Merge tag '9.0.beta10' into t/25828/optional-extension-features

SageMath version 9.0.beta10, Release Date: 2019-12-24

.ci/build-docker.sh

@@ -39,6 +39,12 @@ docker_build --target run-time-dependencies --tag run-time-dependencies:$DOCKER_
 docker_build --target build-time-dependencies --tag build-time-dependencies:$DOCKER_TAG .
 docker_build --target make-all --tag make-all:$DOCKER_TAG .
 
+# Copy docs out of the docker image to save them into browseable GitLab artifacts
+container=$(docker create make-all:$DOCKER_TAG)
+docker cp $container:/home/sage/sage/local/share/doc/sage/html html_
+# GitLab's browser does not like symlinks, so we flatten them
+rsync html_/ html/ -a --copy-links
+
 # Build the release image without build artifacts.
 docker_build --target sagemath --tag "$DOCKER_IMAGE_CLI" .
 # Display the layers of this image

.gitlab-ci.yml

@@ -88,9 +88,10 @@ build-from-latest:
     when: always
     paths:
     - gitlab-build-docker.log
+    - html
     expire_in: 1 month
   script:
-    - apk --update add coreutils
+    - apk --update add coreutils rsync
     # The output of the build can get larger than gitlab.com's limit; only
     # print the first 1MB (and the last 80 lines.) GitLab's limit is 4MB,
     # however, the list of all branches and tags that shows up in the initial
@@ -115,6 +116,12 @@ build-from-latest:
 build-from-clean:
   extends:
     - build-from-latest
+  artifacts:
+    when: always
+    paths:
+    - gitlab-build-docker.log
+    - html
+    expire_in: 99 years
   variables:
     ARTIFACT_BASE: "source-clean"
   only:
@@ -136,18 +143,21 @@ build-from-clean:
 
 test-dev:
   stage: test
+  dependencies: []
   script:
     - . .ci/pull-gitlab.sh sagemath-dev
     - sh .ci/test-dev.sh "$DOCKER_IMAGE"
 
 test-cli:
   stage: test
+  dependencies: []
   script:
     - . .ci/pull-gitlab.sh sagemath
     - sh .ci/test-cli.sh "$DOCKER_IMAGE"
 
 test-jupyter:
   stage: test
+  dependencies: []
   script:
     - . .ci/pull-gitlab.sh sagemath
     - sh .ci/test-jupyter.sh "$DOCKER_IMAGE" docker
@@ -156,6 +166,7 @@ test-jupyter:
 # variables DOCKER_USER and SECRET_DOCKER_PASS have been set up.
 push-dockerhub:
   stage: release
+  dependencies: []
   only:
     refs:
       - branches
@@ -170,6 +181,7 @@ push-dockerhub:
 # variables DOCKER_USER and SECRET_DOCKER_PASS have been set up.
 push-dockerhub-dev:
   stage: release
+  dependencies: []
   only:
     refs:
       - master

.lgtm.yml

@@ -0,0 +1,8 @@
+queries:
+  - exclude: py/call/wrong-named-class-argument
+  - exclude: py/call/wrong-number-class-arguments
+  - exclude: py/unsafe-cyclic-import
+extraction:
+  python:
+    python_setup:
+      version: 3

Makefile

@@ -53,9 +53,11 @@ build/make/Makefile: configure build/make/deps build/make/Makefile.in build/pkgs
 		fi; )
 
 # This is used to monitor progress towards Python 3 and prevent
-# regressions. Should be removed after the full switch to python3
-buildbot-python3: configure
-	./configure --with-python=3
+# regressions. Should be removed after the full switch to python3.
+#
+# As of Sage 9.0: keep the build target for backward compatibility,
+# but it just runs "make".
+buildbot-python3:
 	$(MAKE)
 
 # Preemptively download all standard upstream source tarballs.
@@ -145,7 +147,6 @@ fast-rebuild-clean: misc-clean
 
 TESTALL = ./sage -t --all
 PTESTALL = ./sage -t -p --all
-PTEST_PYTHON3 = cat src/ext/doctest/python3-known-passing.txt | xargs ./sage -t --long -p
 
 # Flags for ./sage -t --all.
 # By default, include all tests marked 'dochtml' -- see
@@ -191,9 +192,6 @@ ptestoptional: all
 ptestoptionallong: all
 	$(PTESTALL) --long --logfile=logs/ptestoptionallong.log
 
-ptest-python3: buildbot-python3
-	$(PTEST_PYTHON3) --logfile=logs/ptest_python3.log
-
 configure: configure.ac src/bin/sage-version.sh m4/*.m4 build/pkgs/*/spkg-configure.m4
 	./bootstrap -d
 
@@ -214,4 +212,4 @@ list:
 	misc-clean bdist-clean distclean bootstrap-clean maintainer-clean \
 	test check testoptional testall testlong testoptionallong testallong \
 	ptest ptestoptional ptestall ptestlong ptestoptionallong ptestallong \
-	buildbot-python3 ptest-python3 list
+	buildbot-python3 list

README.md

@@ -5,7 +5,7 @@
 >   "Creating a Viable Open Source Alternative to
 >    Magma, Maple, Mathematica, and MATLAB"
 
->   Copyright (C) 2005-2018 The Sage Development Team
+>   Copyright (C) 2005-2019 The Sage Development Team
 
    https://www.sagemath.org
 
@@ -17,14 +17,14 @@ and functions list the authors.
 Getting Started
 ---------------
 
-If you downloaded a [binary](http://www.sagemath.org/download.html)
+If you downloaded a [binary](https://www.sagemath.org/download.html)
 (i.e. a version of SageMath prepared for a specific operating system),
 Sage is ready to start -- just open a terminal in the directory where
 you extracted the binary archive and type:
 
     ./sage
 
-If you downloaded the [sources](http://www.sagemath.org/download-source.html),
+If you downloaded the [sources](https://www.sagemath.org/download-source.html),
 please read below on how to build Sage and work around common issues.
 
 If you have questions or encounter problems, please do not hesitate
@@ -177,7 +177,7 @@ More Detailed Instructions to Build from Source
    several jobs in parallel, while the `SAGE_CHECK` environment variable
    controls whether to perform more tests during the installation.  For
    an in-depth discussion of environment variables for building Sage, see
-   [the installation guide](http://doc.sagemath.org/html/en/installation/source.html#environment-variables).
+   [the installation guide](https://doc.sagemath.org/html/en/installation/source.html#environment-variables).
 
    On a machine with 4 processors, say, typing `export MAKE="make -j4"`
    will configure the build script to perform a parallel compilation of
@@ -221,7 +221,7 @@ More Detailed Instructions to Build from Source
 
    Note: if you built for Python 3, you can instead run `make ptest-python3`.
 
-1. The HTML version of the [documentation](http://doc.sagemath.org/html/en/index.html)
+1. The HTML version of the [documentation](https://doc.sagemath.org/html/en/index.html)
    is built during the compilation process of Sage and resides in the directory
    `local/share/doc/sage/html/`.
 

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.0.beta6, Release Date: 2019-11-18
+SageMath version 9.0.beta10, Release Date: 2019-12-24

build/make/deps

@@ -216,7 +216,7 @@ $(SAGE_EXTCODE)/%: $(SAGE_SRC)/ext/%
 # Building the documentation has many dependencies, because all
 # documented modules are imported and because we use matplotlib to
 # produce plots.
-DOC_DEPENDENCIES = sagelib $(inst_sphinx) $(inst_sagenb) \
+DOC_DEPENDENCIES = sagelib $(inst_sphinx) \
 	| $(SAGERUNTIME) $(inst_maxima) $(inst_networkx) $(inst_scipy) $(inst_sympy) \
 	$(inst_matplotlib) $(inst_pillow) $(inst_mathjax) $(inst_mpmath) \
 	$(inst_ipykernel) $(inst_jupyter_client) $(inst_conway_polynomials) \

build/make/install

@@ -55,6 +55,7 @@ fi
 # Dump environment for debugging purposes:
 echo "*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***"
 env | sort
+printf '\E[m'
 echo "***********************************************"
 
 ###############################################################################

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=1c51e1b16652a8f1f16a825560a7d8f06d10cc7c
-md5=2e6fb9d44c7761be23f2e0873619d6cc
-cksum=35665169
+sha1=c992c5f54672201e05e79385de9a2a6ea4233586
+md5=41e4ba80fbdefa79b38a60edb0733422
+cksum=1355983684

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-026a216fa444461e3a5d4b76a11c074784f5fdf7
+0bb0717729c70eb363a18beb3ed37424c5775791

build/pkgs/cvxopt/checksums.ini

@@ -1,4 +1,4 @@
 tarball=cvxopt-VERSION.tar.gz
-sha1=6b6da47c80e5b8fb678bc0ebdc38bddeaa83cc74
-md5=b17c75117b4412b33ea31a47b7e5655e
-cksum=4043372127
+sha1=b16cf3b1c941d763ea0451e947e5661d38ee0473
+md5=aac3db3fc3cf11d9ad2e42d89e94ca5a
+cksum=3018809057

build/pkgs/cvxopt/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) numpy $(BLAS) gsl glpk | pkgconfig pip matplotlib
+$(PYTHON) numpy $(BLAS) gsl glpk suitesparse | pkgconfig pip nose matplotlib
 
 matplotlib is needed to test cvxopt (i.e., if SAGE_CHECK=yes). See #12742.
 

build/pkgs/cvxopt/package-version.txt

@@ -1 +1 @@
-1.1.8.p2
+1.2.3

build/pkgs/cvxopt/spkg-check

@@ -0,0 +1,22 @@
+if [ -z "$SAGE_LOCAL" ]; then
+    echo >&2 "SAGE_LOCAL undefined ... exiting"
+    echo >&2 "Maybe run 'sage --sh'?"
+    exit 1
+fi
+
+cd src
+
+if ! command -v nosetests ; then 
+    echo >&2 'Testing cvxopt requires the package nose to be installed'
+    exit 1
+fi
+
+echo "Testing cvxopt..."
+
+nosetests
+
+if [ $? -ne 0 ]; then
+    echo >&2 "Error running self tests."
+    exit 1
+fi
+

build/pkgs/cvxopt/spkg-install

@@ -5,6 +5,33 @@ if [ "$UNAME" = FreeBSD ]; then
     export CPPFLAGS="$CPPFLAGS -I$SAGE_LOCAL/include"
 fi
 
+# Stolen from Gentoo
+pkg_libs() {
+	pkg-config --libs-only-l $* | \
+		sed -e 's:[ ]-l*\(pthread\|m\)\([ ]\|$\)::g' -e 's:[ ]*$::' | \
+		tr ' ' '\n' | sort -u | sed -e "s:^-l\(.*\):\1:g" | \
+		tr '\n' ';' | sed -e 's:;$::'
+}
+
+
+# configure cvxopt by variables
+# Note that *_INC_DIR variables have to be non-empty.
+# Compilers don't like "-I ".
+export CVXOPT_BLAS_LIB="$(pkg_libs blas)"
+export CVXOPT_BLAS_LIB_DIR="${SAGE_LOCAL}"
+export CVXOPT_LAPACK_LIB="$(pkg_libs lapack)"
+
+export CVXOPT_SUITESPARSE_LIB_DIR="${SAGE_LOCAL}"
+export CVXOPT_SUITESPARSE_INC_DIR="${SAGE_LOCAL}/include"
+
+export CVXOPT_BUILD_GLPK=1
+export CVXOPT_GLPK_LIB_DIR="${SAGE_LOCAL}"
+export CVXOPT_GLPK_INC_DIR="${SAGE_LOCAL}/include"
+
+export CVXOPT_BUILD_GSL=1
+export CVXOPT_GSL_LIB_DIR="${SAGE_LOCAL}"
+export CVXOPT_GSL_INC_DIR="${SAGE_LOCAL}/include"
+
 sdh_pip_install .
 
 if [ "x$SAGE_SPKG_INSTALL_DOCS" = xyes ] ; then

build/pkgs/jmol/spkg-install

@@ -1,8 +1,3 @@
-# Cleanup of previous installation
-rm -rf "${SAGE_SHARE}/jsmol/"
-rm -rf "${SAGE_SHARE}/jmol/"
-rm -f "${SAGE_LOCAL}/bin/jmol"
-
 # jsmol goes in a dedicated directory
 sdh_install src/jsmol "${SAGE_SHARE}/"
 rm -rf src/jsmol