Subject: [PATCH 4/5] gnu: python-flint: Update to 0.5.0 and build with flint@3.

From: Andreas Enge <[email-masked]>
Date: Thu, 25 Jan 2024 14:58:05 +0100

* gnu/packages/patches/python-flint-includes.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Unregister file.
* gnu/packages/algebra.scm (python-flint): Update to 0.5.0.
[source]: Drop patch.
[inputs]: Drop arb.
[native-inputs]: Use python-cython-3.

Change-Id: I5fa9b201efff76e16f957aee0ebcd453ea823e69
---
 gnu/local.mk                                  |   1 -
 gnu/packages/algebra.scm                      |   9 +-
 .../patches/python-flint-includes.patch       | 131 ------------------
 3 files changed, 4 insertions(+), 137 deletions(-)
 delete mode 100644 gnu/packages/patches/python-flint-includes.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 9eac0cae1a..ab63bd5881 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1910,7 +1910,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-piexif-fix-tests-with-pillow-7.2.patch	\
   %D%/packages/patches/python-pillow-CVE-2022-45199.patch	\
   %D%/packages/patches/python-pyfakefs-remove-bad-test.patch	\
-  %D%/packages/patches/python-flint-includes.patch		\
   %D%/packages/patches/python-libxml2-utf8.patch		\
   %D%/packages/patches/python-memcached-syntax-warnings.patch	\
   %D%/packages/patches/python-mox3-python3.6-compat.patch	\
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 43047a9b32..5fd8d0f106 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -494,7 +494,7 @@ (define-public arb
 (define-public python-flint
   (package
     (name "python-flint")
-    (version "0.3.0")
+    (version "0.5.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -503,15 +503,14 @@ (define-public python-flint
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
-              (patches (search-patches "python-flint-includes.patch"))))
+                "10370kqik6q6vdqrqv3gbznsyaxbgqb3rbrff4alpw0sqr5s07c7"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-cython))
+     (list python-cython-3))
     (propagated-inputs
      (list python-numpy))
     (inputs
-     (list arb flint))
+     (list flint))
     (synopsis "Python module wrapping ARB and FLINT")
     (description
      "Python-flint is a Python extension module wrapping FLINT
diff --git a/gnu/packages/patches/python-flint-includes.patch b/gnu/packages/patches/python-flint-includes.patch
deleted file mode 100644
index c0cfe94a04..0000000000
--- a/gnu/packages/patches/python-flint-includes.patch
+++ /dev/null
@@ -1,131 +0,0 @@
-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)
-- 
2.41.0