Rebuild for ntl 11.4.0.

Add primecount support, including the -primecount patch.
Add still more gap packages, nearly finishing the set shipped by upstream.

sagemath-extensions.patch

@@ -1,6 +1,6 @@
 diff -up src/module_list.py.orig src/module_list.py
 --- src/module_list.py.orig	2019-06-26 14:41:04.000000000 -0600
-+++ src/module_list.py	2019-09-11 08:38:22.467995023 -0600
++++ src/module_list.py	2019-09-17 16:06:38.678583204 -0600
 @@ -357,16 +357,16 @@ ext_modules = [
      Extension('sage.graphs.matchpoly',
                sources = ['sage/graphs/matchpoly.pyx']),
@@ -38,6 +38,18 @@ diff -up src/module_list.py.orig src/module_list.py
  
      Extension('sage.graphs.spanning_tree',
                sources = ['sage/graphs/spanning_tree.pyx']),
+@@ -440,9 +440,9 @@ ext_modules = [
+     ##
+     ################################
+ 
+-    OptionalExtension("sage.interfaces.primecount",
++    Extension("sage.interfaces.primecount",
+               ["sage/interfaces/primecount.pyx"],
+-              package = "primecount"),
++              libraries = ["primecount"]),
+ 
+     Extension('*', ['sage/interfaces/*.pyx']),
+ 
 @@ -461,21 +461,19 @@ ext_modules = [
      ##
      ################################

sagemath-primecount.patch

@@ -0,0 +1,110 @@
+diff -up src/sage/interfaces/primecount.pyx.orig src/sage/interfaces/primecount.pyx
+--- src/sage/interfaces/primecount.pyx.orig	2019-06-26 14:41:04.000000000 -0600
++++ src/sage/interfaces/primecount.pyx	2019-09-17 16:13:46.316032782 -0600
+@@ -22,7 +22,7 @@ cdef inline int _do_sig(int64_t n):
+     "threshold for sig_on/sig_off"
+     return n >> 26
+ 
+-cpdef int64_t prime_pi(int64_t n, method=None) except -1:
++cpdef int64_t prime_pi(int64_t n) except -1:
+     r"""
+     Return the number of prime numbers smaller or equal than ``n``.
+ 
+@@ -30,76 +30,22 @@ cpdef int64_t prime_pi(int64_t n, method
+ 
+     - ``n`` - an integer
+ 
+-    - ``method`` - ``None`` or a string that determines the primecount
+-      function to be called
+-
+-        - ``"deleglise_rivat"``
+-        - ``"legendre"``
+-        - ``"lehmer"``
+-        - ``"lmo"``
+-        - ``"meissel"``
+-        - ``"primesieve"``
+-
+     EXAMPLES::
+ 
+         sage: from sage.interfaces.primecount import prime_pi # optional - primecount
+ 
+         sage: prime_pi(1000) == 168                     # optional - primecount
+         True
+-        sage: prime_pi(1000, "deleglise_rivat") == 168  # optional - primecount
+-        True
+-        sage: prime_pi(1000, "legendre") == 168         # optional - primecount
+-        True
+-        sage: prime_pi(1000, "lehmer") == 168           # optional - primecount
+-        True
+-        sage: prime_pi(1000, "lmo") == 168              # optional - primecount
+-        True
+-        sage: prime_pi(1000, "meissel") == 168          # optional - primecount
+-        True
+-        sage: prime_pi(1000, "primesieve") == 168       # optional - primecount
+-        True
+-        sage: prime_pi(1000, "youpi")                   # optional - primecount
+-        Traceback (most recent call last):
+-        ...
+-        ValueError: unknown method 'youpi'
+     """
+     cdef int64_t ans
+-    if method is None:
+-        if _do_sig(n): sig_on()
+-        ans = primecount.pi(n)
+-        if _do_sig(n): sig_off()
+-    elif method == "deleglise_rivat":
+-        if _do_sig(n): sig_on()
+-        ans = primecount.pi_deleglise_rivat(n)
+-        if _do_sig(n): sig_off()
+-    elif method == "legendre":
+-        if _do_sig(n): sig_on()
+-        ans = primecount.pi_legendre(n)
+-        if _do_sig(n): sig_off()
+-    elif method == "lehmer":
+-        if _do_sig(n): sig_on()
+-        ans = primecount.pi_lehmer(n)
+-        if _do_sig(n): sig_off()
+-    elif method == "lmo":
+-        if _do_sig(n): sig_on()
+-        ans = primecount.pi_lmo(n)
+-        if _do_sig(n): sig_off()
+-    elif method == "meissel":
+-        if _do_sig(n): sig_on()
+-        ans = primecount.pi_meissel(n)
+-        if _do_sig(n): sig_off()
+-    elif method == "primesieve":
+-        if _do_sig(n): sig_on()
+-        ans = primecount.pi_primesieve(n)
+-        if _do_sig(n): sig_off()
+-    else:
+-        raise ValueError("unknown method {!r}".format(method))
+-
++    if _do_sig(n): sig_on()
++    ans = primecount.pi(n)
++    if _do_sig(n): sig_off()
+     return ans
+ 
+ cpdef prime_pi_128(n):
+     r"""
+-    Return the number of prime number smaller than ``n``.
++    Return the number of prime numbers smaller than ``n``.
+ 
+     EXAMPLES::
+ 
+diff -up src/sage/libs/primecount.pxd.orig src/sage/libs/primecount.pxd
+--- src/sage/libs/primecount.pxd.orig	2019-06-26 14:41:05.000000000 -0600
++++ src/sage/libs/primecount.pxd	2019-09-17 16:11:06.678851358 -0600
+@@ -9,13 +9,6 @@ cdef extern from "primecount.hpp" namesp
+ 
+     cppstring pi(const cppstring& x)
+ 
+-    int64_t pi_deleglise_rivat(int64_t x)
+-    int64_t pi_legendre(int64_t x)
+-    int64_t pi_lehmer(int64_t x)
+-    int64_t pi_lmo(int64_t x)
+-    int64_t pi_meissel(int64_t x)
+-    int64_t pi_primesieve(int64_t x)
+-
+     int64_t nth_prime(int64_t n)
+ 
+     int64_t phi(int64_t x, int64_t a)

sagemath.spec

@@ -77,7 +77,7 @@
 %endif
 
 # Spkg equivalents of required rpms; we pretend they are installed as spkgs.
-%global SAGE_REQUIRED_PKGS 4ti2-1.6.9 bliss-0.73 cbc-2.10.3 CoCoALib-0.99601 coxeter3-1.1 cryptominisat-5.6.8 database_cremona_ellcurve-%{cremona_ver} gap_packages-4.10.2 gmp-6.1.2 libsirocco-2.0 lrslib-070 mcqd-1.0 qepcad-B.1.72 saclib-2.2.7 surf-1.0.6-gcc6
+%global SAGE_REQUIRED_PKGS 4ti2-1.6.9 bliss-0.73 cbc-2.10.3 CoCoALib-0.99601 coxeter3-1.1 cryptominisat-5.6.8 database_cremona_ellcurve-%{cremona_ver} gap_packages-4.10.2 gmp-6.1.2 libsirocco-2.0 lrslib-070 mcqd-1.0 primecount-5.1 qepcad-B.1.72 saclib-2.2.7 surf-1.0.6-gcc6
 
 %ifarch %{ix86} x86_64
 %global SAGE_REQUIRED_PKGS %{SAGE_REQUIRED_PKGS} fes-0.2
@@ -95,7 +95,7 @@
 Name:		sagemath
 Summary:	A free open-source mathematics software system
 Version:	8.8
-Release:	5%{?dist}
+Release:	6%{?dist}
 # The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file
 # Additionally, every $files section has a comment with the license name
 # before files with that license
@@ -220,6 +220,9 @@ Patch32:	%{name}-sagenb-python3.patch
 # https://git.sagemath.org/sage.git/commit/?id=bbd5b28fc8e451bea4f87c2f2b0c27586386262a
 Patch33:	%{name}-formatargspec.patch
 
+# Adapt to primecount 5.x
+Patch34:	%{name}-primecount.patch
+
 BuildRequires:	4ti2
 BuildRequires:	arb-devel
 BuildRequires:	bliss-devel
@@ -242,6 +245,7 @@ BuildRequires:	gap
 BuildRequires:	GAPDoc
 BuildRequires:	gap-libs
 BuildRequires:	gap-pkg-atlasrep
+BuildRequires:	gap-pkg-corelg
 BuildRequires:	gap-pkg-crime
 BuildRequires:	gap-pkg-design
 BuildRequires:	gap-pkg-forms
@@ -250,6 +254,11 @@ BuildRequires:	gap-pkg-guava
 BuildRequires:	gap-pkg-hapcryst
 BuildRequires:	gap-pkg-hecke
 BuildRequires:	gap-pkg-jupyterviz
+BuildRequires:	gap-pkg-liealgdb
+BuildRequires:	gap-pkg-liepring
+BuildRequires:	gap-pkg-loops
+BuildRequires:	gap-pkg-mapclass
+BuildRequires:	gap-pkg-repsn
 BuildRequires:	gap-pkg-singular
 BuildRequires:	gap-pkg-sonata
 BuildRequires:	gap-pkg-toric
@@ -302,6 +311,7 @@ BuildRequires:	pari-seadata
 BuildRequires:	perl-generators
 BuildRequires:	planarity-devel
 BuildRequires:	ppl-devel
+BuildRequires:	primecount-devel
 BuildRequires:	pynac-devel
 BuildRequires:	python3-devel
 BuildRequires:	python3-cypari2-devel
@@ -419,6 +429,7 @@ Requires:	4ti2
 Requires:	cddlib-tools
 Requires:	gap
 Requires:	gap-pkg-atlasrep
+Requires:	gap-pkg-corelg
 Requires:	gap-pkg-crime
 Requires:	gap-pkg-design
 Requires:	gap-pkg-forms
@@ -427,6 +438,11 @@ Requires:	gap-pkg-guava
 Requires:	gap-pkg-hapcryst
 Requires:	gap-pkg-hecke
 Requires:	gap-pkg-jupyterviz
+Requires:	gap-pkg-liealgdb
+Requires:	gap-pkg-liepring
+Requires:	gap-pkg-loops
+Requires:	gap-pkg-mapclass
+Requires:	gap-pkg-repsn
 Requires:	gap-pkg-sonata
 Requires:	gap-pkg-toric
 Requires:	gfan
@@ -908,6 +924,7 @@ popd
 %patch31
 %patch32
 %patch33
+%patch34
 
 sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
     -e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
@@ -1889,7 +1906,7 @@ rm -fr %{SAGE_LOCAL}/var/lib/sage/installed/database_cremona_ellcurve-%{cremona_
 %lang(uk_UA) %{python3_sitearch}/sagenb/translations/uk_UA
 %if %{with bundled_widgetsnbextension}
 %config(noreplace) %{_sysconfdir}/jupyter/nbconfig/notebook.d/*.json
-%{_datadir}/jupyter/nbextensions/
+%{_datadir}/jupyter/nbextensions/*
 %{python3_sitelib}/widgetsnbextension*
 %endif
 %{_datadir}/jupyter/kernels/sagemath/
@@ -1916,6 +1933,11 @@ rm -fr %{SAGE_LOCAL}/var/lib/sage/installed/database_cremona_ellcurve-%{cremona_
 
 ########################################################################
 %changelog
+* Thu Sep 26 2019 Jerry James <loganjerry@gmail.com> - 8.8-6
+- Rebuild for ntl 11.4.0
+- Add primecount support, including the -primecount patch
+- Add still more gap packages, nearly finishing the set shipped by upstream
+
 * Thu Sep 12 2019 Jerry James <loganjerry@gmail.com> - 8.8-5
 - Improve the -ecm patch
 - Add -formatargspec patch to silence doc-building warnings