Merge tag '9.1.beta9' into t/29415/tox_ini__add_environment_local_conda

SageMath version 9.1.beta9, Release Date: 2020-03-29

.gitignore

@@ -13,9 +13,13 @@
 /config.log
 /config.status
 /configure
+/conftest*
 
 /m4/sage_spkg_configures.m4
 
+# no longer generated, but may still be in user worktrees
+/src/lib/pkgconfig
+
 ###################
 # Temporary Files #
 ###################

Makefile

@@ -33,9 +33,13 @@ sageruntime: base-toolchain
 	+build/bin/sage-logger \
 		"cd build/make && ./install '$@'" logs/install.log
 
+# CONFIG_FILES lists all files that appear in AC_CONFIG_FILES in configure.ac;
+# except for build/make/Makefile-auto, which is unused by the build system
+CONFIG_FILES = build/make/Makefile src/Makefile src/bin/sage-env-config build/bin/sage-build-env-config build/pkgs/sage_conf/src/sage_conf.py build/pkgs/sage_conf/src/setup.cfg
+
 # If configure was run before, rerun it with the old arguments.
 # Otherwise, run configure with argument $PREREQ_OPTIONS.
-build/make/Makefile: configure build/make/deps build/make/Makefile.in build/pkgs/*/*
+build/make/Makefile: configure build/make/deps build/pkgs/*/* $(CONFIG_FILES:%=%.in)
 	rm -f config.log
 	mkdir -p logs/pkgs
 	ln -s logs/pkgs/config.log config.log
@@ -77,6 +81,8 @@ dist: build/make/Makefile
 ssl: all
 	./sage -i pyopenssl
 
+# Deleting src/lib is to get rid of src/lib/pkgconfig
+# that was forgotten to clean in #29082.
 misc-clean:
 	@echo "Deleting build artifacts generated by autoconf, automake, make ..."
 	rm -rf logs
@@ -85,7 +91,7 @@ misc-clean:
 	rm -f aclocal.m4 config.log confcache
 	rm -rf autom4te.cache
 	rm -f build/make/Makefile build/make/Makefile-auto
-	rm -f src/lib/pkgconfig/*
+	rm -rf src/lib
 
 bdist-clean: clean
 	$(MAKE) misc-clean

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.1.beta8, Release Date: 2020-03-18
+SageMath version 9.1.beta9, Release Date: 2020-03-29

build/bin/sage-build-env-config.in

@@ -87,3 +87,5 @@ export SAGE_PARI_CFG="@SAGE_PARI_CFG@"
 
 export SAGE_GLPK_PREFIX="@SAGE_GLPK_PREFIX@"
 export SAGE_FREETYPE_PREFIX="@SAGE_FREETYPE_PREFIX@"
+
+export SAGE_CONFIGURE_FFLAS_FFPACK="@SAGE_CONFIGURE_FFLAS_FFPACK@"

build/bin/sage-pip-install

@@ -38,11 +38,13 @@ fi
 # Note: We need to take care to specify the full path to Sage's Python here
 # to emphasize that this command hould use it, and not the system Python;
 # see https://trac.sagemath.org/ticket/18438
+# But now we delegate this to sage-python23.
+PYTHON=sage-python23
+
+# The PIP variable is only used to determine the name of the lock file.
 if [ "$SAGE_PYTHON3" = yes ]; then
-    PYTHON="$SAGE_LOCAL/bin/python3"
     PIP=pip3
 else
-    PYTHON="$SAGE_LOCAL/bin/python2"
     PIP=pip2
 fi
 

build/bin/sage-system-python

@@ -13,12 +13,21 @@ if [ -z "$SAGE_ORIG_PATH" ]; then
     SAGE_ORIG_PATH="$PATH"
 fi
 
-PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v python)"
-
-# fallback for systems where only the python3 command is available
-# see https://trac.sagemath.org/ticket/26953
-if [ -z "$PYTHON" ]; then
-    PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v python3)"
-fi
+# In particular, it is invoked by "bootstrap -d" for sage-download-file,
+# i.e., before a configure run, and by "sage-spkg", also for sage-download-file.
+# So it needs to find a python that has the urllib module.
+# For example, on Debian buster, the python3-minimal package does NOT provide it.
+#
+# See https://trac.sagemath.org/ticket/29090
 
-exec "$PYTHON" "$@"
+PYTHONS="python3 python3.8 python3.7 python2.7 python python3.6 python2"
+for PY in $PYTHONS; do
+    PYTHON="$(PATH="$SAGE_ORIG_PATH" command -v $PY)"
+    if [[ -n "$PYTHON" ]]; then
+        if "$PYTHON" -c 'import urllib'; then
+            exec "$PYTHON" "$@"
+        fi
+    fi
+done
+echo >&2 "$0: error: none of $PYTHONS is a suitable Python with urllib"
+exit 1

build/bin/sage-venv

@@ -0,0 +1,57 @@
+#!/usr/bin/env python3
+# (Actually, we invoke this script with a specific python3 determined by configure.)
+
+# Adapted from examples in https://docs.python.org/3/library/venv.html
+
+import venv
+import os
+import argparse
+
+parser = argparse.ArgumentParser(prog=__name__,
+                                 description='Creates a virtual Python '
+                                             'environment in a target directory.')
+parser.add_argument('env_dir', metavar='ENV_DIR',
+                    help='A directory in which to create the'
+                         'virtual environment.')
+
+parser.add_argument('--system-site-packages', default=False,
+                    action='store_true', dest='system_site',
+                    help='Give the virtual environment access to the '
+                         'system site-packages dir.')
+
+parser.add_argument('--clear', default=False, action='store_true',
+                    dest='clear', help='Delete the contents of the '
+                                       'virtual environment '
+                                       'directory if it already '
+                                       'exists, before virtual '
+                                       'environment creation.')
+parser.add_argument('--upgrade', default=False, action='store_true',
+                    dest='upgrade', help='Upgrade the virtual '
+                                         'environment directory to '
+                                         'use this version of '
+                                         'Python, assuming Python '
+                                         'has been upgraded '
+                                         'in-place.')
+
+options = parser.parse_args()
+if options.upgrade and options.clear:
+    raise ValueError('you cannot supply --upgrade and --clear together.')
+
+if os.name == 'nt':
+    # default for Windows
+    use_symlinks = False
+else:
+    # default for posix
+    # On macOS, definitely need symlinks=True (which matches what we test in build/pkgs/spkg-configure.m4)
+    # or it may fail with 'dyld: Library not loaded: @executable_path/../Python3' on macOS.
+    use_symlinks = True
+
+b = venv.EnvBuilder(system_site_packages=options.system_site,
+                    clear=options.clear,
+                    upgrade=options.upgrade,
+                    symlinks=use_symlinks)
+c = b.ensure_directories(options.env_dir)
+b.setup_python(c)
+b.create_configuration(c)
+# We do not call setup_scripts, which would install the venv 'activate'/'deactivate' scripts.
+

build/make/Makefile.in

@@ -35,10 +35,22 @@ PYTHON = python@SAGE_PYTHON_VERSION@
 MP_LIBRARY = @SAGE_MP_LIBRARY@
 BLAS = @SAGE_BLAS@
 
-# Because some .pc files are generated at configure time we can't write their
-# names explicitly the Makefile, so we use the wildcard function here at make
-# runtime
-PCFILES = $(subst $(SAGE_SRC),$(SAGE_LOCAL),$(wildcard $(SAGE_SRC)/lib/pkgconfig/*.pc))
+# pkgconfig files generated/installed at build time
+PCFILES = @SAGE_SYSTEM_FACADE_PC_FILES@
+
+LN = ln
+SED = sed
+
+# Generate/install sage-specific .pc files.
+# see build/pkgs/gsl/spkg-configure.m4
+$(SAGE_PKGCONFIG)/gsl.pc:
+	-rm -f $@
+	@SAGE_GSL_PC_COMMAND@
+
+# see build/pkgs/openblas/spkg-configure.m4
+$(SAGE_PKGCONFIG)/blas.pc $(SAGE_PKGCONFIG)/cblas.pc $(SAGE_PKGCONFIG)/lapack.pc:
+	-rm -f $@
+	@SAGE_OPENBLAS_PC_COMMAND@
 
 # Files to track installation of packages
 BUILT_PACKAGES = @SAGE_BUILT_PACKAGES@
@@ -201,6 +213,7 @@ $(1)-clean:
 	sage-spkg-uninstall $(if $(filter $(1),$(TOOLCHAIN_DEPS)),--keep-files) \
 		$(1) '$(SAGE_LOCAL)'
 
+.PHONY: $(1) $(1)-clean
 endef
 
 $(foreach pkgname, $(NORMAL_PACKAGES),\
@@ -219,21 +232,22 @@ endif
 # two rules in the form:
 #
 # <pkgname>: <dependencies>
-#     $(AM_V_at)sage-logger -p 'sage --pip install <pkgname>' '$(SAGE_LOGS)/<pkgname>.log'
+#     $(AM_V_at)sage-logger -p 'sage --pip install ...' '$(SAGE_LOGS)/<pkgname>.log'
 #
 # <pkgname>-clean:
-#     -sage --pip uninstall -y <pkgname>
+#     -sage --pip uninstall -y ...
 
 # Positional arguments:
 #     $(1): package name
 #     $(2): package dependencies
 define PIP_PACKAGE_templ
 $(1): $(2)
-	$(AM_V_at)sage-logger -p 'sage --pip install $(1)' '$$(SAGE_LOGS)/$(1).log'
+	$(AM_V_at)sage-logger -p 'sage --pip install -r "$$(SAGE_ROOT)/build/pkgs/$(1)/requirements.txt"' '$$(SAGE_LOGS)/$(1).log'
 
 $(1)-clean:
-	-sage --pip uninstall -y $(1)
+	-sage --pip uninstall -y -r '$$(SAGE_ROOT)/build/pkgs/$(1)/requirements.txt'
 
+.PHONY: $(1) $(1)-clean
 endef
 
 $(foreach pkgname,$(PIP_PACKAGES),\
@@ -247,41 +261,49 @@ endif
 
 # ============================= script packages ==============================
 # Generate build rules for 'script' packages; this template is used to generate
-# two rules in the form:
+# three rules in the form:
 #
-# <pkgname>: <dependencies>
+# $(INST)/<pkgname>-<pkgvers>: <dependencies>
 #     $(AM_V_at)cd '$SAGE_ROOT' && \\
 #         source '$SAGE_ROOT/src/bin/sage-env' && \\
 #         sage-logger -p '$SAGE_ROOT/build/pkgs/<pkgname>/spkg-install' '$(SAGE_LOGS)/<pkgname>.log'
 #
+# <pkgname>: $(INST)/<pkgname>-<pkgvers>
+#
 # <pkgname>-clean:
 #     -$(AM_V_at)cd '$SAGE_ROOT' && \\
 #         source '$SAGE_ROOT/src/bin/sage-env' && \\
 #         '$SAGE_ROOT/build/pkgs/$PKG_NAME/spkg-uninstall'
 
 # Positional arguments:
 #     $(1): package name
-#     $(2): package dependencies
+#     $(2): package version
+#     $(3): package dependencies
 define SCRIPT_PACKAGE_templ
-$(1): $(2)
+$$(INST)/$(1)-$(2): $(3)
 	$(AM_V_at)cd '$$(SAGE_ROOT)' && \
 		source '$$(SAGE_ROOT)/src/bin/sage-env' && source '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
 		sage-logger -p '$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-install' '$$(SAGE_LOGS)/$(1).log'
+	touch "$$@"
+
+$(1): $$(INST)/$(1)-$(2)
 
 $(1)-clean:
 	-$(AM_V_at)cd '$$(SAGE_ROOT)' && \
 		source '$$(SAGE_ROOT)/src/bin/sage-env' && source '$$(SAGE_ROOT)/build/bin/sage-build-env-config' && \
 		'$$(SAGE_ROOT)/build/pkgs/$(1)/spkg-uninstall'
+	-rm -f "$$(INST)/$(1)-$(2)"
 
+.PHONY: $(1) $(1)-clean
 endef
 
 $(foreach pkgname,$(SCRIPT_PACKAGES),\
-	$(eval $(call SCRIPT_PACKAGE_templ,$(pkgname),$(call pkg_deps,$(pkgname)))))
+	$(eval $(call SCRIPT_PACKAGE_templ,$(pkgname),$(vers_$(pkgname)),$(call pkg_deps,$(pkgname)))))
 
 ifdef DEBUG_RULES
 $(info # Rules for script packages)
 $(foreach pkgname,$(SCRIPT_PACKAGES),\
-	$(info $(call SCRIPT_PACKAGE_templ,$(pkgname),$(call pkg_deps,$(pkgname)))))
+	$(info $(call SCRIPT_PACKAGE_templ,$(pkgname),$(vers_$(pkgname)),$(call pkg_deps,$(pkgname)))))
 endif
 
 

build/make/deps

@@ -29,7 +29,24 @@ STARTED = $(SAGE_LOCAL)/etc/sage-started.txt
 	sagelib \
 	doc doc-html doc-html-jsmath doc-html-mathjax doc-pdf \
 	doc-clean doc-src-clean doc-output-clean \
-	clean sagelib-clean build-clean _clean-broken-gcc
+	clean sagelib-clean build-clean python3_venv _clean-broken-gcc
+
+ifneq ($(PYTHON_FOR_VENV),)
+# Special rule for making the Python virtualenv from the system Python (Python
+# 3 only).  $(PYTHON) is set in Makefile to python3_venv.
+# Thus $(inst_python3_venv) will be the dependency of every Python package.
+#
+# TODO: If we reconfigure to build our own Python after having used the system
+# Python, files installed to create the virtualenv should be *removed*.  That
+# could either be done here by the makefile, or in an spkg-preinst for python3
+ifeq ($(PYTHON),python3)
+PYTHON = python3_venv
+endif
+inst_python3_venv = $(SAGE_LOCAL)/pyvenv.cfg
+
+$(inst_python3_venv):
+	$(PYTHON_FOR_VENV) $(SAGE_ROOT)/build/bin/sage-venv "$(SAGE_LOCAL)"
+endif
 
 # Build everything and start Sage.
 # Note that we put the "doc" target first in the rule below because
@@ -104,7 +121,7 @@ build-start: all-build
 # sage-starts runs sage-location, which should be run after installing
 # any package.
 $(STARTED): $(STANDARD_PACKAGE_INSTS)
-	$(AM_V_at)"$(SAGE_LOCAL)/bin/sage-starts"
+	$(AM_V_at)"$(SAGE_ROOT)/build/bin/sage-starts"
 
 
 ###############################################################################
@@ -193,11 +210,6 @@ sagelib: sagelib-build-deps
 $(SAGE_LOCAL)/bin/%: $(SAGE_SRC)/bin/%
 	$(AM_V_at)cp $< $@
 
-# Install sage-specific generated .pc files
-$(SAGE_PKGCONFIG)/%.pc: $(SAGE_SRC)/lib/pkgconfig/%.pc
-	@mkdir -p "$(@D)"
-	$(AM_V_at)cp -P $< $@
-
 ###############################################################################
 # Building the documentation
 ###############################################################################

build/pkgs/beautifulsoup4/requirements.txt

@@ -0,0 +1 @@
+beautifulsoup4

build/pkgs/beautifulsoup4/type

@@ -1 +1 @@
-pip
+optional

build/pkgs/biopython/requirements.txt

@@ -0,0 +1 @@
+biopython

build/pkgs/biopython/type

@@ -1 +1 @@
-pip
+optional

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=16999eea7613ed2ed183a5b2c3eefc6265685017
-md5=ece66d1eaec2065f7a0e0aad65d71b90
-cksum=906044305
+sha1=61c67b0467fed4e9c3330e74b24eed140d628a3a
+md5=e7e0d1af7ee75e2c10532ec8a3a2ddba
+cksum=2321075386

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-52ba9a76be0b56be044a441ee2448a4f4d93c6c3
+437bbd8e43c5889b8135f4786fed5f4b32cbb46a

build/pkgs/curl/distros/slackware.txt

@@ -1,2 +1,5 @@
 curl
 cyrus-sasl
+# giac build needs libldap
+openldap-client
+libssh2

build/pkgs/cygwin.txt

@@ -13,7 +13,8 @@ binutils
 make
 m4
 # a system python is needed for downloading the sage packages, https://trac.sagemath.org/ticket/29090
-python3
+# as of #27824, we use python3 for venv as well
+python37-urllib python37-devel python37
 perl
 perl-ExtUtils-MakeMaker
 tar

build/pkgs/e_antic/checksums.ini

@@ -1,4 +1,5 @@
 tarball=e-antic-VERSION.tar.gz
-sha1=2a443ab9babf5373a434acd90923a793cd950f10
-md5=c4ffc38b285cd6e81c555e48dbbb529e
-cksum=1444226844
+sha1=582c0c3118410f6d8efe23f8fd679e2c602f09a3
+md5=25e1df644ba85db544209cc1d2056464
+cksum=1577490486
+upstream_url=https://www.labri.fr/perso/vdelecro/e-antic/e-antic-VERSION.tar.gz

build/pkgs/e_antic/package-version.txt

@@ -1 +1 @@
-0.1.3
+0.1.5

build/pkgs/eclib/distros/debian.txt

@@ -1 +1,3 @@
 libec-dev
+# provides the mwrank executable:
+eclib-tools

build/pkgs/fflas_ffpack/spkg-configure.m4

@@ -0,0 +1,16 @@
+SAGE_SPKG_CONFIGURE([fflas_ffpack], [
+  dnl A check for a system package is not implemented yet.
+  sage_spkg_install_fflas_ffpack=yes
+
+  dnl https://github.com/linbox-team/fflas-ffpack/blob/master/macros/instr_set.m4
+  dnl discovers these flags from the processor but fails to check whether
+  dnl compiler (and assembler) actually support these instruction sets.
+
+  AX_CHECK_COMPILE_FLAG([-mavx512f -mavx512vl -mavx512dq], [], [
+    AS_VAR_APPEND([SAGE_CONFIGURE_FFLAS_FFPACK], [" --disable-avx512f --disable-avx512vl --disable-avx512dq"])
+  ])
+  m4_foreach([ISFLAG], [fma, fma4], [
+    AX_CHECK_COMPILE_FLAG([-m]ISFLAG, [], [AS_VAR_APPEND]([SAGE_CONFIGURE_FFLAS_FFPACK], [" --disable-]ISFLAG[ "]))
+  ])
+  AC_SUBST([SAGE_CONFIGURE_FFLAS_FFPACK])
+])