Merge branch 'master' into core-updates

9 files changed, 363 insertions, 25 deletions

diff --git a/gnu/packages/patches/emacs-zones-called-interactively.patch b/gnu/packages/patches/emacs-zones-called-interactively.patch
index b60f390a7e..eefcfdd12e 100644
--- a/gnu/packages/patches/emacs-zones-called-interactively.patch
+++ b/gnu/packages/patches/emacs-zones-called-interactively.patch
@@ -1,4 +1,4 @@
-From fb56fbb706804215ef9af0cc575db97c373046c6 Mon Sep 17 00:00:00 2001
+From 81603e53ebaae0f0b23c4c52c7dab83e808964ec Mon Sep 17 00:00:00 2001
 From: Brian Leung <bkleung89@gmail.com>
 Date: Sun, 17 Mar 2019 01:32:04 +0100
 Subject: [PATCH] This patch silences the byte-compiler.
@@ -8,36 +8,36 @@ Subject: [PATCH] This patch silences the byte-compiler.
  1 file changed, 3 insertions(+), 3 deletions(-)
 
 diff --git a/zones.el b/zones.el
-index 1bf94f0..94fa9a6 100644
+index ca88d48..594ea36 100644
 --- a/zones.el
 +++ b/zones.el
-@@ -1031,7 +1031,7 @@ You can use `C-x n x' to widen to a previous buffer restriction.
+@@ -1075,7 +1075,7 @@ You can use `C-x n x' to widen to a previous buffer restriction.
  
  This is a destructive operation. The list structure of the variable
  value can be modified."
 -  (zz-narrow-advice (interactive-p)))
-+  (zz-narrow-advice (called-interactively-p)))
++  (zz-narrow-advice (called-interactively-p 'interactive)))
  
  (defadvice narrow-to-defun (after zz-add-zone--defun activate)
    "Push the defun limits to the current `zz-izones-var'.
-@@ -1039,7 +1039,7 @@ You can use `C-x n x' to widen to a previous buffer restriction.
+@@ -1083,7 +1083,7 @@ You can use `C-x n x' to widen to a previous buffer restriction.
  
  This is a destructive operation. The list structure of the variable
  value can be modified."
 -  (zz-narrow-advice (interactive-p)))
-+  (zz-narrow-advice (called-interactively-p)))
++  (zz-narrow-advice (called-interactively-p 'interactive)))
  
  ;; Call `zz-add-zone' if interactive or `zz-add-zone-anyway-p'.
  ;;
-@@ -1049,7 +1049,7 @@ You can use `C-x n x' to widen to a previous buffer restriction.
+@@ -1093,7 +1093,7 @@ You can use `C-x n x' to widen to a previous buffer restriction.
  
  This is a destructive operation. The list structure of the variable
  value can be modified."
 -  (zz-narrow-advice (interactive-p)))
-+  (zz-narrow-advice (called-interactively-p)))
++  (zz-narrow-advice (called-interactively-p 'interactive)))
  
  ;;(@* "General Commands")
  
 -- 
-2.21.0
+2.22.0
 
diff --git a/gnu/packages/patches/khmer-use-libraries.patch b/gnu/packages/patches/khmer-use-libraries.patch
deleted file mode 100644
index 47d163a99a..0000000000
--- a/gnu/packages/patches/khmer-use-libraries.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Change setup.cfg so that the bundled zlib and bzip2 are not used.  This cannot
-currently be achieved using "--library z,bz2" as instructed in the setup.py.
-
-diff --git a/setup.cfg b/setup.cfg
-index c054092..080992e 100644
---- a/setup.cfg
-+++ b/setup.cfg
-@@ -1,7 +1,7 @@
- [build_ext]
- define = SEQAN_HAS_BZIP2,SEQAN_HAS_ZLIB
- undef = NO_UNIQUE_RC
--# libraries = z,bz2
-+libraries = z,bz2
- ## if using system libraries
- include-dirs = lib:third-party/zlib:third-party/bzip2:third-party/seqan/core/include:third-party/smhasher
- # include-dirs = lib
diff --git a/gnu/packages/patches/lcalc-default-parameters-1.patch b/gnu/packages/patches/lcalc-default-parameters-1.patch
new file mode 100644
index 0000000000..19b0776320
--- /dev/null
+++ b/gnu/packages/patches/lcalc-default-parameters-1.patch
@@ -0,0 +1,26 @@
+Patch taken from the Sage packaging system.
+
+diff -Naur lcalc-1.23-vanilla/include/Ldirichlet_series.h lcalc-1.23-fixed-gcc.4.9/include/Ldirichlet_series.h
+--- lcalc-1.23-vanilla/include/Ldirichlet_series.h	2012-08-08 23:21:55.000000000 +0200
++++ lcalc-1.23-fixed-gcc.4.9/include/Ldirichlet_series.h	2014-04-21 14:37:59.027464849 +0200
+@@ -43,7 +43,7 @@
+  //XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
+ template <class ttype>
+ Complex L_function <ttype>::
+-dirichlet_series(Complex s, long long N=-1)
++dirichlet_series(Complex s, long long N)
+ {
+     Complex z=0.;
+     long long m,n;
+diff -Naur lcalc-1.23-vanilla/include/L.h lcalc-1.23-fixed-gcc.4.9/include/L.h
+--- lcalc-1.23-vanilla/include/L.h	2012-08-08 23:21:55.000000000 +0200
++++ lcalc-1.23-fixed-gcc.4.9/include/L.h	2014-04-21 14:32:04.003467348 +0200
+@@ -491,7 +491,7 @@
+ 
+     //#include "Ldirichlet_series.h" //for computing Dirichlet series
+     Complex partial_dirichlet_series(Complex s, long long N1, long long N2);
+-    Complex dirichlet_series(Complex s, long long N);
++    Complex dirichlet_series(Complex s, long long N=-1LL);
+ 
+     //#include "Ltaylor_series.h" //for computing taylor series for Dirichlet series
+     //void compute_taylor_series(int N, int K, Complex s_0, Complex *series);
diff --git a/gnu/packages/patches/lcalc-default-parameters-2.patch b/gnu/packages/patches/lcalc-default-parameters-2.patch
new file mode 100644
index 0000000000..1d881ee0c4
--- /dev/null
+++ b/gnu/packages/patches/lcalc-default-parameters-2.patch
@@ -0,0 +1,58 @@
+Patch taken from the Sage packaging system.
+
+--- lcalc-1.23/include/Lgamma.h	2012-08-08 23:21:55.000000000 +0200
++++ lcalc-1.23/include/Lgamma.h	2014-05-18 21:15:27.786889718 +0200
+@@ -77,7 +77,7 @@
+ //n=0 should just give log_GAMMA(z)... thus making log_GAMMA
+ //code obsolete. But leave log_GAMMA intact anyways.
+ template <class ttype>
+-precise(ttype) log_GAMMA (ttype z,int n=0)
++precise(ttype) log_GAMMA (ttype z,int n)
+ {
+     int M;
+     precise(ttype) log_G,r,r2,y;
+@@ -230,7 +230,7 @@
+ //value exp_w which holds exp(-w)
+ //computes G(z,w), so there's an extra w^(-z) factor.
+ template <class ttype>
+-Complex inc_GAMMA (ttype z,ttype w, const char *method="temme", ttype exp_w = 0, bool recycle=false)
++Complex inc_GAMMA (ttype z,ttype w, const char *method, ttype exp_w, bool recycle)
+ {
+ 
+     Complex G;
+@@ -334,7 +334,7 @@
+ 
+ 
+ template <class ttype>
+-ttype cfrac_GAMMA (ttype z,ttype w, ttype exp_w=0, bool recycle=false)  //computes G(z,w) via continued fraction
++ttype cfrac_GAMMA (ttype z,ttype w, ttype exp_w, bool recycle)  //computes G(z,w) via continued fraction
+ {
+ 
+         ttype G;
+@@ -424,7 +424,7 @@
+ }
+ 
+ template <class ttype>
+-ttype asympt_GAMMA (ttype z,ttype w, ttype exp_w = 0, bool recycle=false)  //computes G(z,w) via asymptotic series
++ttype asympt_GAMMA (ttype z,ttype w, ttype exp_w, bool recycle)  //computes G(z,w) via asymptotic series
+ {
+ 
+         if(my_verbose>3) cout << "called asympt_GAMMA("<<z<<","<<w<<")"<< endl;
+@@ -446,7 +446,7 @@
+ 
+ 
+ template <class ttype>
+-ttype comp_inc_GAMMA (ttype z,ttype w,ttype exp_w = 0, bool recycle=false)  //computes g(z,w)
++ttype comp_inc_GAMMA (ttype z,ttype w,ttype exp_w, bool recycle)  //computes g(z,w)
+ {
+ 
+     ttype g;
+@@ -604,7 +604,7 @@
+ }
+ 
+ template <class ttype>
+-Complex gamma_sum(Complex s, int what_type, ttype *coeff, int N, Double g, Complex l, Double Q, Long Period, Complex delta=1, const char *method="temme")
++Complex gamma_sum(Complex s, int what_type, ttype *coeff, int N, Double g, Complex l, Double Q, Long Period, Complex delta, const char *method)
+ {
+     Complex SUM=0;
+ 
diff --git a/gnu/packages/patches/lcalc-lcommon-h.patch b/gnu/packages/patches/lcalc-lcommon-h.patch
new file mode 100644
index 0000000000..897956de64
--- /dev/null
+++ b/gnu/packages/patches/lcalc-lcommon-h.patch
@@ -0,0 +1,13 @@
+Patch taken from the Sage packaging system.
+
+--- src/include/Lcommon.h	2010-01-31 15:16:45.000000000 +0000
++++ src/include/Lcommon.h	2011-03-08 21:19:11.849443238 +0000
+@@ -25,7 +25,7 @@
+ #ifdef USE_MPFR
+ inline double lcalc_to_double(const double& x) { return x; }
+ #endif
+-//inline double lcalc_to_double(const long double& x) { return x; }
++inline double lcalc_to_double(const long double& x) { return x; }
+ inline double lcalc_to_double(const int& x) { return x; }
+ inline double lcalc_to_double(const long long& x) { return x; }
+ inline double lcalc_to_double(const short& x) { return x; }
diff --git a/gnu/packages/patches/lcalc-using-namespace-std.patch b/gnu/packages/patches/lcalc-using-namespace-std.patch
new file mode 100644
index 0000000000..6e0075fdc8
--- /dev/null
+++ b/gnu/packages/patches/lcalc-using-namespace-std.patch
@@ -0,0 +1,43 @@
+Patch taken from the Sage packaging system.
+
+diff --git a/include/Lcommon.h b/include/Lcommon.h
+index 1b3be43..bf40532 100644
+--- a/include/Lcommon.h
++++ b/include/Lcommon.h
+@@ -48,7 +48,7 @@ const bool outputSeries=true;	  // Whether to output the coefficients or just th
+ 
+ // Loop i from m to n
+ // Useful in tidying up most for loops
+-#define loop(i,m,n) for(typeof(m) i=(m); i!=(n); i++)
++#define loop(i,m,n) for(auto i=(m); i!=(n); i++)
+ 
+ // A class for calculations involving polynomials of small degree
+ // Not efficient enough for huge polynomials
+diff --git a/include/Lcommon_ld.h b/include/Lcommon_ld.h
+index 86ae4df..33c560c 100644
+--- a/include/Lcommon_ld.h
++++ b/include/Lcommon_ld.h
+@@ -53,7 +53,7 @@ const bool outputSeries=true;	  // Whether to output the coefficients or just th
+ 
+ // Loop i from m to n
+ // Useful in tidying up most for loops
+-#define loop(i,m,n) for(typeof(m) i=(m); i!=(n); i++)
++#define loop(i,m,n) for(auto i=(m); i!=(n); i++)
+ 
+ // A class for calculations involving polynomials of small degree
+ // Not efficient enough for huge polynomials
+diff --git a/include/Lglobals.h b/include/Lglobals.h
+index 60002e4..ca2606c 100644
+--- a/include/Lglobals.h
++++ b/include/Lglobals.h
+@@ -24,9 +24,9 @@
+ #ifndef Lglobals_H
+ #define Lglobals_H
+ 
++#include <valarray>
+ using namespace std;
+ 
+-#include <valarray>
+ #ifdef USE_MPFR
+     #include "Lgmpfrxx.h"
+     typedef mpfr_class Double;
diff --git a/gnu/packages/patches/leela-zero-gtest.patch b/gnu/packages/patches/leela-zero-gtest.patch
new file mode 100644
index 0000000000..7291b4ab72
--- /dev/null
+++ b/gnu/packages/patches/leela-zero-gtest.patch
@@ -0,0 +1,40 @@
+Use shared gtest instead of submodule
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 617e4b2..2857875 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -18,7 +18,6 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+ include(GNUInstallDirs)
+ 
+ project(leelaz)
+-add_subdirectory(gtest EXCLUDE_FROM_ALL) # We don't want to install gtest, exclude it from `all`
+ 
+ # Required Packages
+ set(Boost_MIN_VERSION "1.58.0")
+@@ -27,6 +26,7 @@ find_package(Boost 1.58.0 REQUIRED program_options filesystem)
+ find_package(Threads REQUIRED)
+ find_package(ZLIB REQUIRED)
+ find_package(OpenCL REQUIRED)
++find_package(GTest REQUIRED)
+ # We need OpenBLAS for now, because we make some specific
+ # calls. Ideally we'd use OpenBLAS is possible and fall back to
+ # not doing those calls if it's not present.
+@@ -93,6 +93,7 @@ include_directories(${IncludePath})
+ include_directories(${Boost_INCLUDE_DIRS})
+ include_directories(${OpenCL_INCLUDE_DIRS})
+ include_directories(${ZLIB_INCLUDE_DIRS})
++include_directories(${GTEST_INCLUDE_DIRS})
+ 
+ if((UNIX AND NOT APPLE) OR WIN32)
+     include_directories(${BLAS_INCLUDE_DIRS})
+@@ -141,7 +142,8 @@ target_link_libraries(tests ${Boost_LIBRARIES})
+ target_link_libraries(tests ${BLAS_LIBRARIES})
+ target_link_libraries(tests ${OpenCL_LIBRARIES})
+ target_link_libraries(tests ${ZLIB_LIBRARIES})
+-target_link_libraries(tests gtest_main ${CMAKE_THREAD_LIBS_INIT})
++target_link_libraries(tests ${GTEST_BOTH_LIBRARIES})
++target_link_libraries(tests ${CMAKE_THREAD_LIBS_INIT})
+ 
+ include(GetGitRevisionDescription)
+ git_describe(VERSION --tags)
diff --git a/gnu/packages/patches/lrcalc-includes.patch b/gnu/packages/patches/lrcalc-includes.patch
new file mode 100644
index 0000000000..e15286905b
--- /dev/null
+++ b/gnu/packages/patches/lrcalc-includes.patch
@@ -0,0 +1,92 @@
+Patch taken from the Sage packaging system.
+
+From 4a5e1c8c3c11efdb1cbb4239825a6bf4bf1c52f8 Mon Sep 17 00:00:00 2001
+From: Anders Skovsted Buch <asbuch@math.rutgers.edu>
+Date: Sun, 29 Nov 2015 16:25:56 -0500
+Subject: [PATCH] Patch by Jeroen Demeyer to change include <vector.h> to
+ "vector.h", plus similar cases.
+
+---
+ src/lrcalc.c   | 2 +-
+ src/maple.c    | 4 ++--
+ src/schublib.h | 2 +-
+ src/symfcn.c   | 6 +++---
+ src/symfcn.h   | 4 ++--
+ 5 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/src/lrcalc.c b/src/lrcalc.c
+index aff3f75..60df49e 100644
+--- a/src/lrcalc.c
++++ b/src/lrcalc.c
+@@ -8,7 +8,7 @@
+ #include <stdlib.h>
+ extern char *optarg;
+ 
+-#include <vectarg.h>
++#include "vectarg.h"
+ 
+ #include "symfcn.h"
+ #include "maple.h"
+diff --git a/src/maple.c b/src/maple.c
+index fdc0768..a5f4d14 100644
+--- a/src/maple.c
++++ b/src/maple.c
+@@ -4,8 +4,8 @@
+  */
+ 
+ #include <stdio.h>
+-#include <vector.h>
+-#include <hashtab.h>
++#include "vector.h"
++#include "hashtab.h"
+ #include "maple.h"
+ 
+ 
+diff --git a/src/schublib.h b/src/schublib.h
+index a8e8511..864850c 100644
+--- a/src/schublib.h
++++ b/src/schublib.h
+@@ -1,7 +1,7 @@
+ #ifndef _SCHUBLIB_H
+ #define _SCHUBLIB_H
+ 
+-#include <hashtab.h>
++#include "hashtab.h"
+ 
+ hashtab *trans(vector *w, int vars, hashtab *res);
+ hashtab *monk(int i, hashtab *slc, int rank);
+diff --git a/src/symfcn.c b/src/symfcn.c
+index 4ffbe4b..fd5df5d 100644
+--- a/src/symfcn.c
++++ b/src/symfcn.c
+@@ -5,9 +5,9 @@
+ 
+ #include <stdio.h>
+ 
+-#include <alloc.h>
+-#include <vector.h>
+-#include <hashtab.h>
++#include "alloc.h"
++#include "vector.h"
++#include "hashtab.h"
+ 
+ #include "symfcn.h"
+ 
+diff --git a/src/symfcn.h b/src/symfcn.h
+index b8543b1..29bb00d 100644
+--- a/src/symfcn.h
++++ b/src/symfcn.h
+@@ -1,8 +1,8 @@
+ #ifndef _SYMFCN_H
+ #define _SYMFCN_H
+ 
+-#include <hashtab.h>
+-#include <vector.h>
++#include "hashtab.h"
++#include "vector.h"
+ 
+ int part_itr_sz(vector *part);
+ int part_itr_sub(vector *part, vector *outer);
+-- 
+2.1.1.1.g1fb337f
+
diff --git a/gnu/packages/patches/python-pyatspi-python-37.patch b/gnu/packages/patches/python-pyatspi-python-37.patch
new file mode 100644
index 0000000000..caa6aea39e
--- /dev/null
+++ b/gnu/packages/patches/python-pyatspi-python-37.patch
@@ -0,0 +1,82 @@
+From 29a7b929f7f1160b643dc5f5911533887173fcff Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Miro=20Hron=C4=8Dok?= <miro@hroncok.cz>
+Date: Thu, 28 Jun 2018 17:10:33 +0200
+Subject: [PATCH] Rename async to asynchronous, keep backwards comaptibility
+
+async is a keyword in Python 3.7 and keeping it results in SyntaxError.
+
+Fixes https://gitlab.gnome.org/GNOME/pyatspi2/issues/1
+---
+ pyatspi/registry.py | 35 +++++++++++++++++++++++++++--------
+ 1 file changed, 27 insertions(+), 8 deletions(-)
+
+diff --git a/pyatspi/registry.py b/pyatspi/registry.py
+index cb28395..f73ee16 100644
+--- a/pyatspi/registry.py
++++ b/pyatspi/registry.py
+@@ -50,9 +50,9 @@ class Registry(object):
+         reference to the Accessibility.Registry singleton. Doing so is harmless and
+         has no point.
+ 
+-        @@ivar async: Should event dispatch to local listeners be decoupled from event
+-                receiving from the registry?
+-        @@type async: boolean
++        @@ivar asynchronous: Should event dispatch to local listeners be decoupled
++                from event receiving from the registry?
++        @@type asynchronous: boolean
+         @@ivar reg: Reference to the real, wrapped registry object
+         @@type reg: Accessibility.Registry
+         @@ivar dev: Reference to the device controller
+@@ -111,25 +111,44 @@ class Registry(object):
+ 
+                 self.has_implementations = True
+ 
+-                self.async = False	# not fully supported yet
++                self.asynchronous = False	# not fully supported yet
+                 self.started = False
+                 self.event_listeners = dict()
+ 
++        def __getattr__(self, name):
++            """
++            For backwards compatibility with old API
++            """
++            if name == 'async':
++                return self.asynchronous
++            return object.__getattr__(self, name)
++
++        def __setattr__(self, name, value):
++            """
++            For backwards compatibility with old API
++            """
++            if name == 'async':
++                self.asynchronous = value
++            object.__setattr__(self, name, value)
++
+         def _set_default_registry (self):
+                 self._set_registry (MAIN_LOOP_GLIB)
+ 
+-        def start(self, async=False, gil=True):
++        def start(self, asynchronous=False, gil=True, **kwargs):
+                 """
+                 Enter the main loop to start receiving and dispatching events.
+ 
+-                @@param async: Should event dispatch be asynchronous (decoupled) from 
+-                        event receiving from the AT-SPI registry?
+-                @@type async: boolean
++                @@param asynchronous: Should event dispatch be asynchronous
++                        (decoupled) from event receiving from the AT-SPI registry?
++                @@type asynchronous: boolean
+                 @@param gil: Add an idle callback which releases the Python GIL for a few
+                         milliseconds to allow other threads to run? Necessary if other threads
+                         will be used in this process.
+                 @@type gil: boolean
+                 """
++                if 'async' in kwargs:
++                    # support previous API
++                    asynchronous = kwargs['async']
+                 if not self.has_implementations:
+                         self._set_default_registry ()
+                 self.started = True
+-- 
+2.22.0
+