Merge tag '10.0.beta8' into sd117_more_optional_doctest_tags

SageMath version 10.0.beta8, Release Date: 2023-04-06

.codecov.yml

@@ -1,5 +1,8 @@
 # https://docs.codecov.com/docs/pull-request-comments#disable-comment
 comment: false
+# https://docs.codecov.com/docs/codecovyml-reference#codecov
+codecov:
+  require_ci_to_pass: false
 # https://docs.codecov.com/docs/commit-status
 coverage:
   status:

.github/workflows/ci-conda.yml

@@ -6,6 +6,9 @@ on:
       - '*'
     branches:
       - 'public/build/**-runci'
+  pull_request:
+    types:
+      - labeled
   workflow_dispatch:
     # Allow to run manually
 
@@ -19,6 +22,13 @@ jobs:
     name: Conda
     runs-on: ${{ matrix.os }}
 
+    # Run on push, workflow dispatch and when certain labels are added 
+    if: |
+      github.event.action != 'labeled' ||
+      github.event.label.name == 'c: packages: optional' || 
+      github.event.label.name == 'c: packages: standard' || 
+      github.event.label.name == 's: run conda ci'
+
     strategy:
       fail-fast: false
       matrix:
@@ -84,13 +94,22 @@ jobs:
           echo "::remove-matcher owner=configure-system-package-warning::"
           echo "::remove-matcher owner=configure-system-package-error::"
 
+          # Manually install ptyprocess for now, until https://github.com/sagemath/sage/issues/32147 is fixed
+          pip install --no-build-isolation -v -v ptyprocess==0.5.1
+
       - name: Build
         shell: bash -l {0}
         run: |
-          pip install --no-build-isolation -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup
-          pip install --no-build-isolation -v -v -e ./src
+          # Use --no-deps and pip check below to verify that all necessary dependencies are installed via conda.
+          pip install --no-build-isolation --no-deps -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup
+          pip install --no-build-isolation --no-deps -v -v -e ./src
         env:
           SAGE_NUM_THREADS: 2
+
+      - name: Verify dependencies
+        if: always()
+        shell: bash -l {0}
+        run: pip check
 
       - name: Test
         shell: bash -l {0}

.github/workflows/doc-publish.yml

@@ -31,15 +31,15 @@ jobs:
         uses: actions/github-script@v6.4.0
         with:
           script: |
-            var artifacts = await github.actions.listWorkflowRunArtifacts({
+            var artifacts = await github.rest.actions.listWorkflowRunArtifacts({
                owner: context.repo.owner,
                repo: context.repo.repo,
                run_id: ${{github.event.workflow_run.id }},
             });
             var matchArtifact = artifacts.data.artifacts.filter((artifact) => {
               return artifact.name == "docs"
             })[0];
-            var download = await github.actions.downloadArtifact({
+            var download = await github.rest.actions.downloadArtifact({
                owner: context.repo.owner,
                repo: context.repo.repo,
                artifact_id: matchArtifact.id,

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 10.0.beta7", 
-    "version": "10.0.beta7", 
+    "title": "sagemath/sage: 10.0.beta8", 
+    "version": "10.0.beta8", 
     "upload_type": "software", 
-    "publication_date": "2023-04-01", 
+    "publication_date": "2023-04-06", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/10.0.beta7", 
+            "identifier": "https://github.com/sagemath/sage/tree/10.0.beta8", 
             "relation": "isSupplementTo"
         }, 
         {

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.0.beta7, Release Date: 2023-04-01
+SageMath version 10.0.beta8, Release Date: 2023-04-06

bootstrap-conda

@@ -11,7 +11,6 @@ STRIP_COMMENTS="sed s/#.*//;"
 shopt -s extglob
 
 DEVELOP_SPKG_PATTERN="@(_develop$(for a in $(head -n 1 build/pkgs/_develop/dependencies); do echo -n "|"$a; done))"
-
 BOOTSTRAP_PACKAGES=$(echo $(${STRIP_COMMENTS} build/pkgs/_bootstrap/distros/conda.txt))
 SYSTEM_PACKAGES=
 OPTIONAL_SYSTEM_PACKAGES=
@@ -37,10 +36,13 @@ for PKG_BASE in $(sage-package list --has-file distros/conda.txt); do
                     ;;
             esac
         else
-            case "$PKG_TYPE" in
-                standard)
+            case "$PKG_BASE:$PKG_TYPE" in
+                *:standard)
                     SAGELIB_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
                     ;;
+                $DEVELOP_SPKG_PATTERN:*)
+                    DEVELOP_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
                 *)
                     SAGELIB_OPTIONAL_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
                     ;;

build/bin/sage-clone-source

@@ -31,11 +31,13 @@ CONFBALL="$SRC/upstream/configure-$CONFVERSION.tar.gz"
 rm -rf "$DST"
 mkdir -p "$DST"
 
-git clone --origin trac "$SRC" "$DST"
+git clone --origin upstream "$SRC" "$DST"
 
 cd "$DST"
-git remote set-url trac "$SAGE_REPO_ANONYMOUS"
-git remote set-url --push trac "$SAGE_REPO_AUTHENTICATED"
+git remote set-url upstream "$SAGE_REPO_ANONYMOUS"
+git remote set-url --push upstream "do not push to upstream"
+git remote add trac https://github.com/sagemath/sagetrac-mirror.git
+git remote set-url --push trac "do not push to trac"
 
 # Save space
 git gc --aggressive --prune=now

build/pkgs/argon2_cffi/dependencies

@@ -1,4 +1,4 @@
-$(PYTHON) six | $(PYTHON_TOOLCHAIN) cffi
+$(PYTHON) argon2_cffi_bindings | $(PYTHON_TOOLCHAIN) flit_core
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/argon2_cffi/spkg-install.in

@@ -1,6 +1,2 @@
 cd src
-if [ "$SAGE_FAT_BINARY" = "yes" ]; then
-   # https://argon2-cffi.readthedocs.io/en/stable/installation.html
-   export ARGON2_CFFI_USE_SSE2=0
-fi
 sdh_pip_install .

build/pkgs/argon2_cffi_bindings/SPKG.rst

@@ -0,0 +1,18 @@
+argon2_cffi_bindings: Low-level CFFI bindings for Argon2
+========================================================
+
+Description
+-----------
+
+Low-level CFFI bindings for Argon2
+
+License
+-------
+
+MIT
+
+Upstream Contact
+----------------
+
+https://pypi.org/project/argon2-cffi-bindings/
+

build/pkgs/argon2_cffi_bindings/checksums.ini

@@ -0,0 +1,5 @@
+tarball=argon2-cffi-bindings-VERSION.tar.gz
+sha1=5a9b8906d9ca73c53c2bf0a2f0a8127fda69e965
+md5=f1591e1af7dea9ef3e5b982e2c196c1d
+cksum=2420586823
+upstream_url=https://pypi.io/packages/source/a/argon2_cffi_bindings/argon2-cffi-bindings-VERSION.tar.gz

build/pkgs/argon2_cffi_bindings/dependencies

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

build/pkgs/argon2_cffi_bindings/install-requires.txt

@@ -0,0 +1 @@
+argon2-cffi-bindings

build/pkgs/argon2_cffi_bindings/package-version.txt

@@ -0,0 +1 @@
+21.2.0

build/pkgs/argon2_cffi_bindings/spkg-install.in

@@ -0,0 +1,6 @@
+cd src
+if [ "$SAGE_FAT_BINARY" = "yes" ]; then
+   # https://argon2-cffi.readthedocs.io/en/stable/installation.html
+   export ARGON2_CFFI_USE_SSE2=0
+fi
+sdh_pip_install .

build/pkgs/argon2_cffi_bindings/type

@@ -0,0 +1 @@
+standard

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=224fa9979ee6d884b708b6e96553c73b170fffcc
-md5=eead1165f89ae4b693dbdb252d4e940c
-cksum=1999003763
+sha1=c809622a8c0b706231b5c8e02c0fb96b940e2a10
+md5=4ab2cb23636289210afe4a6743b36183
+cksum=1470715760

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-ad0ea73c1df909186e435713f1c0d7d34d93cd84
+adaf3af26892f4a3720cc09d0e21c35281b472a3

build/pkgs/gap/distros/conda.txt

@@ -1 +1 @@
-gap-defaults
+gap-defaults>=4.12.2

build/pkgs/ipywidgets/distros/conda.txt

@@ -1 +1 @@
-ipywidgets
+ipywidgets<8.0.0

build/pkgs/lrcalc_python/distros/conda.txt

@@ -1 +1 @@
-python-lrcalc
+python-lrcalc~=2.1

build/pkgs/networkx/distros/conda.txt

@@ -1 +1 @@
-networkx
+networkx<3.0,>=2.4

build/pkgs/openblas/spkg-configure.m4

@@ -7,7 +7,12 @@ SAGE_SPKG_CONFIGURE([openblas], [
   m4_pushdef([SAGE_OPENBLAS_MIN_VERSION_MINOR], [2])
   m4_pushdef([SAGE_OPENBLAS_MIN_VERSION_MICRO], [20])
   m4_pushdef([SAGE_OPENBLAS_MIN_VERSION], [SAGE_OPENBLAS_MIN_VERSION_MAJOR.SAGE_OPENBLAS_MIN_VERSION_MINOR.SAGE_OPENBLAS_MIN_VERSION_MICRO])
-  PKG_CHECK_MODULES([OPENBLAS], [openblas >= ]SAGE_OPENBLAS_MIN_VERSION, [
+  dnl Reject openblas 0.3.22 - https://github.com/sagemath/sage/pull/35371
+  m4_pushdef([SAGE_OPENBLAS_LT_VERSION_MAJOR], [0])
+  m4_pushdef([SAGE_OPENBLAS_LT_VERSION_MINOR], [3])
+  m4_pushdef([SAGE_OPENBLAS_LT_VERSION_MICRO], [22])
+  m4_pushdef([SAGE_OPENBLAS_LT_VERSION], [SAGE_OPENBLAS_LT_VERSION_MAJOR.SAGE_OPENBLAS_LT_VERSION_MINOR.SAGE_OPENBLAS_LT_VERSION_MICRO])
+  PKG_CHECK_MODULES([OPENBLAS], [openblas >= ]SAGE_OPENBLAS_MIN_VERSION [openblas < ]SAGE_OPENBLAS_LT_VERSION, [
     LIBS="$OPENBLAS_LIBS $LIBS"
     CFLAGS="$OPENBLAS_CFLAGS $CFLAGS"
     PKG_CHECK_VAR([OPENBLASPCDIR], [openblas], [pcfiledir], [
@@ -74,6 +79,13 @@ SAGE_SPKG_CONFIGURE([openblas], [
                                                  < 10000 * ]]SAGE_OPENBLAS_MIN_VERSION_MAJOR[[
                                                    + 100 * ]]SAGE_OPENBLAS_MIN_VERSION_MINOR[[
                                                          + ]]SAGE_OPENBLAS_MIN_VERSION_MICRO[[)
+                                               return 1;
+                                             if (  10000 * version[0]
+                                                   + 100 * version[1]
+                                                         + version[2]
+                                                 >=10000 * ]]SAGE_OPENBLAS_LT_VERSION_MAJOR[[
+                                                   + 100 * ]]SAGE_OPENBLAS_LT_VERSION_MINOR[[
+                                                         + ]]SAGE_OPENBLAS_LT_VERSION_MICRO[[)
                                                return 1;]])
                          ], [AS_VAR_SET([HAVE_OPENBLAS], [yes])], [AS_VAR_SET([HAVE_OPENBLAS], [no])],
                             [AS_VAR_SET([HAVE_OPENBLAS], [yes])])

build/pkgs/ptyprocess/distros/conda.txt

@@ -1 +1,3 @@
-ptyprocess
+# The version should be fixed to 0.5.1 (see https://github.com/sagemath/sage/issues/32147), but this is not available on conda-forge
+# thus don't install ptyprocess with conda, but let pip handle it 
+# ptyprocess

build/pkgs/sage_conf/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-conf ~= 10.0b7
+sage-conf ~= 10.0b8

build/pkgs/sage_docbuild/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-docbuild ~= 10.0b7
+sage-docbuild ~= 10.0b8

build/pkgs/sage_setup/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-setup ~= 10.0b7
+sage-setup ~= 10.0b8

build/pkgs/sage_sws2rst/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-sws2rst ~= 10.0b7
+sage-sws2rst ~= 10.0b8

build/pkgs/sagelib/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagelib ~= 10.0b7
+sagelib ~= 10.0b8

build/pkgs/sagemath_categories/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-categories ~= 10.0b7
+sagemath-categories ~= 10.0b8

build/pkgs/sagemath_environment/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-environment ~= 10.0b7
+sagemath-environment ~= 10.0b8

build/pkgs/sagemath_objects/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-objects ~= 10.0b7
+sagemath-objects ~= 10.0b8

build/pkgs/sagemath_repl/install-requires.txt

@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-repl ~= 10.0b7
+sagemath-repl ~= 10.0b8

build/pkgs/scipy/distros/conda.txt

@@ -1 +1 @@
-scipy
+scipy<1.11,>=1.5

build/pkgs/sphinx/distros/conda.txt

@@ -1 +1 @@
-sphinx
+sphinx<6,>=5.2

pkgs/sage-conf/VERSION.txt

@@ -1 +1 @@
-10.0.beta7
+10.0.beta8

pkgs/sage-conf_pypi/VERSION.txt

@@ -1 +1 @@
-10.0.beta7
+10.0.beta8

pkgs/sage-docbuild/VERSION.txt

@@ -1 +1 @@
-10.0.beta7
+10.0.beta8

pkgs/sage-setup/VERSION.txt

@@ -1 +1 @@
-10.0.beta7
+10.0.beta8

pkgs/sage-sws2rst/VERSION.txt

@@ -1 +1 @@
-10.0.beta7
+10.0.beta8

pkgs/sagemath-categories/VERSION.txt

@@ -1 +1 @@
-10.0.beta7
+10.0.beta8

pkgs/sagemath-environment/VERSION.txt

@@ -1 +1 @@
-10.0.beta7
+10.0.beta8

pkgs/sagemath-objects/VERSION.txt

@@ -1 +1 @@
-10.0.beta7
+10.0.beta8

pkgs/sagemath-repl/VERSION.txt

@@ -1 +1 @@
-10.0.beta7
+10.0.beta8

src/.relint.yml

@@ -6,8 +6,8 @@
 - name: 'python3: Python3 incompatible code'
   hint: |
     # ifilter, imap, izip           # __metaclass__
-    Hint: # update raise statements       # except Exception, var
-    Hint: # six is no longer allowed
+    # update raise statements       # except Exception, var
+    # six is no longer allowed
   pattern: '(import.*[, ]ifilter|import.*[, ]imap|import.*[, ]izip|^\s*raise\s*[A-Za-z]*Error\s*,|__metaclass__|except\s*[A-Za-z]\s*,|import six|from six import)'
   filePattern: .*[.](py|pyx|rst)
 
@@ -20,9 +20,9 @@
 - name: 'blocks: wrong syntax for blocks (INPUT, OUTPUT, EXAMPLES, NOTE, etc.)'
   hint: |
     # the correct syntax is .. SEEALSO::
-    Hint: # TESTS and EXAMPLES should be plural, NOTE singular
-    Hint: # no :: after INPUT, OUTPUT, REFERENCE blocks
-    Hint: # no " :" at the end of lines
+    # TESTS and EXAMPLES should be plural, NOTE singular
+    # no :: after INPUT, OUTPUT, REFERENCE blocks
+    # no " :" at the end of lines
   pattern: '(\.\.SEE|SEE ALSO|SEEALSO:($|[^:])|^\s*TEST:|^\s*EXAMPLE:|^\s*NOTES:|^\s*[A-Z]*PUT::|^\s*REFERENCES?::$)'
 
 - name: 'trac_links: bad trac link'
@@ -46,10 +46,10 @@
 - name: 'namespace_pkg_all_import: import from .all of a namespace package'
   hint: |
     Sage library code should not import from sage.PAC.KAGE.all when sage.PAC.KAGE is an implicit
-    Hint: namespace package. Type import_statements("SOME_IDENTIFIER") to find a more specific import,
-    Hint: or use 'sage --fiximports' to fix automatically in the source file.
+    namespace package. Type import_statements("SOME_IDENTIFIER") to find a more specific import,
+    or use 'sage --fiximports' to fix automatically in the source file.
   # Keep in sync with SAGE_ROOT/src/sage/misc/replace_dot_all.py
-  pattern: 'from\s+sage(|[.](arith|categories|combinat|ext|graphs(|[.]decompositions)|interfaces|libs|matrix|misc|numerical(|[.]backends)|rings(|[.]finite_rings)|sets))[.]all\s+import'
+  pattern: 'from\s+sage(|[.](arith|categories|combinat|crypto|databases|data_structures|dynamics|ext|game_theory|games|graphs|groups|interfaces|manifolds|matrix|matroids|misc|modules|monoids|numerical|probability|quadratic_forms|quivers|rings|sat|schemes|sets|stats|tensor)[a-z0-9_.]*|[.]libs)[.]all\s+import'
   # imports from .all are allowed in all.py; also allow in some modules that need sage.all
   filePattern: '(.*/|)(?!(all|benchmark|dev_tools|parsing|sage_eval))[^/.]*[.](py|pyx|pxi)$'
 

src/VERSION.txt

@@ -1 +1 @@
-10.0.beta7
+10.0.beta8

src/bin/sage-env

@@ -305,11 +305,11 @@ if [ -n "$SAGE_LOCAL" ]; then
 fi
 
 if [ -z "$SAGE_REPO_ANONYMOUS" ]; then
-    SAGE_REPO_ANONYMOUS="https://github.com/sagemath/sagetrac-mirror.git"
+    SAGE_REPO_ANONYMOUS="https://github.com/sagemath/sage.git"
     export SAGE_REPO_ANONYMOUS
 fi
 if [ -z "$SAGE_REPO_AUTHENTICATED" ]; then
-        SAGE_REPO_AUTHENTICATED="ssh://git@trac.sagemath.org:2222/sage.git"
+        SAGE_REPO_AUTHENTICATED="https://github.com/sagemath/sage.git"
         export SAGE_REPO_AUTHENTICATED
 fi
 

src/bin/sage-version.sh

@@ -4,6 +4,6 @@
 # which stops "setup.py develop" from rewriting it as a Python file.
 :
 # This file is auto-generated by the sage-update-version script, do not edit!
-SAGE_VERSION='10.0.beta7'
-SAGE_RELEASE_DATE='2023-04-01'
-SAGE_VERSION_BANNER='SageMath version 10.0.beta7, Release Date: 2023-04-01'
+SAGE_VERSION='10.0.beta8'
+SAGE_RELEASE_DATE='2023-04-06'
+SAGE_VERSION_BANNER='SageMath version 10.0.beta8, Release Date: 2023-04-06'