <guix <at> ikherbers.com>

* gnu/packages/graphics.scm (tachyon): New variable.

Change-Id: I57780c08c6b496e40459789d693b9b24fb4a9da8
Co-authored by: Vinicius Monego <monego <at> posteo.net>

Change-Id: I5914afad8d293787b9898a229084e6c79fbe8911
---
 gnu/packages/graphics.scm | 59 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm
index f17511dc94..a0c22bfa35 100644
--- a/gnu/packages/graphics.scm
+++ b/gnu/packages/graphics.scm
@@ -789,6 +789,65 @@ (define-public openshadinglanguage
 materials, lights, displacement, and pattern generation.")
     (license license:bsd-3)))
 
+(define-public tachyon
+  (package
+    (name "tachyon")
+    (version "0.99.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://jedi.ks.uiuc.edu/~johns/raytracer/files/"
+                    version "/tachyon-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1xd6h5d4v6dsnm6w46bdcr15fwkcz44p8dncymfry50i4c83q809"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:tests? #f                  ; no tests
+           #:make-flags #~(list "linux-thr")
+           #:phases
+           #~(modify-phases %standard-phases
+               (delete 'configure)
+               (add-after 'unpack 'prepare-src
+                 (lambda _
+                   (substitute* "unix/Make-arch"
+                     (("CC = cc")
+                      (string-append "CC = " #$(cc-for-target))))
+                   (chdir "unix")))
+               (add-before 'build 'enable-png-jpeg-support
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   (substitute* "Make-config"
+                     (("USEJPEG=")
+                      "USEJPEG = -DUSEJPEG")
+                     (("JPEGLIB=")
+                      "JPEGLIB = -ljpeg")
+                     (("USEPNG=")
+                      "USEPNG = -DUSEPNG")
+                     (("PNGLIB=")
+                      "PNGLIB = -lpng -lz"))))
+               (add-before 'build 'fix-paths
+                 (lambda* (#:key inputs #:allow-other-keys)
+                   (substitute* "Make-config"
+                     (("SHELL=/bin/sh")
+                      (string-append "SHELL=" (which "sh"))))))
+               (replace 'install
+                 (lambda _
+                   (install-file "../compile/linux-thr/tachyon"
+                                 (string-append #$output "/bin"))
+                   (install-file "../compile/linux-thr/libtachyon.a"
+                                 (string-append #$output "/lib")))))))
+    (inputs (list libjpeg-turbo libpng))
+    ;; The server does not seem to be reliably accessible
+    (home-page "http://jedi.ks.uiuc.edu/~johns/raytracer/")
+    (synopsis "Multithreaded ray tracing software")
+    (description
+     "This package contains the Tachyon raytracer.  It supports the typical
+ray tracer features, most of the common geometric primitives, shading and
+texturing modes, etc.  It also supports less common features such as HDR image
+output, ambient occlusion lighting, and support for various triangle mesh and
+volumetric texture formats beneficial for molecular visualization.")
+    (license license:bsd-3)))
+
 (define-public cgal
   (package
     (name "cgal")
-- 
2.39.5

Message #38 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: vicvbcun <guix <at> ikherbers.com>
Subject: [PATCH 11/13] gnu: pari-gp: Use G-Expressions.
Date: Sun, 22 Dec 2024 17:26:55 +0000

From: vicvbcun <guix <at> ikherbers.com>

* gnu/packages/algebra.scm (pari-gp)[arguments]: Use G-Expressions.  Unset
make-flags.

Change-Id: Id2be46acd67b474d6fdb8935070ffb243e87f920
Co-authored by: Vinicius Monego <monego <at> posteo.net>

Change-Id: I7be07998e9e2d1fe9194d4af6a57537467f5e097
---
 gnu/packages/algebra.scm | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 4d7b4001cd..32834f1c15 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -245,16 +245,15 @@ (define-public pari-gp
     (native-inputs (list (texlive-updmap.cfg)))
     (inputs (list gmp libx11 perl readline))
     (arguments
-     '(#:make-flags '("all")
-       #:test-target "dobench"
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'configure
-           (lambda* (#:key outputs #:allow-other-keys)
-             (invoke "./Configure"
-                     "--mt=pthread"
-                     (string-append "--prefix="
-                                    (assoc-ref outputs "out"))))))))
+     (list
+      #:test-target "dobench"
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'configure
+            (lambda _
+              (invoke "./Configure"
+                      "--mt=pthread"
+                      (string-append "--prefix=" #$output)))))))
     (synopsis "PARI/GP, a computer algebra system for number theory")
     (description
      "PARI/GP is a widely used computer algebra system designed for fast
-- 
2.39.5

Message #41 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: vicvbcun <guix <at> ikherbers.com>
Subject: [PATCH 12/13] gnu: pari-gp: Install galdata.
Date: Sun, 22 Dec 2024 17:26:56 +0000

From: vicvbcun <guix <at> ikherbers.com>

* gnu/packages/algebra.scm (pari-galdata): New variable.
(pari-gp)[arguments]<#:phases>: Add phase "install-galdata".

Change-Id: Iaec77b0ab60d8ff59c8a36e7e0a7878b58742751
Co-authored by: Vinicius Monego <monego <at> posteo.net>

Change-Id: Id74aa6ce315df48a2d917baf1a436ba54b1b5185
---
 gnu/packages/algebra.scm | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 32834f1c15..5da77b6318 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -229,6 +229,16 @@ (define-public python-fpylll
     (description "fpylll is a Python wrapper for fplll.")
     (license license:gpl2+)))
 
+(define pari-galdata
+  ;; version from 2008-04-12
+  (origin
+    (method url-fetch)
+    ;; no versioning, old files seem to be moved to `old/...' on update
+    (uri "https://pari.math.u-bordeaux.fr/pub/pari/packages/galdata.tgz")
+    (sha256
+     (base32
+      "1pch6bk76f1i6cwwgm7hhxi5h71m52lqayp4mnyj0jmjk406bhdp"))))
+
 (define-public pari-gp
   (package
     (name "pari-gp")
@@ -253,7 +263,13 @@ (define-public pari-gp
             (lambda _
               (invoke "./Configure"
                       "--mt=pthread"
-                      (string-append "--prefix=" #$output)))))))
+                      (string-append "--prefix=" #$output))))
+          (add-after 'install 'install-galdata
+            (lambda _
+              (invoke "tar" "-xvf" #$pari-galdata)
+              (copy-recursively "data/" (string-append
+                                         #$output
+                                         "/share/pari")))))))
     (synopsis "PARI/GP, a computer algebra system for number theory")
     (description
      "PARI/GP is a widely used computer algebra system designed for fast
-- 
2.39.5

Message #44 received at 75032 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 75032 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 13/13] gnu: Add python-sphinx-inline-tabs.
Date: Sun, 22 Dec 2024 17:26:57 +0000

* gnu/packages/sphinx.scm (python-sphinx-inline-tabs): New variable.

Change-Id: I92516cdc404cdcaee74cb8cf19f255c049c43021
---
 gnu/packages/sphinx.scm | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 72f1513f34..f7f3286b7b 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -15,7 +15,7 @@
 ;;; Copyright © 2019 Brett Gilio <brettg <at> gnu.org>
 ;;; Copyright © 2020 Giacomo Leidi <goodoldpaul <at> autistici.org>
 ;;; Copyright © 2021 Eric Bavier <bavier <at> posteo.net>
-;;; Copyright © 2021, 2022 Vinicius Monego <monego <at> posteo.net>
+;;; Copyright © 2021, 2022, 2024 Vinicius Monego <monego <at> posteo.net>
 ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte <at> inria.fr>
 ;;; Copyright © 2021, 2022, 2024 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
 ;;; Copyright © 2024 Troy Figiel <troy <at> troyfigiel.com>
@@ -519,6 +519,27 @@ (define-public python-sphinxcontrib-newsfeed
     (home-page "https://bitbucket.org/prometheus/sphinxcontrib-newsfeed")
     (license license:bsd-2)))
 
+(define-public python-sphinx-inline-tabs
+  (package
+    (name "python-sphinx-inline-tabs")
+    (version "2023.4.21")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "sphinx_inline_tabs" version))
+       (sha256
+        (base32 "1g5yhdk208i8maippnbnijd1knpai809wl3cbwzqy59cc0zz3wjx"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f)) ; no tests in the release, only in the main branch
+    (native-inputs (list python-flit-core
+                         python-sphinx))
+    (home-page "https://github.com/pradyunsg/sphinx-inline-tabs")
+    (synopsis "Add inline tabbed content to your Sphinx documentation")
+    (description "This package provides a Sphinx plugin to add inline tabbed
+content to your Sphinx documentation.")
+    (license license:expat)))
+
 (define-public python-sphinx-issues
   (package
     (name "python-sphinx-issues")
-- 
2.39.5

Message #49 received at 75032-done <at> debbugs.gnu.org (full text, mbox):

From: dannym <at> friendly-machines.com
To: 75032-done <at> debbugs.gnu.org
Subject: merged sagemath dependencies
Date: Wed, 01 Jan 2025 13:16:33 +0100

Hi,

I've merged those sagemath dependencies, through guix commit 
07a352738ad36ba152bd485975a3c90b43e9c2f5.

I have the following notes:

- pari-gp is not and was not reproducible (because dvi)
- compilation of palp-2.21 gives a lot of scary warnings
- sagemath-data-polytopes-db: We could maybe use PALP to generate those.
- sagemath-data-graphs: It's a research summary.
- sagemath-data-combinatorial-designs: Use Handbook of Combinatorial 
Designs, 2ed to generate those?! [latin squares]
- pari-galdata: Not sure whether those can be autogenerated.

Cheers,
   Danny

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