Merge pull request #219 from oscarbenjamin/pr_bindings

Backdate autogenerated bindings to FLINT 3.1.3-p1

src/flint/flintlib/README.md

@@ -0,0 +1,35 @@
+Cython declarations for functions exported by libflint
+======================================================
+
+This directory contains Cython declarations for functions exported by libflint.
+The declarations under the `types` directory are for the types defined in
+libflint and are hand-written. The declarations under the `functions` directory
+are for the functions defined in libflint and are generated by running:
+```console
+$ bin/all_rst_to_pxd.sh /path/to/flint/doc/source
+```
+where `/path/to/flint/doc/source` is the path to the source directory of the
+flint documentation. This command should always be run on the FLINT docs of the
+version of FLINT that is used by default in python-flint's wheels which is the
+version shown in the `bin/build_variables.sh` script. Typically this just means
+the latest released version of FLINT.
+
+It is important not to edit any of the files in `functions` manually because a
+subsequent run of `bin/all_rst_to_pxd.sh` will overwrite them. There are
+several reasons why manual editing may be needed but usually it is because
+either:
+
+1. The function is not documented in the FLINT docs.
+2. The function is a macro and not a function.
+
+In either case, we need to manually write the declaration for the function but
+it cannot be done in the `functions` directory. Instead, it should be added
+somewhere in the `types` directory.
+
+Generally undocumented functions should be reported/fixed upstream in FLINT.
+
+It might be better to list macros (and undocumented functions) in the
+`bin/rst_to_pxd.py` script so that it can add them to the generated files
+automatically. Then we can keep them out of the hand-written code but also keep
+track of them with a goal of eventually getting all of them added to the FLINT
+docs.

src/flint/flintlib/functions/acb_poly.pxd

@@ -236,6 +236,7 @@ cdef extern from "flint/acb_poly.h":
     void acb_poly_root_bound_fujiwara(mag_t bound, acb_poly_t poly)
     void _acb_poly_root_inclusion(acb_t r, const acb_t m, acb_srcptr poly, acb_srcptr polyder, slong len, slong prec)
     slong _acb_poly_validate_roots(acb_ptr roots, acb_srcptr poly, slong len, slong prec)
+    void _acb_poly_refine_roots_durand_kerner(acb_ptr roots, acb_srcptr poly, slong len, slong prec)
     slong _acb_poly_find_roots(acb_ptr roots, acb_srcptr poly, acb_srcptr initial, slong len, slong maxiter, slong prec)
     slong acb_poly_find_roots(acb_ptr roots, const acb_poly_t poly, acb_srcptr initial, slong maxiter, slong prec)
     int _acb_poly_validate_real_roots(acb_srcptr roots, acb_srcptr poly, slong len, slong prec)

src/flint/flintlib/functions/arb.pxd

@@ -1,6 +1,6 @@
 from flint.flintlib.types.arb cimport arb_ptr, arb_srcptr, arb_t, mag_srcptr, mag_t
 from flint.flintlib.types.arf cimport arf_rnd_t, arf_srcptr, arf_t
-from flint.flintlib.types.flint cimport flint_bitcnt_t, flint_rand_t, fmpz_struct, fmpz_t, nn_ptr, nn_srcptr, slong, ulong
+from flint.flintlib.types.flint cimport flint_bitcnt_t, flint_rand_t, fmpz_struct, fmpz_t, mp_limb_t, mp_ptr, mp_size_t, mp_srcptr, slong, ulong
 from flint.flintlib.types.fmpq cimport fmpq_t
 
 # unknown type FILE
@@ -318,14 +318,14 @@ cdef extern from "flint/arb.h":
     void arb_partitions_ui(arb_t res, ulong n, slong prec)
     void arb_primorial_nth_ui(arb_t res, ulong n, slong prec)
     void arb_primorial_ui(arb_t res, ulong n, slong prec)
-    void _arb_atan_taylor_naive(nn_ptr y, ulong * error, nn_srcptr x, slong xn, ulong N, int alternating)
-    void _arb_atan_taylor_rs(nn_ptr y, ulong * error, nn_srcptr x, slong xn, ulong N, int alternating)
-    void _arb_exp_taylor_naive(nn_ptr y, ulong * error, nn_srcptr x, slong xn, ulong N)
-    void _arb_exp_taylor_rs(nn_ptr y, ulong * error, nn_srcptr x, slong xn, ulong N)
-    void _arb_sin_cos_taylor_naive(nn_ptr ysin, nn_ptr ycos, ulong * error, nn_srcptr x, slong xn, ulong N)
-    void _arb_sin_cos_taylor_rs(nn_ptr ysin, nn_ptr ycos, ulong * error, nn_srcptr x, slong xn, ulong N, int sinonly, int alternating)
-    int _arb_get_mpn_fixed_mod_log2(nn_ptr w, fmpz_t q, ulong * error, const arf_t x, slong wn)
-    int _arb_get_mpn_fixed_mod_pi4(nn_ptr w, fmpz_t q, int * octant, ulong * error, const arf_t x, slong wn)
+    void _arb_atan_taylor_naive(mp_ptr y, mp_limb_t * error, mp_srcptr x, mp_size_t xn, ulong N, int alternating)
+    void _arb_atan_taylor_rs(mp_ptr y, mp_limb_t * error, mp_srcptr x, mp_size_t xn, ulong N, int alternating)
+    void _arb_exp_taylor_naive(mp_ptr y, mp_limb_t * error, mp_srcptr x, mp_size_t xn, ulong N)
+    void _arb_exp_taylor_rs(mp_ptr y, mp_limb_t * error, mp_srcptr x, mp_size_t xn, ulong N)
+    void _arb_sin_cos_taylor_naive(mp_ptr ysin, mp_ptr ycos, mp_limb_t * error, mp_srcptr x, mp_size_t xn, ulong N)
+    void _arb_sin_cos_taylor_rs(mp_ptr ysin, mp_ptr ycos, mp_limb_t * error, mp_srcptr x, mp_size_t xn, ulong N, int sinonly, int alternating)
+    int _arb_get_mpn_fixed_mod_log2(mp_ptr w, fmpz_t q, mp_limb_t * error, const arf_t x, mp_size_t wn)
+    int _arb_get_mpn_fixed_mod_pi4(mp_ptr w, fmpz_t q, int * octant, mp_limb_t * error, const arf_t x, mp_size_t wn)
     slong _arb_exp_taylor_bound(slong mag, slong prec)
     void arb_exp_arf_bb(arb_t z, const arf_t x, slong prec, int m1)
     void _arb_exp_sum_bs_simple(fmpz_t T, fmpz_t Q, flint_bitcnt_t * Qexp, const fmpz_t x, flint_bitcnt_t r, slong N)

src/flint/flintlib/functions/arf.pxd

@@ -1,6 +1,6 @@
 from flint.flintlib.types.arb cimport mag_t
 from flint.flintlib.types.arf cimport arf_rnd_t, arf_srcptr, arf_t
-from flint.flintlib.types.flint cimport flint_rand_t, fmpz_t, nn_ptr, nn_srcptr, slong, ulong
+from flint.flintlib.types.flint cimport flint_rand_t, fmpz_t, mp_limb_t, mp_ptr, mp_size_t, mp_srcptr, slong, ulong
 from flint.flintlib.types.fmpq cimport fmpq_t
 
 # unknown type FILE
@@ -161,8 +161,8 @@ cdef extern from "flint/arf.h":
     int arf_complex_mul(arf_t e, arf_t f, const arf_t a, const arf_t b, const arf_t c, const arf_t d, slong prec, arf_rnd_t rnd)
     int arf_complex_mul_fallback(arf_t e, arf_t f, const arf_t a, const arf_t b, const arf_t c, const arf_t d, slong prec, arf_rnd_t rnd)
     int arf_complex_sqr(arf_t e, arf_t f, const arf_t a, const arf_t b, slong prec, arf_rnd_t rnd)
-    int _arf_get_integer_mpn(nn_ptr y, nn_srcptr xp, slong xn, slong exp)
-    int _arf_set_mpn_fixed(arf_t z, nn_srcptr xp, slong xn, slong fixn, int negative, slong prec, arf_rnd_t rnd)
+    int _arf_get_integer_mpn(mp_ptr y, mp_srcptr xp, mp_size_t xn, slong exp)
+    int _arf_set_mpn_fixed(arf_t z, mp_srcptr xp, mp_size_t xn, mp_size_t fixn, int negative, slong prec, arf_rnd_t rnd)
     int _arf_set_round_ui(arf_t z, ulong x, int sgnbit, slong prec, arf_rnd_t rnd)
-    int _arf_set_round_uiui(arf_t z, slong * fix, ulong hi, ulong lo, int sgnbit, slong prec, arf_rnd_t rnd)
-    int _arf_set_round_mpn(arf_t z, slong * exp_shift, nn_srcptr x, slong xn, int sgnbit, slong prec, arf_rnd_t rnd)
+    int _arf_set_round_uiui(arf_t z, slong * fix, mp_limb_t hi, mp_limb_t lo, int sgnbit, slong prec, arf_rnd_t rnd)
+    int _arf_set_round_mpn(arf_t z, slong * exp_shift, mp_srcptr x, mp_size_t xn, int sgnbit, slong prec, arf_rnd_t rnd)

src/flint/flintlib/functions/arith.pxd

@@ -1,4 +1,4 @@
-from flint.flintlib.types.flint cimport fmpz_struct, fmpz_t, nmod_t, nn_ptr, slong, ulong
+from flint.flintlib.types.flint cimport fmpz_struct, fmpz_t, mp_limb_t, mp_ptr, nmod_t, slong, ulong
 from flint.flintlib.types.fmpq cimport fmpq_poly_t, fmpq_struct, fmpq_t
 from flint.flintlib.types.fmpz cimport fmpz_mat_t, fmpz_poly_t
 
@@ -7,6 +7,7 @@ from flint.flintlib.types.fmpz cimport fmpz_mat_t, fmpz_poly_t
 
 
 cdef extern from "flint/arith.h":
+    void arith_primorial(fmpz_t res, slong n)
     void _arith_harmonic_number(fmpz_t num, fmpz_t den, slong n)
     void arith_harmonic_number(fmpq_t x, slong n)
     void arith_stirling_number_1u(fmpz_t s, ulong n, ulong k)
@@ -27,11 +28,11 @@ cdef extern from "flint/arith.h":
     void arith_bell_number_vec(fmpz_struct * b, slong n)
     void arith_bell_number_vec_recursive(fmpz_struct * b, slong n)
     void arith_bell_number_vec_multi_mod(fmpz_struct * b, slong n)
-    ulong arith_bell_number_nmod(ulong n, nmod_t mod)
-    void arith_bell_number_nmod_vec(nn_ptr b, slong n, nmod_t mod)
-    void arith_bell_number_nmod_vec_recursive(nn_ptr b, slong n, nmod_t mod)
-    void arith_bell_number_nmod_vec_ogf(nn_ptr b, slong n, nmod_t mod)
-    int arith_bell_number_nmod_vec_series(nn_ptr b, slong n, nmod_t mod)
+    mp_limb_t arith_bell_number_nmod(ulong n, nmod_t mod)
+    void arith_bell_number_nmod_vec(mp_ptr b, slong n, nmod_t mod)
+    void arith_bell_number_nmod_vec_recursive(mp_ptr b, slong n, nmod_t mod)
+    void arith_bell_number_nmod_vec_ogf(mp_ptr b, slong n, nmod_t mod)
+    int arith_bell_number_nmod_vec_series(mp_ptr b, slong n, nmod_t mod)
     double arith_bell_number_size(ulong n)
     void _arith_bernoulli_number(fmpz_t num, fmpz_t den, ulong n)
     void arith_bernoulli_number(fmpq_t x, ulong n)
@@ -46,14 +47,22 @@ cdef extern from "flint/arith.h":
     void arith_euler_number_vec(fmpz_struct * res, slong n)
     double arith_euler_number_size(ulong n)
     void arith_euler_polynomial(fmpq_poly_t poly, ulong n)
+    void arith_euler_phi(fmpz_t res, const fmpz_t n)
+    int arith_moebius_mu(const fmpz_t n)
+    void arith_divisor_sigma(fmpz_t res, ulong k, const fmpz_t n)
     void arith_divisors(fmpz_poly_t res, const fmpz_t n)
     void arith_ramanujan_tau(fmpz_t res, const fmpz_t n)
     void arith_ramanujan_tau_series(fmpz_poly_t res, slong n)
     void arith_landau_function_vec(fmpz_struct * res, slong len)
+    void arith_dedekind_sum_naive(fmpq_t s, const fmpz_t h, const fmpz_t k)
+    double arith_dedekind_sum_coprime_d(double h, double k)
+    void arith_dedekind_sum_coprime_large(fmpq_t s, const fmpz_t h, const fmpz_t k)
+    void arith_dedekind_sum_coprime(fmpq_t s, const fmpz_t h, const fmpz_t k)
+    void arith_dedekind_sum(fmpq_t s, const fmpz_t h, const fmpz_t k)
     void arith_number_of_partitions_vec(fmpz_struct * res, slong len)
-    void arith_number_of_partitions_nmod_vec(nn_ptr res, slong len, nmod_t mod)
+    void arith_number_of_partitions_nmod_vec(mp_ptr res, slong len, nmod_t mod)
     # void trig_prod_init(trig_prod_t prod)
-    # void arith_hrr_expsum_factored(trig_prod_t prod, ulong k, ulong n)
+    # void arith_hrr_expsum_factored(trig_prod_t prod, mp_limb_t k, mp_limb_t n)
     # void arith_number_of_partitions_mpfr(mpfr_t x, ulong n)
     void arith_number_of_partitions(fmpz_t x, ulong n)
     void arith_sum_of_squares(fmpz_t r, ulong k, const fmpz_t n)

src/flint/flintlib/functions/fmpq_mpoly.pxd

@@ -1,4 +1,4 @@
-from flint.flintlib.types.flint cimport flint_bitcnt_t, flint_rand_t, fmpz_struct, fmpz_t, slong, ulong
+from flint.flintlib.types.flint cimport flint_bitcnt_t, flint_rand_t, fmpz_struct, fmpz_t, mp_limb_t, slong, ulong
 from flint.flintlib.types.fmpq cimport fmpq_mpoly_ctx_t, fmpq_mpoly_struct, fmpq_mpoly_t, fmpq_poly_struct, fmpq_poly_t, fmpq_struct, fmpq_t
 from flint.flintlib.types.fmpz cimport fmpz_mpoly_struct
 from flint.flintlib.types.mpoly cimport ordering_t
@@ -95,9 +95,9 @@ cdef extern from "flint/fmpq_mpoly.h":
     void fmpq_mpoly_sort_terms(fmpq_mpoly_t A, const fmpq_mpoly_ctx_t ctx)
     void fmpq_mpoly_combine_like_terms(fmpq_mpoly_t A, const fmpq_mpoly_ctx_t ctx)
     void fmpq_mpoly_reverse(fmpq_mpoly_t A, const fmpq_mpoly_t B, const fmpq_mpoly_ctx_t ctx)
-    void fmpq_mpoly_randtest_bound(fmpq_mpoly_t A, flint_rand_t state, slong length, ulong coeff_bits, ulong exp_bound, const fmpq_mpoly_ctx_t ctx)
-    void fmpq_mpoly_randtest_bounds(fmpq_mpoly_t A, flint_rand_t state, slong length, ulong coeff_bits, ulong * exp_bounds, const fmpq_mpoly_ctx_t ctx)
-    void fmpq_mpoly_randtest_bits(fmpq_mpoly_t A, flint_rand_t state, slong length, ulong coeff_bits, ulong exp_bits, const fmpq_mpoly_ctx_t ctx)
+    void fmpq_mpoly_randtest_bound(fmpq_mpoly_t A, flint_rand_t state, slong length, mp_limb_t coeff_bits, ulong exp_bound, const fmpq_mpoly_ctx_t ctx)
+    void fmpq_mpoly_randtest_bounds(fmpq_mpoly_t A, flint_rand_t state, slong length, mp_limb_t coeff_bits, ulong * exp_bounds, const fmpq_mpoly_ctx_t ctx)
+    void fmpq_mpoly_randtest_bits(fmpq_mpoly_t A, flint_rand_t state, slong length, mp_limb_t coeff_bits, mp_limb_t exp_bits, const fmpq_mpoly_ctx_t ctx)
     void fmpq_mpoly_add_fmpq(fmpq_mpoly_t A, const fmpq_mpoly_t B, const fmpq_t c, const fmpq_mpoly_ctx_t ctx)
     void fmpq_mpoly_add_fmpz(fmpq_mpoly_t A, const fmpq_mpoly_t B, const fmpz_t c, const fmpq_mpoly_ctx_t ctx)
     void fmpq_mpoly_add_ui(fmpq_mpoly_t A, const fmpq_mpoly_t B, ulong c, const fmpq_mpoly_ctx_t ctx)