Merge tag '9.5.beta5' into t/29039/pip_installable_package_sage_boots…

…trap

SageMath version 9.5.beta5, Release Date: 2021-10-28

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.5.beta4", 
-    "version": "9.5.beta4", 
+    "title": "sagemath/sage: 9.5.beta5", 
+    "version": "9.5.beta5", 
     "upload_type": "software", 
-    "publication_date": "2021-10-19", 
+    "publication_date": "2021-10-28", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta4", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta5", 
             "relation": "isSupplementTo"
         }, 
         {

Pipfile.m4

@@ -24,7 +24,6 @@ numpy = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../numpy/package-version.txt)')"
 cysignals = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../cysignals/package-version.txt)')"
 cypari2 = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../cypari/package-version.txt)')"
 gmpy2 = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../gmpy2/package-version.txt)')"
-psutil = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../psutil/package-version.txt)')"
 pexpect = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../pexpect/package-version.txt)')"
 ipython = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../ipython/package-version.txt)')"
 sympy = "==esyscmd(`printf $(sed "s/[.]p.*//;" ../sympy/package-version.txt)')"

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.5.beta4, Release Date: 2021-10-19
+SageMath version 9.5.beta5, Release Date: 2021-10-28

build/bin/sage-dist-helpers

@@ -306,6 +306,17 @@ sdh_store_and_pip_install_wheel() {
         local sudo=""
         local root=""
     fi
+    # Trac #32659: pip no longer reinstalls local wheels if the version is the same.
+    # Because neither (1) applying patches nor (2) local changes (in the case
+    # of sage-conf, sage-setup, etc.) bump the version number, we need to
+    # override this behavior.  The pip install option --force-reinstall does too
+    # much -- it also reinstalls all dependencies, which we do not want.
+    wheel_basename="${wheel##*/}"
+    distname="${wheel_basename%%-*}"
+    $sudo sage-pip-uninstall "$distname"
+    if [ $? -ne 0 ]; then
+        echo "(ignoring error)" >&2
+    fi
     $sudo sage-pip-install $root $pip_options "$wheel" || \
         sdh_die "Error installing ${wheel##*/}"
     if [ -n "${SAGE_PKG_DIR}" ]; then
@@ -316,11 +327,7 @@ sdh_store_and_pip_install_wheel() {
 }
 
 sdh_pip_uninstall() {
-    # --disable-pip-version-check: Don't periodically check PyPI to determine whether a new version of pip is available
-    # --no-input: Disable prompting for input.
-    # --yes: Don't ask for confirmation of uninstall deletions
-    # See sage-pip-install for a discussion of the other flags.
-    python3 -m pip uninstall --isolated --disable-pip-version-check --yes --no-input "$@"
+    sage-pip-uninstall "$@"
     if [ $? -ne 0 ]; then
         echo "Warning: pip exited with status $?" >&2
     fi

build/bin/sage-pip-uninstall

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+# This command ensures that any previous installations of the same package
+# are uninstalled.
+
+# Note: "sage-pip-uninstall" is meant to be run after $(PYTHON) has
+# been installed (either as an spkg or as a venv over a system python3).
+# It is then guaranteed by sage-env that PATH is set in a way that "python3"
+# refers to the correct python3.
+PYTHON=python3
+
+# The PIP variable is only used to determine the name of the lock file.
+PIP=pip3
+
+# We should avoid running pip while uninstalling a package because that
+# is prone to race conditions. Therefore, we use a lockfile while
+# running pip. This is implemented in the Python script sage-flock
+LOCK="$SAGE_LOCAL/var/lock/$PIP.lock"
+
+    # --disable-pip-version-check: Don't periodically check PyPI to determine whether a new version of pip is available
+    # --no-input: Disable prompting for input.
+    # --yes: Don't ask for confirmation of uninstall deletions
+    # See sage-pip-install for a discussion of the other flags.
+sage-flock -x $LOCK $PYTHON -m pip uninstall --isolated --disable-pip-version-check --yes --no-input "$@"

build/make/Makefile.in

@@ -287,8 +287,7 @@ python3-SAGE_VENV-no-deps: setuptools-clean
 
 # Everything needed to start up Sage using "./sage".  Of course, not
 # every part of Sage will work.  It does not include Maxima for example.
-SAGERUNTIME = sagelib $(inst_ipython) $(inst_pexpect) \
-		$(inst_psutil)
+SAGERUNTIME = sagelib $(inst_ipython) $(inst_pexpect)
 
 all-sageruntime: toolchain-deps
 	+$(MAKE_REC) $(SAGERUNTIME)

build/pkgs/4ti2/spkg-configure.m4

@@ -1,5 +1,5 @@
 SAGE_SPKG_CONFIGURE([4ti2], [
-    SAGE_SPKG_DEPCHECK([gmp mpir glpk zlib], [
+    SAGE_SPKG_DEPCHECK([gmp glpk zlib], [
         dnl Debian installs these programs with an executable prefix "4ti2-",
         dnl OpenSUSE uses the prefix "4ti2_".
         dnl Singular checks for unprefixed and prefixed with "4ti2-".

build/pkgs/argcomplete/type

@@ -1 +1 @@
-optional
+standard

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=1df4c487d374a7ea9eeda3a9234cc6eed81c1443
-md5=83d4327261e545f26d4ad318030823e8
-cksum=2968565921
+sha1=ab6592f2216c48049bbbcfb3a42c3e157f44d917
+md5=fc3a50e0f47802e55969eade44648af4
+cksum=3704729867

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-e8ab458165ec5e5832adf702099f47f4cff94596
+c5a87834e7e2939b878a5134cd240e6c712bd573

build/pkgs/gfortran/SPKG.rst

@@ -22,7 +22,7 @@ Dependencies
 ------------
 
 -  zlib
--  MPIR
+-  GMP 
 -  MPFR
 -  MPC
 

build/pkgs/mpc/spkg-install.in

@@ -1,7 +1,7 @@
 cd src
 
 # Unset CC and CFLAGS.  This will make mpc use the same configuration
-# as MPIR, which is probably a good thing.
+# as GMP, which is probably a good thing.
 unset CC
 unset CFLAGS