Merge remote-tracking branch 'trac/u/dkrenn/k-regular-warning' into u/dkrenn/k-regular-trunk

* trac/u/dkrenn/k-regular-warning: (2124 commits)
  Follow-up from Trac #21325 review comment 19: shift_left+right: test equality
  Trac #21325 review comment 19: shift_left, shift_right
  Trac #21325 review comment 18: deal with remaining block vectors
  Trac #21325 review comment 17: simpler (more readable) construction of block matrix
  Trac #21325 review comment 14+15: rewrite construction dict
  Trac #21325 review comment 13: use .linear representation in examples partial_sum
  Trac #21325 review comment 12: fixup docstring partial_sums
  Trac #21325 review comment 11: simplify construction and code for left vector
  Trac #21325 review comment 9: add comment in inner loop
  Trac #21325 review comment 8: more rewriting to use block structure
  Trac #21325 review comment 8: rewrite subsequences to use block matrices
  Trac #21325 review comment 7: rewrite dict-constrution
  Trac #21325 review comment 6: test matrices of output
  Trac #21325 review comment 4: explicitly state vector in example
  Trac #21325 review comment 5: use .linear_representation
  Trac #21325 review comment 4: simplify lineare representation of example-sequence (subsequence)
  Trac #21325 review comment 3: revise description of parameter b of subsequence
  Trac #21325 review comment 2: PEP8 in examples of pad_right
  Trac #21325 review comment 1: fix docstring formatting in pad_right
  Updated SageMath version to 9.4
  ...

Author: dkrenn

.github/workflows/ci-cygwin-minimal.yml

@@ -13,7 +13,7 @@ env:
   MAKE: make -j8
   SAGE_NUM_THREADS: 3
   CYGWIN: winsymlinks:native
-  CONFIGURE_ARGS: --enable-experimental-packages --enable-download-from-upstream-url --enable-fat-binary
+  EXTRA_CONFIGURE_ARGS: --enable-fat-binary
   SAGE_LOCAL: /opt/sage-${{ github.sha }}
 
 jobs:

.github/workflows/ci-cygwin-standard.yml

@@ -13,7 +13,7 @@ env:
   MAKE: make -j8
   SAGE_NUM_THREADS: 3
   CYGWIN: winsymlinks:native
-  CONFIGURE_ARGS: --enable-experimental-packages --enable-download-from-upstream-url --enable-fat-binary
+  EXTRA_CONFIGURE_ARGS: --enable-fat-binary
   SAGE_LOCAL: /opt/sage-${{ github.sha }}
 
 jobs:

.github/workflows/lint.yml

@@ -30,7 +30,7 @@ jobs:
     - name: Install relint
       run: pip install tox relint
     - name: Lint using relint
-      run: tox -e relint src/
+      run: tox -e relint src/sage/
   lint-pyright:
     name: Static type check with pyright
     runs-on: ubuntu-latest

.github/workflows/tox-experimental.yml

@@ -38,7 +38,9 @@ jobs:
       fail-fast: false
       max-parallel: 6
       matrix:
-        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7, centos-8, gentoo, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386]
+        # This list is different from the one in tox.yml:
+        # Trac #31526 switches gcc 4.x-based distributions to using the gcc_spkg configuration factor
+        tox_system_factor: [ubuntu-trusty-gcc_spkg, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17-gcc_spkg, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-gcc_spkg]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:
@@ -112,54 +114,35 @@ jobs:
       fail-fast: false
       max-parallel: 3
       matrix:
-        tox_system_factor: [homebrew-macos, conda-forge-macos]
-        tox_packages_factor: [minimal, standard]
+        tox_system_factor: [homebrew-macos, conda-forge-macos, homebrew-macos-python3_xcode]
+        tox_packages_factor: [maximal]
         # As of 2021-03, default xcode is 12.4
         # https://github.com/actions/virtual-environments/blob/main/images/macos/macos-10.15-Readme.md#xcode
         xcode_version_factor: [default]
+        targets_pattern: [0-g, h-o, p, q-z]
         os: [ macos-10.15, macos-11.0 ]
         include:
           # Test xcode 11.7 only on macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: minimal
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: 0-g
             os: macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: standard
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: h-o
             os: macos-10.15
-          # python3_xcode is only accepted if enough packages are available from the system
-          # --> to test "minimal", we will need https://trac.sagemath.org/ticket/30949
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: p
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
+            xcode_version_factor: 11.7
+            targets_pattern: q-z
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: homebrew-macos-python3_xcode-nokegonly
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # likewise for python3_pythonorg
-          - tox_system_factor: homebrew-macos-python3_pythonorg
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # conda-forge-macos-environment
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment-optional
-            xcode_version_factor: default
-            os: macos-11.0
     env:
       TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}-${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}

.github/workflows/tox-optional.yml

@@ -38,7 +38,9 @@ jobs:
       fail-fast: false
       max-parallel: 6
       matrix:
-        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7, centos-8, gentoo, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386]
+        # This list is different from the one in tox.yml:
+        # Trac #31526 switches gcc 4.x-based distributions to using the gcc_spkg configuration factor
+        tox_system_factor: [ubuntu-trusty-gcc_spkg, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie-gcc_spkg, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17-gcc_spkg, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7-gcc_spkg, centos-8, gentoo, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-gcc_spkg]
         tox_packages_factor: [maximal]
         targets_pattern: [0-g, h-o, p, q-z]
     env:
@@ -114,54 +116,35 @@ jobs:
       fail-fast: false
       max-parallel: 3
       matrix:
-        tox_system_factor: [homebrew-macos, conda-forge-macos]
-        tox_packages_factor: [minimal, standard]
+        tox_system_factor: [homebrew-macos, conda-forge-macos, homebrew-macos-python3_xcode]
+        tox_packages_factor: [maximal]
         # As of 2021-03, default xcode is 12.4
         # https://github.com/actions/virtual-environments/blob/main/images/macos/macos-10.15-Readme.md#xcode
         xcode_version_factor: [default]
+        targets_pattern: [0-g, h-o, p, q-z]
         os: [ macos-10.15, macos-11.0 ]
         include:
           # Test xcode 11.7 only on macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: minimal
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: 0-g
             os: macos-10.15
           - tox_system_factor: homebrew-macos
-            tox_packages_factor: standard
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: h-o
             os: macos-10.15
-          # python3_xcode is only accepted if enough packages are available from the system
-          # --> to test "minimal", we will need https://trac.sagemath.org/ticket/30949
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
             xcode_version_factor: 11.7
+            targets_pattern: p
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
+          - tox_system_factor: homebrew-macos
+            tox_packages_factor: maximal
+            xcode_version_factor: 11.7
+            targets_pattern: q-z
             os: macos-10.15
-          - tox_system_factor: homebrew-macos-python3_xcode
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: homebrew-macos-python3_xcode-nokegonly
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # likewise for python3_pythonorg
-          - tox_system_factor: homebrew-macos-python3_pythonorg
-            tox_packages_factor: standard
-            xcode_version_factor: default
-            os: macos-11.0
-          # conda-forge-macos-environment
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment
-            xcode_version_factor: default
-            os: macos-11.0
-          - tox_system_factor: conda-forge-macos
-            tox_packages_factor: environment-optional
-            xcode_version_factor: default
-            os: macos-11.0
     env:
       TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
       LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}-${{ matrix.os }}-xcode_${{ matrix.xcode_version_factor }}

.github/workflows/tox.yml

@@ -38,7 +38,7 @@ jobs:
       fail-fast: false
       max-parallel: 20
       matrix:
-        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, centos-7, centos-8, gentoo, gentoo-python3.7, archlinux-latest, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386]
+        tox_system_factor: [ubuntu-trusty, ubuntu-xenial, ubuntu-bionic, ubuntu-focal, ubuntu-groovy, ubuntu-hirsute, ubuntu-impish, debian-jessie, debian-stretch, debian-buster, debian-bullseye, debian-sid, linuxmint-17, linuxmint-18, linuxmint-19, linuxmint-19.3, linuxmint-20.1, linuxmint-20.2, fedora-26, fedora-27, fedora-28, fedora-29, fedora-30, fedora-31, fedora-32, fedora-33, fedora-34, fedora-35, centos-7, centos-8, gentoo, gentoo-python3.7, archlinux-latest, opensuse-15, opensuse-15.3, opensuse-tumbleweed, slackware-14.2, conda-forge, ubuntu-bionic-i386, manylinux-2_24-i686, debian-buster-i386, centos-7-i386]
         tox_packages_factor: [minimal, standard]
     env:
       TOX_ENV: docker-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}

.gitignore

@@ -1,4 +1,6 @@
-*.pyc
+## We use this file both as .gitignore and .dockerignore,
+## which have different semantics.
+
 /dist
 /local
 /logs
@@ -23,17 +25,31 @@
 /src/environment.yml
 /src/environment-optional.yml
 
+/src/setup.cfg
+/src/requirements.txt
+/src/pyproject.toml
+/src/Pipfile
+/src/Pipfile.lock
+/Pipfile
+/Pipfile.lock
+
 # Various editors
 *~
+**/*~
 
 # Emacs
 \#*\#
+**/\#*\#
 .\#*
+**/.\#*
 
 # Vim
 *.swp
+**/*.swp
 *.swo
+**/*.swo
 *.swn
+**/*.swn
 *.un~
 .netrwhist
 
@@ -43,6 +59,7 @@
 
 # VSCode
 .vscode/*
+**/.vscode/*
 
 # XCode
 xcuserdata/
@@ -53,6 +70,7 @@ xcuserdata/
 .metadata
 *.tmp
 *.bak
+**/*.bak
 *.swp
 *~.nib
 .classpath
@@ -64,6 +82,7 @@ xcuserdata/
 
 # OSX specific temporary files
 .DS_Store
+**/.DS_Store
 ._*
 .AppleDouble
 .LSOverride
@@ -90,46 +109,69 @@ gitlab-build-docker.log
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
+**/__pycache__
 *.py[cod]
+**/*.py[cod]
 *$py.class
 
+# Generated by sage_setup.autogen
+/src/sage/ext/interpreters
+
 # Generated Cython files
 *.so
-src/sage/**/*.c
-src/sage/**/*.cpp
-src/sage/modular/arithgroup/farey_symbol.h
-!src/sage/cpython/debugimpl.c
-!src/sage/graphs/base/boost_interface.cpp
-!src/sage/graphs/cliquer/cl.c
-!src/sage/graphs/graph_decompositions/sage_tdlib.cpp
-!src/sage/libs/eclib/wrap.cpp
-!src/sage/misc/inherit_comparison_impl.c
-!src/sage/modular/arithgroup/farey.cpp
-!src/sage/modular/arithgroup/sl2z.cpp
-!src/sage/rings/bernmm/bern_modp.cpp
-!src/sage/rings/bernmm/bern_modp_util.cpp
-!src/sage/rings/bernmm/bern_rat.cpp
-!src/sage/rings/bernmm/bernmm-test.cpp
-!src/sage/rings/padics/transcendantal.c
-!src/sage/rings/polynomial/weil/power_sums.c
-!src/sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.cpp
-!src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.cpp
-!src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_zn_poly.cpp
-!src/sage/stats/distributions/dgs_bern.c
-!src/sage/stats/distributions/dgs_gauss_dp.c
-!src/sage/stats/distributions/dgs_gauss_mp.c
+**/*.so
+/src/sage/**/*.c
+/src/sage/**/*.cpp
+/src/sage/modular/arithgroup/farey_symbol.h
+!/src/sage/cpython/debugimpl.c
+!/src/sage/graphs/base/boost_interface.cpp
+!/src/sage/graphs/cliquer/cl.c
+!/src/sage/graphs/graph_decompositions/sage_tdlib.cpp
+!/src/sage/libs/eclib/wrap.cpp
+!/src/sage/libs/linkages/padics/relaxed/flint_helper.c
+!/src/sage/misc/inherit_comparison_impl.c
+!/src/sage/modular/arithgroup/farey.cpp
+!/src/sage/modular/arithgroup/sl2z.cpp
+!/src/sage/rings/bernmm/bern_modp.cpp
+!/src/sage/rings/bernmm/bern_modp_util.cpp
+!/src/sage/rings/bernmm/bern_rat.cpp
+!/src/sage/rings/bernmm/bernmm-test.cpp
+!/src/sage/rings/padics/transcendantal.c
+!/src/sage/rings/polynomial/weil/power_sums.c
+!/src/sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.cpp
+!/src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.cpp
+!/src/sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_zn_poly.cpp
+!/src/sage/stats/distributions/dgs_bern.c
+!/src/sage/stats/distributions/dgs_gauss_dp.c
+!/src/sage/stats/distributions/dgs_gauss_mp.c
 /src/cython_debug
 
 # Temporary build files
 build/temp.*/
 build/bin/sage-build-env-config
 
+# Generated files in the top-level source trees
+/pkgs/*/build
+/pkgs/*/dist
+/pkgs/*/MANIFEST
+/pkgs/*/*.egg-info
+/pkgs/*/.tox
+
+# same for old locations - before Trac #31577
 /build/pkgs/*/src/build
 /build/pkgs/*/src/dist
 /build/pkgs/*/src/MANIFEST
 /build/pkgs/*/src/*.egg-info
 /build/pkgs/*/src/.tox
 
+# Generated by docbuild
+/src/doc/en/reference/*/sage
+/src/doc/en/reference/sage
+/src/doc/en/reference/spkg/*.rst
+/src/doc/output
+/src/doc/en/installation/*.txt
+/src/doc/en/reference/repl/*.txt
+
 # Distribution / packaging
 src/*.egg-info/
 /src/.cython_version
@@ -152,5 +194,10 @@ src/venv.bak/
 
 # tox generated files
 /.tox
+/build/.tox
+**/.tox
 /prefix
+
+# git worktree
 worktree*
+**/worktree*

.homebrew-build-env

@@ -31,7 +31,7 @@ for l in readline bzip2 ntl; do
         CPATH="$HOMEBREW/opt/$l/include:$CPATH"
     fi
 done
-for l in "gcc/lib/gcc/10 gcc/lib/gcc/9"; do
+for l in "gcc/lib/gcc/11 gcc/lib/gcc/10 gcc/lib/gcc/9"; do
     if [ -d "$HOMEBREW/opt/$l" ]; then
         LIBRARY_PATH="$HOMEBREW/opt/$l:$LIBRARY_PATH"
         break

.zenodo.json

@@ -1,10 +1,10 @@
 {
     "description": "Mirror of the Sage https://sagemath.org/ source tree", 
     "license": "other-open", 
-    "title": "sagemath/sage: 9.3", 
-    "version": "9.3", 
+    "title": "sagemath/sage: 9.4", 
+    "version": "9.4", 
     "upload_type": "software", 
-    "publication_date": "2021-05-09", 
+    "publication_date": "2021-08-22", 
     "creators": [
         {
             "affiliation": "SageMath.org", 
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url", 
-            "identifier": "https://github.com/sagemath/sage/tree/9.3", 
+            "identifier": "https://github.com/sagemath/sage/tree/9.4", 
             "relation": "isSupplementTo"
         }, 
         {