Trac #25009: update and promote spkg primecount

The `prime_pi` function is currently a symbolic function that can hold
its argument as in
{{{
sage: n = SR.var('n')
sage: prime_pi(n)
prime_pi(n)
}}}
that also contains the Cython code for evaluating it
{{{
sage: prime_pi(13543)
1603
}}}
Unfortunately, it is buggy, see #24960 (fixed in #32894, using this
ticket). We will promote the spkg `primecount` to standard and use it
instead. This ticket does this part, and reverts deprecations from
#32412. It also removes obsolete deprecation warning, and the
corresponding no longer available parameter.

Upstream patch: kimwalisch/primesieve#107
(rejected)

-------------
Below is the original part, no longer too relevant.
-------------
We move the evaluation part as a standalone function in `arith/` and
provide alternative implementations
 - using `PARI/GP` (only efficient in the range of tabulated primes)
 - using the different algorithms in the library primecount that is
packaged in #24966

URL: https://trac.sagemath.org/25009
Reported by: vdelecroix
Ticket author(s): Dima Pasechnik
Reviewer(s): Matthias Koeppe

build/pkgs/primecount/checksums.ini

@@ -1,4 +1,5 @@
 tarball=primecount-VERSION.tar.gz
-sha1=d7a2c660eb64d14c951feeaee1d94d220c68c23e
-md5=ab925094a104499cfc21db2532e65517
-cksum=2340721037
+sha1=845b863f2007dc90d83c199db0af8fc20fd5092e
+md5=b855038556de3f0ec8210b54e4057a65
+cksum=2388953073
+upstream_url=https://github.com/kimwalisch/primecount/archive/refs/tags/vVERSION.tar.gz

build/pkgs/primecount/dependencies

@@ -1 +1 @@
-cmake
+primesieve | cmake

build/pkgs/primecount/distros/fedora.txt

@@ -0,0 +1,2 @@
+primecount
+primecount-devel

build/pkgs/primecount/package-version.txt

@@ -1 +1 @@
-5.1
+7.1

build/pkgs/primecount/patches/sieve_version.patch

@@ -0,0 +1,13 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index d1fb69a..d9d6d43 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -267,7 +267,7 @@ if(BUILD_LIBPRIMESIEVE)
+     set(BUILD_MANPAGE "${COPY_BUILD_MANPAGE}" CACHE BOOL "Regenerate man page using a2x" FORCE)
+     set(BUILD_TESTS "${COPY_BUILD_TESTS}" CACHE BOOL "Build test programs" FORCE)
+ else()
+-    find_package(primesieve REQUIRED)
++    find_package(primesieve 7.6 REQUIRED)
+ endif()
+
+ # Testing ############################################################

build/pkgs/primecount/spkg-check.in

@@ -1,8 +1,2 @@
-###############################################################################
-#
-# primecount Sage check script
-#
-###############################################################################
-
 cd src
 $MAKE test

build/pkgs/primecount/spkg-configure.m4

@@ -0,0 +1,32 @@
+SAGE_SPKG_CONFIGURE([primecount], [
+    m4_pushdef([SAGE_PRIMECOUNT_MINVER],[7.1])
+    m4_pushdef([SAGE_PRIMECOUNT_MAJOR],[7])
+    m4_pushdef([SAGE_PRIMECOUNT_MINOR],[1])
+    SAGE_SPKG_DEPCHECK([primesieve], [
+      dnl Checking for primecount with pkg-config
+      PKG_CHECK_MODULES([PRIMECOUNT], [primecount >= SAGE_PRIMECOUNT_MINVER], [ ], [
+          AC_CHECK_HEADER([primecount.h], [
+           AC_SEARCH_LIBS([primecount_pi], [primecount], [
+             AC_MSG_CHECKING([checking primecount version directly])
+             AC_RUN_IFELSE([AC_LANG_PROGRAM([
+                      [#include <primecount.h>
+                      ]],[[
+                       if (PRIMECOUNT_VERSION_MAJOR > ]] SAGE_PRIMECOUNT_MAJOR [[ ) return 0;
+                       if (PRIMECOUNT_VERSION_MAJOR == ]] SAGE_PRIMECOUNT_MAJOR [[  &&
+                           PRIMECOUNT_VERSION_MINOR >= ]] SAGE_PRIMECOUNT_MINOR [[ ) return 0;
+                       else return 1;
+                      ]])],
+                     [AC_MSG_RESULT([Good.])],
+                     [AC_MSG_RESULT([Too old.])
+                      sage_spkg_install_primecount=yes],
+                     []) dnl cross-compilation - noop
+           ],
+              [sage_spkg_install_primecount=yes])
+          ], [sage_spkg_install_primecount=yes])
+      ])
+    ])
+    m4_popdef([SAGE_PRIMECOUNT_MINVER])
+    m4_popdef([SAGE_PRIMECOUNT_MAJOR])
+    m4_popdef([SAGE_PRIMECOUNT_MINOR])
+])
+

build/pkgs/primecount/spkg-install.in

@@ -1,22 +1,23 @@
-###############################################################################
-#
-# primecount Sage install script
-#
-###############################################################################
-
 cd src
 
 if [ "$SAGE_FAT_BINARY" = yes ]; then
     EXTRA_OPTS="-DWITH_POPCNT=OFF"
 fi
 
-echo "Configuring primecount."
+primc_config(){
+echo "Configuring primecount: building primesieve $1"
 sdh_cmake -DCMAKE_VERBOSE_MAKEFILE=ON \
           -DBUILD_STATIC_LIBS=OFF \
           -DBUILD_SHARED_LIBS=ON \
           -DBUILD_TESTS=ON \
-          ${EXTRA_OPTS}
+	  -DBUILD_LIBPRIMESIEVE=$1 \
+	  -DCMAKE_FIND_ROOT_PATH=$SAGE_LOCAL/lib/cmake \
+	  -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=BOTH \
+	  -DCMAKE_INSTALL_PREFIX=$SAGE_LOCAL \
+          ${EXTRA_OPTS} && sdh_make_install
+}
 
-sdh_make
+# we try to use the external primesieve first, and if
+# cmake cannot find it, we build a vendored copy
 
-sdh_make_install
+(primc_config OFF) || primc_config ON

build/pkgs/primecount/type

@@ -1 +1 @@
-optional
+standard

build/pkgs/primesieve/SPKG.rst

@@ -0,0 +1,20 @@
+primesieve: CLI program and C/C++ library for generating primes 
+===============================================================
+
+Description
+-----------
+
+A CLI program and C/C++ library for quickly generating prime numbers.
+https://github.com/kimwalisch/primesieve
+
+A dependency of the standard spkg primecount.
+
+License
+-------
+
+BSD-2-clause
+
+Upstream Contact
+----------------
+
+- https://github.com/kimwalisch/primesieve

build/pkgs/primesieve/checksums.ini

@@ -0,0 +1,5 @@
+tarball=primesieve-VERSION.tar.gz
+sha1=b78579e0c78fedb75dc9a58b4be3b092eefbcfcb
+md5=65eb8972819e47f552f563dc7699be8a
+cksum=51195771
+upstream_url=https://github.com/kimwalisch/primesieve/archive/refs/tags/vVERSION.tar.gz

build/pkgs/primesieve/dependencies

@@ -0,0 +1 @@
+| cmake

build/pkgs/primesieve/distros/alpine.txt

@@ -0,0 +1,2 @@
+primesieve-dev
+primesieve

build/pkgs/primesieve/distros/arch.txt

@@ -0,0 +1 @@
+primesieve

build/pkgs/primesieve/distros/debian.txt

@@ -0,0 +1 @@
+libprimesieve-dev

build/pkgs/primesieve/distros/fedora.txt

@@ -0,0 +1,2 @@
+primesieve-devel
+primesieve

build/pkgs/primesieve/distros/homebrew.txt

@@ -0,0 +1 @@
+primesieve

build/pkgs/primesieve/distros/opensuse.txt

@@ -0,0 +1 @@
+primesieve

build/pkgs/primesieve/distros/repology.txt

@@ -0,0 +1 @@
+primesieve

build/pkgs/primesieve/package-version.txt

@@ -0,0 +1 @@
+7.6

build/pkgs/primesieve/patches/107.patch

@@ -0,0 +1,54 @@
+From 1f8d0470b4e9d50393032b86d21a7a2fcc512355 Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
+Date: Sat, 27 Nov 2021 10:50:09 -0800
+Subject: [PATCH] src/MemoryPool.cpp: Work around missing std::align on GCC 4.x
+
+---
+ src/MemoryPool.cpp | 27 ++++++++++++++++++++++++++-
+ 1 file changed, 26 insertions(+), 1 deletion(-)
+
+diff --git a/src/MemoryPool.cpp b/src/MemoryPool.cpp
+index 7a4a4006..60f62101 100644
+--- a/src/MemoryPool.cpp
++++ b/src/MemoryPool.cpp
+@@ -26,6 +26,31 @@
+
+ using std::size_t;
+
++#if defined(__GNUC__) && __GNUC__ == 4
++
++// gcc 4.9 does not implement std::align.
++// Use the implementation from
++// https://gcc.gnu.org/bugzilla/show_bug.cgi?id=57350#c11
++
++using std::uintptr_t;
++
++static inline void *align(size_t alignment, size_t size,
++                          void *&ptr, size_t &space)
++{
++  uintptr_t pn = reinterpret_cast<uintptr_t>(ptr);
++  uintptr_t aligned = (pn + alignment - 1) & -alignment;
++  size_t padding = aligned - pn;
++  if (space < size + padding) return nullptr;
++  space -= padding;
++  return ptr = reinterpret_cast<void *>(aligned);
++}
++
++#else
++
++using std::align;
++
++#endif
++
+ namespace primesieve {
+
+ void MemoryPool::addBucket(SievingPrime*& sievingPrime)
+@@ -70,7 +95,7 @@ void MemoryPool::allocateBuckets()
+   void* ptr = memory;
+
+   // Align pointer address to sizeof(Bucket)
+-  if (!std::align(sizeof(Bucket), sizeof(Bucket), ptr, bytes))
++  if (!align(sizeof(Bucket), sizeof(Bucket), ptr, bytes))
+     throw primesieve_error("MemoryPool: failed to align memory!");
+
+   initBuckets(ptr, bytes);

build/pkgs/primesieve/spkg-check.in

@@ -0,0 +1,2 @@
+cd src
+$MAKE test

build/pkgs/primesieve/spkg-configure.m4

@@ -0,0 +1,8 @@
+SAGE_SPKG_CONFIGURE([primesieve], [
+    m4_pushdef([SAGE_PRIMESIEVE_MINVER],[7.6])
+    dnl Checking for primesieve with pkg-config
+    PKG_CHECK_MODULES([PRIMESIEVE], [primesieve >= SAGE_PRIMESIEVE_MINVER], [ ], [
+        sage_spkg_install_primesieve=yes])
+    m4_popdef([SAGE_PRIMESIEVE_MINVER])
+])
+

build/pkgs/primesieve/spkg-install.in

@@ -0,0 +1,14 @@
+cd src
+
+if [ "$SAGE_FAT_BINARY" = yes ]; then
+    EXTRA_OPTS="-DWITH_POPCNT=OFF"
+fi
+
+echo "Configuring primesieve."
+sdh_cmake -DCMAKE_VERBOSE_MAKEFILE=ON \
+          -DBUILD_STATIC_LIBS=OFF \
+          -DBUILD_SHARED_LIBS=ON \
+          -DBUILD_TESTS=ON \
+          ${EXTRA_OPTS}
+
+sdh_make_install

build/pkgs/primesieve/type

@@ -0,0 +1 @@
+standard

build/pkgs/sagelib/dependencies

@@ -1,4 +1,4 @@
-FORCE $(SCRIPTS) arb boost_cropped $(BLAS) brial cliquer cypari cysignals cython ecl eclib ecm flint libgd gap giac givaro glpk gmpy2 gsl iml jinja2 jupyter_core lcalc lrcalc libbraiding libhomfly libpng linbox m4ri m4rie memory_allocator mpc mpfi mpfr $(MP_LIBRARY) ntl numpy pari pip pkgconfig planarity ppl pplpy pycygwin $(PYTHON) ratpoints rw sage_conf singular symmetrica zn_poly $(PCFILES) | $(PYTHON_TOOLCHAIN) sage_setup
+FORCE $(SCRIPTS) arb boost_cropped $(BLAS) brial cliquer cypari cysignals cython ecl eclib ecm flint libgd gap giac givaro glpk gmpy2 gsl iml jinja2 jupyter_core lcalc lrcalc libbraiding libhomfly libpng linbox m4ri m4rie memory_allocator mpc mpfi mpfr $(MP_LIBRARY) ntl numpy pari pip pkgconfig planarity ppl pplpy primesieve primecount pycygwin $(PYTHON) ratpoints rw sage_conf singular symmetrica zn_poly $(PCFILES) | $(PYTHON_TOOLCHAIN) sage_setup
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/scipoptsuite/spkg-install.in

@@ -3,7 +3,7 @@ echo "Building scipoptsuite with cmake"
 cd src
 mkdir build
 cd build
-cmake .. -DCMAKE_INSTALL_PREFIX="${SAGE_LOCAL}"/ -DCMAKE_VERBOSE_MAKEFILE=ON -DGMP_DIR="${SAGE_LOCAL}" -DZLIB_ROOT="${SAGE_LOCAL}" -DReadline_ROOT_DIR="${SAGE_LOCAL}" -DBLISS_DIR="${SAGE_LOCAL}" -DIPOPT=FALSE
+cmake .. -DCMAKE_VERBOSE_MAKEFILE=ON -DGMP_DIR="${SAGE_LOCAL}" -DZLIB_ROOT="${SAGE_LOCAL}" -DReadline_ROOT_DIR="${SAGE_LOCAL}" -DBLISS_DIR="${SAGE_LOCAL}" -DIPOPT=FALSE
 make
 make install
 

build/pkgs/symengine/spkg-install.in

@@ -1,8 +1,7 @@
 cd src
 mkdir build
 cd build
-cmake -DCMAKE_INSTALL_PREFIX="$SAGE_LOCAL" \
-      -DCMAKE_PREFIX_PATH="$SAGE_LOCAL" \
+cmake -DCMAKE_PREFIX_PATH="$SAGE_LOCAL" \
       -DWITH_SYMENGINE_THREAD_SAFE=yes \
       -DWITH_ECM=yes \
       -DWITH_FLINT=yes \

src/sage/interfaces/primecount.pyx

@@ -1,5 +1,3 @@
-# sage_setup: distribution = sagemath-primecount
-
 r"""
 Interface to the primecount library
 """
@@ -17,12 +15,6 @@ from libcpp.string cimport string as cppstring
 from cpython.int cimport PyInt_FromString
 
 from cysignals.signals cimport sig_on, sig_off
-
-
-from sage.misc.superseded import deprecation
-deprecation(32412, "the module sage.interfaces.primecount is deprecated")
-
-
 cimport sage.libs.primecount as primecount
 
 cdef inline int _do_sig(int64_t n):
@@ -37,29 +29,15 @@ cpdef int64_t prime_pi(int64_t n, method=None) except -1:
 
     - ``n`` - an integer
 
-    - ``method`` - deprecated, no longer supported in primecount 5
-
     EXAMPLES::
 
-        sage: from sage.interfaces.primecount import prime_pi # optional - primecount
-        doctest:warning
-        ...
-        DeprecationWarning: the module sage.interfaces.primecount is deprecated
-        See https://trac.sagemath.org/32412 for details.
-
-        sage: prime_pi(1000) == 168                     # optional - primecount
+        sage: from sage.interfaces.primecount import prime_pi
+        sage: prime_pi(1000) == 168
         True
-        sage: prime_pi(1000, method='deleglise_rivat') == 168 # optional - primecount
-        doctest:warning
-        ...
-        DeprecationWarning: primecount 5 no longer supports the 'method' parameter
-        See https://trac.sagemath.org/28493 for details.
+        sage: prime_pi(1000, method='deleglise_rivat') == 168
         True
     """
     cdef int64_t ans
-    if method is not None:
-        from sage.misc.superseded import deprecation_cython as deprecation
-        deprecation(28493, "primecount 5 no longer supports the 'method' parameter")
     if _do_sig(n): sig_on()
     ans = primecount.pi(n)
     if _do_sig(n): sig_off()
@@ -71,9 +49,9 @@ cpdef prime_pi_128(n):
 
     EXAMPLES::
 
-        sage: from sage.interfaces.primecount import prime_pi_128 # optional - primecount
+        sage: from sage.interfaces.primecount import prime_pi_128
 
-        sage: prime_pi_128(1000)     # optional - primecount
+        sage: prime_pi_128(1000)
         168
         sage: nth_prime_128(2**65)   # not tested
         ?
@@ -91,9 +69,9 @@ cpdef int64_t nth_prime(int64_t n) except -1:
 
     EXAMPLES::
 
-        sage: from sage.interfaces.primecount import nth_prime # optional - primecount
+        sage: from sage.interfaces.primecount import nth_prime
 
-        sage: nth_prime(168) == 997  # optional - primecount
+        sage: nth_prime(168) == 997
         True
     """
     if n <= 0:
@@ -114,11 +92,11 @@ cpdef int64_t phi(int64_t x, int64_t a):
 
     EXAMPLES::
 
-         sage: from sage.interfaces.primecount import phi # optional - primecount
+         sage: from sage.interfaces.primecount import phi
 
-         sage: phi(1000, 3) == 266 # optional - primecount
+         sage: phi(1000, 3) == 266
          True
-         sage: phi(2**30, 100) == 95446716 # optional - primecount
+         sage: phi(2**30, 100) == 95446716
          True
     """
     return primecount.phi(x, a)

src/sage/libs/primecount.pxd

@@ -1,4 +1,4 @@
-# distutils: libraries = primecount
+# distutils: libraries = primecount primesieve
 # distutils: language = c++
 
 # Use of this file is deprecated.

tox.ini

@@ -241,6 +241,7 @@ setenv =
     fedora-29:        BASE_TAG=29
     fedora-29:                                 IGNORE_MISSING_SYSTEM_PACKAGES=yes
     fedora-30:        BASE_TAG=30
+    fedora-30:                                 IGNORE_MISSING_SYSTEM_PACKAGES=yes
     fedora-31:        BASE_TAG=31
     fedora-32:        BASE_TAG=32
     fedora-33:        BASE_TAG=33