01/01: gnu: Add python-flint.

[guix-commits]

andreas pushed a commit to branch master
in repository guix.

commit 1d6589db81c7c390e04795805e684b01f5a0c45f
Author: Andreas Enge <address@hidden>
Date:   Tue Mar 19 10:44:15 2019 +0100

    gnu: Add python-flint.
    
    * gnu/packages/algebra.scm (python-flint): New variable.
    * gnu/packages/patches/python-flint-includes.patch: New file.
    * gnu/local.mk (dist_patch_DATA): Register the patch.
---
 gnu/local.mk                                     |   1 +
 gnu/packages/algebra.scm                         |  34 ++++++
 gnu/packages/patches/python-flint-includes.patch | 131 +++++++++++++++++++++++
 3 files changed, 166 insertions(+)

diff --git a/gnu/local.mk b/gnu/local.mk
index 0a7e9bb..87bed6e 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1176,6 +1176,7 @@ dist_patch_DATA =                                         
\
   %D%/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch \
   %D%/packages/patches/python-configobj-setuptools.patch       \
   %D%/packages/patches/python-faker-fix-build-32bit.patch      \
+  %D%/packages/patches/python-flint-includes.patch             \
   %D%/packages/patches/python-mox3-python3.6-compat.patch      \
   %D%/packages/patches/python-testtools.patch                  \
   %D%/packages/patches/python-paste-remove-timing-test.patch   \
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 2849a56..e272cd9 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -43,6 +43,7 @@
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages shells)
   #:use-module (gnu packages tex)
@@ -52,6 +53,7 @@
   #:use-module (guix build-system ant)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system python)
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
@@ -421,6 +423,38 @@ real and complex numbers, with automatic, rigorous error 
control.")
     (license license:lgpl2.1+)
     (home-page "http://fredrikj.net/arb/";)))
 
+(define-public python-flint
+  (package
+    (name "python-flint")
+    (version "0.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url 
"https://github.com/fredrik-johansson/python-flint.git";)
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
+              (patches (search-patches "python-flint-includes.patch"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-cython" ,python-cython)))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)))
+    (inputs
+     `(("arb" ,arb)
+       ("flint" ,flint)))
+    (synopsis "Python module wrapping ARB and FLINT")
+    (description
+     "Python-flint is a Python extension module wrapping FLINT
+(Fast Library for Number Theory) and Arb (arbitrary-precision ball
+arithmetic).  It supports integers, rationals, modular integers,
+real and complex ball arithmetic, polynomials and matrices over all
+these types and other mathematical functions.")
+    (license license:expat)
+    (home-page "http://fredrikj.net/python-flint/";)))
+
 (define-public ntl
   (package
    (name "ntl")
diff --git a/gnu/packages/patches/python-flint-includes.patch 
b/gnu/packages/patches/python-flint-includes.patch
new file mode 100644
index 0000000..c0cfe94
--- /dev/null
+++ b/gnu/packages/patches/python-flint-includes.patch
@@ -0,0 +1,131 @@
+The following patch, authored by Andreas Enge, looks for the flint include
+files in the correct subdirectory.
+
+diff -u -r python-flint-old/src/flint.pxd python-flint-new/src/flint.pxd
+--- python-flint-old/src/flint.pxd     2019-03-19 10:26:11.055748626 +0100
++++ python-flint-new/src/flint.pxd     2019-03-19 10:35:23.269341203 +0100
+@@ -27,7 +27,7 @@
+ 
+ ctypedef long fmpz_struct
+ 
+-cdef extern from "flint.h":
++cdef extern from "flint/flint.h":
+     ctypedef void * flint_rand_t
+     void flint_randinit(flint_rand_t state)
+     void flint_randclear(flint_rand_t state)
+@@ -35,7 +35,7 @@
+     long flint_get_num_threads()
+     void flint_cleanup()
+ 
+-cdef extern from "nmod_vec.h":
++cdef extern from "flint/nmod_vec.h":
+     ctypedef struct nmod_t:
+        mp_limb_t n
+        mp_limb_t ninv
+@@ -47,7 +47,7 @@
+     mp_limb_t nmod_mul(mp_limb_t a, mp_limb_t b, nmod_t mod)
+     mp_limb_t nmod_div(mp_limb_t a, mp_limb_t b, nmod_t mod)
+ 
+-cdef extern from "nmod_poly.h":
++cdef extern from "flint/nmod_poly.h":
+     ctypedef struct nmod_poly_struct:
+         mp_ptr coeffs
+         long alloc
+@@ -129,7 +129,7 @@
+     void nmod_poly_factor_init(nmod_poly_factor_t fac)
+     void nmod_poly_factor_clear(nmod_poly_factor_t fac)
+ 
+-cdef extern from "nmod_mat.h":
++cdef extern from "flint/nmod_mat.h":
+     ctypedef struct nmod_mat_struct:
+         mp_limb_t * entries
+         long r
+@@ -178,7 +178,7 @@
+     long nmod_mat_rref(nmod_mat_t A)
+     long nmod_mat_nullspace(nmod_mat_t X, nmod_mat_t A)
+ 
+-cdef extern from "fmpz.h":
++cdef extern from "flint/fmpz.h":
+     ctypedef fmpz_struct fmpz_t[1]
+     int COEFF_IS_MPZ(fmpz_struct v)
+     void fmpz_init(fmpz_t op)
+@@ -268,7 +268,7 @@
+     void fmpz_rfac_uiui(fmpz_t r, ulong x, ulong n)
+     void fmpz_primorial(fmpz_t res, ulong n)
+ 
+-cdef extern from "fmpz_factor.h":
++cdef extern from "flint/fmpz_factor.h":
+     ctypedef struct fmpz_factor_struct:
+         int sign
+         fmpz_struct * p
+@@ -280,7 +280,7 @@
+     void fmpz_factor_clear(fmpz_factor_t factor)
+     void fmpz_factor(fmpz_factor_t factor, fmpz_t n)
+ 
+-cdef extern from "fmpz_poly.h":
++cdef extern from "flint/fmpz_poly.h":
+     ctypedef struct fmpz_poly_struct:
+         fmpz_struct * coeffs
+         long alloc
+@@ -390,14 +390,14 @@
+     void fmpz_poly_cos_minpoly(fmpz_poly_t, ulong)
+     void fmpz_poly_swinnerton_dyer(fmpz_poly_t, ulong)
+ 
+-cdef extern from "fmpz_poly_factor.h":
++cdef extern from "flint/fmpz_poly_factor.h":
+     void fmpz_poly_factor_init(fmpz_poly_factor_t fac)
+     void fmpz_poly_factor_clear(fmpz_poly_factor_t fac)
+     void fmpz_poly_factor_zassenhaus(fmpz_poly_factor_t fac, fmpz_poly_t G)
+     void fmpz_poly_factor(fmpz_poly_factor_t fac, fmpz_poly_t G)
+     void fmpz_poly_factor_squarefree(fmpz_poly_factor_t fac, fmpz_poly_t G)
+ 
+-cdef extern from "fmpz_mat.h":
++cdef extern from "flint/fmpz_mat.h":
+     ctypedef struct fmpz_mat_struct:
+         fmpz_struct * entries
+         long r
+@@ -448,7 +448,7 @@
+     void fmpz_mat_snf(fmpz_mat_t S, const fmpz_mat_t A)
+     int fmpz_mat_is_in_snf(const fmpz_mat_t A)
+ 
+-cdef extern from "fmpz_lll.h":
++cdef extern from "flint/fmpz_lll.h":
+     ctypedef struct fmpz_lll_struct:
+         double delta
+         double eta
+@@ -461,7 +461,7 @@
+     void fmpz_lll(fmpz_mat_t B, fmpz_mat_t U, const fmpz_lll_t fl)
+ 
+ 
+-cdef extern from "fmpq.h":
++cdef extern from "flint/fmpq.h":
+     ctypedef struct fmpq_struct:
+         fmpz_struct num
+         fmpz_struct den
+@@ -506,7 +506,7 @@
+     void fmpq_next_signed_minimal(fmpq_t res, fmpq_t x)
+     void fmpq_harmonic_ui(fmpq_t res, ulong n)
+ 
+-cdef extern from "fmpq_poly.h":
++cdef extern from "flint/fmpq_poly.h":
+     ctypedef struct fmpq_poly_struct:
+         fmpz_struct * coeffs
+         fmpz_t den
+@@ -620,7 +620,7 @@
+     void fmpq_poly_compose_series(fmpq_poly_t res, fmpq_poly_t poly1, 
fmpq_poly_t poly2, long n)
+     void fmpq_poly_revert_series(fmpq_poly_t res, fmpq_poly_t poly1, long n)
+ 
+-cdef extern from "fmpq_mat.h":
++cdef extern from "flint/fmpq_mat.h":
+     ctypedef struct fmpq_mat_struct:
+         fmpq_struct * entries
+         long r
+@@ -672,7 +672,7 @@
+     long fmpq_mat_rref(fmpq_mat_t B, fmpq_mat_t A)
+     void fmpq_mat_transpose(fmpq_mat_t B, fmpq_mat_t A)
+ 
+-cdef extern from "arith.h":
++cdef extern from "flint/arith.h":
+     void arith_number_of_partitions(fmpz_t res, ulong n)
+     int arith_moebius_mu(fmpz_t n)
+     void arith_divisor_sigma(fmpz_t v, fmpz_t n, ulong k)