Merge sagemath#29865

.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

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.5.beta1", 
-    "version": "9.5.beta1", 
+    "title": "sagemath/sage: 9.5.beta2", 
+    "version": "9.5.beta2", 
     "upload_type": "software", 
-    "publication_date": "2021-09-13", 
+    "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.beta1", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.5.beta2", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.5.beta1, Release Date: 2021-09-13
+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 .
@@ -275,6 +275,17 @@ 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_SUDO" ]; then
         # Trac #29585: Do the SAGE_DESTDIR staging of the wheel installation
@@ -295,7 +306,7 @@ sdh_store_and_pip_install_wheel() {
         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 [email protected], including the build log of this package."
+    fi
 fi

build/make/Makefile.in

@@ -534,8 +534,10 @@ $(1)-$(4)-no-deps:
 $(1)-no-deps: $(1)-$(4)-no-deps
 
 $(1)-$(4)-clean:
-	sage-spkg-uninstall $(if $(filter $(1),$(TOOLCHAIN_DEPS)),--keep-files) \
-		$(1) '$$($(4))'
+	if [ -d '$$($(4))' ]; then \
+	    sage-spkg-uninstall $(if $(filter $(1),$(TOOLCHAIN_DEPS)),--keep-files) \
+		$(1) '$$($(4))'; \
+	fi
 
 $(1)-clean: $(1)-$(4)-clean
 

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/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=c68b33782a9f983d5cd132cdb85b9cdc424d5c04
-md5=be4260558a6cf800a2e9eda789efc32b
-cksum=344926279
+sha1=9b22a30a08e51ba00cd1d83434baaefd3185301e
+md5=0ac843dd51c77c37da876beae77af4bf
+cksum=1637280499

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-a2af3f6a457f4c5618b72690a5c0be2b02360afb
+0a4f2a302c23d9c821b7be2cd6a7429075b7da60

build/pkgs/database_knotinfo/checksums.ini

@@ -1,5 +1,5 @@
 tarball=database_knotinfo-VERSION.tar.gz
-sha1=2d758c5f8bf346162d13bec1d5bccfec9d27baa1
-md5=ec20d43af0c4ecf59dfd281c6ccc4ef0
-cksum=2792610748
+sha1=549e3162b2ba6942dede30366072d10e26643f54
+md5=c6487321cd2e0fd6b9f9ee7bdfa19993
+cksum=2255768788
 upstream_url=https://pypi.io/packages/source/d/database_knotinfo/database_knotinfo-VERSION.tar.gz

build/pkgs/database_knotinfo/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) | $(PYTHON_TOOLCHAIN)
+$(PYTHON) | $(PYTHON_TOOLCHAIN) $(and $(filter-out no,$(SAGE_CHECK_database_knotinfo)), $(SAGERUNTIME) ipywidgets sympy singular gap libhomfly libbraiding matplotlib)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/database_knotinfo/package-version.txt

@@ -1 +1 @@
-0.7
+2021.9.1

build/pkgs/database_knotinfo/spkg-check.in

@@ -1,10 +1,5 @@
 cd $SAGE_ROOT/src/sage/
 
-echo "Testing databases/knotinfo_db.py"
-sage -t --long --optional="sage,database_knotinfo" databases/knotinfo_db.py  || sdh_die "Error testing KnotInfo databases"
-
-echo "Testing knots/knotinfo.py"
-sage -t --optional="sage,database_knotinfo" knots/knotinfo.py  || sdh_die "Error testing KnotInfo funcionality"
-
-echo "Testing knots/link.py"
-sage -t --optional="sage,database_knotinfo" knots/link.py  || sdh_die "Error testing KnotInfo funcionality"
+FILES="databases/ features/ knots/"
+echo "Testing: "$FILES
+sage -tp --long --optional="sage,database_knotinfo" $FILES  || sdh_die "Error testing KnotInfo databases"

build/pkgs/database_knotinfo/spkg-install.in

@@ -1,9 +1,2 @@
 cd src
 sdh_pip_install .
-
-FILECACHE="${SAGE_SHARE}/knotinfo"
-if [ -d $FILECACHE ]
-then
-    echo "Clearing former filecache of knotinfo"
-    rm -rf $FILECACHE
-fi

build/pkgs/distlib/checksums.ini

@@ -1,5 +1,5 @@
 tarball=distlib-VERSION.zip
-sha1=1c575431e31c32d25596c360e81bba7fe4638669
-md5=4baf787d8aceb260d6f77cb31bf27cf6
-cksum=2902365751
+sha1=b36dcbb9542fa58ada97ab27269176ff7d170724
+md5=50196f22cc2ed82fe2cf6c8fa3220d78
+cksum=801947531
 upstream_url=https://pypi.io/packages/source/d/distlib/distlib-VERSION.zip

build/pkgs/distlib/package-version.txt

@@ -1 +1 @@
-0.3.1
+0.3.2

build/pkgs/flit_core/dependencies

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

build/pkgs/html5lib/dependencies

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

build/pkgs/importlib_metadata/checksums.ini

@@ -1,5 +1,5 @@
 tarball=importlib_metadata-VERSION.tar.gz
-sha1=9a41be5cdf1fb347fca35640d607cbb27873cd02
-md5=de8753734db41db35d763475b3cf56be
-cksum=2900617554
+sha1=1572500dd099439cbd86bb70bfe1d206fbc844f6
+md5=5b944bce3fccaf848f0cba7a07f850a1
+cksum=416853070
 upstream_url=https://pypi.io/packages/source/i/importlib_metadata/importlib_metadata-VERSION.tar.gz

build/pkgs/importlib_metadata/package-version.txt

@@ -1 +1 @@
-4.0.1
+4.8.1

build/pkgs/importlib_resources/checksums.ini

@@ -1,5 +1,5 @@
 tarball=importlib_resources-VERSION.tar.gz
-sha1=d4b853132e9b9a0c58610e23df380c84be428c08
-md5=a4586b3cbb3d39c7a5e7ffc49d9ceb53
-cksum=1484460315
+sha1=d1f2742895a68f3f8d19dd7285df1687877fb15a
+md5=5db738106ca7c05340495c36357986a2
+cksum=1338307365
 upstream_url=https://pypi.io/packages/source/i/importlib_resources/importlib_resources-VERSION.tar.gz

build/pkgs/importlib_resources/dependencies

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

build/pkgs/importlib_resources/package-version.txt

@@ -1 +1 @@
-5.1.4
+5.2.2

build/pkgs/ipykernel/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) | ipython jupyter_client $(PYTHON_TOOLCHAIN) scandir
+$(PYTHON) debugpy matplotlib_inline ipython jupyter_client scandir | $(PYTHON_TOOLCHAIN)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/jupyterlab_pygments/dependencies

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

build/pkgs/matplotlib_inline/dependencies

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

build/pkgs/nbclient/dependencies

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

build/pkgs/nbconvert/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) | $(PYTHON_TOOLCHAIN) mistune jinja2 pygments traitlets jupyter_core nbformat entrypoints bleach pandocfilters testpath defusedxml
+$(PYTHON)  mistune jinja2 pygments traitlets jupyter_core nbformat entrypoints bleach pandocfilters testpath defusedxml jupyter_client jupyterlab_pygments nbclient | $(PYTHON_TOOLCHAIN)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/numpy/checksums.ini

@@ -1,5 +1,5 @@
 tarball=numpy-VERSION.zip
-sha1=56731f9eedf3bd42de2940515cfe3fadea7dfcca
-md5=949d9114af9accc25ede1daa359c4227
-cksum=2320980313
+sha1=c7eb91a2232f7843301c355795860baaa0280909
+md5=5638d5dae3ca387be562912312db842e
+cksum=2204147896
 upstream_url=https://pypi.io/packages/source/n/numpy/numpy-VERSION.zip

build/pkgs/numpy/package-version.txt

@@ -1 +1 @@
-1.20.3
+1.21.2

build/pkgs/openssl/checksums.ini

@@ -1,5 +1,5 @@
 tarball=openssl-VERSION.tar.gz
-sha1=261ea1ad4bbf7738622bea5caa97da0283fc3166
-md5=53807796206619b62037a178846ebe7e
-cksum=980103943
+sha1=3be896f1b33bc01af874ccca701a6f700af9de20
+md5=43c5ab628b7ab899d7cd4a4c7fe4067f
+cksum=2515710600
 upstream_url=https://www.openssl.org/source/openssl-VERSION.tar.gz

build/pkgs/openssl/package-version.txt

@@ -1 +1 @@
-3.0.0-beta2
+3.0.0

build/pkgs/packaging/checksums.ini

@@ -1,5 +1,5 @@
 tarball=packaging-VERSION.tar.gz
-sha1=6f8880ab84f05714a2549c1b54314b4f79fee319
-md5=5377308b3ba89f2d78c05e7f485be65d
-cksum=1567718319
+sha1=6ba3b8ff3ee43d1d4c0b658241f4fd6036ee7c78
+md5=240ba5823ed31051a1254e74c9d18d55
+cksum=3836397838
 upstream_url=https://pypi.io/packages/source/p/packaging/packaging-VERSION.tar.gz

build/pkgs/packaging/dependencies

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

build/pkgs/packaging/package-version.txt

@@ -1 +1 @@
-20.9
+21.0

build/pkgs/pip/checksums.ini

@@ -1,5 +1,5 @@
 tarball=pip-VERSION.tar.gz
-sha1=b26e4afd5524f5613edf5b1b94dd1b6e9a2e1f87
-md5=a867fd51eacfd5293f5b7e0c2e7867a7
-cksum=2004742197
+sha1=c6c9348c79a7f8448cd14b9e53baf141ea185dee
+md5=efbdb4201a5e6383fb4d12e26f78f355
+cksum=2583473334
 upstream_url=https://pypi.io/packages/source/p/pip/pip-VERSION.tar.gz

build/pkgs/pip/package-version.txt

@@ -1 +1 @@
-21.1.2
+21.2.4