Merge tag '9.6.beta4' into t/33465/sage_graphs__use_executable_absolu…

…te_filename__

SageMath version 9.6.beta4, Release Date: 2022-03-08

.github/workflows/build.yml

@@ -22,7 +22,10 @@ jobs:
         run: |
           # Reuse built SAGE_LOCAL contained in the Docker image 
           ./bootstrap
-          ./configure --enable-build-as-root --prefix=/sage/local --with-sage-venv
+          ./configure --enable-build-as-root --prefix=/sage/local --with-sage-venv --enable-editable
+          # Install test tools
+          apt-get install -y git
+          ./sage -python -m pip install coverage
       
       - name: Build
         run: make build
@@ -31,4 +34,18 @@ jobs:
           SAGE_NUM_THREADS: 2
 
       - name: Test
-        run: ./sage -t --all -p0
+        run: ../sage -python -m coverage run ./bin/sage-runtests --all -p2
+        working-directory: ./src
+
+      - name: Prepare coverage results
+        if: always()
+        run: |
+          ./venv/bin/python3 -m coverage combine src/.coverage/
+          ./venv/bin/python3 -m coverage xml
+          find . -name *coverage*
+      
+      - name: Upload coverage to codecov
+        if: always()
+        uses: codecov/codecov-action@v2
+        with:
+          files: ./coverage.xml

.github/workflows/ci-cygwin-minimal.yml

@@ -217,7 +217,7 @@ jobs:
     env:
       STAGE: ii-b
       PREVIOUS_STAGES: i-*
-      TARGETS: singular maxima gap pari gfan palp flintqs ratpoints arb ecm givaro
+      TARGETS: singular maxima gap pari gfan palp flintqs arb ecm givaro
       LOCAL_ARTIFACT_NAME: sage-local-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
 

.github/workflows/ci-cygwin-standard.yml

@@ -217,7 +217,7 @@ jobs:
     env:
       STAGE: ii-b
       PREVIOUS_STAGES: i-*
-      TARGETS: singular maxima gap pari gfan palp flintqs ratpoints arb ecm givaro
+      TARGETS: singular maxima gap pari gfan palp flintqs arb ecm givaro
       LOCAL_ARTIFACT_NAME: sage-local-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
 

.github/workflows/lint.yml

@@ -2,6 +2,11 @@ name: Lint
 
 on: [push, pull_request]
 
+concurrency:
+  # Cancel previous runs of this workflow for the same branch
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   lint-pycodestyle:
     name: Code style check with pycodestyle

.gitignore

@@ -213,6 +213,9 @@ src/venv.bak/
 **/.tox
 /prefix
 
+# code coverage generated files
+src/.coverage/
+
 # git worktree
 worktree*
 **/worktree*

.vscode/settings.json

@@ -1,16 +1,22 @@
 {
-    "python.defaultInterpreterPath": "./venv/bin/python",
-    "python.pythonPath": "./venv/bin/python",
+    "python.defaultInterpreterPath": "./venv/bin/python3",
     "files.exclude": {
         "**/__pycache__": true,
         "src/**/*.cpp": true,
         "src/**/*.so": true,
-        "build/pkgs/sagelib/src": true
+    },
+    "search.exclude": {
+        "build/pkgs/sagemath_categories/src": true,
+        "build/pkgs/sagemath_objects/src": true,
+        "build/pkgs/sagelib/src": true,
+        "pkgs/sage-conf_pypi/sage_root/build": true,
+        "pkgs/sagemath-categories/sage": true,
+        "pkgs/sagemath-objects/sage": true,
+        "pkgs/sagemath-standard/sage": true,
     },
     "python.testing.pytestEnabled": true,
     "python.testing.pytestArgs": [
         "src"
     ],
-    "python.testing.nosetestsEnabled": false,
     "python.testing.unittestEnabled": false,
 }

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.6.beta3", 
-    "version": "9.6.beta3", 
+    "title": "sagemath/sage: 9.6.beta4", 
+    "version": "9.6.beta4", 
     "upload_type": "software", 
-    "publication_date": "2022-02-27", 
+    "publication_date": "2022-03-08", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.6.beta3", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.6.beta4", 
             "relation": "isSupplementTo"
         }, 
         {

COPYING.txt

@@ -107,7 +107,6 @@ pynac                       GPLv2+
 pyparsing                   MIT License
 python                      Python License (see below)
 R                           GPLv2+
-ratpoints                   GPLv2+
 readline                    GPLv3+
 rpy                         GPLv2+
 rubiks/dietz                GPL, any version

Makefile

@@ -194,7 +194,6 @@ micro_release:
 	@echo "Removing documentation. Inspection in IPython still works."
 	rm -rf local/share/doc local/share/*/doc local/share/*/examples local/share/singular/html
 	@echo "Removing unnecessary files & directories - make will not be functional afterwards anymore"
-	@# We need src/doc/common, src/doc/en/introspect for introspection with "??"
 	@# We keep src/sage for some doctests that it expect it to be there and
 	@# also because it does not add any weight with rdfind below.
 	@# We need src/sage/bin/ for the scripts that invoke Sage
@@ -203,7 +202,7 @@ micro_release:
 	@# We keep VERSION.txt.
 	@# We keep COPYING.txt so we ship a license with this distribution.
 	find . -name . -o -prune ! -name config.status ! -name src ! -name sage ! -name local ! -name VERSION.txt ! -name COPYING.txt ! -name build -exec rm -rf \{\} \;
-	cd src && find . -name . -o -prune ! -name sage ! -name bin ! -name doc -exec rm -rf \{\} \;
+	cd src && find . -name . -o -prune ! -name sage ! -name bin -exec rm -rf \{\} \;
 	if command -v rdfind > /dev/null; then \
 		echo "Hardlinking identical files."; \
 		rdfind -makeresultsfile false -makehardlinks true .; \

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.6.beta3, Release Date: 2022-02-27
+SageMath version 9.6.beta4, Release Date: 2022-03-08

bootstrap

@@ -79,9 +79,11 @@ install_config_rpath() {
 
 
 bootstrap () {
+    if [ "${BOOTSTRAP_QUIET}" = "no" ]; then
+        echo "bootstrap:$LINENO: installing 'm4/sage_spkg_configures.m4'"
+    fi
     rm -f m4/sage_spkg_configures.m4
     spkg_configures=""
-
     # initialize SAGE_ENABLE... options for standard packages
     for pkgname in $(./sage --package list :standard: | sort); do
         spkg_configures="$spkg_configures
@@ -101,16 +103,43 @@ AC_SUBST(SAGE_ENABLE_$pkgname, [if_installed])"
                             if [ -f build/pkgs/$pkgname/spkg-install -o -f build/pkgs/$pkgname/spkg-install.in ]; then
                                 # Trac #31163: Not just an optional dummy package
                                 spkg_configures="$spkg_configures
-SAGE_SPKG_ENABLE([$pkgname], [$pkgtype], [$(head -n1 build/pkgs/$pkgname/SPKG.rst 2>/dev/null || echo $pkgname)])"
+SAGE_SPKG_ENABLE([$pkgname], [$pkgtype], [$(grep -v ^= build/pkgs/$pkgname/SPKG.rst | head -n1 2>/dev/null || echo $pkgname)])"
                             fi
                             ;;
                     esac
                 fi
     done
     for pkgname in $(./sage --package list --has-file spkg-configure.m4 | sort); do
-        echo "m4_sinclude([build/pkgs/$pkgname/spkg-configure.m4])" >> m4/sage_spkg_configures.m4
+        echo "m4_sinclude([build/pkgs/$pkgname/spkg-configure.m4])"
         spkg_configures="$spkg_configures
 SAGE_SPKG_CONFIGURE_$(echo ${pkgname} | tr '[a-z]' '[A-Z]')"
+    done >> m4/sage_spkg_configures.m4
+    for pkgname in $(./sage --package list | sort); do
+        DIR=build/pkgs/$pkgname
+        pkgtype="$(cat $DIR/type)"
+        if test -f "$DIR/requirements.txt"; then
+            SPKG_SOURCE=pip
+        elif test ! -f "$DIR/checksums.ini"; then
+            if test -f "$DIR/spkg-install"; then
+                SPKG_SOURCE=script
+            else
+                # a dummy script package
+                SPKG_SOURCE=none
+            fi
+        else
+            SPKG_SOURCE=normal
+        fi
+        if test -f "$DIR/trees.txt"; then
+            SPKG_TREE_VAR="$(sed "s/#.*//;" "$DIR/trees.txt")"
+        else
+            SPKG_TREE_VAR=SAGE_LOCAL
+            if test -f "$DIR/requirements.txt" -o -f "$DIR/install-requires.txt"; then
+                # A Python package
+                SPKG_TREE_VAR=SAGE_VENV
+            fi
+        fi
+        spkg_configures="$spkg_configures
+SAGE_SPKG_FINALIZE([$pkgname], [$pkgtype], [$SPKG_SOURCE], [$SPKG_TREE_VAR])"
     done
     echo "$spkg_configures" >> m4/sage_spkg_configures.m4
 

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=e097e1c5bf49ece5ef27101143c5b0a89ae77714
-md5=206b6e2055e09a0bd00c54e2065c430a
-cksum=1007778800
+sha1=0fa6909f982efbd452287651f58854ffdce6a588
+md5=80324f006d5a30d741ec34235c0220e0
+cksum=2324005793

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-0fed9a145e65dfe3989e9383aa93c4137806fb03
+b845564e0439f7178a40c8f28983aa039364209b

build/pkgs/ecl/SPKG.rst

@@ -19,20 +19,20 @@ Solaris and Windows, running on top of the Intel, Sparc, Alpha and
 PowerPC processors. Porting to other architectures should be rather
 easy.
 
-Website: http://ecls.sourceforge.net/
+Website: https://common-lisp.net/project/ecl/
 
 License
 -------
 
 -  LGPL V2+ or compatible - for details see
 
-   http://ecls.sourceforge.net/license.html
+   https://common-lisp.net/project/ecl/static/manual/Copyrights.html#Copyright-of-ECL
 
 
 Upstream Contact
 ----------------
 
--  the ECL mailing list - see http://ecls.sourceforge.net/resources.html
+-  the ECL mailing list - see https://mailman.common-lisp.net/listinfo/ecl-devel
 
 Special Update/Build Instructions
 ---------------------------------

build/pkgs/python3/patches/0001-bpo-22699-Allow-compiling-on-debian-ubuntu-with-a-di.patch

@@ -0,0 +1,64 @@
+From aef4a7749dec9ecf942647af39d7a1303c758131 Mon Sep 17 00:00:00 2001
+From: Isuru Fernando <isuruf@gmail.com>
+Date: Thu, 16 Sep 2021 15:46:09 -0500
+Subject: [PATCH 08/24] bpo-22699: Allow compiling on debian/ubuntu with a
+ different compiler
+
+This PR fixes one issue mentioned in the bpo
+https://bugs.python.org/issue22699#msg364685 with a slightly better
+patch than given
+---
+ setup.py | 19 ++++++++++++++++++-
+ 1 file changed, 18 insertions(+), 1 deletion(-)
+
+diff --git a/setup.py b/setup.py
+index 8fb8ea5c47..783d20bdcd 100644
+--- a/setup.py
++++ b/setup.py
+@@ -663,9 +663,30 @@ def add_multiarch_paths(self):
+         # Debian/Ubuntu multiarch support.
+         # https://wiki.ubuntu.com/MultiarchSpec
+         cc = sysconfig.get_config_var('CC')
+-        tmpfile = os.path.join(self.build_temp, 'multiarch')
+         if not os.path.exists(self.build_temp):
+             os.makedirs(self.build_temp)
++
++        tmpfile_sysroot = os.path.join(self.build_temp, 'sysroot')
++        ret_sysroot = run_command(
++            '%s -print-sysroot > %s 2> /dev/null' % (cc, tmpfile_sysroot))
++
++        try:
++            if ret_sysroot == 0:
++                with open(tmpfile_sysroot) as fp:
++                    sysroot = fp.readline().strip()
++                    # if the sysroot is not /, then we are not using
++                    # the compiler from debian/ubuntu
++                    if sysroot not in ['', '/']:
++                        add_dir_to_list(self.compiler.library_dirs,
++                            sysroot + '/usr/lib')
++                        add_dir_to_list(self.compiler.include_dirs,
++                            sysroot + '/usr/include')
++                        return
++        finally:
++            os.unlink(tmpfile_sysroot)
++
++        tmpfile = os.path.join(self.build_temp, 'multiarch')
++
+         ret = run_command(
+             '%s -print-multiarch > %s 2> /dev/null' % (cc, tmpfile))
+         multiarch_path_component = ''
+--- a/setup.py    2021-09-28 23:49:53.193868987 -0700
++++ b/setup.py    2021-09-28 23:50:13.554098642 -0700
+@@ -738,7 +738,8 @@
+         for env_var, arg_name, dir_list in (
+                 ('LDFLAGS', '-R', self.compiler.runtime_library_dirs),
+                 ('LDFLAGS', '-L', self.compiler.library_dirs),
+-                ('CPPFLAGS', '-I', self.compiler.include_dirs)):
++                ('CPPFLAGS', '-I', self.compiler.include_dirs),
++                ('CPPFLAGS', '-isystem', self.compiler.include_dirs)):
+             env_val = sysconfig.get_config_var(env_var)
+             if env_val:
+                 parser = argparse.ArgumentParser()
+-- 
+2.30.2
+

build/pkgs/python3/spkg-build.in

@@ -90,7 +90,7 @@ sdh_configure --enable-shared $PYTHON_CONFIGURE
 # we need to provide paths into $SAGE_LOCAL, so that setup.py finds
 # the libraries needed for the extension modules - in particular sqlite3.
 # (The search code there does not know about CPATH and LIBRARY_PATH.)
-make_LDFLAGS="-L. -L$SAGE_LOCAL/lib $LDFLAGS"
+make_LDFLAGS="-L. -Wl,-rpath,. -L$SAGE_LOCAL/lib $LDFLAGS"
 make_CPPFLAGS="-I$SAGE_LOCAL/include $CPPFLAGS"
 
 # Also, we need to add an rpath, like we do for SAGE_LOCAL in src/bin/sage-env.