Trac #29766: Upgrade NumPy to 1.19.1, scipy to 1.5.2, networkx to 2.4…

…, add pybind11 package

Follow-up from the update of numpy to 1.16.6 (#29429):

We update
 * https://pypi.org/project/numpy/ to 1.19.1 (latest as of 2020-07-21)
 * https://pypi.org/project/scipy/ to 1.5.2 (latest as of 2020-07-31)
 * networkx to the latest release, 2.4 (latest as of 2020-07-04)
All of the above versions support Python >= 3.6.

One deprecation warning is removed here, another suppressed (from
#29425),
the rest it trivial.

Tarballs: see checksums.ini [upstream_url]

URL: https://trac.sagemath.org/29766
Reported by: dimpase
Ticket author(s): Dima Pasechnik, Matthias Koeppe
Reviewer(s): Travis Scrimshaw, Isuru Fernando, Dima Pasechnik

build/make/Makefile.in

@@ -465,28 +465,35 @@ $(foreach pkgname, $(NORMAL_PACKAGES),\
 	                                   $(call pkg_deps,$(pkgname)))))
 endif
 
-# SAGE_CHECK_PACKAGES: if this contains "!pkg", skip tests for "pkg",
-# so set SAGE_CHECK=no.  If this contains "pkg", run tests, so set
-# SAGE_CHECK=yes.  Check this now and export SAGE_CHECK so that the
-# package's spkg-install script can use this variable.
+# Parsing the SAGE_CHECK_PACKAGES variable:
+# - if this contains "!pkg", set SAGE_CHECK_pkg=no.
+# - if this contains "?pkg", set SAGE_CHECK_pkg=warn.
+# - if this contains "pkg",  set SAGE_CHECK_pkg=yes.
+#
+# We check this now and export SAGE_CHECK_pkg for
+# dependencies and the Makefile rules.
 #
 # Since Python's self-tests seem to fail on all platforms, we disable
-# its test suite by default.  However, if SAGE_CHECK=warn, we do not
-# do that.
-SAGE_CHECK_PACKAGES_DEFAULT := !python3
+# its test suite by default.
+# However, if SAGE_CHECK=warn, we do not do that.
+SAGE_CHECK_PACKAGES_DEFAULT_yes := !python3
+SAGE_CHECK_PACKAGES_DEFAULT_warn :=
+SAGE_CHECK_PACKAGES_DEFAULT_no :=
 comma := ,
 ifeq "$(origin SAGE_CHECK_PACKAGES)" "undefined"
-SAGE_CHECK_PACKAGES := $(if $(findstring yes,$(SAGE_CHECK)),$(SAGE_CHECK_PACKAGES_DEFAULT))
+SAGE_CHECK_PACKAGES := $(SAGE_CHECK_PACKAGES_DEFAULT$(SAGE_CHECK))
 endif
-SAGE_CHECK_PACKAGES := $(subst $(comma), ,$(SAGE_CHECK_PACKAGES))
-SAGE_CHECK_PACKAGES := $(subst :, ,$(SAGE_CHECK_PACKAGES))
+SAGE_CHECK_PACKAGES_sep := $(subst $(comma), ,$(SAGE_CHECK_PACKAGES))
+SAGE_CHECK_PACKAGES_sep := $(subst :, ,$(SAGE_CHECK_PACKAGES_sep))
 define SET_SAGE_CHECK
 $(eval SAGE_CHECK_$(1) := $(2))
 endef
-$(foreach clause, $(SAGE_CHECK_PACKAGES), \
-     $(if $(findstring !,$(clause)), \
-	             $(eval $(call SET_SAGE_CHECK,$(subst !,,$(clause)),no)), \
-		     $(eval $(call SET_SAGE_CHECK,$(clause),yes))))
+$(foreach clause, $(SAGE_CHECK_PACKAGES_sep),					\
+     $(if $(findstring !,$(clause)),						\
+	  $(eval $(call SET_SAGE_CHECK,$(subst !,,$(clause)),no)),		\
+	  $(if $(findstring ?,$(clause)),					\
+	       $(eval $(call SET_SAGE_CHECK,$(subst ?,,$(clause)),warn)),	\
+	       $(eval $(call SET_SAGE_CHECK,$(clause),yes)))))
 debug-check:
 	@echo $(foreach pkgname, $(NORMAL_PACKAGES), SAGE_CHECK_$(pkgname) = $(SAGE_CHECK_$(pkgname)))
 

build/pkgs/networkx/checksums.ini

@@ -1,4 +1,5 @@
 tarball=networkx-VERSION.zip
-sha1=a68f8faa3726c220b93d68cfa28bed24874ba3fc
-md5=82608a3686fb3e61f20cf13bfd3c1b4a
-cksum=539980282
+sha1=b440621c1f597b6dff46c1150541a48601a180cc
+md5=95617052af8998381ff3bc9c88ffeaa3
+cksum=2271648010
+upstream_url=https://github.com/networkx/networkx/archive/networkx-2.4.zip

build/pkgs/networkx/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) decorator | $(PYTHON_TOOLCHAIN) nose scipy
+$(PYTHON) decorator | $(PYTHON_TOOLCHAIN) scipy $(and $(filter-out no,$(SAGE_CHECK_networkx)), nose pytest)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/networkx/package-version.txt

@@ -1 +1 @@
-2.2
+2.4

build/pkgs/numpy/checksums.ini

@@ -1,5 +1,5 @@
-tarball=numpy-VERSION.tar.gz
-sha1=9171cd372c79bbc542aa2f945936b3431fa27adf
-md5=5e958c603605f3168b7b29f421f64cdd
-cksum=3517639766
-upstream_url=https://github.com/numpy/numpy/releases/download/vVERSION/numpy-VERSION.tar.gz
+tarball=numpy-VERSION.zip
+sha1=0d6b62fbf723f5d91ab289766a252a30467609f1
+md5=2ccca1881b2766040149629614d22a3f
+cksum=3596367842
+upstream_url=https://pypi.io/packages/source/n/numpy/numpy-VERSION.zip

build/pkgs/numpy/package-version.txt

@@ -1 +1 @@
-1.16.6
+1.19.1