Merge branch 'develop' into pep8_structure

fchapoton · web-flow · commit 4adf519a6b6a · 2024-11-30T14:47:44.000+01:00
diff --git a/.github/workflows/ci-linux.yml b/.github/workflows/ci-linux.yml
@@ -50,6 +50,7 @@ jobs:
       tox_packages_factors: >-
         ["standard"]
       docker_push_repository: ghcr.io/${{ github.repository }}/
+      logs_artifact: false
 
   # All platforms. This duplicates the default platform, but why not,
   # it makes it more robust regarding random timeouts.
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -85,6 +85,9 @@ on:
         description: 'Elapsed time (seconds) at which to kill the build'
         default: 20000
         type: number
+      logs_artifact:
+        default: true
+        type: boolean
       #
       # Publishing to GitHub Packages
       #
@@ -260,11 +263,12 @@ jobs:
           cp -r .tox/$TOX_ENV/* "artifacts/$LOGS_ARTIFACT_NAME"
           rm -rf "artifacts/$LOGS_ARTIFACT_NAME"/{bin,lib,pyvenv.cfg}
         if: always()
-      - uses: actions/upload-artifact@v4
+      - name: Upload logs artifact
+        uses: actions/upload-artifact@v4
         with:
           path: artifacts
           name: ${{ env.LOGS_ARTIFACT_NAME }}
-        if: always()
+        if: always() && inputs.logs_artifact
       - name: Print out logs for immediate inspection
         # and markup the output with GitHub Actions logging commands
         run: |
diff --git a/CITATION.cff b/CITATION.cff
@@ -4,8 +4,8 @@ title: SageMath
 abstract: SageMath is a free open-source mathematics software system.
 authors:
 - name: "The SageMath Developers"
-version: 10.5.rc1
+version: 10.5.rc2
 doi: 10.5281/zenodo.8042260
-date-released: 2024-11-23
+date-released: 2024-11-30
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"
diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-SageMath version 10.5.rc1, Release Date: 2024-11-23
+SageMath version 10.5.rc2, Release Date: 2024-11-30
diff --git a/build/pkgs/configure/checksums.ini b/build/pkgs/configure/checksums.ini
@@ -1,3 +1,3 @@
 tarball=configure-VERSION.tar.gz
-sha1=4b08e1c0e6b812bfbade59ef7c751619d8e44f81
-sha256=9ae6ed35a2391f1af02ed2c7b855670d3db0bb421a69064a2c907b4f3a584eb4
+sha1=4d6de7b4a5aff43a508a1e64078fe409554869fe
+sha256=18cc6fa95c0bd6ae0bf1f9b447ae2dd9da7d596d17bec5e961b980b9687e1a7e
diff --git a/build/pkgs/configure/package-version.txt b/build/pkgs/configure/package-version.txt
@@ -1 +1 @@
-95eb9b8c8642831f849b5fec82a0b545a95e9ca6
+68f446ad3f1abcea6e1a9b679a04242597f439f6
diff --git a/build/pkgs/ecm/patches/assembler.patch b/build/pkgs/ecm/patches/assembler.patch
diff --git a/build/pkgs/sage_conf/version_requirements.txt b/build/pkgs/sage_conf/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-conf ~= 10.5rc1
+sage-conf ~= 10.5rc2
diff --git a/build/pkgs/sage_docbuild/version_requirements.txt b/build/pkgs/sage_docbuild/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-docbuild ~= 10.5rc1
+sage-docbuild ~= 10.5rc2
diff --git a/build/pkgs/sage_setup/version_requirements.txt b/build/pkgs/sage_setup/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-setup ~= 10.5rc1
+sage-setup ~= 10.5rc2
diff --git a/build/pkgs/sage_sws2rst/version_requirements.txt b/build/pkgs/sage_sws2rst/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sage-sws2rst ~= 10.5rc1
+sage-sws2rst ~= 10.5rc2
diff --git a/build/pkgs/sagelib/version_requirements.txt b/build/pkgs/sagelib/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-standard ~= 10.5rc1
+sagemath-standard ~= 10.5rc2
diff --git a/build/pkgs/sagemath_bliss/version_requirements.txt b/build/pkgs/sagemath_bliss/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-bliss ~= 10.5rc1
+sagemath-bliss ~= 10.5rc2
diff --git a/build/pkgs/sagemath_categories/version_requirements.txt b/build/pkgs/sagemath_categories/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-categories ~= 10.5rc1
+sagemath-categories ~= 10.5rc2
diff --git a/build/pkgs/sagemath_coxeter3/version_requirements.txt b/build/pkgs/sagemath_coxeter3/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-coxeter3 ~= 10.5rc1
+sagemath-coxeter3 ~= 10.5rc2
diff --git a/build/pkgs/sagemath_environment/version_requirements.txt b/build/pkgs/sagemath_environment/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-environment ~= 10.5rc1
+sagemath-environment ~= 10.5rc2
diff --git a/build/pkgs/sagemath_mcqd/version_requirements.txt b/build/pkgs/sagemath_mcqd/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-mcqd ~= 10.5rc1
+sagemath-mcqd ~= 10.5rc2
diff --git a/build/pkgs/sagemath_meataxe/version_requirements.txt b/build/pkgs/sagemath_meataxe/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-meataxe ~= 10.5rc1
+sagemath-meataxe ~= 10.5rc2
diff --git a/build/pkgs/sagemath_objects/version_requirements.txt b/build/pkgs/sagemath_objects/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-objects ~= 10.5rc1
+sagemath-objects ~= 10.5rc2
diff --git a/build/pkgs/sagemath_repl/version_requirements.txt b/build/pkgs/sagemath_repl/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-repl ~= 10.5rc1
+sagemath-repl ~= 10.5rc2
diff --git a/build/pkgs/sagemath_sirocco/version_requirements.txt b/build/pkgs/sagemath_sirocco/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-sirocco ~= 10.5rc1
+sagemath-sirocco ~= 10.5rc2
diff --git a/build/pkgs/sagemath_tdlib/version_requirements.txt b/build/pkgs/sagemath_tdlib/version_requirements.txt
@@ -1,2 +1,2 @@
 # This file is updated on every release by the sage-update-version script
-sagemath-tdlib ~= 10.5rc1
+sagemath-tdlib ~= 10.5rc2
diff --git a/pkgs/sage-conf/VERSION.txt b/pkgs/sage-conf/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sage-conf_conda/VERSION.txt b/pkgs/sage-conf_conda/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sage-conf_pypi/VERSION.txt b/pkgs/sage-conf_pypi/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sage-docbuild/VERSION.txt b/pkgs/sage-docbuild/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sage-setup/VERSION.txt b/pkgs/sage-setup/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sage-sws2rst/VERSION.txt b/pkgs/sage-sws2rst/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sagemath-bliss/VERSION.txt b/pkgs/sagemath-bliss/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sagemath-categories/VERSION.txt b/pkgs/sagemath-categories/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sagemath-coxeter3/VERSION.txt b/pkgs/sagemath-coxeter3/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sagemath-environment/VERSION.txt b/pkgs/sagemath-environment/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sagemath-mcqd/VERSION.txt b/pkgs/sagemath-mcqd/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sagemath-meataxe/VERSION.txt b/pkgs/sagemath-meataxe/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sagemath-objects/VERSION.txt b/pkgs/sagemath-objects/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sagemath-repl/VERSION.txt b/pkgs/sagemath-repl/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sagemath-sirocco/VERSION.txt b/pkgs/sagemath-sirocco/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/pkgs/sagemath-tdlib/VERSION.txt b/pkgs/sagemath-tdlib/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/src/VERSION.txt b/src/VERSION.txt
@@ -1 +1 @@
-10.5.rc1
+10.5.rc2
diff --git a/src/bin/sage-version.sh b/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='10.5.rc1'
-SAGE_RELEASE_DATE='2024-11-23'
-SAGE_VERSION_BANNER='SageMath version 10.5.rc1, Release Date: 2024-11-23'
+SAGE_VERSION='10.5.rc2'
+SAGE_RELEASE_DATE='2024-11-30'
+SAGE_VERSION_BANNER='SageMath version 10.5.rc2, Release Date: 2024-11-30'
diff --git a/src/doc/en/developer/coding_basics.rst b/src/doc/en/developer/coding_basics.rst
@@ -6,7 +6,6 @@
 General Conventions
 ===================
 
-
 There are many ways to contribute to Sage, including sharing scripts
 and Jupyter notebooks that implement new functionality using Sage,
 improving to the Sage library, or to working on the many underlying
@@ -1256,17 +1255,38 @@ framework. Here is a comprehensive list:
      Neither of this applies to files or directories which are explicitly given
      as command line arguments: those are always tested.
 
-- **optional/needs:** A line tagged with ``optional - FEATURE``
-  or ``needs FEATURE`` is not tested unless the ``--optional=KEYWORD`` flag
-  is passed to ``sage -t`` (see
-  :ref:`section-optional-doctest-flag`). The main applications are:
+- **optional** or **needs:** A line tagged with ``optional - FEATURE`` or
+  ``needs FEATURE`` is tested if the feature is available in Sage. If
+  ``FEATURE`` starts with an exclamation point ``!``, then the condition is
+  negated, that is, the doctest runs only if the feature is not available.
+
+  If the feature is included in the ``--optional=KEYWORD`` flag passed to
+  ``sage -t`` (see :ref:`section-optional-doctest-flag`), then the line is
+  tested regardless of the feature availability.
+
+  The main applications are:
 
   - **optional packages:** When a line requires an optional package to be
-    installed (e.g. the ``sloane_database`` package)::
+    installed (e.g. the ``rubiks`` package)::
+
+      sage: C = RubiksCube("R*L")
+      sage: C.solve()                    # optional - rubiks (a hybrid algorithm is used)
+      'L R'
+      sage: C.solve()                    # optional - !rubiks (GAP is used)
+      'L*R'
+
+  - **features:** When a line requires a feature to be present::
 
       sage: SloaneEncyclopedia[60843]    # optional - sloane_database
+      [1, 6, 21, 107, 47176870]
+
+      sage: SloaneEncyclopedia[60843]    # optional - !sloane_database
+      Traceback (most recent call last):
+      ...
+      OSError: The Sloane Encyclopedia database must be installed. Use e.g.
+      'SloaneEncyclopedia.install()' to download and install it.
 
-  - **internet:** For lines that require an internet connection::
+    For lines that require an internet connection::
 
        sage: oeis(60843)                 # optional - internet
        A060843: Busy Beaver problem: a(n) = maximal number of steps that an
diff --git a/src/meson.build b/src/meson.build
@@ -78,11 +78,7 @@ endif
 # that too to make the fallback detection with CMake work
 blas_order += ['cblas', 'openblas', 'OpenBLAS', 'flexiblas', 'blis', 'blas']
 blas = dependency(blas_order)
-gsl = dependency(
-  'gsl',
-  version: '>=2.5',
-  required: true,
-)
+gsl = dependency('gsl', version: '>=2.5', required: true)
 gd = cc.find_library('gd')
 # Only some platforms have a standalone math library (https://mesonbuild.com/howtox.html#add-math-library-lm-portably)
 m = cc.find_library('m', required: false)
diff --git a/src/sage/databases/sloane.py b/src/sage/databases/sloane.py
@@ -12,7 +12,7 @@
 ::
 
     sage: SloaneEncyclopedia[60843]  # optional - sloane_database
-    [1, 6, 21, 107]
+    [1, 6, 21, 107, 47176870]
 
 To get the name of a sequence, type
 
@@ -149,6 +149,17 @@ def __len__(self):
         self.load()
         return len(self.__data__)
 
+    def is_installed(self):
+        """
+        Check if a local copy of the encyclopedia is installed.
+
+        EXAMPLES::
+
+            sage: SloaneEncyclopedia.is_installed()  # optional - sloane_database
+            True
+        """
+        return os.path.exists(self.__file__) and os.path.exists(self.__file_names__)
+
     def find(self, seq, maxresults=30):
         """
         Return a list of all sequences which have seq as a subsequence, up
@@ -274,7 +285,7 @@ def load(self):
         for L in file_seq:
             if len(L) == 0:
                 continue
-            m = entry.search(L)
+            m = entry.search(L.decode('utf-8'))
             if m:
                 seqnum = int(m.group('num'))
                 msg = m.group('body').strip()
@@ -287,10 +298,13 @@ def load(self):
             for L in file_names:
                 if not L:
                     continue
-                m = entry.search(L)
+                m = entry.search(L.decode('utf-8'))
                 if m:
                     seqnum = int(m.group('num'))
-                    self.__data__[seqnum][3] = m.group('body').strip()
+                    if seqnum in self.__data__:
+                        self.__data__[seqnum][3] = m.group('body').strip()
+                    else:
+                        self.__data__[seqnum] = [seqnum, None, 'unknown', m.group('body').strip()]
             file_names.close()
             self.__loaded_names__ = True
         except KeyError:
diff --git a/src/sage/doctest/parsing.py b/src/sage/doctest/parsing.py
@@ -58,7 +58,7 @@
 special_optional_regex = (
     "py2|long time|not implemented|not tested|optional|needs|known bug"
 )
-tag_with_explanation_regex = r"((?:\w|[.])*)\s*(?:\((?P<cmd_explanation>.*?)\))?"
+tag_with_explanation_regex = r"((?:!?\w|[.])*)\s*(?:\((?P<cmd_explanation>.*?)\))?"
 optional_regex = re.compile(
     rf"[^ a-z]\s*(?P<cmd>{special_optional_regex})(?:\s|[:-])*(?P<tags>(?:(?:{tag_with_explanation_regex})\s*)*)",
     re.IGNORECASE,
@@ -1124,14 +1124,14 @@ def check_and_clear_tag_counts():
                             continue
 
                     if self.optional_tags is not True:
-                        extra = {
-                            tag
-                            for tag in optional_tags
-                            if (
-                                tag not in self.optional_tags
-                                and tag not in available_software
-                            )
-                        }
+                        extra = set()
+                        for tag in optional_tags:
+                            if tag not in self.optional_tags:
+                                if tag.startswith('!'):
+                                    if tag[1:] in available_software:
+                                        extra.add(tag)
+                                elif tag not in available_software:
+                                    extra.add(tag)
                         if extra and any(tag in ["bug"] for tag in extra):
                             # Bug only occurs on a specific platform?
                             bug_platform = optional_tags_with_values.get("bug")
diff --git a/src/sage/features/dot2tex.py b/src/sage/features/dot2tex.py
diff --git a/src/sage/features/sloane_database.py b/src/sage/features/sloane_database.py
diff --git a/src/sage/graphs/graph_latex.py b/src/sage/graphs/graph_latex.py
diff --git a/src/sage/groups/perm_gps/cubegroup.py b/src/sage/groups/perm_gps/cubegroup.py
diff --git a/src/sage/matroids/meson.build b/src/sage/matroids/meson.build
diff --git a/src/sage/rings/meson.build b/src/sage/rings/meson.build
diff --git a/src/sage/version.py b/src/sage/version.py

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-SageMath version 10.5.rc1, Release Date: 2024-11-23`
	`1`	`+SageMath version 10.5.rc2, Release Date: 2024-11-30`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-95eb9b8c8642831f849b5fec82a0b545a95e9ca6`
	`1`	`+68f446ad3f1abcea6e1a9b679a04242597f439f6`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`# This file is updated on every release by the sage-update-version script`
`2`		`-sage-conf ~= 10.5rc1`
	`2`	`+sage-conf ~= 10.5rc2`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`# This file is updated on every release by the sage-update-version script`
`2`		`-sage-docbuild ~= 10.5rc1`
	`2`	`+sage-docbuild ~= 10.5rc2`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`# This file is updated on every release by the sage-update-version script`
`2`		`-sage-setup ~= 10.5rc1`
	`2`	`+sage-setup ~= 10.5rc2`