internlm/SWE-Fixer-Train-110K huggingface dataset:
Repository: sagemath/sage

Issue:
sage-download-file: Limit number of mirrors contacted
<div id="comment:0"></div>

In particular when `--enable-download-from-upstream-url` is in use.

CC:  @jhpalmieri @dimpase @vbraun @williamstein

Component: **build**

_Issue created by migration from https://trac.sagemath.org/ticket/34411_




Discussion:
<div id="comment:1" align="right">comment:1</div>

https://github.com/sagemath/sage-prod/blob/develop/build/sage_bootstrap/download/mirror_list.py#L203 falls back to the server http://sagepad.org/

Who runs this server? Is this fallback still needed? 

This server is not mentioned in https://trac.sagemath.org/wiki/Infrastructure
<div id="comment:2" align="right">comment:2</div>

Sagepad seems to belong to Volker, so I would guess that this is his server, and I hope he can tell you whether it is obsolete.  See
https://www.openhub.net/p/sagepad and https://github.com/vbraun/sagepad
<div id="comment:3" align="right">comment:3</div>

it seems that `sagepad` project has not been touched for 10 years. The server just gives a default Centos web server page, nothing there it seems.

Resolving patch:
diff --git a/build/sage_bootstrap/download/mirror_list.py b/build/sage_bootstrap/download/mirror_list.py
--- a/build/sage_bootstrap/download/mirror_list.py
+++ b/build/sage_bootstrap/download/mirror_list.py
@@ -170,9 +170,7 @@ def _rank_mirrors(self):
         timed_mirrors = []
         import time, socket
         log.info('Searching fastest mirror')
-        timeout = socket.getdefaulttimeout()
-        if timeout is None:
-            timeout = 1
+        timeout = 1
         for mirror in self.mirrors:
             if not mirror.startswith('http'):
                 log.debug('we currently can only handle http, got %s', mirror)
@@ -190,6 +188,11 @@ def _rank_mirrors(self):
             result_ms = int(1000 * result)
             log.info(str(result_ms).rjust(5) + 'ms: ' + mirror)
             timed_mirrors.append((result, mirror))
+            timed_mirrors.sort()
+            if len(timed_mirrors) >= 5 and timed_mirrors[4][0] < 0.3:
+                # We don't need more than 5 decent mirrors
+                break
+
         if len(timed_mirrors) == 0:
             # We cannot reach any mirror directly, most likely firewall issue
             if 'http_proxy' not in os.environ:
@@ -197,7 +200,6 @@ def _rank_mirrors(self):
                 raise MirrorListException('Failed to connect to any mirror, probably no internet connection')
             log.info('Cannot time mirrors via proxy, using default order')
         else:
-            timed_mirrors.sort()
             self._mirrors = [m[1] for m in timed_mirrors]
         log.info('Fastest mirror: ' + self.fastest)
 


Test patch:
Repository: sagemath/sage

Issue:
typo in documentation
### Steps To Reproduce

https://doc.sagemath.org/html/en/reference/groups/sage/groups/perm_gps/permgroup.html#index-of-methods


### Expected Behavior

`Here are the methods of a`

### Actual Behavior

`Here are the method of a`

### Additional Information

Can we run a grammar checking tool over all of the documentation?

### Environment

```markdown
irrelevant.
```


### Checklist

- [X] I have searched the existing issues for a bug report that matches the one I want to file, without success.
- [X] I have read the documentation and troubleshoot guide


Discussion:

Resolving patch:
diff --git a/src/sage/groups/perm_gps/permgroup.py b/src/sage/groups/perm_gps/permgroup.py
--- a/src/sage/groups/perm_gps/permgroup.py
+++ b/src/sage/groups/perm_gps/permgroup.py
@@ -29,7 +29,7 @@
 Index of methods
 ----------------
 
-Here are the method of a :func:`PermutationGroup`
+Here are the methods of a :func:`PermutationGroup`
 
 {METHODS_OF_PermutationGroup_generic}
 


Test patch:
Repository: sagemath/sage

Issue:
update qepcad to B 1.74, add spkg-configure
Debian and Ubuntu 22 carry qepcad B 1.74, from 2021. It's newer than ours, and might work better e.g, on arm64, cf. #36831

the canonical source is [chriswestbrown/qepcad](https://github.com/chriswestbrown/qepcad) and B.1.74 was introduced in https://github.com/chriswestbrown/qepcad/commit/185cd845bbd8b4ccb79958b101dc0fd68fe5352e

Debian and Fedora fixed more bugs, cf e.g. https://bugs.debian.org/996561 and https://github.com/chriswestbrown/qepcad/pulls

So we can use Debian's tarball from https://packages.debian.org/sid/qepcad




Discussion:

Resolving patch:
diff --git a/src/sage/interfaces/qepcad.py b/src/sage/interfaces/qepcad.py
--- a/src/sage/interfaces/qepcad.py
+++ b/src/sage/interfaces/qepcad.py
@@ -1090,7 +1090,7 @@ def _parse_answer_stats(self):
             sage: ans
             'x^2 - 2 > 0'
             sage: stats
-            '-----------------------------------------------------------------------------\r\n0 Garbage collections, 0 Cells and 0 Arrays reclaimed, in 0 milliseconds.\r\n492514 Cells in AVAIL, 500000 Cells in SPACE.\r\n\r\nSystem time: 16 milliseconds.\r\nSystem time after the initialization: 4 milliseconds.\r\n-----------------------------------------------------------------------------\r\n'
+            '-----------------------------------------------------------------------------\r\n0 Garbage collections, 0 Cells and 0 Arrays reclaimed, in 0 ...
         """
         if self.phase() != 'EXITED':
             raise ValueError("QEPCAD is not finished yet")


Test patch:
Repository: sagemath/sage

Issue:
old Polymake incompatibility with system Perl 5.38 (Fedora 39) - update to polymake 4.11
https://forum.polymake.org/viewtopic.php?t=1914

Polymake recommends installing suitable Perl via perlbrew:
https://polymake.org/doku.php/install/install#perlbrew

Polymake also provides BinaryBuilder.org/JLL-based binaries that ship a suitable Perl (and all libraries include gmp, ...). 
- https://polymake.org/doku.php/install/jll
- ... made using https://github.com/JuliaPackaging/JLLPrefixes.jl and https://github.com/benlorenz/pmjll
- ... from https://github.com/JuliaBinaryWrappers/Perl_jll.jl (built from https://github.com/JuliaPackaging/Yggdrasil/tree/master/P/Perl/bundled)
- ... from https://github.com/JuliaBinaryWrappers/polymake_jll.jl 
- etc.



Discussion:
Polymake is masked for removal on Gentoo too for the same issue.
https://github.com/polymake/polymake/releases/tag/V4.11 has perl 5.38 support, all rejoice please

Resolving patch:
diff --git a/src/sage/geometry/polyhedron/base.py b/src/sage/geometry/polyhedron/base.py
--- a/src/sage/geometry/polyhedron/base.py
+++ b/src/sage/geometry/polyhedron/base.py
@@ -1175,12 +1175,13 @@ def _polymake_init_(self):
 
         Floating-point polyhedron::
 
-            sage: P = polytopes.dodecahedron(exact=False); P                            # needs sage.groups
+            sage: # optional - jupymake, needs sage.groups
+            sage: P = polytopes.dodecahedron(exact=False); P
             A 3-dimensional polyhedron in RDF^3 defined as the convex hull of 20 vertices
-            sage: print("Maybe recompile warning"); PP = polymake(P); PP        # optional - jupymake, needs sage.groups
+            sage: print("There may be a recompilation warning"); PP = polymake(P); PP
             There may be a recompilation warning...
             Polytope<Float>[...]
-            sage: sorted(PP.VERTICES[:], key=repr)[0]                           # optional - jupymake, needs sage.groups
+            sage: sorted(PP.VERTICES[:], key=repr)[0]
             1 -0.472135955 0 -1.236067978
 
         """


Test patch:
Repository: sagemath/sage

Issue:
RegularSequence.subsequence broken for zero sequence
### Steps To Reproduce

```python
R = RegularSequenceRing(2, QQ)
z = R.zero()
z.subsequence(1, 1)
```

### Expected Behavior

```
2-regular sequence 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ...
```

### Actual Behavior

```
Traceback (most recent call last):
...
  File "/local/cheuberg/local/sage-10.3.beta7/src/sage/combinat/regular_sequence.py", line 850, in subsequence
    vector(chain.from_iterable(
  File "sage/modules/free_module_element.pyx", line 587, in sage.modules.free_module_element.vector
  File "sage/modules/free_module_element.pyx", line 690, in sage.modules.free_module_element.prepare
TypeError: unable to find a common ring for all elements
```

### Additional Information

Cc: @dkrenn 

### Environment

```markdown
- **OS**: Ubuntu 20.04
- **Sage Version**: 10.3.beta7
```


### Checklist

- [X] I have searched the existing issues for a bug report that matches the one I want to file, without success.
- [X] I have read the documentation and troubleshoot guide


Discussion:

Resolving patch:
diff --git a/src/sage/combinat/regular_sequence.py b/src/sage/combinat/regular_sequence.py
--- a/src/sage/combinat/regular_sequence.py
+++ b/src/sage/combinat/regular_sequence.py
@@ -762,6 +762,12 @@ def subsequence(self, a, b):
 
             sage: S.regenerated().subsequence(1, -4)
             2-regular sequence 0, 0, 0, 0, 1, 3, 6, 9, 12, 18, ...
+
+        Check that the zero sequence is handled correctly (issue:`37282`)
+        ::
+
+            sage: Seq2.zero().subsequence(1, 1)
+            2-regular sequence 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ...
         """
         from itertools import chain
         from sage.rings.integer_ring import ZZ
@@ -835,14 +841,16 @@ def matrix_row(r, c):
             d, f = rule[r, c]
             return [self.mu[f] if d == j else zero_M for j in kernel]
 
+        # We explicitly set the ring when creating vectors in order to avoid
+        # problems with the zero sequence, see issue:`37282`.
         result = P.element_class(
             P,
             {r: Matrix.block([matrix_row(r, c) for c in kernel])
              for r in A},
-            vector(chain.from_iterable(
+            vector(P.coefficient_ring(), chain.from_iterable(
                 b.get(c, 0) * self.left
                 for c in kernel)),
-            vector(chain.from_iterable(
+            vector(P.coefficient_ring(), chain.from_iterable(
                 (self.coefficient_of_n(c, multiply_left=False) if c >= 0 else zero_R)
                 for c in kernel)))
 


Test patch:
Repository: sagemath/sage

Issue:
Cannot convert PermutationGroup element into sized Permutation
### Steps To Reproduce

The following code shows that an element of `PermutationGroup` can be converted into a sizeless `Permutation` and then into a sized one, but not directly.

```
PG = PermutationGroup(SymmetricGroup(5).gens())
P5 = Permutations(5)
p = PG.an_element()
print(p.parent())
q = Permutation(p)
print(q.parent())
r = P5(q)
print(r.parent())
s = P5(p)            # <----- this one fails
```

### Expected Behavior

It should be possible to convert a `PermutationGroup` directly into into a sized `Permutation`.

### Actual Behavior

The output is

> Permutation Group with generators [(1,2), (1,2,3,4,5)]
> Standard permutations
> Standard permutations of 5

and then 

> TypeError: object of type 'sage.groups.perm_gps.permgroup_element.PermutationGroupElement' has no len()

### Additional Information

_No response_

### Environment

```markdown
- **OS**: Ubuntu 22.04.3 LTS
- **Sage Version**: 10.2.beta5
```


### Checklist

- [X] I have searched the existing issues for a bug report that matches the one I want to file, without success.
- [X] I have read the documentation and troubleshoot guide


Discussion:

Resolving patch:
diff --git a/src/sage/combinat/permutation.py b/src/sage/combinat/permutation.py
--- a/src/sage/combinat/permutation.py
+++ b/src/sage/combinat/permutation.py
@@ -7092,7 +7092,19 @@ def _element_constructor_(self, x, check=True):
             [1, 4, 5, 2, 3, 6]
             sage: Permutations(6)(x)            # known bug
             [1, 4, 5, 2, 3, 6]
+
+        Ensure that :issue:`37284` is fixed::
+
+            sage: PG = PermutationGroup([[(1,2,3),(5,6)],[(7,8)]])
+            sage: P8 = Permutations(8)
+            sage: p = PG.an_element()
+            sage: q = P8(p); q
+            [2, 3, 1, 4, 6, 5, 8, 7]
+            sage: q.parent()
+            Standard permutations of 8
         """
+        if isinstance(x, PermutationGroupElement):
+            return self. _from_permutation_group_element(x)
         if len(x) < self.n:
             x = list(x) + list(range(len(x) + 1, self.n + 1))
         return self.element_class(self, x, check=check)


Test patch:
Repository: sagemath/sage

Issue:
Improve the documentation of discrete dynamical systems
### Steps To Reproduce

There are typos and repeated sentences in https://doc.sagemath.org/html/en/reference/dynamics/sage/dynamics/finite_dynamical_system.html

### Expected Behavior

There shouldn't be any typos!

### Actual Behavior

There are typos!

### Additional Information

Tthis, A discrete dynamical system (henceforth DDS) is a pair of a set and a map . This set is called the ground set of the DDS, while the map is called the evolution of the DDS.

A discrete dynamical system (short: DDS) is a pair of a set and a map .

### Environment

```markdown
irrelevant
```


### Checklist

- [X] I have searched the existing issues for a bug report that matches the one I want to file, without success.
- [X] I have read the documentation and troubleshoot guide


Discussion:
i am working on this..
Hello,
Is this issue still open?

If so, I would like to work on this.
Thank you :-)
Oh, that would be wonderful!  You have done a great job on the other issue!
Thank you.
I will start working on this.

Resolving patch:
diff --git a/src/sage/dynamics/finite_dynamical_system.py b/src/sage/dynamics/finite_dynamical_system.py
--- a/src/sage/dynamics/finite_dynamical_system.py
+++ b/src/sage/dynamics/finite_dynamical_system.py
@@ -98,22 +98,15 @@ class DiscreteDynamicalSystem(SageObject, metaclass=ClasscallMetaclass):
 
     A *discrete dynamical system* (henceforth *DDS*) is a
     pair `(X, \phi)` of a set `X` and a map `\phi : X \to X`.
-    This set `X` is called the *ground set* of the DDS, while
-    the map `\phi` is called the *evolution* of the DDS.
-
-    A *discrete dynamical system* (short: *DDS*) is a pair
-    `(X, \phi)` of a set `X` and a map `\phi : X \to X`.
-    (This is one of several things known as a "discrete
-    dynamical system" in mathematics.)
-    Thus, a DDS is the same as an endomorphism of a set.
-    The DDS is said to be *finite* if `X` is finite.
-    The DDS is said to be *invertible* if the map `\phi` is
-    invertible.
     The set `X` is called the *ground set* of the DDS;
     the map `\phi` is called the *evolution* of the DDS;
     the inverse map `\phi^{-1}` (when it exists) is called the
     *inverse evolution* of the DDS.
 
+    The DDS is called *finite* if `X` is finite.
+    The DDS is called *invertible* if the map `\phi` is
+    invertible.
+
     Given a DDS `(X, \phi)`, we can study
 
     * its orbits (i.e., the lists
@@ -138,7 +131,7 @@ class DiscreteDynamicalSystem(SageObject, metaclass=ClasscallMetaclass):
 
     - ``X`` -- set, list, tuple, or another iterable, or
       ``None`` (default: ``None``); the ground set for the DDS.
-      Tthis can be ``None`` (in which case Sage will not know
+      This can be ``None`` (in which case Sage will not know
       the ground set, but can still apply evolution to any
       elements that are provided to it).
       Make sure to set the ``create_tuple`` argument to


Test patch:
Repository: sagemath/sage

Issue:
Wrong link to Sphinx’ documentation
<div id="comment:0"></div>

https://doc.sagemath.org/html/en/developer/sage_manuals.html#chapter-sage-manuals

makes a reference to 
"See Sphinx’ documentation." at http://sphinx.pocoo.org/markup/inline.html
but that link is not operational.

Component: **documentation**

_Issue created by migration from https://trac.sagemath.org/ticket/31281_




Discussion:
<div id="comment:1" align="right">comment:1</div>

could use https://www.sphinx-doc.org/en/1.8/usage/restructuredtext/roles.html
<div id="comment:2" align="right">comment:2</div>

see also #27495
<div id="comment:3" align="right">comment:3</div>

Moving to 9.4, as 9.3 has been released.

Resolving patch:
diff --git a/src/sage/misc/sageinspect.py b/src/sage/misc/sageinspect.py
--- a/src/sage/misc/sageinspect.py
+++ b/src/sage/misc/sageinspect.py
@@ -2577,10 +2577,6 @@ def sage_getvariablename(self, omit_underscore_names=True):
     ``omit_underscore_names`` is True (the default) then omit names
     starting with an underscore "_".
 
-    This is a modified version of code taken from
-    http://pythonic.pocoo.org/2009/5/30/finding-objects-names,
-    written by Georg Brandl.
-
     EXAMPLES::
 
         sage: # needs sage.modules
@@ -2597,6 +2593,9 @@ def sage_getvariablename(self, omit_underscore_names=True):
         sage: sage_getvariablename(random_matrix(ZZ, 60))                               # needs sage.modules
         []
     """
+    # This is a modified version of code taken from
+    # https://web.archive.org/web/20100416095847/http://pythonic.pocoo.org/2009/5/30/finding-objects-names
+    # written by Georg Brandl.
     result = []
     for frame in inspect.stack():
         for name, obj in frame[0].f_globals.items():


Test patch:
Repository: sagemath/sage

Issue:
graphs.triangulations(3) does not return the triangle
### Steps To Reproduce

len(list(graphs.triangulations(3)))

### Expected Behavior

1

### Actual Behavior

0

### Additional Information

The triangle (complete graph on 3 vertices) should be considered as a triangulation and returned by the iterator. 

### Environment

```markdown
- **OS**: Ubuntu 22.04
- **Sage Version**: 10.1
```


### Checklist

- [X] I have searched the existing issues for a bug report that matches the one I want to file, without success.
- [X] I have read the documentation and troubleshoot guide


Discussion:
While surprising, this is actually the correct documented behavior. Note that it requires the degree to be $\geq 3$, but the triangle (cycle graph on 3 vertices) only has degree 2.

That being said, it likely wouldn't be a bad thing to special case that. @dcoudert might have some thoughts on this.
To add a special case for the triangle, we must first specify the expected behavior for the combinations with other parameters. For instance which dual is expected ? what to return if the minimum connectivity is set to 3 ? etc. Help is more than welcome here.
Indeed, the possible combinations of minimum degree and minimum connectivity make the triangle impossible. Also the dual is a multigraph, so this might be an issue too. Perhaps, simply adding in the documentation of the function that the triangle is excluded, would be sufficient.
To be fair, it is already documented (by the degree condition). However, an example for the 3 vertex case explaining why it’s empty could make it more clear.

Resolving patch:
diff --git a/src/sage/graphs/graph_generators.py b/src/sage/graphs/graph_generators.py
--- a/src/sage/graphs/graph_generators.py
+++ b/src/sage/graphs/graph_generators.py
@@ -2237,6 +2237,12 @@ def triangulations(self, order, minimum_degree=None, minimum_connectivity=None,
             sage: g.is_isomorphic(graphs.OctahedralGraph())           # optional - plantri
             True
 
+        The minimum degree of a triangulation is 3, so the method can not output
+        a triangle::
+
+            sage: list(graphs.triangulations(3))                      # optional - plantri
+            []
+
         An overview of the number of 5-connected triangulations on up to 22 vertices. This
         agrees with :oeis:`A081621`::
 


Test patch:
Repository: sagemath/sage

Issue:
`bool(Poset())` evaluates to `True`
### Steps To Reproduce

```
sage: bool(set())
False
sage: bool([])
False
sage: bool(Poset())
True
```

### Expected Behavior

Similarly to other empty objects, boolean value of the empty poset should be `False`.



### Actual Behavior

`bool(Poset())` evaluates to `True`.

### Additional Information

_No response_

### Environment

```markdown
- **OS**: Ubuntu 22.04.4 LTS
- **Sage Version**: 10.3.beta7
```


### Checklist

- [X] I have searched the existing issues for a bug report that matches the one I want to file, without success.
- [X] I have read the documentation and troubleshoot guide


Discussion:

Resolving patch:
diff --git a/src/sage/combinat/posets/posets.py b/src/sage/combinat/posets/posets.py
--- a/src/sage/combinat/posets/posets.py
+++ b/src/sage/combinat/posets/posets.py
@@ -1230,6 +1230,21 @@ def unwrap(self, element):
         else:
             return element.element
 
+    def __bool__(self) -> bool:
+        r"""
+        Return if ``self`` is empty or not.
+
+        EXAMPLES::
+
+            sage: P = Poset((divisors(15), attrcall("divides")), facade=True)
+            sage: bool(P)
+            True
+            sage: P = Poset()
+            sage: bool(P)
+            False
+        """
+        return bool(self._elements)
+
     def __contains__(self, x) -> bool:
         r"""
         Return ``True`` if ``x`` is an element of the poset.


Test patch:
Repository: sagemath/sage

Issue:
RST liner is failing due to RST304 failure
### Steps To Reproduce

```
Jack: sage % ./sage --version                                                           
SageMath version 10.4.beta1, Release Date: 2024-03-31
Jack: sage % ./sage -tox -e rst -- ./src/sage                          
rst: commands[0] /Users/Jack/sage/sage/src> flake8 --select=RST sage
sage/algebras/quantum_groups/quantum_group_gap.py:8:1: RST304 Unknown interpreted text role "gap_package".
sage/combinat/designs/incidence_structures.py:1812:1: RST304 Unknown interpreted text role "gap_package".
sage/groups/cubic_braid.py:272:1: RST304 Unknown interpreted text role "gap".
sage/groups/generic.py:1626:1: RST304 Unknown interpreted text role "gap".
sage/groups/matrix_gps/finitely_generated_gap.py:225:1: RST304 Unknown interpreted text role "gap".
rst: exit 1 (54.79 seconds) /Users/Jack/sage/sage/src> flake8 --select=RST sage pid=9808
  rst: FAIL code 1 (54.86=setup[0.07]+cmd[54.79] seconds)
  evaluation failed :( (55.02 seconds)
```

### Expected Behavior

All listing should pass on the develop branch

### Actual Behavior

Linting has failures on the develop branch

### Additional Information

_No response_

### Environment

```markdown
- **OS**: MacOS 14.3.1
- **Sage Version**: 10.4.beta1
```


### Checklist

- [X] I have searched the existing issues for a bug report that matches the one I want to file, without success.
- [X] I have read the documentation and troubleshoot guide


Discussion:
Oh is this an issue because the linter is being run before the new docs have been built? Maybe patience is the solution here.
Examples of failing PR:

https://github.com/sagemath/sage/pull/37441
https://github.com/sagemath/sage/pull/37513
https://github.com/sagemath/sage/pull/37615
Thanks. I'm preparing a fix.

Resolving patch:
diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py
--- a/src/sage/misc/sagedoc.py
+++ b/src/sage/misc/sagedoc.py
@@ -502,7 +502,10 @@ def process_dollars(s):
     return s
 
 
-# Sage github issue shortcuts. For example, :issue:`7549` .
+# When adding roles here, also add them to SAGE_ROOT/src/tox.ini [flake8]
+# and document them in SAGE_ROOT/src/doc/en/developer/sage_manuals.rst
+#
+# Sage github issue shortcuts. For example, :issue:`7549`.
 pythonversion = sys.version.split(' ')[0]
 extlinks = {
     'python': (f'https://docs.python.org/release/{pythonversion}/%s', None),


Test patch: