Merge tag '9.5.beta2' into t/32442/__configure__make___with_sage_venv…

…_the_default

SageMath version 9.5.beta2, Release Date: 2021-09-26

.github/workflows/lint.yml

@@ -31,17 +31,3 @@ jobs:
       run: pip install tox relint
     - name: Lint using relint
       run: tox -e relint src/sage/
-  lint-pyright:
-    name: Static type check with pyright
-    runs-on: ubuntu-latest
-    steps:
-    - name: Checkout
-      uses: actions/checkout@v2
-    - name: Set up node to install pyright
-      uses: actions/setup-node@v1
-      with:
-        node-version: '12'
-    - name: Install pyright
-      run: npm install -g pyright
-    - name: Lint using pyright
-      run: pyright

.github/workflows/sdist.yml

@@ -0,0 +1,45 @@
+name: Prepare source distributions
+
+on:
+  push:
+    tags:
+      # Match all release tags including beta, rc
+      - '[0-9]+.[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+'
+      - '[0-9]+.[0-9]+.beta[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+.beta[0-9]+'
+      - '[0-9]+.[0-9]+.rc[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+.rc[0-9]+'
+
+  workflow_dispatch:
+    # Allow to run manually
+
+jobs:
+
+  release_dist:
+
+    # This job, in contrast to "dist" in tox.yml,
+    # does not use "configure --enable-download-from-upstream-url".
+    #
+    # In this way, we check that all necessary package tarballs
+    # have already been uploaded to the Sage server at the time
+    # of pushing a release tag.
+    #
+    # It also uses "bootstrap -D", thus checking that the "configure"
+    # tarball has been uploaded to the Sage server at the time
+    # of pushing a release tag.
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install bootstrap prerequisites
+        run: |
+          sudo DEBIAN_FRONTEND=noninteractive apt-get update
+          sudo DEBIAN_FRONTEND=noninteractive apt-get install $(build/bin/sage-get-system-packages debian _bootstrap)
+      - name: make dist
+        run: |
+          ./bootstrap -D && ./configure && make dist
+      - uses: actions/upload-artifact@v2
+        with:
+          path: "dist/*.tar.gz"
+          name: release_dist

.github/workflows/tox-gcc_spkg.yml

@@ -27,7 +27,7 @@ on:
     # Allow to run manually
 
 env:
-  TARGETS_PRE: sagelib-build-deps
+  TARGETS_PRE: all-sage-local
   TARGETS: build doc-html
   TARGETS_OPTIONAL: ptest
 

.github/workflows/tox.yml

@@ -27,7 +27,7 @@ on:
     # Allow to run manually
 
 env:
-  TARGETS_PRE: sagelib-build-deps
+  TARGETS_PRE: all-sage-local
   TARGETS: build doc-html
   TARGETS_OPTIONAL: ptest
 
@@ -257,7 +257,7 @@ jobs:
           SAGE_ROOT=. SAGE_SRC=./src src/bin/sage-update-version $(git describe) || echo "(ignoring error)"
       - name: make dist
         run: |
-          ./configure && make dist
+          ./configure --enable-download-from-upstream-url && make dist
       - uses: actions/upload-artifact@v2
         with:
           path: "dist/*.tar.gz"

.gitignore

@@ -144,6 +144,7 @@ __pycache__/
 !/src/sage/stats/distributions/dgs_bern.c
 !/src/sage/stats/distributions/dgs_gauss_dp.c
 !/src/sage/stats/distributions/dgs_gauss_mp.c
+!/src/sage/symbolic/ginac/*.cpp
 /src/cython_debug
 
 # Temporary build files

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.5.beta0", 
-    "version": "9.5.beta0", 
+    "title": "sagemath/sage: 9.5.beta2", 
+    "version": "9.5.beta2", 
     "upload_type": "software", 
-    "publication_date": "2021-08-31", 
+    "publication_date": "2021-09-26", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta0", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta2", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.5.beta0, Release Date: 2021-08-31
+SageMath version 9.5.beta2, Release Date: 2021-09-26

build/bin/sage-dist-helpers

@@ -240,7 +240,7 @@ sdh_pip_install() {
     echo "Installing $PKG_NAME"
     mkdir -p dist
     rm -f dist/*.whl
-    python3 -m pip wheel --use-feature=in-tree-build --wheel-dir=dist --no-binary :all: --verbose --no-deps --no-index --isolated --no-build-isolation "$@" || \
+    python3 -m pip wheel --use-feature=in-tree-build --wheel-dir=dist --no-binary :all: --verbose --no-deps --no-index --isolated --no-build-isolation --ignore-requires-python "$@" || \
         sdh_die "Error building a wheel for $PKG_NAME"
 
     sdh_store_and_pip_install_wheel .
@@ -275,16 +275,38 @@ sdh_store_wheel() {
 }
 
 sdh_store_and_pip_install_wheel() {
+    local pip_options=""
+    while [ $# -gt 0 ]; do
+        case $1 in
+            -*) pip_options="$pip_options $1"
+                ;;
+            *)
+                break
+                ;;
+        esac
+        shift
+    done
     sdh_store_wheel "$@"
-    if [ -n "$SAGE_DESTDIR" ]; then
-        local sudo=""
-        # --no-warn-script-location: Suppress a warning caused by --root
-        local root="--root=$SAGE_DESTDIR --no-warn-script-location"
+    if [ -n "$SAGE_SUDO" ]; then
+        # Trac #29585: Do the SAGE_DESTDIR staging of the wheel installation
+        # ONLY if SAGE_SUDO is set (in that case, we still do the staging so
+        # that we do not invoke pip as root).
+        if [ -n "$SAGE_DESTDIR" ]; then
+            # --no-warn-script-location: Suppress a warning caused by --root
+            local sudo=""
+            local root="--root=$SAGE_DESTDIR --no-warn-script-location"
+        else
+            # Trac #32361: Of course, this can only be done for normal packages,
+            # whose installation goes through sage-spkg.
+            # For script packages, we do have to invoke pip as root.
+            local sudo="$SAGE_SUDO"
+            local root=""
+        fi
     else
-        local sudo="$SAGE_SUDO"
+        local sudo=""
         local root=""
     fi
-    $sudo sage-pip-install $root "$wheel" || \
+    $sudo sage-pip-install $root $pip_options "$wheel" || \
         sdh_die "Error installing ${wheel##*/}"
     if [ -n "${SAGE_PKG_DIR}" ]; then
         # Record name of installed distribution name for uninstallation.

build/bin/sage-pip-install

@@ -3,16 +3,15 @@
 # built wheel.
 
 # Default arguments for all packages installed with `pip install`
-# --ignore-installed : Force pip to re-install package even if it thinks it's
-#                      already installed (for which it sometimes gets false
-#                      positives for partially-installed packages).
 # --verbose          : Display the output when running setup.py.
-# --no-deps          : Don't install runtime dependencies from PyPI.
 # --no-index         : Don't look at the package index.
-#                      This also disables pip's version self-check.
+# --disable-pip-version-check : Disables pip's version self-check.
 # --isolated         : Don't read configuration files such as
 #                      ~/.pydistutils.cfg
-pip_install_flags="--ignore-installed --verbose --no-deps --no-index --isolated"
+# --no-cache-dir     : Disable the cache.
+#                      (so that no previously built wheels can sneak in to
+#                      resolve runtime dependencies)
+pip_install_flags="--verbose --no-index --find-links=$SAGE_SPKG_WHEELS --disable-pip-version-check --isolated --no-cache-dir"
 
 # Note: "sage-pip-install" is meant to be run after $(PYTHON) has
 # been installed (either as an spkg or as a venv over a system python3).
@@ -35,6 +34,17 @@ LOCK="$SAGE_LOCAL/var/lock/$PIP.lock"
 # to apply a shared lock)
 sage-flock -s $LOCK $PYTHON -m pip install $pip_install_flags "$@"
 if [ $? -ne 0 ]; then
-    echo >&2 "Error: installing with $PIP failed"
-    exit 3
+    # --ignore-installed : Force pip to re-install package even if it thinks it's
+    #                      already installed (for which it sometimes gets false
+    #                      positives for partially-installed packages).
+    # --no-deps          : Don't install runtime dependencies from PyPI.
+    extra_pip_install_flags="--no-deps --ignore-installed --ignore-requires-python"
+    echo >&2 "Warning: installing with \"$PYTHON -m pip install $pip_install_flags\" failed. Retrying, adding \"$extra_pip_install_flags\""
+    sage-flock -s $LOCK $PYTHON -m pip install $pip_install_flags $extra_pip_install_flags "$@"
+    if [ $? -ne 0 ]; then
+        echo >&2 "Error: installing with pip  failed"
+        exit 3
+    else
+        echo >&2 "Warning: The installation needed to use \"$extra_pip_install_flags\" to succeed. This means that a dependencies file in build/pkgs/ needs to be updated. Please report this to sage-devel@googlegroups.com, including the build log of this package."
+    fi
 fi

build/bin/write-dockerfile.sh

@@ -230,7 +230,7 @@ ARG USE_MAKEFLAGS="-k V=0"
 ENV SAGE_CHECK=warn
 ENV SAGE_CHECK_PACKAGES="!gfan,!cython,!r,!python3,!python2,!nose,!pathpy,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!networkx,!rpy2,!symengine_py,!sage_sws2rst"
 #:make:
-ARG TARGETS_PRE="sagelib-build-deps"
+ARG TARGETS_PRE="all-sage-local"
 $RUN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS_PRE} $ENDRUN
 
 FROM with-targets-pre as with-targets

build/make/Makefile.in

@@ -379,6 +379,9 @@ sagelib-clean:
 sage_docbuild-clean:
 	(cd "$(SAGE_ROOT)/build/pkgs/sage_docbuild/src" && rm -rf build)
 
+sage_setup-clean:
+	(cd "$(SAGE_ROOT)/build/pkgs/sage_setup/src" && rm -rf build)
+
 build-clean: clean doc-clean sagelib-clean sage_docbuild-clean
 
 # Special target for cleaning up a broken GCC install detected by configure
@@ -654,6 +657,8 @@ $(1)-$(4)-uninstall:
 
 $(1)-uninstall: $(1)-$(4)-uninstall
 
+$(1)-clean: $(1)-uninstall
+
 .PHONY: $(1) $(1)-uninstall $(1)-build-deps $(1)-no-deps $(1)-clean
 endef
 

build/pkgs/appnope/SPKG.rst

@@ -1,12 +1,18 @@
-appnope: Disable App Nap on OS X
-================================
+appnope: Disable App Nap on macOS >= 10.9
+=========================================
 
 Description
 -----------
 
-Disable App Nap on OS X 10.9
+Disable App Nap on macOS >= 10.9
+
+License
+-------
+
+BSD
 
 Upstream Contact
 ----------------
 
-https://github.com/minrk/appnope
+https://pypi.org/project/appnope/
+

build/pkgs/appnope/checksums.ini

@@ -1,4 +1,5 @@
 tarball=appnope-VERSION.tar.gz
-sha1=838158bf881f3e8538b7bfeff4ad289a6623cdda
-md5=932fbaa73792c9b06754755a774dcac5
-cksum=4167491137
+sha1=2613cb737d132ee929e09924b19eb6eb088592c4
+md5=16198e5c4f2b049dc98aa444e96ca554
+cksum=224603249
+upstream_url=https://pypi.io/packages/source/a/appnope/appnope-VERSION.tar.gz

build/pkgs/appnope/package-version.txt

@@ -1 +1 @@
-0.1.0.p0
+0.1.2

build/pkgs/attrs/checksums.ini

@@ -1,5 +1,5 @@
 tarball=attrs-VERSION.tar.gz
-sha1=5cad208b39fe854745c35b75f667eaf6400e2720
-md5=5b2db50fcc31be34d32798183c9bd062
-cksum=2725988683
+sha1=d0c0f0d92f4860821c5aaeb9e07646dc22bc31d3
+md5=06af884070d9180694becdb106e5cd65
+cksum=4087843587
 upstream_url=https://pypi.io/packages/source/a/attrs/attrs-VERSION.tar.gz

build/pkgs/attrs/package-version.txt

@@ -1 +1 @@
-19.3.0
+21.2.0

build/pkgs/backcall/checksums.ini

@@ -1,5 +1,5 @@
 tarball=backcall-VERSION.tar.gz
-sha1=e0ca4c1bde8f0a198505a090cd585a325789def1
-md5=87ce0c7839808e6a3427d57df6a792e7
-cksum=3908868358
+sha1=5bc62d540af1534f23560c0c32aac1e129518cd5
+md5=1f4c9a370c78743406296f48e56e8821
+cksum=3815916908
 upstream_url=https://pypi.io/packages/source/b/backcall/backcall-VERSION.tar.gz

build/pkgs/backcall/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) | $(PYTHON_TOOLCHAIN)
+$(PYTHON) | $(PYTHON_TOOLCHAIN) flit_core toml
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/backcall/package-version.txt

@@ -1 +1 @@
-0.1.0
+0.2.0

build/pkgs/bleach/checksums.ini

@@ -1,5 +1,5 @@
 tarball=bleach-VERSION.tar.gz
-sha1=3034291f3ec699d76aafefa00282007064a90312
-md5=63cae08551307156ec636465aff5183e
-cksum=3471185424
+sha1=6adfc1d0374305cce7c4dc92fdb9a241b81400f7
+md5=41e70ac58aa7bc5ff96c8fef24b9d659
+cksum=2710248571
 upstream_url=https://pypi.io/packages/source/b/bleach/bleach-VERSION.tar.gz

build/pkgs/bleach/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) | $(PYTHON_TOOLCHAIN)
+$(PYTHON) packaging six | $(PYTHON_TOOLCHAIN)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/bleach/package-version.txt

@@ -1 +1 @@
-3.1.5
+4.1.0

build/pkgs/cddlib/spkg-configure.m4

@@ -49,9 +49,9 @@ EOF
     dnl for now. Once all of cddlib's consumers know about the new (or
     dnl both) locations, we can update this check to support them.
     dnl See https://trac.sagemath.org/ticket/29413
-    AC_CHECK_HEADER([cdd.h],[],[sage_spkg_install_cddlib=yes],[
-      #include <setoper.h>
-      #include <cddmp.h>
+    AC_CHECK_HEADER([cddlib/cdd.h],[],[sage_spkg_install_cddlib=yes],[
+      #include <cddlib/setoper.h>
+      #include <cddlib/cddmp.h>
     ])
 
     dnl Both lattE and gfan try to link against libcddgmp (as

build/pkgs/certifi/checksums.ini

@@ -1,5 +1,5 @@
 tarball=certifi-VERSION.tar.gz
-sha1=dde31a44f2c2e36f007f6cd97ebec5a15070b1bb
-md5=b25267355218d11652c707e46accd059
-cksum=3624975010
+sha1=93145f31550b5e11dc323085d75a227856b93fd4
+md5=4b38238b7305fcb3ffbc4368be4e8845
+cksum=3424910066
 upstream_url=https://pypi.io/packages/source/c/certifi/certifi-VERSION.tar.gz

build/pkgs/certifi/package-version.txt

@@ -1 +1 @@
-2020.11.8
+2021.5.30

build/pkgs/cffi/checksums.ini

@@ -1,5 +1,5 @@
 tarball=cffi-VERSION.tar.gz
-sha1=21cdeccd7b7b121d35eae1b8e91d78f9ec83da98
-md5=272cb183bf0365530e3c0d8f446cd89d
-cksum=4039836079
+sha1=35bb24955834ecb5b7173e625fa95b02d638fcfd
+md5=5c118a18ea897df164dbff67a32876fc
+cksum=2930209167
 upstream_url=https://pypi.io/packages/source/c/cffi/cffi-VERSION.tar.gz

build/pkgs/cffi/package-version.txt

@@ -1 +1 @@
-1.14.5
+1.14.6

build/pkgs/charset_normalizer/SPKG.rst

@@ -0,0 +1,18 @@
+charset_normalizer: The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet.
+===========================================================================================================================
+
+Description
+-----------
+
+The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet.
+
+License
+-------
+
+MIT
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/charset-normalizer/
+

build/pkgs/charset_normalizer/checksums.ini

@@ -0,0 +1,5 @@
+tarball=charset-normalizer-VERSION.tar.gz
+sha1=8eec37b27487fa08532914f4c96ad3d7001d379e
+md5=40ecb4aa5ac6f08f87513a2ca0b32238
+cksum=1993471876
+upstream_url=https://pypi.io/packages/source/c/charset_normalizer/charset-normalizer-VERSION.tar.gz

build/pkgs/charset_normalizer/dependencies

@@ -0,0 +1,4 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.