Merge branch 'develop' into barvinok0417

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -3,33 +3,11 @@ description: Report a bug
 title: "<title>"
 labels: "t: bug"
 body:
-  - type: checkboxes
-    attributes:
-      label: Is there an existing issue for this?
-      description: Please search to see if an issue already exists for the bug you encountered.
-      options:
-      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
-        required: true
-  - type: checkboxes
-    attributes:
-      label: Did you read the documentation and troubleshoot guide?
-      description: Please read [README.md](https://github.com/sagemath/sage/blob/develop/README.md) and [the Troubleshooting section in the Installation Guide](https://doc.sagemath.org/html/en/installation/troubles.html).
-      options:
-      - label: I have read the documentation and troubleshoot guide
-        required: true
-  - type: textarea
+  - type: markdown
     attributes:
-      label: Environment
-      description: |
-        examples:
-          - **OS**: Ubuntu 20.04
-          - Sage Version: 9.2
       value: |
-          - **OS**:
-          - **Sage Version**: 
-      render: markdown
-    validations:
-      required: true
+        * Please search to see if an issue already exists for the bug you encountered.
+        * Please read [README.md](https://github.com/sagemath/sage/blob/develop/README.md) and [the Troubleshooting section in the Installation Guide](https://doc.sagemath.org/html/en/installation/troubles.html).
   - type: textarea
     attributes:
       label: Steps To Reproduce
@@ -60,3 +38,24 @@ body:
         Links? References? Anything that will give us more context about the issue you are encountering!
     validations:
       required: false
+  - type: textarea
+    attributes:
+      label: Environment
+      description: |
+        examples:
+          - **OS**: Ubuntu 20.04
+          - Sage Version: 9.2
+      value: |
+          - **OS**:
+          - **Sage Version**:
+      render: markdown
+    validations:
+      required: true
+  - type: checkboxes
+    attributes:
+      label: Checklist
+      options:
+      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
+        required: true
+      - label: I have read the documentation and troubleshoot guide
+        required: true

.github/ISSUE_TEMPLATE/failure_building_from_source.yml

@@ -4,20 +4,11 @@ title: "<title>"
 labels: ['c: build', 't: bug']
 assignees: []
 body:
-  - type: checkboxes
+  - type: markdown
     attributes:
-      label: Is there an existing issue for this?
-      description: Please search to see if an issue already exists for the bug you encountered.
-      options:
-      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
-        required: true
-  - type: checkboxes
-    attributes:
-      label: Did you read the documentation and troubleshoot guide?
-      description: Please read [README.md](https://github.com/sagemath/sage/blob/develop/README.md) and [the Troubleshooting sectionin the Installation Guide](https://doc.sagemath.org/html/en/installation/troubles.html).
-      options:
-      - label: I have read the documentation and troubleshoot guide
-        required: true
+      value: |
+        * Please search to see if an issue already exists for the bug you encountered.
+        * Please read [README.md](https://github.com/sagemath/sage/blob/develop/README.md) and [the Troubleshooting section in the Installation Guide](https://doc.sagemath.org/html/en/installation/troubles.html).
   - type: textarea
     attributes:
       label: Environment
@@ -65,3 +56,11 @@ body:
         Links? References? Anything that will give us more context about the issue you are encountering!
     validations:
       required: false
+  - type: checkboxes
+    attributes:
+      label: Checklist
+      options:
+      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
+        required: true
+      - label: I have read the documentation and troubleshoot guide
+        required: true

.github/ISSUE_TEMPLATE/feature_report.yml

@@ -3,13 +3,10 @@ description: Suggest an idea
 title: "<title>"
 labels: "t: enhancement"
 body:
-  - type: checkboxes
+  - type: markdown
     attributes:
-      label: Is there an existing issue for this?
-      description: Please search to see if an issue already exists for the bug you encountered.
-      options:
-      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
-        required: true
+      value: |
+        * Please search to see if an issue already exists for the bug you encountered.
   - type: textarea
     attributes:
       label: Problem Description
@@ -34,3 +31,9 @@ body:
       description: Add any other context about the problem here.
     validations:
       required: false
+  - type: checkboxes
+    attributes:
+      label: Is there an existing issue for this?
+      options:
+      - label: I have searched the existing issues for a bug report that matches the one I want to file, without success.
+        required: true

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,17 +1,20 @@
-<!-- Please provide a concise, informative and self-explanatory title. -->
-<!-- Don't put issue numbers in the title. Put it in the Description below. -->
-<!-- For example, instead of "Fixes #12345", use "Add a new method to multiply two integers" -->
-
-### :books: Description
+<!-- ^^^^^
+Please provide a concise, informative and self-explanatory title.
+Don't put issue numbers in there, do this in the PR body below.
+For example, instead of "Fixes #1234" use "Introduce new method to calculate 1+1"
+-->
+<!-- Describe your changes here in detail -->
 
-<!-- Describe your changes here in detail. -->
 <!-- Why is this change required? What problem does it solve? -->
 <!-- If this PR resolves an open issue, please link to it here. For example "Fixes #12345". -->
 <!-- If your change requires a documentation PR, please link it appropriately. -->
 
 ### :memo: Checklist
 
-<!-- Put an `x` in all the boxes that apply. It should be `[x]` not `[x ]`. -->
+<!-- Put an `x` in all the boxes that apply. -->
+<!-- If your change requires a documentation PR, please link it appropriately -->
+<!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
+<!-- Feel free to remove irrelevant items. -->
 
 - [ ] The title is concise, informative, and self-explanatory.
 - [ ] The description explains in detail what this PR is about.

.github/workflows/build.yml

@@ -60,11 +60,13 @@ jobs:
           # (This keeps mtimes of unchanged files unchanged and mtimes of changed files newer than unchanged files.)
           # Finally we reset the index to "old". (This keeps all mtimes unchanged.)
           # The changed files now show up as uncommitted changes.
+          # The final "git add -N" makes sure that files that were added in "new" do not show
+          # as untracked files, which would be removed by "git clean -fx".
           git worktree add --detach worktree-image
           rm -rf /sage/.git && mv worktree-image/.git /sage/
           rm -rf worktree-image && ln -s /sage worktree-image
           if [ ! -f worktree-image/.gitignore ]; then cp .gitignore worktree-image/; fi
-          (cd worktree-image && git add -A && git commit --allow-empty -m "old" -a && git tag -f old && git reset --hard new && git reset old)
+          (cd worktree-image && git add -A && git commit --quiet --allow-empty -m "old" -a && git tag -f old && git reset --hard new && git reset --quiet old && git add -N . && git status)
 
       - name: Incremental build, test changed files (sage -t --new)
         id: incremental

.github/workflows/doc-build.yml

@@ -44,13 +44,15 @@ jobs:
           # (This keeps mtimes of unchanged files unchanged and mtimes of changed files newer than unchanged files.)
           # Finally we reset the index to "old". (This keeps all mtimes unchanged.)
           # The changed files now show up as uncommitted changes.
+          # The final "git add -N" makes sure that files that were added in "new" do not show
+          # as untracked files, which would be removed by "git clean -fx".
           git worktree add --detach worktree-image
           rm -rf /sage/.git && mv worktree-image/.git /sage/
           rm -rf worktree-image && ln -s /sage worktree-image
           if [ ! -f worktree-image/.gitignore ]; then cp .gitignore worktree-image/; fi
-          (cd worktree-image && git add -A && git commit --allow-empty -m "old" -a && git tag -f old && git reset --hard new && git reset old)
+          (cd worktree-image && git add -A && git commit --quiet --allow-empty -m "old" -a && git tag -f old && git reset --hard new && git reset --quiet old && git add -N . && git status)
           # Keep track of changes to built HTML
-          (cd /sage/local/share/doc/sage/html/en && find . -name "*.html" | xargs sed -i '/class="sidebar-brand-text"/s/Sage [0-9a-z.]* /Sage dev /'; git init && (echo ".buildinfo"; echo ".inv") > .gitignore; git add -A && git commit --quiet -m "old")
+          new_version=$(cat src/VERSION.txt); (cd /sage/local/share/doc/sage/html/en && find . -name "*.html" | xargs sed -i '/class="sidebar-brand-text"/s/Sage [0-9a-z.]* /Sage '$new_version' /'; git init && (echo "*.svg binary"; echo "*.pdf binary") >> .gitattributes && (echo ".buildinfo"; echo '*.inv'; echo '.git*'; echo '*.svg'; echo '*.pdf'; echo '*.png'; echo 'searchindex.js') > .gitignore; git add -A && git commit --quiet -m "old")
 
       - name: Incremental build
         id: incremental
@@ -80,7 +82,10 @@ jobs:
         # incremental docbuild may introduce broken links (inter-file references) though build succeeds
         run: |
           set -ex
-          make doc-clean doc-uninstall sagelib-clean && git clean -fx src/sage && ./config.status && make doc-html
+          mv /sage/local/share/doc/sage/html/en/.git /sage/.git-doc
+          make doc-clean doc-uninstall sagelib-clean && git clean -fx src/sage
+          mkdir -p /sage/local/share/doc/sage/html/en/ && mv /sage/.git-doc /sage/local/share/doc/sage/html/en/.git
+          ./config.status && make doc-html
         working-directory: ./worktree-image
         env:
           MAKE: make -j2
@@ -94,7 +99,7 @@ jobs:
           mkdir -p ./docs
           # Create changelog
           echo '## Preview of CHANGES.html'
-          (cd /sage/local/share/doc/sage/html/en && find . -name "*.html" | xargs sed -i '/class="sidebar-brand-text"/s/Sage [0-9a-z.]* /Sage dev /'; git diff --name-only) | tee ./docs/CHANGES.txt
+          (cd /sage/local/share/doc/sage/html/en && git diff --name-only) | tee ./docs/CHANGES.txt
           (cd /sage/local/share/doc/sage/html/en && git diff; rm -rf .git) > ./docs/html.diff
           echo '## Preview of html.diff'; head -n 400 ./docs/html.diff
           (echo '<p><a href="html.diff">HTML diff</a>'; sed -E 's,(.*),<p><a href="\1">\1</a>,' ./docs/CHANGES.txt) > ./docs/CHANGES.html

.github/workflows/docker.yml

@@ -50,6 +50,8 @@ on:
            "centos-7-devtoolset-gcc_11",
            "centos-stream-8-python3.9",
            "centos-stream-9-python3.9",
+           "almalinux-8-python3.9",
+           "almalinux-9-python3.11",
            "gentoo-python3.10",
            "gentoo-python3.11",
            "archlinux-latest",

.gitignore

@@ -22,6 +22,7 @@
 /confdefs.h
 
 /m4/sage_spkg_configures.m4
+/m4/sage_spkg_versions*.m4
 
 # no longer generated, but may still be in user worktrees
 /src/lib/pkgconfig

.vscode/settings.json

@@ -27,7 +27,7 @@
     "python.linting.enabled": true,
     // The following pycodestyle arguments are the same as the pycodestyle-minimal
     // tox environnment, see the file SAGE_ROOT/src/tox.ini
-    "python.linting.pycodestyleArgs": ["--select= E111,E211,E271,E303,E306,E401,E502,E701,E702,E703,E714,W291,W293,W391,W605,E711,E712,E713,E721,E722"],
+    "python.linting.pycodestyleArgs": ["--select= E111,E21,E222,E227,E251,E271,E303,E306,E401,E502,E701,E702,E703,E71,E72,W291,W293,W391,W605"],
     "cSpell.words": [
         "furo",
         "Conda",

CITATION.cff

@@ -4,8 +4,8 @@ title: SageMath
 abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
-version: 10.1.beta4
+version: 10.1.beta6
 doi: 10.5281/zenodo.593563
-date-released: 2023-06-21
+date-released: 2023-07-09
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"

VERSION.txt

@@ -1 +1 @@
-SageMath version 10.1.beta4, Release Date: 2023-06-21
+SageMath version 10.1.beta6, Release Date: 2023-07-09

bootstrap

@@ -35,10 +35,16 @@ CONFVERSION=$(cat $PKG/package-version.txt)
 
 
 bootstrap () {
-    if [ "${BOOTSTRAP_QUIET}" = "no" ]; then
-        echo "bootstrap:$LINENO: installing 'm4/sage_spkg_configures.m4'"
-    fi
-    rm -f m4/sage_spkg_configures.m4
+    for a in m4/sage_spkg_configures.m4 m4/sage_spkg_versions.m4 m4/sage_spkg_versions_toml.m4; do
+        if [ "${BOOTSTRAP_QUIET}" = "no" ]; then
+            echo "bootstrap:$LINENO: installing '"$a"'"
+        fi
+        rm -f $a
+        echo "# Generated by SAGE_ROOT/bootstrap; do not edit" > $a
+    done
+    for a in m4/sage_spkg_versions.m4 m4/sage_spkg_versions_toml.m4; do
+        echo 'changequote(`>>>'"'"', `<<<'"')dnl" >> $a
+    done
     spkg_configures=""
     # initialize SAGE_ENABLE... options for standard packages
     for pkgname in $(sage-package list :standard: | sort); do
@@ -92,12 +98,17 @@ SAGE_SPKG_CONFIGURE_$(echo ${pkgname} | tr '[a-z]' '[A-Z]')"
             if test -f "$DIR/requirements.txt" -o -f "$DIR/install-requires.txt"; then
                 # A Python package
                 SPKG_TREE_VAR=SAGE_VENV
+                echo "define(>>>SPKG_INSTALL_REQUIRES_${pkgname}<<<, >>>$(echo $(sage-get-system-packages install-requires ${pkgname}))<<<)dnl" >> m4/sage_spkg_versions.m4
+                echo "define(>>>SPKG_INSTALL_REQUIRES_${pkgname}<<<, >>>$(echo $(sage-get-system-packages install-requires-toml ${pkgname}))<<<)dnl" >> m4/sage_spkg_versions_toml.m4
             fi
         fi
         spkg_configures="$spkg_configures
 SAGE_SPKG_FINALIZE([$pkgname], [$pkgtype], [$SPKG_SOURCE], [$SPKG_TREE_VAR])"
     done
     echo "$spkg_configures" >> m4/sage_spkg_configures.m4
+    for a in m4/sage_spkg_versions.m4 m4/sage_spkg_versions_toml.m4; do
+        echo 'changequote(>>>`<<<, >>>'"'"'<<<)dnl' >> $a
+    done
 
     for pkgname in $(sage-package list --has-file bootstrap); do
         (cd build/pkgs/$pkgname && ./bootstrap) || exit 1

build/bin/sage-get-system-packages

@@ -12,16 +12,16 @@ if [ -z "$SAGE_ROOT" ]; then
 fi
 case "$SYSTEM" in
     install-requires)
-        # Collect install-requires.txt and output it in the format
+        # Collect install-requires.txt (falling back to requirements.txt) and output it in the format
         # needed by setup.cfg [options] install_requires=
-        SYSTEM_PACKAGES_FILE_NAMES="install-requires.txt"
+        SYSTEM_PACKAGES_FILE_NAMES="install-requires.txt requirements.txt"
         STRIP_COMMENTS="sed s/#.*//;/^[[:space:]]*$/d;"
         COLLECT=
         ;;
     install-requires-toml)
-        # Collect install-requires.txt and output it in the format
+        # Collect install-requires.txt (falling back to requirements.txt) and output it in the format
         # needed by pyproject.toml [build-system] requires=
-        SYSTEM_PACKAGES_FILE_NAMES="install-requires.txt"
+        SYSTEM_PACKAGES_FILE_NAMES="install-requires.txt requirements.txt"
         STRIP_COMMENTS="sed s/#.*//;/^[[:space:]]*$/d;s/^/'/;s/$/',/;"
         COLLECT=
         ;;

build/pkgs/bliss/SPKG.rst

@@ -10,17 +10,21 @@ canonical forms of graphs.
 License
 -------
 
-LGPL
+LGPL3
 
 
 Upstream Contact
 ----------------
 
-Bliss is currently being maintained by Tommi Junttila and Petteri Kaski.
+Bliss is currently being maintained by Tommi Junttila at
+
+https://users.aalto.fi/~tjunttil/bliss/index.html
+
+Bliss used to be maintained by Tommi Junttila and Petteri Kaski up to version 0.73 at
 
 http://www.tcs.tkk.fi/Software/bliss/index.html
 
-We apply patches generated from https://github.com/mkoeppe/bliss (branch
-apply_debian_patches) as our upstream. This tracks the patches from the
-Debian package, adding an autotools build system and adjusting the
-include file locations.
+Dependencies
+------------
+
+None

build/pkgs/bliss/checksums.ini

@@ -1,4 +1,5 @@
-tarball=bliss-VERSION.tar.gz
-sha1=1da8f098046824fbfff4c64c337e28b2a082f74f
-md5=452aea8737d3c4ad0d8ff39180be8004
-cksum=2193930007
+tarball=bliss-VERSION.zip
+sha1=c91c9dcbc11d66ffbcf6415e09ebe793df37be2a
+md5=5707cbfd9fd00980571c64ab3584c505
+cksum=1626493724
+upstream_url=https://users.aalto.fi/~tjunttil/bliss/downloads/bliss-VERSION.zip

build/pkgs/bliss/dependencies

@@ -1,4 +1,4 @@
-# no dependencies
+| cmake
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/bliss/package-version.txt

@@ -1 +1 @@
-0.73+debian-1+sage-2016-08-02.p0
+0.77

build/pkgs/bliss/patches/bliss-0.77-install.patch

@@ -0,0 +1,32 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 01ed093..cfdb0a6 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -62,3 +62,27 @@ if(USE_GMP)
+   target_link_libraries(bliss-executable ${GMP_LIBRARIES})
+ endif(USE_GMP)
+ set_target_properties(bliss-executable PROPERTIES OUTPUT_NAME bliss)
++
++include(GNUInstallDirs)
++
++set(
++  BLISS_HEADERS
++  src/bliss_C.h
++  src/uintseqhash.hh
++  src/abstractgraph.hh
++  src/stats.hh
++  src/digraph.hh
++  src/defs.hh
++  src/heap.hh
++  src/graph.hh
++  src/partition.hh
++  src/kqueue.hh
++  src/utils.hh
++  src/orbit.hh
++  src/timer.hh
++  src/bignum.hh
++)
++
++install(TARGETS bliss-executable RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
++install(TARGETS bliss LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
++install(FILES ${BLISS_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/bliss)

build/pkgs/bliss/spkg-install.in

@@ -1,4 +1,4 @@
 cd src
-sdh_configure --disable-gmp
+sdh_cmake -DUSE_GMP=OFF -DCMAKE_VERBOSE_MAKEFILE=ON
 sdh_make
 sdh_make_install