Merge tag '9.1.beta2' into t/29053/installation_manual__generate__apt…

…_get_install__and__yum_install__lines_from_build_pkgs_at___bootstrap_time

SageMath version 9.1.beta2, Release Date: 2020-01-26

.lgtm.yml

@@ -6,6 +6,11 @@ path_classifiers:
   imports_only:
     - "**/all.py"
     - "**/*catalog*.py"
+    - "**/species/library.py"
+    - "**/matroids/advanced.py"
+    - "**/categories/basic.py"
+    - "**/interacts/geometry.py"
+    - "**/combinat/ribbon.py"
 extraction:
   python:
     python_setup:

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.1.beta1, Release Date: 2020-01-21
+SageMath version 9.1.beta2, Release Date: 2020-01-26

bootstrap

@@ -75,7 +75,7 @@ install_config_rpath() {
 bootstrap () {
     rm -f m4/sage_spkg_configures.m4
     spkg_configures=""
-    for filename in $(find build/pkgs -type f -name spkg-configure.m4); do
+    for filename in $(find build/pkgs -type f -name spkg-configure.m4 | sort); do
         pkgname="$(echo $filename | cut -d/ -f3)"
         echo "m4_sinclude([$filename])" >> m4/sage_spkg_configures.m4
         spkg_configures="$spkg_configures

build/make/deps

@@ -170,6 +170,7 @@ sagelib: \
 		$(inst_ratpoints) \
 		$(inst_readline) \
 		$(inst_rw) \
+		$(inst_sage_conf) \
 		$(inst_singular) \
 		$(inst_six) \
 		$(inst_symmetrica) \

build/make/install

@@ -72,38 +72,51 @@ The following package(s) may have failed to build (not necessarily
 during this run of 'make $@'):
 EOF
 
-    for f in "$SAGE_LOGS"/*.log; do
+    # Sort in chronological order by log file.
+    for f in `ls -tr "$SAGE_LOGS"/*.log 2>/dev/null`; do
         # Look for recent error message in log file.
         # Note that "tail -n 20 ..." doesn't work on Solaris.
         if tail -20 "$f" 2>/dev/null | grep "^Error" &>/dev/null; then
             base_f=`basename $f .log`
+            # stat(1) is not portable between Linux and macOS, so we extract it from ls -lf
+            timestamp=`ls -l $f | awk -F' ' '{print $6, $7, $8}'` 2> /dev/null
             cat >&2 <<EOF
 
-* package: $base_f
-  log file: $f
-  build directory: ${SAGE_BUILD_DIR:-$SAGE_LOCAL/var/tmp/sage/build}/$base_f
+* package:         $base_f
+  last build time: $timestamp
+  log file:        $f
 EOF
+            build_dir="${SAGE_BUILD_DIR:-$SAGE_LOCAL/var/tmp/sage/build}/$base_f"
+            if [ -d "$build_dir" ]; then
+                cat >&2 <<EOF
+  build directory: $build_dir
+EOF
+            fi
         fi
     done
 
-    for f in "$SAGE_LOGS"/../doc*.log; do
+    for f in `ls -tr "$SAGE_LOGS"/../doc*.log 2>/dev/null`; do
         # Look for recent error message in log file.
         # Note that "tail -n 20 ..." doesn't work on Solaris.
         if tail -100 "$f" 2>/dev/null | grep "^Error" &>/dev/null; then
             base_f=`basename $f .log`
+            # stat(1) is not portable between Linux and macOS, so we extract it from ls -lf
+            timestamp=`ls -l $f | awk -F' ' '{print $6, $7, $8}'` 2> /dev/null
             cat >&2 <<EOF
 
-* documentation: $base_f
-  log file: $f
+* documentation:   $base_f
+  last build time: $timestamp
+  log file:        $f
 EOF
         fi
     done
     cat >&2 <<EOF
 
-The build directory may contain configuration files and other potentially
-helpful information. WARNING: if you now run 'make' again, the build
-directory will, by default, be deleted. Set the environment variable
-SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.
+It is safe to delete any log files and build directories, but they
+contain information that is helpful for debugging build problems.
+WARNING: If you now run 'make' again, the build directory of the
+same version of the package will, by default, be deleted. Set the
+environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
 
 EOF
     exit 1

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=029fe778cefcb82231353c0dab72a75769ffdcf9
-md5=b4231b3e4ce67fc656ba9532b123485a
-cksum=3808756319
+sha1=bbd3a48fc6eb8028e3a868f51d0412a564e4ec78
+md5=d90a07adfc2c87e48c9b8c54bc3d3b33
+cksum=1392125278

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-4fd5d56ecea2c81d58e9e43bd5f07b05e863bc7c
+fb9218e13b0d6e9ddfd7453d41e8111780b40214

build/pkgs/m4ri/checksums.ini

@@ -1,4 +1,4 @@
 tarball=m4ri-VERSION.tar.gz
-sha1=87d9ad087938f32ada502b12991f02f4e20224ff
-md5=91d964b6c6754499da81277433605199
-cksum=4106591812
+sha1=7d0d680f1e983c1d5b24e49f25194e2f327690b4
+md5=3fb6a27437bf535128d605fe47c8fae8
+cksum=1002661464

build/pkgs/m4ri/package-version.txt

@@ -1 +1 @@
-20140914.p0
+20200115

build/pkgs/m4ri/patches/mzd_fix.patch

@@ -0,0 +1,76 @@
+diff --git a/m4ri/mzd.c b/m4ri/mzd.c
+index 861905c..922dc3c 100644
+--- a/m4ri/mzd.c
++++ b/m4ri/mzd.c
+@@ -1894,7 +1894,7 @@ mzd_t *mzd_submatrix(mzd_t *S, mzd_t const *M, rci_t const startrow, rci_t const
+   } else {
+     wi_t j;
+     for(rci_t i=0; i<nrows; i++) {
+-      for(j=0; j+m4ri_radix<=ncols; j+=m4ri_radix)
++      for(j=0; j+m4ri_radix<ncols; j+=m4ri_radix)
+         S->rows[i][j/m4ri_radix] = mzd_read_bits(M, startrow+i, startcol+j, m4ri_radix);
+       S->rows[i][j/m4ri_radix] &= ~S->high_bitmask;
+       S->rows[i][j/m4ri_radix] |= mzd_read_bits(M, startrow+i, startcol+j, ncols - j) & S->high_bitmask;
+diff --git a/tests/test_misc.c b/tests/test_misc.c
+index a9a9547..b1a2e32 100644
+--- a/tests/test_misc.c
++++ b/tests/test_misc.c
+@@ -76,6 +76,31 @@ int test_png(rci_t m, rci_t n) {
+   return ret;
+ }
+
++int test_submatrix(const rci_t m, const rci_t n, const rci_t lowr, const rci_t lowc, const rci_t highr, const rci_t highc) {
++  printf("submatrix: m: %4d, n: %4d, (%4d, %4d, %4d, %4d)", m, n, lowr, lowc, highr, highc);
++  assert(highr-lowr > 0);
++  assert(highc-lowc > 0);
++  mzd_t *M = mzd_init(m, n);
++  mzd_randomize(M);
++  mzd_t *S = mzd_init(highr-lowr, highc-lowc);
++  mzd_submatrix(S, M, lowr, lowc, highr, highc);
++  int ret = 0;
++  for(rci_t i=0; i<highr-lowr; i++) {
++    for(rci_t j=0; j<highc-lowc; j++) {
++      ret += (mzd_read_bit(M, lowr+i, lowc+j) ^ mzd_read_bit(S, i, j));
++    }
++  }
++
++  mzd_free(M);
++  mzd_free(S);
++
++  if(ret==0) {
++    printf(" ... passed\n");
++  } else {
++    printf(" ... FAILED\n");
++  }
++  return ret;
++}
+
+ int main(int argc, char *argv[]) {
+   int status = 0;
+@@ -99,6 +124,23 @@ int main(int argc, char *argv[]) {
+   status += test_png(126,12);
+   status += test_png(128,200);
+
++  status += test_submatrix(2, 127, 1, 1, 2, 127);
++  status += test_submatrix(2, 128, 1, 1, 2, 128);
++  status += test_submatrix(2, 129, 1, 1, 2, 129);
++  status += test_submatrix(2, 130, 1, 1, 2, 130);
++  status += test_submatrix(2, 131, 1, 1, 2, 131);
++
++  status += test_submatrix(2, 63, 1, 1, 1, 63);
++  status += test_submatrix(2, 64, 1, 1, 1, 64);
++  status += test_submatrix(2, 65, 1, 1, 1, 65);
++  status += test_submatrix(2, 66, 1, 1, 1, 66);
++  status += test_submatrix(2, 67, 1, 1, 1, 67);
++
++  status += test_submatrix(2, 127, 1, 63, 2, 127);
++  status += test_submatrix(2, 128, 1, 64, 2, 128);
++  status += test_submatrix(2, 129, 1, 65, 2, 129);
++  status += test_submatrix(2, 130, 1, 66, 2, 130);
++
+   if (!status) {
+     printf("All tests passed.\n");
+   } else {
+-- 
+2.10.5
+

build/pkgs/m4rie/checksums.ini

@@ -1,4 +1,4 @@
 tarball=m4rie-VERSION.tar.gz
-sha1=d0c5407046131184fc34056d478c8b4e9e22bb1a
-md5=c2c04cbfcc5d56ffdeb5133109272b8c
-cksum=1547829740
+sha1=728524509dd30da2dc960814b61d0bae67f83043
+md5=e7685c63e7bab4c5a0922a161499ba83
+cksum=127676695

build/pkgs/m4rie/package-version.txt

@@ -1 +1 @@
-20150908.p0
+20200115

build/pkgs/planarity/spkg-configure.m4

@@ -0,0 +1,20 @@
+SAGE_SPKG_CONFIGURE([planarity], [
+     AC_LANG_PUSH([C])
+     AC_CHECK_HEADER([planarity/planarity.h], [
+        AC_CHECK_LIB([planarity], [gp_InitGraph], [
+         AC_MSG_CHECKING([for planarity version 3.0 or later])
+         AC_COMPILE_IFELSE(
+          [AC_LANG_PROGRAM(
+            [[#include <planarity/graphStructures.h>]],
+            [[vertexRec v;]
+             [v.link[0]=1;]])
+          ], [
+           AC_MSG_RESULT([yes])
+          ], [
+           AC_MSG_RESULT([no])
+           sage_spkg_install_planarity=yes
+        ])
+       ], [sage_spkg_install_planarity=yes])
+        ], [sage_spkg_install_planarity=yes])
+     AC_LANG_POP()
+])

build/pkgs/sage_conf/README.rst

@@ -0,0 +1,2 @@
+This is a module that provides configuration information to sagelib
+at the time of its installation and at its runtime.

build/pkgs/sage_conf/dependencies

@@ -0,0 +1 @@
+$(PYTHON) ../pkgs/sage_conf/src/sage_conf.py ../pkgs/sage_conf/src/setup.cfg | pip setuptools

build/pkgs/sage_conf/spkg-install

@@ -0,0 +1,12 @@
+#! /usr/bin/env bash
+# From sage-spkg.
+# For type=script packages, the build rule in build/make/Makefile sources
+# sage-env but not sage-dist-helpers.
+lib="$SAGE_ROOT/build/bin/sage-dist-helpers"
+source "$lib"
+if [ $? -ne 0 ]; then
+    echo >&2 "Error: failed to source $lib"
+    echo >&2 "Is $SAGE_ROOT the correct SAGE_ROOT?"
+    exit 1
+fi
+cd $SAGE_ROOT/build/pkgs/sage_conf/src && sdh_pip_install .

build/pkgs/sage_conf/src/.gitignore

@@ -0,0 +1,2 @@
+/sage_conf.py
+/setup.cfg

build/pkgs/sage_conf/src/sage_conf.py.in

@@ -0,0 +1,31 @@
+# @configure_input@
+
+VERSION = "@PACKAGE_VERSION@"
+
+MAXIMA = "@prefix@/bin/maxima"
+
+# The following must not be used during build to determine source or installation
+# location of sagelib.  See comments in SAGE_ROOT/src/Makefile.in
+SAGE_LOCAL = "@prefix@"
+SAGE_ROOT = "@abs_top_srcdir@"
+
+# Entry point 'sage-config'.  It does not depend on any packages.
+
+def _main():
+    from argparse import ArgumentParser
+    from sys import exit, stdout
+    parser = ArgumentParser()
+    parser.add_argument('--version', help="show version", action="version",
+                       version='%(prog)s ' + VERSION)
+    parser.add_argument("VARIABLE", nargs='?', help="output the value of VARIABLE")
+    args = parser.parse_args()
+    d = globals()
+    if args.VARIABLE:
+        stdout.write('{}\n'.format(d[args.VARIABLE]))
+    else:
+        for k, v in d.items():
+            if not k.startswith('_'):
+                stdout.write('{}={}\n'.format(k, v))
+
+if __name__ == "__main__":
+    _main()

build/pkgs/sage_conf/src/setup.cfg.in

@@ -0,0 +1,19 @@
+# @configure_input@
+
+[metadata]
+name = sage_conf
+version = @PACKAGE_VERSION@
+description = Sage: Open Source Mathematics Software: Configuration for sagelib
+long_description = file: README.rst
+license = GNU General Public License (GPL) v3 or later
+author = The Sage Developers
+author_email = https://groups.google.com/group/sage-support
+url = https://www.sagemath.org
+
+[options]
+py_modules =
+    sage_conf
+
+[options.entry_points]
+console_scripts =
+    sage-config = sage_conf:_main

build/pkgs/sage_conf/src/setup.py

@@ -0,0 +1,2 @@
+from setuptools import setup
+setup()

build/pkgs/sage_conf/type

@@ -0,0 +1 @@
+script

build/pkgs/sqlite/spkg-configure.m4

@@ -0,0 +1,34 @@
+SAGE_SPKG_CONFIGURE([sqlite], [
+  m4_pushdef([SAGE_SQLITE3_MIN_VERSION_MAJOR], [3])
+  m4_pushdef([SAGE_SQLITE3_MIN_VERSION_MINOR], [8])
+  m4_pushdef([SAGE_SQLITE3_MIN_VERSION_MICRO], [7])
+  m4_pushdef([SAGE_SQLITE3_MIN_VERSION], [SAGE_SQLITE3_MIN_VERSION_MAJOR.SAGE_SQLITE3_MIN_VERSION_MINOR.SAGE_SQLITE3_MIN_VERSION_MICRO])
+  AC_MSG_CHECKING([libsqlite3 >= sqlite3_min_version])
+                     dnl https://www.sqlite.org/c3ref/libversion.html
+                     dnl https://www.sqlite.org/c3ref/c_source_id.html
+                     SQLITE_SAVED_LIBS="$LIBS"
+                     LIBS="$LIBS -lsqlite3"
+                     AC_RUN_IFELSE([
+                       AC_LANG_PROGRAM([[
+                                         #include <sqlite3.h>
+                                         #include <assert.h>
+                                         #include <stdlib.h>
+                                         #include <string.h>
+                                       ]],
+                                       [[
+                                         assert( strcmp(sqlite3_libversion(),SQLITE_VERSION)==0 );
+                                         if (SQLITE_VERSION_NUMBER < ]]SAGE_SQLITE3_MIN_VERSION_MAJOR[[*1000000 + ]]SAGE_SQLITE3_MIN_VERSION_MINOR[[*1000 + ]]SAGE_SQLITE3_MIN_VERSION_MICRO[[)
+                                           exit(1);
+                                         else
+                                           exit(0);
+                                       ]])
+                       ],
+                       [AC_MSG_RESULT([yes])],
+                       [AC_MSG_RESULT([no])
+                        LIBS="$SQLITE_SAVED_LIBS"
+                        sage_spkg_install_sqlite=yes])
+  m4_popdef([SAGE_SQLITE3_MIN_VERSION_MAJOR])
+  m4_popdef([SAGE_SQLITE3_MIN_VERSION_MINOR])
+  m4_popdef([SAGE_SQLITE3_MIN_VERSION_MICRO])
+  m4_popdef([SAGE_SQLITE3_MIN_VERSION])
+])

build/pkgs/tides/spkg-check

@@ -1,2 +1,2 @@
 cd src
-$MAKE check
+sdh_make check AM_CFLAGS="" AM_FFLAGS=""

build/sage_bootstrap/download/app.py

@@ -4,18 +4,16 @@
 """
 
 
-#*****************************************************************************
+# ****************************************************************************
 #       Copyright (C) 2016 Volker Braun <vbraun.name@gmail.com>
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 2 of the License, or
 # (at your option) any later version.
-#                  http://www.gnu.org/licenses/
-#*****************************************************************************
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
 
-import os
-import sys
 import logging
 log = logging.getLogger()