From f98bc6e48426cca78812c169af091554ed5433e5 Mon Sep 17 00:00:00 2001
From: dcoudert <david.coudert@inria.fr>
Date: Fri, 10 May 2024 16:57:54 +0200
Subject: [PATCH 01/51] cographs generator

---
 src/doc/en/reference/graphs/index.rst     |   1 +
 src/doc/en/reference/references/index.rst |   5 +
 src/sage/graphs/cographs.py               | 571 ++++++++++++++++++++++
 src/sage/graphs/graph_generators.py       |   3 +
 4 files changed, 580 insertions(+)
 create mode 100644 src/sage/graphs/cographs.py

diff --git a/src/doc/en/reference/graphs/index.rst b/src/doc/en/reference/graphs/index.rst
index 496f00ebcba..f681c083a08 100644
--- a/src/doc/en/reference/graphs/index.rst
+++ b/src/doc/en/reference/graphs/index.rst
@@ -78,6 +78,7 @@ Libraries of algorithms
    sage/graphs/centrality
    sage/graphs/asteroidal_triples
    sage/graphs/independent_sets
+   sage/graphs/cographs
    sage/graphs/comparability
    sage/graphs/line_graph
    sage/graphs/spanning_tree
diff --git a/src/doc/en/reference/references/index.rst b/src/doc/en/reference/references/index.rst
index 894b680b2a9..556a3ed9c5d 100644
--- a/src/doc/en/reference/references/index.rst
+++ b/src/doc/en/reference/references/index.rst
@@ -3624,6 +3624,11 @@ REFERENCES:
 .. [Jon2005] \V. Jones, The Jones Polynomial, 2005.
              https://math.berkeley.edu/~vfr/jones.pdf
 
+.. [JPD2018] Átila A. Jones, Fábio Protti and Renata R. Del-Vecchio:
+             *Cograph generation with linear delay*.
+             Theoretical Computer Science, 713:1-10, 2018.
+             :doi:`10.1016/j.tcs.2017.12.037`
+
 .. [JRJ94] Jourdan, Guy-Vincent; Rampon, Jean-Xavier; Jard, Claude
            (1994), "Computing on-line the lattice of maximal antichains
            of posets", Order 11 (3) p. 197-210, :doi:`10.1007/BF02115811`
diff --git a/src/sage/graphs/cographs.py b/src/sage/graphs/cographs.py
new file mode 100644
index 00000000000..516b9fb89b5
--- /dev/null
+++ b/src/sage/graphs/cographs.py
@@ -0,0 +1,571 @@
+r"""
+Cographs
+
+A cograph is a `P_4`-free graph, that is a graph without induced path of order
+4. Any cograph may be constructed, starting from the single vertex graph, by a
+sequence of join and disjoint union operations. See the :wikipedia:`Cograph` for
+more details on this graph class, and :oeis:`A000084` to know the number of
+cographs of order `n \geq 1`.
+
+This module implements the folowing methods concerning cographs:
+
+.. csv-table::
+    :class: contentstable
+    :widths: 30, 70
+    :delim: |
+
+    :meth:`cographs` | Return an iterator over the cographs of order `n`.
+
+Methods
+-------
+"""
+# ****************************************************************************
+#       Copyright (C)      2024 David Coudert <david.coudert@inria.fr>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#                  https://www.gnu.org/licenses/
+# ****************************************************************************
+
+
+class CoTree:
+    """
+    Generic cotree node.
+
+    This data structure is used for the generation of cographs in
+    :meth:`cographs`.
+    """
+    def __init__(self, name='root'):
+        r"""
+        Initialize a cotree.
+
+        INPUT:
+
+        - ``name`` -- either an operation ('U' or 'J') or the size of the
+          subtree rooted at this node
+
+        EXAMPLES::
+
+            sage: from sage.graphs.cographs import CoTree
+            sage: CoTree(1)
+            ( 1 )
+            sage: CoTree()
+            ( root )
+        """
+        self.name = name
+        self.children = []
+        self.info = None
+        self.parent = None
+
+    def __repr__(self):
+        r"""
+        Return a string representation of ``self``.
+
+        EXAMPLES::
+
+            sage: from sage.graphs.cographs import CoTree
+            sage: CoTree(1)
+            ( 1 )
+            sage: CoTree('J')
+            [ J ]
+            sage: next(graphs.cographs(4, as_graph=False))  # indirect doctest
+            [ J ( 0 ) ( 1 ) ( 2 ) ( 3 ) ]
+        """
+        return self.__str__()
+
+    def __str__(self):
+        r"""
+        Return a string representation of ``self``.
+
+        The subtree of a node is inside brackets and starts with the operation
+        to perform between the children ('J' for join or 'U' for disjoint
+        union).
+
+        EXAMPLES::
+
+            sage: from sage.graphs.cographs import CoTree
+            sage: CoTree(1)
+            ( 1 )
+            sage: CoTree('J')
+            [ J ]
+            sage: next(graphs.cographs(4, as_graph=False))  # indirect doctest
+            [ J ( 0 ) ( 1 ) ( 2 ) ( 3 ) ]
+        """
+        first = '[' if self.name in ['J', 'U'] else '('
+        last = ' ]' if self.name in ['J', 'U'] else ' )'
+        s = f"{first} {self.name}"
+        for child in self.children:
+            s += f' {child}'
+        s += last
+        return s
+
+
+    def add_child(self, node):
+        r"""
+        Add cotree ``node`` in the list of children of ``self``.
+
+        INPUT:
+
+        - ``node`` -- a CoTree
+
+        EXAMPLES::
+
+            sage: from sage.graphs.cographs import CoTree
+            sage: T = CoTree('J')
+            sage: T.add_child(CoTree(1))
+            sage: T
+            [ J ( 1 ) ]
+        """
+        assert isinstance(node, CoTree)
+        self.children.append(node)
+        node.parent = self
+
+    def copy_tree(self, T):
+        r"""
+        Make `T` a copy of ``self``.
+
+        INPUT:
+
+        - ``T`` -- a CoTree
+
+        EXAMPLES::
+
+            sage: from sage.graphs.cographs import CoTree
+            sage: T = CoTree('J')
+            sage: T.add_child(CoTree(1))
+            sage: T.add_child(CoTree(2))
+            sage: T
+            [ J ( 1 ) ( 2 ) ]
+            sage: B =  CoTree('U')
+            sage: T.copy_tree(B)
+            sage: B
+            [ U ( 1 ) ( 2 ) ]
+        """
+        for i, child in enumerate(self.children):
+            T.add_child(CoTree(child.name))
+            child.copy_tree(T.children[i])
+
+    def reset_info(self):
+        r"""
+        Reset parameter ``info`` from all nodes of ``self``.
+
+        EXAMPLES::
+
+            sage: from sage.graphs.cographs import CoTree
+            sage: T = CoTree(1)
+            sage: B = CoTree(2)
+            sage: T.add_child(B)
+            sage: C = CoTree(3)
+            sage: B.add_child(C)
+            sage: C.info = 'info'
+            sage: T.reset_info()
+            sage: C.info is None
+            True
+        """
+        for child in self.children:
+            child.reset_info()
+        self.info = None
+
+
+def next_partition(P):
+    r"""
+    Return the next partition after `P`, if any.
+
+    This is a helper method to method :meth:`cographs`.
+
+    INPUT:
+
+    - ``P`` -- a list encoding a partition of a number `n`
+
+    EXAMPLES::
+
+        sage: from sage.graphs.cographs import next_partition
+        sage: P = [1, 1, 1, 1, 1, 1]
+        sage: while P:
+        ....:     print(P)
+        ....:     P = next_partition(P)
+        [1, 1, 1, 1, 1, 1]
+        [1, 1, 1, 1, 2]
+        [1, 1, 1, 3]
+        [1, 1, 2, 2]
+        [1, 1, 4]
+        [1, 2, 3]
+        [1, 5]
+        [2, 2, 2]
+        [2, 4]
+        [3, 3]
+    """
+    if len(P) < 2:
+        raise ValueError("the length of the input partition must be at least 2") 
+    n = sum(P)
+    if P[0] != n//2:
+        if P[-1] - P[-2] <= 1:
+            return P[:-2] + [P[-2] + P[-1]]
+
+        x = P[-2] + 1
+        y = P[-1] - 1
+        q = y // x
+        if q > 1:
+            r = y % x
+            return P[:-2] + [x]*q + [x + r]
+        return P[:-2] + [x, y]
+
+    if n == 3 and P[1] != n//2 + n%2:
+        return [1, 2]
+    return None
+
+
+def rebuild_node(u, P):
+    r"""
+    Replace the subtree rooted at `u` by a subtree induced by partition `P`.
+
+    This is a helper method to method :meth:`cographs`.
+
+    INPUT:
+
+    - ``u`` -- a ``CoTree``
+
+    - ``P`` -- a partition encoding the new structure of the children of `u`
+
+    EXAMPLES::
+
+        sage: next(graphs.cographs(3, as_graph=True)).vertices()  # indirect doctest
+        [0, 1, 2]
+    """
+    u.children = []  # delete the subtree rooted at u
+    for value in P:
+        this_child = CoTree(value)
+        u.add_child(this_child)
+        if value > 1:
+            for j in range(value):
+                this_child.add_child(CoTree(1))
+
+
+def find_pivot(T):
+    r"""
+    Seach for a pivot node in `T`.
+
+    This is a helper method to method :meth:`cographs`.
+
+    A node in `T` is a ``pivot`` if it is not a leaf, it does not induce a
+    maximum partition and it is the first such node in the inverse postorder
+    traversal.
+
+    INPUT:
+
+    - ``T`` -- a ``CoTree``
+
+    EXAMPLES::
+
+        sage: next(graphs.cographs(3, as_graph=True)).vertices()  # indirect doctest
+        [0, 1, 2]
+    """
+    for child in reversed(T.children):
+        pivot = find_pivot(child)
+        if pivot is not None:
+            return pivot
+
+    # Check if T is a pivot
+    i = T.name
+    if (i != 1 and ((i//2 != T.children[0].name) or
+                    (i//2 + i%2 != T.children[1].name))): 
+        T.info = 'p'  # pivot mark
+        return T
+    return None
+
+
+def next_tree(T):
+    r"""
+    Check if there is another tree after `T`.
+
+    This is a helper method to method :meth:`cographs`.
+
+    This methods returns ``True`` if there is a tree after `T`, and if so it
+    modifies the input tree `T` that becomes the next tree.
+
+    INPUT:
+
+    - ``T`` -- a ``CoTree``
+
+    EXAMPLES::
+
+        sage: next(graphs.cographs(3, as_graph=True)).vertices()  # indirect doctest
+        [0, 1, 2]
+    """
+    pivot = find_pivot(T)
+    if pivot is None:
+        return False
+
+    # Find the next partition induced by the subtree pivot
+    partition = [c.name for c in pivot.children]
+    P = next_partition(partition)
+    # and rebuild the subtree of pivot accordingly
+    rebuild_node(pivot, P)
+
+    x = pivot
+    while x.parent is not None:
+        ancestor = x.parent
+        # Modify the bigger siblings of x (i.e., the siblings placed after
+        # x in the list of children of ancestor)
+        is_bigger_sibling = False
+        for y, this_child in enumerate(ancestor.children):
+            if this_child.info == 'p':
+                is_bigger_sibling = True
+            elif is_bigger_sibling:  # true only for bigger siblings of x
+                if x.name == this_child.name: 
+                    temp = CoTree(x.name)
+                    x.copy_tree(temp)
+                    ancestor.children[y] = temp  # copy subtree T(x) in T(y)
+                    temp.parent = ancestor
+                else:
+                    P = [1] * ancestor.children[y].name
+                    rebuild_node(ancestor.children[y], P)
+
+        # Make the parent of x (if any) the new pivot
+        x.info = None  # reset the pivot mark
+        ancestor.info = 'p'  # parent gets the pivot mark
+        x = ancestor
+
+    return True
+
+
+def cographs(n, as_graph=True, immutable=False):
+    r"""
+    Return an iterator over the cographs of order `n`.
+
+    A cograph is a `P_4`-free graph, that is a graph without induced path of
+    order 4. Any cograph may be constructed, starting from the single vertex
+    graph, by a sequence of :meth:`sage.graphs.graph.Graph.join` and
+    :meth:`sage.graphs.generic_graph.GenericGraph.disjoint_union` operations.
+    See the :wikipedia:`Cograph` for more details.
+
+    This method implements the generator of all cographs of order `n` proposd
+    in [JPD2018]_. The algorithm generates one by one every cotree with `n` nodes,
+    and each cotree is generated by using its previous cotree. The time to
+    construct the first cotree is `O(n)` and the time spent between two
+    consecutive outputs is `O(n)`. Hence, the overall complexity of the algorithm
+    is `O(n*Mn)`, where `n` is the number of nodes and `Mn` is the total number of
+    cographs with `n` nodes (see :oeis:`A000084`).
+
+    INPUT:
+
+    - ``n`` -- an integer larger or equal to 1
+
+    - ``as_graph`` -- boolean (default: ``True``); whether to return graphs or
+      the tree data structure encoding the graph
+
+    - ``immutable`` -- boolean (default: ``False``); whether to return an
+      immutable or a mutable graph. This parameter is used only when ``as_graph
+      is True``.
+
+    EXAMPLES:
+
+    The output can be either cotrees or graphs::
+
+        sage: for t in graphs.cographs(3, as_graph=False):
+        ....:     print(t)
+        [ J ( 0 ) ( 1 ) ( 2 ) ]
+        [ J [ U ( 0 ) ( 1 ) ( 2 ) ] ]
+        [ J ( 0 ) [ U ( 1 ) ( 2 ) ] ]
+        [ J [ U ( 0 ) [ J ( 1 ) ( 2 ) ] ] ]
+        sage: for g in graphs.cographs(3, as_graph=True):
+        ....:     print(g.edges(labels=False, sort=True))
+        [(0, 1), (0, 2), (1, 2)]
+        []
+        [(0, 1), (0, 2)]
+        [(1, 2)]
+
+    Check that we agree with :oeis:`A000084`::
+
+        sage: [sum(1 for _ in graphs.cographs(n, as_graph=False))
+        ....:  for n in range(1, 8)]
+        [1, 2, 4, 10, 24, 66, 180]
+
+    TESTS::
+
+        sage: g = next(graphs.cographs(2, as_graph=True, immutable=False))
+        sage: g.is_immutable()
+        False
+        sage: g = next(graphs.cographs(2, as_graph=True, immutable=True))
+        sage: g.is_immutable()
+        True
+        sage: next(graphs.cographs(0))
+        Traceback (most recent call last):
+        ...
+        ValueError: parameter n must be at least >= 1
+    """
+    if n < 1:
+        raise ValueError('parameter n must be at least >= 1')
+    if as_graph:
+        def func(T):
+            return tree_to_graph(T, immutable=immutable)
+    else:
+        def func(T):
+            return T
+
+    if n == 1:
+        T = CoTree('J')
+        B = CoTree('U')
+        B.add_child(CoTree(0))
+        T.add_child(B)
+        yield func(T)
+        return
+
+    # Construct the minimum tree
+    T = CoTree(n)
+    for j in range(n):
+        T.add_child(CoTree(1))
+
+    while True:
+        # T corresponds to 2 cotrees: one with 'U' root and one with 'J' root
+        tree_J = CoTree(T.name)
+        T.copy_tree(tree_J)
+        tree_U = CoTree(T.name)
+        T.copy_tree(tree_U)
+        # tree_J has root 'J'
+        change_label(tree_J, True, [0])
+        # tree 0 has root 'U'
+        change_label(tree_U, False, [0])
+        tree_UU = CoTree('J')
+        tree_UU.add_child(tree_U)
+        yield func(tree_J)
+        yield func(tree_UU)
+        if not next_tree(T):
+            break
+
+
+def change_label(tree, status, counter):
+    """
+    Set the names of the nodes of ``tree``.
+
+    This is a helper method to method :meth:`cographs`.
+
+    The input ``tree`` is such that each node has as label its number of
+    children.  This method changes the label of each node so that a parallel
+    node is labeled 'U', a series node is labeled 'J' and a leaf node gets a
+    unique number.
+
+    INPUT:
+
+    - ``tree`` -- the tree to relabel
+
+    - ``status`` -- boolean; used to to detect series (``True``) and parallel
+      (``False``) internal nodes
+
+    - ``counter`` -- list; the first integer of the list is used to assign a
+      unique number to the leaves of the tree
+
+    EXAMPLES::
+
+        sage: next(graphs.cographs(4, as_graph=True)).vertices()  # indirect doctest
+        [0, 1, 2, 3]
+    """
+    if tree.name != 1:
+        tree.name = 'J' if status else 'U'
+    else:
+        tree.name = counter[0]
+        counter[0] += 1
+    for child in tree.children:
+        if child is not None:
+            change_label(child, not status, counter)
+
+
+def tree_to_graph(tree, immutable=False):
+    r"""
+    Return the cograph represented by ``tree``.
+
+    This is a helper method to method :meth:`cographs`.
+
+    EXAMPLES::
+
+        sage: for t in graphs.cographs(3, as_graph=True):  # indirect doctest
+        ....:     print(t.edges(labels=False, sort=True))  # indirect doctest
+        [(0, 1), (0, 2), (1, 2)]
+        []
+        [(0, 1), (0, 2)]
+        [(1, 2)]
+    """
+    from sage.graphs.graph import Graph
+    g = Graph()
+    _tree_to_graph_rec(tree, g)
+    return g.copy(immutable=True) if immutable else g
+
+
+def _tree_to_graph_rec(tree, g):
+    r"""
+    Add recursively one by one the vertices and edges of ``tree`` to ``g``.
+
+    This is a helper method to method :meth:`tree_to_graph`.
+
+    EXAMPLES::
+
+        sage: for t in graphs.cographs(3, as_graph=True):  # indirect doctest
+        ....:     print(t.edges(labels=False, sort=True))  # indirect doctest
+        [(0, 1), (0, 2), (1, 2)]
+        []
+        [(0, 1), (0, 2)]
+        [(1, 2)]
+    """
+    for child in tree.children:
+        _tree_to_graph_rec(child, g)
+    if tree.name not in ['J', 'U']:
+        tree.info = 'v'
+        g.add_vertex(tree.name)
+        _find_neighbors(tree, g)
+        tree.reset_info()
+
+
+def _find_neighbors(tree, g):
+    r"""
+    Identify the neighbors of node ``tree`` in ``g`` and add needed edges.
+
+    This is a helper method to method :meth:`tree_to_graph`.
+
+    EXAMPLES::
+
+        sage: for t in graphs.cographs(3, as_graph=True):  # indirect doctest
+        ....:     print(t.edges(labels=False, sort=True))  # indirect doctest
+        [(0, 1), (0, 2), (1, 2)]
+        []
+        [(0, 1), (0, 2)]
+        [(1, 2)]
+    """
+    ancestor = tree.parent
+    ancestor.info = 'v'
+    while ancestor is not None:
+        if ancestor.name == 'J':
+            for sibling in ancestor.children:
+                if sibling != tree and sibling.info != 'v':
+                    _add_edge(tree, sibling, g)
+        elif ancestor.name == 'U':
+            ancestor.info = 'v'
+        ancestor = ancestor.parent
+
+
+def _add_edge(u, v, g):
+    r"""
+    Add an edge in `g` between the nodes associated to the cotrees `u` and `v`.
+
+    This is a helper method to method :meth:`tree_to_graph`.
+
+    If `v` is not a leaf, then the method add edges between `u` and all leaves
+    of the subtree rooted at `v`.
+
+    The method assumes that `u` is a leaf (not tested).
+
+    EXAMPLES::
+
+        sage: for t in graphs.cographs(3, as_graph=True):  # indirect doctest
+        ....:     print(t.edges(labels=False, sort=True))  # indirect doctest
+        [(0, 1), (0, 2), (1, 2)]
+        []
+        [(0, 1), (0, 2)]
+        [(1, 2)]
+    """
+    if v.name in ['J', 'U']:
+        for child in v.children:
+            _add_edge(u, child, g)
+    else:
+        g.add_edge(u.name, v.name)
diff --git a/src/sage/graphs/graph_generators.py b/src/sage/graphs/graph_generators.py
index 5a09c617ba2..d7b5af8fc22 100644
--- a/src/sage/graphs/graph_generators.py
+++ b/src/sage/graphs/graph_generators.py
@@ -232,6 +232,7 @@ def wrap_name(x):
      "CaiFurerImmermanGraph",
      "chang_graphs",
      "CirculantGraph",
+     "cographs",
      "cospectral_graphs",
      "CubeGraph",
      "CubeConnectedCycle",
@@ -2632,6 +2633,7 @@ def quadrangulations(self, order, minimum_degree=None, minimum_connectivity=None
 ###########################################################################
 # Families
 ###########################################################################
+    from . import cographs as cographs_module
     from .generators import families
     from . import strongly_regular_db
     AlternatingFormsGraph = staticmethod(distance_regular.AlternatingFormsGraph)
@@ -2643,6 +2645,7 @@ def quadrangulations(self, order, minimum_degree=None, minimum_connectivity=None
     CaiFurerImmermanGraph = staticmethod(families.CaiFurerImmermanGraph)
     chang_graphs = staticmethod(families.chang_graphs)
     CirculantGraph = staticmethod(families.CirculantGraph)
+    cographs = staticmethod(cographs_module.cographs)
     CubeGraph = staticmethod(families.CubeGraph)
     CubeConnectedCycle = staticmethod(families.CubeConnectedCycle)
     DipoleGraph = staticmethod(families.DipoleGraph)

From 6323dab97388d09b0957e72482c9a6eeaf4ff058 Mon Sep 17 00:00:00 2001
From: dcoudert <david.coudert@inria.fr>
Date: Fri, 10 May 2024 17:14:31 +0200
Subject: [PATCH 02/51] fix lint

---
 src/sage/graphs/cographs.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/sage/graphs/cographs.py b/src/sage/graphs/cographs.py
index 516b9fb89b5..e816166d6dc 100644
--- a/src/sage/graphs/cographs.py
+++ b/src/sage/graphs/cographs.py
@@ -481,7 +481,7 @@ def tree_to_graph(tree, immutable=False):
     EXAMPLES::
 
         sage: for t in graphs.cographs(3, as_graph=True):  # indirect doctest
-        ....:     print(t.edges(labels=False, sort=True))  # indirect doctest
+        ....:     print(t.edges(labels=False, sort=True))
         [(0, 1), (0, 2), (1, 2)]
         []
         [(0, 1), (0, 2)]
@@ -502,7 +502,7 @@ def _tree_to_graph_rec(tree, g):
     EXAMPLES::
 
         sage: for t in graphs.cographs(3, as_graph=True):  # indirect doctest
-        ....:     print(t.edges(labels=False, sort=True))  # indirect doctest
+        ....:     print(t.edges(labels=False, sort=True))
         [(0, 1), (0, 2), (1, 2)]
         []
         [(0, 1), (0, 2)]
@@ -526,7 +526,7 @@ def _find_neighbors(tree, g):
     EXAMPLES::
 
         sage: for t in graphs.cographs(3, as_graph=True):  # indirect doctest
-        ....:     print(t.edges(labels=False, sort=True))  # indirect doctest
+        ....:     print(t.edges(labels=False, sort=True))
         [(0, 1), (0, 2), (1, 2)]
         []
         [(0, 1), (0, 2)]
@@ -558,7 +558,7 @@ def _add_edge(u, v, g):
     EXAMPLES::
 
         sage: for t in graphs.cographs(3, as_graph=True):  # indirect doctest
-        ....:     print(t.edges(labels=False, sort=True))  # indirect doctest
+        ....:     print(t.edges(labels=False, sort=True))
         [(0, 1), (0, 2), (1, 2)]
         []
         [(0, 1), (0, 2)]

From 8b603483b9f40d300bb4432b8e4b848e6e34c9d5 Mon Sep 17 00:00:00 2001
From: dcoudert <david.coudert@inria.fr>
Date: Fri, 10 May 2024 17:26:20 +0200
Subject: [PATCH 03/51] more lint issues

---
 src/sage/graphs/cographs.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/sage/graphs/cographs.py b/src/sage/graphs/cographs.py
index e816166d6dc..67fb3d72c36 100644
--- a/src/sage/graphs/cographs.py
+++ b/src/sage/graphs/cographs.py
@@ -101,7 +101,6 @@ def __str__(self):
         s += last
         return s
 
-
     def add_child(self, node):
         r"""
         Add cotree ``node`` in the list of children of ``self``.
@@ -198,7 +197,7 @@ def next_partition(P):
         [3, 3]
     """
     if len(P) < 2:
-        raise ValueError("the length of the input partition must be at least 2") 
+        raise ValueError("the length of the input partition must be at least 2")
     n = sum(P)
     if P[0] != n//2:
         if P[-1] - P[-2] <= 1:
@@ -212,7 +211,7 @@ def next_partition(P):
             return P[:-2] + [x]*q + [x + r]
         return P[:-2] + [x, y]
 
-    if n == 3 and P[1] != n//2 + n%2:
+    if n == 3 and P[1] != n//2 + n % 2:
         return [1, 2]
     return None
 
@@ -270,7 +269,7 @@ def find_pivot(T):
     # Check if T is a pivot
     i = T.name
     if (i != 1 and ((i//2 != T.children[0].name) or
-                    (i//2 + i%2 != T.children[1].name))): 
+                    (i//2 + i % 2 != T.children[1].name))):
         T.info = 'p'  # pivot mark
         return T
     return None
@@ -314,7 +313,7 @@ def next_tree(T):
             if this_child.info == 'p':
                 is_bigger_sibling = True
             elif is_bigger_sibling:  # true only for bigger siblings of x
-                if x.name == this_child.name: 
+                if x.name == this_child.name:
                     temp = CoTree(x.name)
                     x.copy_tree(temp)
                     ancestor.children[y] = temp  # copy subtree T(x) in T(y)

From a70f6c2cbdcbe34f501ef69d1bcb360093ac04b3 Mon Sep 17 00:00:00 2001
From: dcoudert <david.coudert@inria.fr>
Date: Sun, 12 May 2024 14:29:50 +0200
Subject: [PATCH 04/51] fix typos

---
 src/sage/graphs/cographs.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/sage/graphs/cographs.py b/src/sage/graphs/cographs.py
index 67fb3d72c36..a85ba748a6a 100644
--- a/src/sage/graphs/cographs.py
+++ b/src/sage/graphs/cographs.py
@@ -31,7 +31,7 @@
 
 
 class CoTree:
-    """
+    r"""
     Generic cotree node.
 
     This data structure is used for the generation of cographs in
@@ -340,13 +340,13 @@ def cographs(n, as_graph=True, immutable=False):
     :meth:`sage.graphs.generic_graph.GenericGraph.disjoint_union` operations.
     See the :wikipedia:`Cograph` for more details.
 
-    This method implements the generator of all cographs of order `n` proposd
-    in [JPD2018]_. The algorithm generates one by one every cotree with `n` nodes,
-    and each cotree is generated by using its previous cotree. The time to
-    construct the first cotree is `O(n)` and the time spent between two
-    consecutive outputs is `O(n)`. Hence, the overall complexity of the algorithm
-    is `O(n*Mn)`, where `n` is the number of nodes and `Mn` is the total number of
-    cographs with `n` nodes (see :oeis:`A000084`).
+    This method implements the generator of all cographs of order `n` proposed
+    in [JPD2018]_. The algorithm generates one by one every cotree with `n`
+    nodes, and each cotree is generated by using its previous cotree. The time
+    to construct the first cotree is `O(n)` and the time spent between two
+    consecutive outputs is `O(n)`. Hence, the overall complexity of the
+    algorithm is `O(n*M_n)`, where `n` is the number of nodes and `M_n` is the
+    total number of cographs with `n` nodes (see :oeis:`A000084`).
 
     INPUT:
 
@@ -436,7 +436,7 @@ def func(T):
 
 
 def change_label(tree, status, counter):
-    """
+    r"""
     Set the names of the nodes of ``tree``.
 
     This is a helper method to method :meth:`cographs`.

From 421b552c5da6805e7867228ad2f1ca973ad6866d Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Sun, 2 Jun 2024 22:50:23 -0700
Subject: [PATCH 05/51] .github/workflows/ci-linux-incremental.yml
 (sitepackages): Remove label condition

---
 .github/workflows/ci-linux-incremental.yml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/.github/workflows/ci-linux-incremental.yml b/.github/workflows/ci-linux-incremental.yml
index 88a31a5ce42..5613a4b71a3 100644
--- a/.github/workflows/ci-linux-incremental.yml
+++ b/.github/workflows/ci-linux-incremental.yml
@@ -107,14 +107,6 @@ jobs:
 
   site:
     needs: [changed_files]
-    if: |
-      github.event_name != 'pull_request' ||
-      ((github.event.action != 'labeled' &&
-         (contains(github.event.pull_request.labels.*.name, 'c: packages: standard') ||
-          contains(github.event.pull_request.labels.*.name, 'c: packages: optional'))) ||
-       (github.event.action == 'labeled' &&
-         (github.event.label.name == 'c: packages: optional' ||
-          github.event.label.name == 'c: packages: standard')))
     uses: ./.github/workflows/docker.yml
     with:
       # Build incrementally from published Docker image

From e90d73704bef9cf52d1678e4f6affea96baacda3 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Sun, 2 Jun 2024 23:22:24 -0700
Subject: [PATCH 06/51] .github/workflows/build.yml: Determine build_targets
 (adapted from ci-linux-incremental.yml)

---
 .github/workflows/build.yml | 46 +++++++++++++++++++++++++++++++++----
 1 file changed, 42 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 161704a280c..9d355e29482 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -78,6 +78,8 @@ env:
 jobs:
   test-new:
     runs-on: ubuntu-latest
+    outputs:
+      build_targets:     ${{ steps.build-targets.outputs.build_targets }}
     services:
       # https://docs.docker.com/build/ci/github-actions/local-registry/
       registry:
@@ -98,6 +100,42 @@ jobs:
       - name: Checkout
         id: checkout
         uses: actions/checkout@v4
+      - name: Get all packages that have changed
+        id: changed-packages
+        uses: tj-actions/changed-files@v44
+        with:
+          files_yaml: |
+            configures:
+              - 'build/pkgs/*/spkg-configure.m4'
+            pkgs:
+              - 'build/pkgs/**'
+              - 'pkgs/**'
+      - name: Determine targets to build
+        id: build-targets
+        run: |
+          uninstall_targets=$(echo $(for a in '' ${{ steps.changed-packages.outputs.configures_all_changed_files }}; do echo $a | sed -E 's,build/pkgs/([a-z0-9][_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'; done | sort -u))
+          build_targets=$(echo $(for a in '' ${{ steps.changed-packages.outputs.pkgs_all_changed_files }}; do SPKG=$(echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([a-z0-9][-_.a-z0-9]*)/[^ ]* *,\2,;'); if [ -f "build/pkgs/$SPKG/checksums.ini" -o -f "build/pkgs/$SPKG/requirements.txt" -o -f "build/pkgs/$SPKG/spkg-install" ]; then echo "$SPKG-ensure"; fi; done | sort -u))
+          if [ -n "$uninstall_targets" ]; then
+              echo "build_targets=$uninstall_targets reconfigure $build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+          else
+              echo "build_targets=$build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+          fi
+          cat $GITHUB_OUTPUT
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.base_ref }}
+          path: worktree-base
+        if: github.base_ref && steps.changed-packages.outputs.pkgs_all_changed_files
+      - name: Compute metrics
+        run: |
+          export PATH=build/bin:$PATH
+          if [ -d worktree-base ]; then
+            (echo "# $GITHUB_BASE_REF"; SAGE_ROOT=worktree-base sage-package metrics :all:) > base-metrics.txt
+            (echo "# $GITHUB_REF"; sage-package metrics :all:) > metrics.txt
+            diff --color=always --width=100 --side-by-side --left-column base-metrics.txt metrics.txt || true
+          else
+            sage-package metrics :all:
+          fi
       - name: Install test prerequisites
         # From docker.yml
         run: |
@@ -153,7 +191,7 @@ jobs:
             NUMPROC=6
             USE_MAKEFLAGS=-k V=0 SAGE_NUM_THREADS=4 --output-sync=recurse
             TARGETS_PRE=build/make/Makefile
-            TARGETS=ci-build-with-fallback
+            TARGETS=${{ steps.build-targets.outputs.build_targets }}
 
       - name: Start container
         run: |
@@ -266,7 +304,7 @@ jobs:
             NUMPROC=6
             USE_MAKEFLAGS=-k V=0 SAGE_NUM_THREADS=4 --output-sync=recurse
             TARGETS_PRE=build/make/Makefile
-            TARGETS=ci-build-with-fallback
+            TARGETS=${{ needs.test-new.outputs.build_targets }}
 
       - name: Start container
         run: |
@@ -361,7 +399,7 @@ jobs:
             NUMPROC=6
             USE_MAKEFLAGS=-k V=0 SAGE_NUM_THREADS=4 --output-sync=recurse
             TARGETS_PRE=build/make/Makefile
-            TARGETS=ci-build-with-fallback
+            TARGETS=${{ needs.test-new.outputs.build_targets }}
 
       - name: Start container
         id: container
@@ -473,7 +511,7 @@ jobs:
             NUMPROC=6
             USE_MAKEFLAGS=-k V=0 SAGE_NUM_THREADS=4 --output-sync=recurse
             TARGETS_PRE=build/make/Makefile
-            TARGETS=ci-build-with-fallback
+            TARGETS=${{ needs.test-new.outputs.build_targets }}
 
       - name: Start container
         id: container

From dae0ff152b11481dab1358ce7ef4bd2075c07284 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Sun, 2 Jun 2024 23:54:06 -0700
Subject: [PATCH 07/51] .github/workflows/build.yml: Combine calls of
 tj-actions/changed-files

---
 .github/workflows/build.yml | 26 +++++++++++---------------
 1 file changed, 11 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 9d355e29482..45a8bb56e8d 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -100,21 +100,25 @@ jobs:
       - name: Checkout
         id: checkout
         uses: actions/checkout@v4
-      - name: Get all packages that have changed
-        id: changed-packages
+      - name: Get changed files and packages
+        id: changed-files
         uses: tj-actions/changed-files@v44
         with:
+          # File extensions for doctests per sage.doctest.control.skipfile
           files_yaml: |
             configures:
               - 'build/pkgs/*/spkg-configure.m4'
             pkgs:
               - 'build/pkgs/**'
               - 'pkgs/**'
+            doctests:
+              - 'src/**/*.{py,pyx,pxd,pxi,sage,spyx,rst,tex}'
+              - '!src/{setup,conftest*}.py'
       - name: Determine targets to build
         id: build-targets
         run: |
-          uninstall_targets=$(echo $(for a in '' ${{ steps.changed-packages.outputs.configures_all_changed_files }}; do echo $a | sed -E 's,build/pkgs/([a-z0-9][_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'; done | sort -u))
-          build_targets=$(echo $(for a in '' ${{ steps.changed-packages.outputs.pkgs_all_changed_files }}; do SPKG=$(echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([a-z0-9][-_.a-z0-9]*)/[^ ]* *,\2,;'); if [ -f "build/pkgs/$SPKG/checksums.ini" -o -f "build/pkgs/$SPKG/requirements.txt" -o -f "build/pkgs/$SPKG/spkg-install" ]; then echo "$SPKG-ensure"; fi; done | sort -u))
+          uninstall_targets=$(echo $(for a in '' ${{ steps.changed-files.outputs.configures_all_changed_files }}; do echo $a | sed -E 's,build/pkgs/([a-z0-9][_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'; done | sort -u))
+          build_targets=$(echo $(for a in '' ${{ steps.changed-files.outputs.pkgs_all_changed_files }}; do SPKG=$(echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([a-z0-9][-_.a-z0-9]*)/[^ ]* *,\2,;'); if [ -f "build/pkgs/$SPKG/checksums.ini" -o -f "build/pkgs/$SPKG/requirements.txt" -o -f "build/pkgs/$SPKG/spkg-install" ]; then echo "$SPKG-ensure"; fi; done | sort -u))
           if [ -n "$uninstall_targets" ]; then
               echo "build_targets=$uninstall_targets reconfigure $build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
           else
@@ -125,7 +129,7 @@ jobs:
         with:
           ref: ${{ github.base_ref }}
           path: worktree-base
-        if: github.base_ref && steps.changed-packages.outputs.pkgs_all_changed_files
+        if: github.base_ref && steps.changed-files.outputs.pkgs_all_changed_files
       - name: Compute metrics
         run: |
           export PATH=build/bin:$PATH
@@ -213,20 +217,12 @@ jobs:
           ./sage -python -m pytest -c tox.ini -qq --doctest --collect-only || true
         shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
 
-      - name: Get changed files
-        id: changed-files
-        uses: tj-actions/changed-files@v44
-        with:
-          # File extensions per sage.doctest.control.skipfile
-          files: src/**/*.{py,pyx,pxd,pxi,sage,spyx,rst,tex}
-          files_ignore: src/{setup,conftest*}.py
-
       - name: Test changed files (sage -t --new)
-        if: steps.changed-files.outputs.all_changed_files
+        if: steps.changed-files.outputs.doctests_all_changed_files
         run: |
           export MAKE="make -j2 --output-sync=recurse" SAGE_NUM_THREADS=4
           # https://github.com/tj-actions/changed-files?tab=readme-ov-file#outputs-
-          ./sage -t --long --format github -p4 ${{ steps.changed-files.outputs.all_changed_files }}
+          ./sage -t --long --format github -p4 ${{ steps.changed-files.outputs.doctests_all_changed_files }}
         shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
 
   test-mod:

From 62ade48069563b91335ee7361c14f7427ed55343 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 3 Jun 2024 00:55:52 -0700
Subject: [PATCH 08/51] .github/workflows/build.yml (test-new): Do not push and
 do not start container if nothing to be tested

---
 .github/workflows/build.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 45a8bb56e8d..605707ffd9e 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -184,7 +184,7 @@ jobs:
           # more reliable than "load", for which we observed random failure
           # conditions in which the built image could not be found.
           #
-          push:       true
+          push:       ${{ steps.changed-files.outputs.doctests_all_changed_files && true || false }}
           load:       false
           context:    .
           tags:       ${{ env.BUILD_IMAGE }}
@@ -198,6 +198,7 @@ jobs:
             TARGETS=${{ steps.build-targets.outputs.build_targets }}
 
       - name: Start container
+        if: steps.changed-files.outputs.doctests_all_changed_files
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -207,6 +208,7 @@ jobs:
       # Testing
 
       - name: Check that all modules can be imported
+        if: steps.changed-files.outputs.doctests_all_changed_files
         run: |
           # Increase the length of the lines in the "short summary"
           export COLUMNS=120

From a1b3a44fcc55bed6a9c3718f9382fd165a09984a Mon Sep 17 00:00:00 2001
From: dcoudert <david.coudert@inria.fr>
Date: Mon, 3 Jun 2024 11:58:46 +0200
Subject: [PATCH 09/51] use AccelAsc_next

---
 src/sage/graphs/cographs.py | 63 +++++++------------------------------
 1 file changed, 11 insertions(+), 52 deletions(-)

diff --git a/src/sage/graphs/cographs.py b/src/sage/graphs/cographs.py
index a85ba748a6a..8a141b1088a 100644
--- a/src/sage/graphs/cographs.py
+++ b/src/sage/graphs/cographs.py
@@ -20,7 +20,8 @@
 -------
 """
 # ****************************************************************************
-#       Copyright (C)      2024 David Coudert <david.coudert@inria.fr>
+#       Copyright (C) 2017-2024 Marianna Spyrakou
+#                          2024 David Coudert <david.coudert@inria.fr>
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -29,6 +30,8 @@
 #                  https://www.gnu.org/licenses/
 # ****************************************************************************
 
+from sage.combinat.partitions import AccelAsc_next
+
 
 class CoTree:
     r"""
@@ -168,54 +171,6 @@ def reset_info(self):
         self.info = None
 
 
-def next_partition(P):
-    r"""
-    Return the next partition after `P`, if any.
-
-    This is a helper method to method :meth:`cographs`.
-
-    INPUT:
-
-    - ``P`` -- a list encoding a partition of a number `n`
-
-    EXAMPLES::
-
-        sage: from sage.graphs.cographs import next_partition
-        sage: P = [1, 1, 1, 1, 1, 1]
-        sage: while P:
-        ....:     print(P)
-        ....:     P = next_partition(P)
-        [1, 1, 1, 1, 1, 1]
-        [1, 1, 1, 1, 2]
-        [1, 1, 1, 3]
-        [1, 1, 2, 2]
-        [1, 1, 4]
-        [1, 2, 3]
-        [1, 5]
-        [2, 2, 2]
-        [2, 4]
-        [3, 3]
-    """
-    if len(P) < 2:
-        raise ValueError("the length of the input partition must be at least 2")
-    n = sum(P)
-    if P[0] != n//2:
-        if P[-1] - P[-2] <= 1:
-            return P[:-2] + [P[-2] + P[-1]]
-
-        x = P[-2] + 1
-        y = P[-1] - 1
-        q = y // x
-        if q > 1:
-            r = y % x
-            return P[:-2] + [x]*q + [x + r]
-        return P[:-2] + [x, y]
-
-    if n == 3 and P[1] != n//2 + n % 2:
-        return [1, 2]
-    return None
-
-
 def rebuild_node(u, P):
     r"""
     Replace the subtree rooted at `u` by a subtree induced by partition `P`.
@@ -233,6 +188,8 @@ def rebuild_node(u, P):
         sage: next(graphs.cographs(3, as_graph=True)).vertices()  # indirect doctest
         [0, 1, 2]
     """
+    if P is None:
+        print('P is None')
     u.children = []  # delete the subtree rooted at u
     for value in P:
         this_child = CoTree(value)
@@ -244,7 +201,7 @@ def rebuild_node(u, P):
 
 def find_pivot(T):
     r"""
-    Seach for a pivot node in `T`.
+    Search for a pivot node in `T`.
 
     This is a helper method to method :meth:`cographs`.
 
@@ -297,9 +254,11 @@ def next_tree(T):
     if pivot is None:
         return False
 
-    # Find the next partition induced by the subtree pivot
+    # Find the next partition induced by the subtree pivot.
+    # Partitions are represented in ascending order (i.e., `P_i \leq P_{i+1}`)
+    # and we search for the next partition in lexicographic order.
     partition = [c.name for c in pivot.children]
-    P = next_partition(partition)
+    P = AccelAsc_next(partition)
     # and rebuild the subtree of pivot accordingly
     rebuild_node(pivot, P)
 

From 9d3a3f23c052ef89fd175085acd8003c587eb67b Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 3 Jun 2024 11:42:51 -0700
Subject: [PATCH 10/51] .github/workflows/ci-linux-incremental.yml: Remove
 duplicate testing of the default platform (ubuntu-jammy)

---
 .github/workflows/ci-linux-incremental.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci-linux-incremental.yml b/.github/workflows/ci-linux-incremental.yml
index 5613a4b71a3..e63c097bec3 100644
--- a/.github/workflows/ci-linux-incremental.yml
+++ b/.github/workflows/ci-linux-incremental.yml
@@ -91,7 +91,6 @@ jobs:
       targets: "${{needs.changed_files.outputs.uninstall_targets}} reconfigure ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
       tox_system_factors: >-
         ["ubuntu-focal",
-         "ubuntu-jammy",
          "ubuntu-mantic",
          "debian-bullseye",
          "debian-bookworm",

From cacd8d8230f6885f597a8959a68dfe85a766cc64 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 3 Jun 2024 12:12:11 -0700
Subject: [PATCH 11/51] build/pkgs/scip: Update to 9.0.1

---
 build/pkgs/scip/checksums.ini       | 4 ++--
 build/pkgs/scip/package-version.txt | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/build/pkgs/scip/checksums.ini b/build/pkgs/scip/checksums.ini
index d99a2b7930f..25100a06dad 100644
--- a/build/pkgs/scip/checksums.ini
+++ b/build/pkgs/scip/checksums.ini
@@ -1,4 +1,4 @@
 tarball=scip-${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_MICRO}.tar.gz
-sha1=bb28aef4bad00a1ff2c7f4ee982961709d15b9f8
-sha256=ee221bd13a6b24738f2e74321e2efdebd6d7c603574ca6f6cb9d4472ead2c22f
+sha1=7bae5feab37e6e602d25d9468d003479d268d6a8
+sha256=08ad3e7ad6f84f457d95bb70ab21fa7fc648dd43103099359ef8a8f30fcce32e
 upstream_url=https://github.com/scipopt/scip/archive/refs/tags/v${VERSION_MAJOR}${VERSION_MINOR}${VERSION_MICRO}.tar.gz
diff --git a/build/pkgs/scip/package-version.txt b/build/pkgs/scip/package-version.txt
index 486ff8cd7ba..37ad5c8b19d 100644
--- a/build/pkgs/scip/package-version.txt
+++ b/build/pkgs/scip/package-version.txt
@@ -1 +1 @@
-9.0.0.p0
+9.0.1

From a86b8413680aebe6674da0825557f8d41901f260 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 3 Jun 2024 12:12:19 -0700
Subject: [PATCH 12/51] build/pkgs/soplex: Update to 7.0.1

---
 build/pkgs/soplex/checksums.ini       | 4 ++--
 build/pkgs/soplex/package-version.txt | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/build/pkgs/soplex/checksums.ini b/build/pkgs/soplex/checksums.ini
index 4eb6d430aff..eadf0896fcf 100644
--- a/build/pkgs/soplex/checksums.ini
+++ b/build/pkgs/soplex/checksums.ini
@@ -1,4 +1,4 @@
 tarball=soplex-VERSION.tar.gz
-sha1=5d0e7fa41b45aa0877134a5b8e261d9608505636
-sha256=ab1906d3afb1793a6f129a5baef9dd8eee929ee945aade427cb9f0b17888239c
+sha1=a53fecd8d916751ee6e9a8daee0be795ed5222a6
+sha256=80cce994dcbe45fd52b60e31a3aeb5d2c60a7ddbaae495e0ce6bf58481675696
 upstream_url=https://github.com/scipopt/soplex/archive/refs/tags/release-${VERSION_MAJOR}${VERSION_MINOR}${VERSION_MICRO}.tar.gz
diff --git a/build/pkgs/soplex/package-version.txt b/build/pkgs/soplex/package-version.txt
index 66ce77b7ead..9fe9ff9d996 100644
--- a/build/pkgs/soplex/package-version.txt
+++ b/build/pkgs/soplex/package-version.txt
@@ -1 +1 @@
-7.0.0
+7.0.1

From c095189add5d5c3af4dbf57e2d64a483ec66a94c Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 3 Jun 2024 12:12:39 -0700
Subject: [PATCH 13/51] build/pkgs/papilo: Update to 2.2.1

---
 build/pkgs/papilo/checksums.ini       | 4 ++--
 build/pkgs/papilo/package-version.txt | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/build/pkgs/papilo/checksums.ini b/build/pkgs/papilo/checksums.ini
index 831334dbdb9..d99180dc1e1 100644
--- a/build/pkgs/papilo/checksums.ini
+++ b/build/pkgs/papilo/checksums.ini
@@ -1,4 +1,4 @@
 tarball=papilo-VERSION.tar.gz
-sha1=069f64ff25cfb08c9b2a416d1d215bd5b907c877
-sha256=4ed759e55fe1c74be779137e4e3cdae67e1b64bd62ca31793ca3b321509c27a8
+sha1=55e8416d5512d3f823ae87c4161ccff30e76f4a1
+sha256=b022af82bda3db1a594fe67524d98be82e67279f9d9d645b2fcdfc9349cdc6f7
 upstream_url=https://github.com/scipopt/papilo/archive/refs/tags/vVERSION.tar.gz
diff --git a/build/pkgs/papilo/package-version.txt b/build/pkgs/papilo/package-version.txt
index ccbccc3dc62..c043eea7767 100644
--- a/build/pkgs/papilo/package-version.txt
+++ b/build/pkgs/papilo/package-version.txt
@@ -1 +1 @@
-2.2.0
+2.2.1

From b07fa20c3be88e2e7b600b92d2de603e026ad790 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 3 Jun 2024 12:13:05 -0700
Subject: [PATCH 14/51] build/pkgs/onetbb: Update to 2021.12.0

---
 build/pkgs/onetbb/checksums.ini       | 4 ++--
 build/pkgs/onetbb/package-version.txt | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/build/pkgs/onetbb/checksums.ini b/build/pkgs/onetbb/checksums.ini
index 6573c2f7b99..c7b278c01af 100644
--- a/build/pkgs/onetbb/checksums.ini
+++ b/build/pkgs/onetbb/checksums.ini
@@ -1,4 +1,4 @@
 tarball=onetbb-VERSION.tar.gz
-sha1=740e86b703f42446ddde392b73a9db3dc0f5f4cd
-sha256=782ce0cab62df9ea125cdea253a50534862b563f1d85d4cda7ad4e77550ac363
+sha1=bd663861ab6bfec2469f3a8133c3ac1244f260cb
+sha256=c7bb7aa69c254d91b8f0041a71c5bcc3936acb64408a1719aec0b2b7639dd84f
 upstream_url=https://github.com/oneapi-src/oneTBB/archive/refs/tags/vVERSION.tar.gz
diff --git a/build/pkgs/onetbb/package-version.txt b/build/pkgs/onetbb/package-version.txt
index 90431db79ad..5c5abc38ec9 100644
--- a/build/pkgs/onetbb/package-version.txt
+++ b/build/pkgs/onetbb/package-version.txt
@@ -1 +1 @@
-2021.11.0
+2021.12.0

From 4db331384bb68a7b1e9899ac6bd6c148cc1642aa Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 3 Jun 2024 11:46:40 -0700
Subject: [PATCH 15/51] .github/workflows/ci-linux-incremental.yml: Replace
 ubuntu-mantic, fedora-38 by latest

---
 .github/workflows/ci-linux-incremental.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci-linux-incremental.yml b/.github/workflows/ci-linux-incremental.yml
index e63c097bec3..a74eb4e0597 100644
--- a/.github/workflows/ci-linux-incremental.yml
+++ b/.github/workflows/ci-linux-incremental.yml
@@ -91,11 +91,11 @@ jobs:
       targets: "${{needs.changed_files.outputs.uninstall_targets}} reconfigure ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
       tox_system_factors: >-
         ["ubuntu-focal",
-         "ubuntu-mantic",
+         "ubuntu-noble",
          "debian-bullseye",
          "debian-bookworm",
          "fedora-30",
-         "fedora-38",
+         "fedora-40",
          "gentoo-python3.11",
          "debian-bullseye-i386"]
       tox_packages_factors: >-

From 358609098cb3d951b829fd25af0d80980a11de69 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 3 Jun 2024 12:07:15 -0700
Subject: [PATCH 16/51] .github/workflows/ci-linux-incremental.yml: Update
 build_target script from build.yml, use ptest-nodoc to avoid duplicate
 doc-html build

---
 .github/workflows/ci-linux-incremental.yml | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci-linux-incremental.yml b/.github/workflows/ci-linux-incremental.yml
index a74eb4e0597..ce468ff3a42 100644
--- a/.github/workflows/ci-linux-incremental.yml
+++ b/.github/workflows/ci-linux-incremental.yml
@@ -41,12 +41,11 @@ jobs:
     runs-on: ubuntu-latest
     name: List changed packages
     outputs:
-      uninstall_targets: ${{ steps.build-targets.outputs.uninstall_targets }}
       build_targets:     ${{ steps.build-targets.outputs.build_targets }}
     steps:
       - uses: actions/checkout@v4
       - name: Get all packages that have changed
-        id: changed-packages
+        id: changed-files
         uses: tj-actions/changed-files@v44
         with:
           files_yaml: |
@@ -58,14 +57,19 @@ jobs:
       - name: Determine targets to build
         id: build-targets
         run: |
-          echo "uninstall_targets=$(echo $(for a in '' ${{ steps.changed-packages.outputs.configures_all_changed_files }}; do echo $a | sed -E 's,build/pkgs/([a-z0-9][_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'; done | sort -u))" >> $GITHUB_OUTPUT
-          echo "build_targets=$(echo $(for a in '' ${{ steps.changed-packages.outputs.pkgs_all_changed_files }}; do SPKG=$(echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([a-z0-9][-_.a-z0-9]*)/[^ ]* *,\2,;'); if [ -f "build/pkgs/$SPKG/checksums.ini" -o -f "build/pkgs/$SPKG/requirements.txt" -o -f "build/pkgs/$SPKG/spkg-install" ]; then echo "$SPKG-ensure"; fi; done | sort -u))" >> $GITHUB_OUTPUT
+          uninstall_targets=$(echo $(for a in '' ${{ steps.changed-files.outputs.configures_all_changed_files }}; do echo $a | sed -E 's,build/pkgs/([a-z0-9][_.a-z0-9]*)/spkg-configure[.]m4 *,\1-uninstall,'; done | sort -u))
+          build_targets=$(echo $(for a in '' ${{ steps.changed-files.outputs.pkgs_all_changed_files }}; do SPKG=$(echo $a | sed -E 's,-,_,g;s,(build/)?pkgs/([a-z0-9][-_.a-z0-9]*)/[^ ]* *,\2,;'); if [ -f "build/pkgs/$SPKG/checksums.ini" -o -f "build/pkgs/$SPKG/requirements.txt" -o -f "build/pkgs/$SPKG/spkg-install" ]; then echo "$SPKG-ensure"; fi; done | sort -u))
+          if [ -n "$uninstall_targets" ]; then
+              echo "build_targets=$uninstall_targets reconfigure $build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+          else
+              echo "build_targets=$build_targets ci-build-with-fallback" >> $GITHUB_OUTPUT
+          fi
           cat $GITHUB_OUTPUT
       - uses: actions/checkout@v4
         with:
           ref: ${{ github.base_ref }}
           path: worktree-base
-        if: github.base_ref
+        if: github.base_ref && steps.changed-files.outputs.pkgs_all_changed_files
       - name: Compute metrics
         run: |
           export PATH=build/bin:$PATH
@@ -88,7 +92,7 @@ jobs:
       from_docker_target: "with-targets"
       from_docker_tag: "dev"
       docker_targets: "with-targets"
-      targets: "${{needs.changed_files.outputs.uninstall_targets}} reconfigure ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
+      targets: "${{needs.changed_files.outputs.build_targets}} doc-html ptest-nodoc"
       tox_system_factors: >-
         ["ubuntu-focal",
          "ubuntu-noble",
@@ -115,7 +119,7 @@ jobs:
       from_docker_target: "with-targets"
       from_docker_tag: "dev"
       docker_targets: "with-targets"
-      targets: "${{needs.changed_files.outputs.uninstall_targets}} reconfigure ${{needs.changed_files.outputs.build_targets}} build doc-html ptest"
+      targets: "${{needs.changed_files.outputs.build_targets}} doc-html ptest-nodoc"
       # Only test systems with a usable system python (>= 3.9)
       # with only a small number of test failures as of 10.2.rc0
       tox_system_factors: >-

From 1df4f5a5c508dfdbb8779161283cf780459dd908 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 3 Jun 2024 18:27:13 -0700
Subject: [PATCH 17/51] .ci/retrofit-worktree.sh: Commit /new

---
 .ci/retrofit-worktree.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.ci/retrofit-worktree.sh b/.ci/retrofit-worktree.sh
index eba1b674ecb..4c283f7ff4a 100755
--- a/.ci/retrofit-worktree.sh
+++ b/.ci/retrofit-worktree.sh
@@ -23,9 +23,10 @@ set -x
 # If actions/checkout downloaded our source tree using the GitHub REST API
 # instead of with git (because do not have git installed in our image),
 # we first make the source tree a repo.
-if [ ! -d .git ]; then git init && git add -A && git commit --quiet -m "new"; fi
+if [ ! -d .git ]; then git init; fi
 
-# Tag this state of the source tree "new". This is what we want to build and test.
+# Commit and tag this state of the source tree "new". This is what we want to build and test.
+git add -A && git commit --quiet --allow-empty -m "new"
 git tag -f new
 
 # Our container image contains a source tree in $WORKTREE_DIRECTORY with a full build of Sage.

From 44903a34f188a355e5901398e75b52ab12833ce5 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 3 Jun 2024 15:50:24 -0700
Subject: [PATCH 18/51] build/pkgs/scip/patches/struct_symmetry_header.patch:
 Remove

---
 .../pkgs/scip/patches/struct_symmetry_header.patch | 14 --------------
 1 file changed, 14 deletions(-)
 delete mode 100644 build/pkgs/scip/patches/struct_symmetry_header.patch

diff --git a/build/pkgs/scip/patches/struct_symmetry_header.patch b/build/pkgs/scip/patches/struct_symmetry_header.patch
deleted file mode 100644
index 39d9114a58e..00000000000
--- a/build/pkgs/scip/patches/struct_symmetry_header.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-From https://github.com/scipopt/SCIP-SDP/issues/12#issuecomment-1969453709
-
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index 5392127c5d..b66e86dec5 100644
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -991,6 +991,7 @@ set(scipheaders
- set(symheaders
-   symmetry/build_sassy_graph.h
-   symmetry/compute_symmetry.h
-+  symmetry/struct_symmetry.h
-   symmetry/type_symmetry.h
- )
-

From 5d1fc2aec090c301d9a187af4eb32d5e45e251df Mon Sep 17 00:00:00 2001
From: David Coudert <david.coudert@inria.fr>
Date: Tue, 4 Jun 2024 12:59:03 +0200
Subject: [PATCH 19/51] Update src/sage/graphs/cographs.py

Co-authored-by: Travis Scrimshaw <clfrngrown@aol.com>
---
 src/sage/graphs/cographs.py | 16 +---------------
 1 file changed, 1 insertion(+), 15 deletions(-)

diff --git a/src/sage/graphs/cographs.py b/src/sage/graphs/cographs.py
index 8a141b1088a..44a0c736060 100644
--- a/src/sage/graphs/cographs.py
+++ b/src/sage/graphs/cographs.py
@@ -62,21 +62,7 @@ def __init__(self, name='root'):
         self.info = None
         self.parent = None
 
-    def __repr__(self):
-        r"""
-        Return a string representation of ``self``.
-
-        EXAMPLES::
-
-            sage: from sage.graphs.cographs import CoTree
-            sage: CoTree(1)
-            ( 1 )
-            sage: CoTree('J')
-            [ J ]
-            sage: next(graphs.cographs(4, as_graph=False))  # indirect doctest
-            [ J ( 0 ) ( 1 ) ( 2 ) ( 3 ) ]
-        """
-        return self.__str__()
+    __repr__ = __str__
 
     def __str__(self):
         r"""

From c8a1949968e557a98919b901cb646a441e33ec23 Mon Sep 17 00:00:00 2001
From: dcoudert <david.coudert@inria.fr>
Date: Tue, 4 Jun 2024 16:04:36 +0200
Subject: [PATCH 20/51] fix error

---
 src/sage/graphs/cographs.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/sage/graphs/cographs.py b/src/sage/graphs/cographs.py
index 44a0c736060..b921375f643 100644
--- a/src/sage/graphs/cographs.py
+++ b/src/sage/graphs/cographs.py
@@ -62,8 +62,6 @@ def __init__(self, name='root'):
         self.info = None
         self.parent = None
 
-    __repr__ = __str__
-
     def __str__(self):
         r"""
         Return a string representation of ``self``.
@@ -90,6 +88,8 @@ def __str__(self):
         s += last
         return s
 
+    __repr__ = __str__
+
     def add_child(self, node):
         r"""
         Add cotree ``node`` in the list of children of ``self``.

From a872aacc3f879472a98de7796b0c48c0e6d39899 Mon Sep 17 00:00:00 2001
From: Giacomo Pope <giacomopope@gmail.com>
Date: Tue, 4 Jun 2024 17:42:54 +0100
Subject: [PATCH 21/51] fix slow columns

---
 src/sage/matrix/matrix_mod2_dense.pyx | 41 +++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/src/sage/matrix/matrix_mod2_dense.pyx b/src/sage/matrix/matrix_mod2_dense.pyx
index 0d3c15be395..1bbb41fe205 100644
--- a/src/sage/matrix/matrix_mod2_dense.pyx
+++ b/src/sage/matrix/matrix_mod2_dense.pyx
@@ -526,6 +526,47 @@ cdef class Matrix_mod2_dense(matrix_dense.Matrix_dense):   # dense or sparse
             mzd_submatrix(z._entries, self._entries, i, 0, i+1, self._ncols)
         return z
 
+    def columns(self, copy=True):
+        """
+        Return list of the columns of self.
+
+        INPUT:
+
+        - ``copy`` - (default: True) if True, return a copy so you can
+          modify it safely
+
+        EXAMPLES:
+
+        An example with a small 3x3 matrix::
+
+            sage: M2 = Matrix(GF(2), [[1, 0, 0], [0, 1, 0], [0, 1, 1]])
+            sage: M2.columns()
+            [(1, 0, 0), (0, 1, 1), (0, 0, 1)]
+
+        """
+        x = self.fetch('columns')
+        if x is not None:
+            if copy: return list(x)
+            return x
+        cdef Py_ssize_t i
+
+        # Note: due to the way M4ri represents values, extracting rows
+        #       if fast, but columns are slow. Therefore we transpose
+        #       then take rows. For more information, see the issue
+        #       https://github.com/sagemath/sage/issues/38150
+        C = self.transpose().rows()
+
+        # Make the vectors immutable since we are caching them
+        for x in C:
+            x.set_immutable()
+
+        # cache result
+        self.cache('columns', C)
+        if copy:
+            return list(C)
+        else:
+            return C
+
     ########################################################################
     # LEVEL 2 functionality
     #   * def _pickle

From 74b12f423b71a7dd9b34b0bce7d134a0bb0d5ad5 Mon Sep 17 00:00:00 2001
From: Giacomo Pope <44242839+GiacomoPope@users.noreply.github.com>
Date: Tue, 4 Jun 2024 17:55:40 +0100
Subject: [PATCH 22/51] fix a typo in comment

---
 src/sage/matrix/matrix_mod2_dense.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sage/matrix/matrix_mod2_dense.pyx b/src/sage/matrix/matrix_mod2_dense.pyx
index 1bbb41fe205..14eb6f02539 100644
--- a/src/sage/matrix/matrix_mod2_dense.pyx
+++ b/src/sage/matrix/matrix_mod2_dense.pyx
@@ -551,7 +551,7 @@ cdef class Matrix_mod2_dense(matrix_dense.Matrix_dense):   # dense or sparse
         cdef Py_ssize_t i
 
         # Note: due to the way M4ri represents values, extracting rows
-        #       if fast, but columns are slow. Therefore we transpose
+        #       is fast, but columns are slow. Therefore we transpose
         #       then take rows. For more information, see the issue
         #       https://github.com/sagemath/sage/issues/38150
         C = self.transpose().rows()

From 8d0c849d0d1f4d6a4b45d857722f0dfe8f43240e Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 4 Jun 2024 15:07:45 -0700
Subject: [PATCH 23/51] .ci/write-dockerfile.sh: Remove old /new at the
 beginning, remove new /new at the end

---
 .ci/write-dockerfile.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.ci/write-dockerfile.sh b/.ci/write-dockerfile.sh
index 67ef594729c..ffdfa5404f6 100755
--- a/.ci/write-dockerfile.sh
+++ b/.ci/write-dockerfile.sh
@@ -264,6 +264,7 @@ cat <<EOF
 
 FROM with-system-packages as bootstrapped
 #:bootstrapping:
+RUN rm -rf /new
 $ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap bootstrap-conda configure.ac sage .homebrew-build-env tox.ini Pipfile.m4 .gitignore /new/
 $ADD config/config.rpath /new/config/config.rpath
 $ADD src/doc/bootstrap /new/src/doc/bootstrap
@@ -347,7 +348,8 @@ RUN cd /new && rm -rf .git && \
         rm -rf /sage/src;                                    \
         mv src /sage/src;                                    \
         cd /sage && ./bootstrap && ./config.status;          \
-    fi
+    fi; \
+    cd /sage && rm -rf /new
 
 ARG TARGETS="build"
 $RUN $CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS} $ENDRUN $THEN_SAVE_STATUS

From d068c8dcc82e667006ecd298a761aff8335a3654 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 4 Jun 2024 15:09:09 -0700
Subject: [PATCH 24/51] .ci/write-dockerfile.sh: Remove duplicated ADD

---
 .ci/write-dockerfile.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.ci/write-dockerfile.sh b/.ci/write-dockerfile.sh
index ffdfa5404f6..beee1440368 100755
--- a/.ci/write-dockerfile.sh
+++ b/.ci/write-dockerfile.sh
@@ -339,7 +339,6 @@ ENV SAGE_CHECK=warn
 ENV SAGE_CHECK_PACKAGES="!cython,!r,!python3,!gap,!cysignals,!linbox,!git,!ppl,!cmake,!rpy2,!sage_sws2rst"
 $ADD .gitignore /new/.gitignore
 $ADD src /new/src
-ADD .ci /.ci
 RUN cd /new && rm -rf .git && \
     if /.ci/retrofit-worktree.sh worktree-pre /sage; then \
         cd /sage && touch configure build/make/Makefile; \

From 7fb032388d799a2e06d9a41dd60a7a6dde32bf6a Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 4 Jun 2024 16:46:13 -0700
Subject: [PATCH 25/51] .ci/write-dockerfile.sh: Remove old .git file at the
 beginning, remove new .git file at the end

---
 .ci/write-dockerfile.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.ci/write-dockerfile.sh b/.ci/write-dockerfile.sh
index beee1440368..3a4ae5b152d 100755
--- a/.ci/write-dockerfile.sh
+++ b/.ci/write-dockerfile.sh
@@ -264,7 +264,7 @@ cat <<EOF
 
 FROM with-system-packages as bootstrapped
 #:bootstrapping:
-RUN rm -rf /new
+RUN rm -rf /new /sage/.git
 $ADD Makefile VERSION.txt COPYING.txt condarc.yml README.md bootstrap bootstrap-conda configure.ac sage .homebrew-build-env tox.ini Pipfile.m4 .gitignore /new/
 $ADD config/config.rpath /new/config/config.rpath
 $ADD src/doc/bootstrap /new/src/doc/bootstrap
@@ -348,7 +348,7 @@ RUN cd /new && rm -rf .git && \
         mv src /sage/src;                                    \
         cd /sage && ./bootstrap && ./config.status;          \
     fi; \
-    cd /sage && rm -rf /new
+    cd /sage && rm -rf /new .git
 
 ARG TARGETS="build"
 $RUN $CHECK_STATUS_THEN make SAGE_SPKG="sage-spkg -y -o" \${USE_MAKEFLAGS} \${TARGETS} $ENDRUN $THEN_SAVE_STATUS

From 212552ec52cb7b22bad8b9aaff823637fef79b2d Mon Sep 17 00:00:00 2001
From: Dima Pasechnik <dimpase@gmail.com>
Date: Tue, 26 Mar 2024 10:00:26 +0000
Subject: [PATCH 26/51] convert pycryptosat into pip package

---
 build/pkgs/cryptominisat/SPKG.rst             | 38 ----------------
 build/pkgs/cryptominisat/checksums.ini        |  4 --
 build/pkgs/cryptominisat/dependencies         |  4 --
 build/pkgs/cryptominisat/distros/conda.txt    |  1 -
 build/pkgs/cryptominisat/distros/homebrew.txt |  1 -
 build/pkgs/cryptominisat/distros/repology.txt |  1 -
 build/pkgs/cryptominisat/package-version.txt  |  1 -
 build/pkgs/cryptominisat/patches/679.patch    | 43 -------------------
 ...tominisat-5.8.0-rm_extra_python_vars.patch | 37 ----------------
 build/pkgs/cryptominisat/spkg-install.in      |  5 ---
 build/pkgs/cryptominisat/type                 |  1 -
 build/pkgs/pycryptosat/SPKG.rst               | 17 +++++++-
 build/pkgs/pycryptosat/checksums.ini          |  1 -
 build/pkgs/pycryptosat/dependencies           |  2 +-
 build/pkgs/pycryptosat/package-version.txt    |  1 -
 build/pkgs/pycryptosat/patches                |  1 -
 build/pkgs/pycryptosat/spkg-install.in        |  9 ----
 .../pkgs/pycryptosat/version_requirements.txt |  1 -
 18 files changed, 16 insertions(+), 152 deletions(-)
 delete mode 100644 build/pkgs/cryptominisat/SPKG.rst
 delete mode 100644 build/pkgs/cryptominisat/checksums.ini
 delete mode 100644 build/pkgs/cryptominisat/dependencies
 delete mode 100644 build/pkgs/cryptominisat/distros/conda.txt
 delete mode 100644 build/pkgs/cryptominisat/distros/homebrew.txt
 delete mode 100644 build/pkgs/cryptominisat/distros/repology.txt
 delete mode 100644 build/pkgs/cryptominisat/package-version.txt
 delete mode 100644 build/pkgs/cryptominisat/patches/679.patch
 delete mode 100644 build/pkgs/cryptominisat/patches/cryptominisat-5.8.0-rm_extra_python_vars.patch
 delete mode 100644 build/pkgs/cryptominisat/spkg-install.in
 delete mode 100644 build/pkgs/cryptominisat/type
 delete mode 120000 build/pkgs/pycryptosat/checksums.ini
 delete mode 120000 build/pkgs/pycryptosat/package-version.txt
 delete mode 120000 build/pkgs/pycryptosat/patches
 delete mode 100644 build/pkgs/pycryptosat/spkg-install.in
 delete mode 100644 build/pkgs/pycryptosat/version_requirements.txt

diff --git a/build/pkgs/cryptominisat/SPKG.rst b/build/pkgs/cryptominisat/SPKG.rst
deleted file mode 100644
index 45c987baf84..00000000000
--- a/build/pkgs/cryptominisat/SPKG.rst
+++ /dev/null
@@ -1,38 +0,0 @@
-cryptominisat: A SAT solver
-===========================
-
-Description
------------
-
-   CryptoMiniSat is a SAT solver that aims to become a premiere SAT
-   solver with all the features and speed of successful SAT solvers,
-   such as MiniSat and PrecoSat. The long-term goals of CryptoMiniSat
-   are to be an efficient sequential, parallel and distributed
-   solver. There are solvers that are good at one or the other,
-   e.g. ManySat (parallel) or PSolver (distributed), but we wish to
-   excel at all.
-
-   CryptoMiniSat 2.5 won the SAT Race 2010 among 20 solvers submitted
-   by researchers and industry.
-
-License
--------
-
-MIT License
-
-
-Upstream Contact
-----------------
-
--  Authors: Mate Soos
--  Email: soos.mate@gmail.com
--  Website: http://www.msoos.org/
--  Releases: https://github.com/msoos/cryptominisat/releases
-
-
-Special Update/Build Instructions
----------------------------------
-
-CryptoMiniSat's tarball downloaded from github is called VERSION.tar.gz
-and should be renamed to cryptominisat-VERSION.tar.gz
-Its Python module is installed by the pycryptosat spkg.
diff --git a/build/pkgs/cryptominisat/checksums.ini b/build/pkgs/cryptominisat/checksums.ini
deleted file mode 100644
index f3838f6618c..00000000000
--- a/build/pkgs/cryptominisat/checksums.ini
+++ /dev/null
@@ -1,4 +0,0 @@
-tarball=cryptominisat-VERSION.tar.gz
-sha1=f79dfa1ffc6c9c75b3a33f76d3a89a3df2b3f4c2
-sha256=50153025c8503ef32f32fff847ee24871bb0fc1f0b13e17fe01aa762923f6d94
-upstream_url=https://github.com/msoos/cryptominisat/archive/refs/tags/VERSION.tar.gz
diff --git a/build/pkgs/cryptominisat/dependencies b/build/pkgs/cryptominisat/dependencies
deleted file mode 100644
index e30473e40f6..00000000000
--- a/build/pkgs/cryptominisat/dependencies
+++ /dev/null
@@ -1,4 +0,0 @@
- m4ri zlib libpng | cmake boost_cropped $(PYTHON)
-
-----------
-All lines of this file are ignored except the first.
diff --git a/build/pkgs/cryptominisat/distros/conda.txt b/build/pkgs/cryptominisat/distros/conda.txt
deleted file mode 100644
index 5ba98aa9061..00000000000
--- a/build/pkgs/cryptominisat/distros/conda.txt
+++ /dev/null
@@ -1 +0,0 @@
-cryptominisat
diff --git a/build/pkgs/cryptominisat/distros/homebrew.txt b/build/pkgs/cryptominisat/distros/homebrew.txt
deleted file mode 100644
index 5ba98aa9061..00000000000
--- a/build/pkgs/cryptominisat/distros/homebrew.txt
+++ /dev/null
@@ -1 +0,0 @@
-cryptominisat
diff --git a/build/pkgs/cryptominisat/distros/repology.txt b/build/pkgs/cryptominisat/distros/repology.txt
deleted file mode 100644
index 5ba98aa9061..00000000000
--- a/build/pkgs/cryptominisat/distros/repology.txt
+++ /dev/null
@@ -1 +0,0 @@
-cryptominisat
diff --git a/build/pkgs/cryptominisat/package-version.txt b/build/pkgs/cryptominisat/package-version.txt
deleted file mode 100644
index 11d9efa3d5a..00000000000
--- a/build/pkgs/cryptominisat/package-version.txt
+++ /dev/null
@@ -1 +0,0 @@
-5.8.0
diff --git a/build/pkgs/cryptominisat/patches/679.patch b/build/pkgs/cryptominisat/patches/679.patch
deleted file mode 100644
index a7dec833f6f..00000000000
--- a/build/pkgs/cryptominisat/patches/679.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-From a01179ffd6b0dd47bfdef2d9350d80b575571f24 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Maciej=20Bar=C4=87?= <xgqt@gentoo.org>
-Date: Sun, 3 Apr 2022 20:02:59 +0200
-Subject: [PATCH] python/setup.py.in: import sysconfig instead of importing it
- from distutils
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-setuptools 61 dropped sysconfig module
-
-Ref: https://github.com/stamparm/pcapy-ng/commit/f6ce5248f78ac0a247d76e48cff152f4e3f26482
-Bug: https://bugs.gentoo.org/836684
-
-Signed-off-by: Maciej Barć <xgqt@gentoo.org>
----
- python/setup.py.in | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/python/setup.py.in b/python/setup.py.in
-index b3ab64af4..293eb1f80 100644
---- a/python/setup.py.in
-+++ b/python/setup.py.in
-@@ -27,7 +27,7 @@ import sys
- import os
- import platform
- from distutils.core import setup, Extension
--from distutils import sysconfig
-+import sysconfig
- from distutils.cmd import Command
- 
- __PACKAGE_VERSION__ = "0.2.0"
-@@ -59,8 +59,8 @@ def _init_posix(init):
-     Forces g++ instead of gcc on most systems
-     credits to eric jones (eric@enthought.com) (found at Google Groups)
-     """
--    def wrapper():
--        init()
-+    def wrapper(vars):
-+        init(vars)
- 
-         config_vars = sysconfig.get_config_vars()  # by reference
-         if config_vars["MACHDEP"].startswith("sun"):
diff --git a/build/pkgs/cryptominisat/patches/cryptominisat-5.8.0-rm_extra_python_vars.patch b/build/pkgs/cryptominisat/patches/cryptominisat-5.8.0-rm_extra_python_vars.patch
deleted file mode 100644
index 5ef6f21c948..00000000000
--- a/build/pkgs/cryptominisat/patches/cryptominisat-5.8.0-rm_extra_python_vars.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
-index f549ca7..4a9f0d8 100644
---- a/python/CMakeLists.txt
-+++ b/python/CMakeLists.txt
-@@ -25,19 +25,6 @@ import sysconfig;
- print(sysconfig.get_config_var('CFLAGS'), end = '')"
-     OUTPUT_VARIABLE PY_C_CONFIG)
- 
--execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "
--from __future__ import print_function;
--import sysconfig;
--print(sysconfig.get_config_var('SHLIBS'), end = '')"
--    OUTPUT_VARIABLE PY_LD_CONFIG)
--
--
--execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "
--from __future__ import print_function;
--import sysconfig;
--print(sysconfig.get_config_var('LINKFORSHARED'), end = '')"
--    OUTPUT_VARIABLE PY_LINKFORSHARED_CONFIG)
--
- if(DEFINED ENV{PYCRYPTOSAT_INSTALL_PATH})
-     set(PY_INSTALL_PREFIX "--prefix=$ENV{PYCRYPTOSAT_INSTALL_PATH}")
- elseif(DEFINED ENV{VIRTUAL_ENV})
-@@ -47,12 +34,8 @@ else()
- endif()
- 
- string(REPLACE "\n" " " PY_C_CONFIG ${PY_C_CONFIG})
--string(REPLACE "\n" " " PY_LD_CONFIG ${PY_LD_CONFIG})
--string(REPLACE "\n" " " PY_LINKFORSHARED_CONFIG ${PY_LINKFORSHARED_CONFIG})
- 
- message(STATUS "Python CFLAGS:  '${PY_C_CONFIG}'")
--message(STATUS "Python LDFLAGS: '${PY_LD_CONFIG}'")
--message(STATUS "Python LINKFORSHARED flags: '${PY_LINKFORSHARED_CONFIG}'")
- message(STATUS "Python module installation prefix: ${PY_INSTALL_PREFIX}")
- 
- set(PY_LD_CONFIG "${PY_LD_CONFIG} ${PY_LINKFORSHARED_CONFIG}")
diff --git a/build/pkgs/cryptominisat/spkg-install.in b/build/pkgs/cryptominisat/spkg-install.in
deleted file mode 100644
index edcbcf4f0b2..00000000000
--- a/build/pkgs/cryptominisat/spkg-install.in
+++ /dev/null
@@ -1,5 +0,0 @@
-cd src
-
-sdh_cmake -DUSE_GAUSS='ON' -DENABLE_PYTHON_INTERFACE=OFF $EXTRA_OPTS
-sdh_make VERBOSE=ON
-sdh_make_install VERBOSE=ON
diff --git a/build/pkgs/cryptominisat/type b/build/pkgs/cryptominisat/type
deleted file mode 100644
index 134d9bc32d5..00000000000
--- a/build/pkgs/cryptominisat/type
+++ /dev/null
@@ -1 +0,0 @@
-optional
diff --git a/build/pkgs/pycryptosat/SPKG.rst b/build/pkgs/pycryptosat/SPKG.rst
index a0b0ef6a510..c61a3a69bc3 100644
--- a/build/pkgs/pycryptosat/SPKG.rst
+++ b/build/pkgs/pycryptosat/SPKG.rst
@@ -4,8 +4,21 @@ pycryptosat: Python module of cryptominisat
 Description
 -----------
 
-   Build and install pycryptosat into appropriate venv.
-   See cryptominisat for more details.
+   Build and install pycryptosat (Python frontend to CryptoMiniSat, which will be built if needed too)
+   into appropriate venv.
+
+
+
+   CryptoMiniSat is a SAT solver that aims to become a premiere SAT solver
+   with all the features and speed of successful SAT solvers, such as MiniSat
+   and PrecoSat. The long-term goals of CryptoMiniSat are to be an efficient
+   sequential, parallel and distributed solver. There are solvers that are
+   good at one or the other, e.g. ManySat (parallel) or PSolver (distributed),
+   but we wish to excel at all.
+
+   CryptoMiniSat 2.5 won the SAT Race 2010 among 20 solvers submitted by researchers and industry.
+
+
 
 License
 -------
diff --git a/build/pkgs/pycryptosat/checksums.ini b/build/pkgs/pycryptosat/checksums.ini
deleted file mode 120000
index 93cecdab18f..00000000000
--- a/build/pkgs/pycryptosat/checksums.ini
+++ /dev/null
@@ -1 +0,0 @@
-../cryptominisat/checksums.ini
\ No newline at end of file
diff --git a/build/pkgs/pycryptosat/dependencies b/build/pkgs/pycryptosat/dependencies
index c51735427aa..58247760d8a 100644
--- a/build/pkgs/pycryptosat/dependencies
+++ b/build/pkgs/pycryptosat/dependencies
@@ -1,4 +1,4 @@
- m4ri zlib libpng cryptominisat | cmake boost_cropped $(PYTHON_TOOLCHAIN) $(PYTHON)
+ m4ri zlib libpng | cmake boost_cropped $(PYTHON_TOOLCHAIN) $(PYTHON)
 
 ----------
 All lines of this file are ignored except the first.
diff --git a/build/pkgs/pycryptosat/package-version.txt b/build/pkgs/pycryptosat/package-version.txt
deleted file mode 120000
index 1743d5359eb..00000000000
--- a/build/pkgs/pycryptosat/package-version.txt
+++ /dev/null
@@ -1 +0,0 @@
-../cryptominisat/package-version.txt
\ No newline at end of file
diff --git a/build/pkgs/pycryptosat/patches b/build/pkgs/pycryptosat/patches
deleted file mode 120000
index a9b6b7c63e5..00000000000
--- a/build/pkgs/pycryptosat/patches
+++ /dev/null
@@ -1 +0,0 @@
-../cryptominisat/patches
\ No newline at end of file
diff --git a/build/pkgs/pycryptosat/spkg-install.in b/build/pkgs/pycryptosat/spkg-install.in
deleted file mode 100644
index b218fe1a924..00000000000
--- a/build/pkgs/pycryptosat/spkg-install.in
+++ /dev/null
@@ -1,9 +0,0 @@
-cd src
-
-sdh_cmake -DUSE_GAUSS='ON' $EXTRA_OPTS
-
-cd pycryptosat
-
-export CFLAGS="$CFLAGS -std=gnu++11"
-
-sdh_pip_install .
diff --git a/build/pkgs/pycryptosat/version_requirements.txt b/build/pkgs/pycryptosat/version_requirements.txt
deleted file mode 100644
index a6b5d27edc4..00000000000
--- a/build/pkgs/pycryptosat/version_requirements.txt
+++ /dev/null
@@ -1 +0,0 @@
-pycryptosat

From 6692a941c603eb03d3df1278d5c40cf56be9aeee Mon Sep 17 00:00:00 2001
From: Dima Pasechnik <dima@pasechnik.info>
Date: Wed, 17 Apr 2024 11:04:25 +0100
Subject: [PATCH 27/51] correct spkg name

---
 src/sage/sat/solvers/cryptominisat.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sage/sat/solvers/cryptominisat.py b/src/sage/sat/solvers/cryptominisat.py
index 82f1ffd9086..0a968dbde65 100644
--- a/src/sage/sat/solvers/cryptominisat.py
+++ b/src/sage/sat/solvers/cryptominisat.py
@@ -26,7 +26,7 @@
 from sage.misc.lazy_import import lazy_import
 from sage.features import PythonModule
 lazy_import('pycryptosat', ['Solver'],
-            feature=PythonModule('pycryptosat', spkg='cryptominisat'))
+            feature=PythonModule('pycryptosat', spkg='pycryptosat'))
 
 
 class CryptoMiniSat(SatSolver):

From 8f2a0a00c91b7a43bc62005c845e70f5deb7dfd1 Mon Sep 17 00:00:00 2001
From: Dima Pasechnik <dima@pasechnik.info>
Date: Thu, 18 Apr 2024 08:34:22 +0100
Subject: [PATCH 28/51] added the elusive requirements.txt

---
 build/pkgs/pycryptosat/requirements.txt | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 build/pkgs/pycryptosat/requirements.txt

diff --git a/build/pkgs/pycryptosat/requirements.txt b/build/pkgs/pycryptosat/requirements.txt
new file mode 100644
index 00000000000..a6b5d27edc4
--- /dev/null
+++ b/build/pkgs/pycryptosat/requirements.txt
@@ -0,0 +1 @@
+pycryptosat

From b5ae24b8213519e78ca767b855effbdce48b7ba2 Mon Sep 17 00:00:00 2001
From: Dima Pasechnik <dima@pasechnik.info>
Date: Thu, 18 Apr 2024 08:50:18 +0100
Subject: [PATCH 29/51] remove/update outdated comments

---
 src/sage/sat/solvers/cryptominisat.py | 2 --
 src/sage/sat/solvers/satsolver.pyx    | 2 +-
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/sage/sat/solvers/cryptominisat.py b/src/sage/sat/solvers/cryptominisat.py
index 0a968dbde65..27955c43eef 100644
--- a/src/sage/sat/solvers/cryptominisat.py
+++ b/src/sage/sat/solvers/cryptominisat.py
@@ -3,8 +3,6 @@
 
 This solver relies on Python bindings provided by upstream cryptominisat.
 
-The ``cryptominisat`` package should be installed on your Sage installation.
-
 AUTHORS:
 
 - Thierry Monteil (2017): complete rewrite, using upstream Python bindings,
diff --git a/src/sage/sat/solvers/satsolver.pyx b/src/sage/sat/solvers/satsolver.pyx
index 2f9ed49bcc0..7b63a1ee87d 100644
--- a/src/sage/sat/solvers/satsolver.pyx
+++ b/src/sage/sat/solvers/satsolver.pyx
@@ -322,7 +322,7 @@ def SAT(solver=None, *args, **kwds):
 
     - ``solver`` (string) -- select a solver. Admissible values are:
 
-        - ``"cryptominisat"`` -- note that the cryptominisat package must be
+        - ``"cryptominisat"`` -- note that the pycryptosat package must be
           installed.
 
         - ``"picosat"`` -- note that the pycosat package must be installed.

From a21881a20e39020c2a2524f5dd21602608ba9de7 Mon Sep 17 00:00:00 2001
From: Dima Pasechnik <dima@pasechnik.info>
Date: Sat, 20 Apr 2024 16:25:16 +0100
Subject: [PATCH 30/51] Update SPKG.rst

---
 build/pkgs/pycryptosat/SPKG.rst | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/build/pkgs/pycryptosat/SPKG.rst b/build/pkgs/pycryptosat/SPKG.rst
index c61a3a69bc3..d09e5b7f6cb 100644
--- a/build/pkgs/pycryptosat/SPKG.rst
+++ b/build/pkgs/pycryptosat/SPKG.rst
@@ -4,19 +4,16 @@ pycryptosat: Python module of cryptominisat
 Description
 -----------
 
-   Build and install pycryptosat (Python frontend to CryptoMiniSat, which will be built if needed too)
-   into appropriate venv.
+Build and install pycryptosat (Python frontend to CryptoMiniSat, which will be built if needed too).
 
+CryptoMiniSat is a SAT solver that aims to become a premiere SAT solver
+with all the features and speed of successful SAT solvers, such as MiniSat
+and PrecoSat. The long-term goals of CryptoMiniSat are to be an efficient
+sequential, parallel and distributed solver. There are solvers that are
+good at one or the other, e.g. ManySat (parallel) or PSolver (distributed),
+but we wish to excel at all.
 
-
-   CryptoMiniSat is a SAT solver that aims to become a premiere SAT solver
-   with all the features and speed of successful SAT solvers, such as MiniSat
-   and PrecoSat. The long-term goals of CryptoMiniSat are to be an efficient
-   sequential, parallel and distributed solver. There are solvers that are
-   good at one or the other, e.g. ManySat (parallel) or PSolver (distributed),
-   but we wish to excel at all.
-
-   CryptoMiniSat 2.5 won the SAT Race 2010 among 20 solvers submitted by researchers and industry.
+CryptoMiniSat 2.5 won the SAT Race 2010 among 20 solvers submitted by researchers and industry.
 
 
 

From 601631c6b564ea046845fefcd2fc1d12a36b8123 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 4 Jun 2024 18:24:17 -0700
Subject: [PATCH 31/51] build/pkgs/cryptominisat: Remove leftover file

---
 build/pkgs/cryptominisat/math | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 build/pkgs/cryptominisat/math

diff --git a/build/pkgs/cryptominisat/math b/build/pkgs/cryptominisat/math
deleted file mode 100644
index e69de29bb2d..00000000000

From 41b88e19f4a203c36558b85eadc6dfc0eaa0bf88 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 16 Apr 2024 18:52:21 -0700
Subject: [PATCH 32/51] build/pkgs/igraph: Update to 0.10.11

---
 build/pkgs/igraph/checksums.ini       | 5 +++--
 build/pkgs/igraph/package-version.txt | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/build/pkgs/igraph/checksums.ini b/build/pkgs/igraph/checksums.ini
index 6d63bbce214..1f4fc517e29 100644
--- a/build/pkgs/igraph/checksums.ini
+++ b/build/pkgs/igraph/checksums.ini
@@ -1,4 +1,5 @@
 tarball=igraph-VERSION.tar.gz
-sha1=40efbd2adf3c1cc0a2bb3e14f4c7898d053f1fe4
-sha256=ac5fa94ae6fd1eace651e4b235e99c056479a5c5d0d641aed30240ac33b19403
+sha1=ca6752410ad8593b60de2fb6e1e2644ba009e62a
+md5=024e65e7e4c32949f71f1469b57bbff7
+cksum=773092395
 upstream_url=https://github.com/igraph/igraph/releases/download/VERSION/igraph-VERSION.tar.gz
diff --git a/build/pkgs/igraph/package-version.txt b/build/pkgs/igraph/package-version.txt
index 1a46c7f13e7..223df198464 100644
--- a/build/pkgs/igraph/package-version.txt
+++ b/build/pkgs/igraph/package-version.txt
@@ -1 +1 @@
-0.10.8
+0.10.11

From 2299e0624db940c1a6fca7d08ea087332409cd14 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 16 Apr 2024 19:02:55 -0700
Subject: [PATCH 33/51] build/pkgs/python_igraph/spkg-install.in: We can pass
 another --config-settings now, as we have setuptools>=64 with
 https://github.com/pypa/setuptools/issues/3380

---
 build/pkgs/python_igraph/spkg-install.in | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/build/pkgs/python_igraph/spkg-install.in b/build/pkgs/python_igraph/spkg-install.in
index bafbbda375e..ea42c2d9241 100644
--- a/build/pkgs/python_igraph/spkg-install.in
+++ b/build/pkgs/python_igraph/spkg-install.in
@@ -2,9 +2,4 @@ cd src
 # Use --use-pep517 because https://github.com/igraph/python-igraph as of 0.9.11 does not have pyproject.toml
 # and so "pip wheel" would use a legacy build method, ignoring --config-settings.
 #
-# TODO: With setuptools 63.2.0, passing another --config-settings "--global-option=--no-wait" (not really needed)
-# kills the "--global-option=--use-pkg-config".
-# https://github.com/pypa/setuptools/issues/3380 makes changes to this, so we can revisit this after
-# the next setuptools upgrade.
-#
-sdh_pip_install --use-pep517 --config-settings "--global-option=--use-pkg-config"  .
+sdh_pip_install --use-pep517 --config-settings "--global-option=--use-pkg-config" --config-settings "--global-option=--no-wait" .

From 0a9bf9fc82bf82a0010210580e62dae7c258f9b7 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 16 Apr 2024 19:03:44 -0700
Subject: [PATCH 34/51] build/pkgs/python_igraph/spkg-install.in: No more need
 to use --use-pep-517 explicitly

---
 build/pkgs/python_igraph/spkg-install.in | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/build/pkgs/python_igraph/spkg-install.in b/build/pkgs/python_igraph/spkg-install.in
index ea42c2d9241..07408c34b0d 100644
--- a/build/pkgs/python_igraph/spkg-install.in
+++ b/build/pkgs/python_igraph/spkg-install.in
@@ -1,5 +1,2 @@
 cd src
-# Use --use-pep517 because https://github.com/igraph/python-igraph as of 0.9.11 does not have pyproject.toml
-# and so "pip wheel" would use a legacy build method, ignoring --config-settings.
-#
-sdh_pip_install --use-pep517 --config-settings "--global-option=--use-pkg-config" --config-settings "--global-option=--no-wait" .
+sdh_pip_install --config-settings "--global-option=--use-pkg-config" --config-settings "--global-option=--no-wait" .

From 176cbaf81759e6db4b57a325ff85a5f280b2c4e1 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 16 Apr 2024 19:17:10 -0700
Subject: [PATCH 35/51] build/pkgs/igraph/spkg-check.in: Fix

---
 build/pkgs/igraph/spkg-check.in | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/build/pkgs/igraph/spkg-check.in b/build/pkgs/igraph/spkg-check.in
index 27cd9419538..29b0a04f2cc 100644
--- a/build/pkgs/igraph/spkg-check.in
+++ b/build/pkgs/igraph/spkg-check.in
@@ -1,2 +1,3 @@
 cd src
-$MAKE check
+cd build
+sdh_make_check

From 8010f7f5ef0fc56ddb7173795d4bdf01f06bdd1d Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Wed, 17 Apr 2024 12:29:50 -0700
Subject: [PATCH 36/51] build/pkgs/igraph/spkg-configure.m4: Accept system
 igraph 0.10.11

---
 build/pkgs/igraph/spkg-configure.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/pkgs/igraph/spkg-configure.m4 b/build/pkgs/igraph/spkg-configure.m4
index 5133fce98da..22823f5ae8d 100644
--- a/build/pkgs/igraph/spkg-configure.m4
+++ b/build/pkgs/igraph/spkg-configure.m4
@@ -3,7 +3,7 @@ SAGE_SPKG_CONFIGURE([igraph], [
     dnl check for igraph with pkg-config
     dnl Per upstream in https://github.com/sagemath/sage/pull/36750#issuecomment-1826998762:
     dnl each python-igraph release is only guaranteed to be compatible with the same C/igraph that it bundles
-    PKG_CHECK_MODULES([IGRAPH], [igraph >= 0.10.8 igraph < 0.10.9], [], [
+    PKG_CHECK_MODULES([IGRAPH], [igraph >= 0.10.8 igraph < 0.10.12], [], [
         sage_spkg_install_igraph=yes])
   ])
 ])

From 645757c9af8ccda1fcd4412dc00770a81cd10a03 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Wed, 17 Apr 2024 17:47:40 -0700
Subject: [PATCH 37/51] build/pkgs/python_igraph: Update to 0.11.4

---
 build/pkgs/python_igraph/checksums.ini       | 5 +++--
 build/pkgs/python_igraph/package-version.txt | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/build/pkgs/python_igraph/checksums.ini b/build/pkgs/python_igraph/checksums.ini
index ecdc7ea2dfe..2e820f171fd 100644
--- a/build/pkgs/python_igraph/checksums.ini
+++ b/build/pkgs/python_igraph/checksums.ini
@@ -1,4 +1,5 @@
 tarball=python-igraph-VERSION.tar.gz
-sha1=ef7ee85cb1bc83109c744d5dd6bbe5e37598ce3f
-sha256=e55df60f882a51b8e8c1c5e7e940c5f90685d75634ea6df63bebcc983397adfa
+sha1=ab9e19b43b598b15c8cd671f73efa0bbce98395f
+md5=909d1b330e317d5b8cc9ac37096c94c1
+cksum=1231908814
 upstream_url=https://pypi.io/packages/source/i/igraph/igraph-VERSION.tar.gz
diff --git a/build/pkgs/python_igraph/package-version.txt b/build/pkgs/python_igraph/package-version.txt
index 1a96df19c09..35ad34429be 100644
--- a/build/pkgs/python_igraph/package-version.txt
+++ b/build/pkgs/python_igraph/package-version.txt
@@ -1 +1 @@
-0.11.3
+0.11.4

From bd02730f7b9bc6168e0c3a5462adcf4091905ebf Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 4 Jun 2024 19:02:00 -0700
Subject: [PATCH 38/51] build/pkgs/igraph: Update to 0.10.12

---
 build/pkgs/igraph/checksums.ini       | 5 ++---
 build/pkgs/igraph/package-version.txt | 2 +-
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/build/pkgs/igraph/checksums.ini b/build/pkgs/igraph/checksums.ini
index 1f4fc517e29..62eafa1aec9 100644
--- a/build/pkgs/igraph/checksums.ini
+++ b/build/pkgs/igraph/checksums.ini
@@ -1,5 +1,4 @@
 tarball=igraph-VERSION.tar.gz
-sha1=ca6752410ad8593b60de2fb6e1e2644ba009e62a
-md5=024e65e7e4c32949f71f1469b57bbff7
-cksum=773092395
+sha1=3789f61beac1f1231f8c3832102dcb2720f2a0c9
+sha256=b011f7f9f38a3e59924cc9ff652e6d33105fa03fcaf3792f47d752626a0a4625
 upstream_url=https://github.com/igraph/igraph/releases/download/VERSION/igraph-VERSION.tar.gz
diff --git a/build/pkgs/igraph/package-version.txt b/build/pkgs/igraph/package-version.txt
index 223df198464..70016a7c6ad 100644
--- a/build/pkgs/igraph/package-version.txt
+++ b/build/pkgs/igraph/package-version.txt
@@ -1 +1 @@
-0.10.11
+0.10.12

From 735a90e29fad0a969cb8deea9db44e2a0c2fe6d5 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 4 Jun 2024 19:02:28 -0700
Subject: [PATCH 39/51] build/pkgs/python_igraph: Update to 0.11.5

---
 build/pkgs/python_igraph/checksums.ini       | 5 ++---
 build/pkgs/python_igraph/package-version.txt | 2 +-
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/build/pkgs/python_igraph/checksums.ini b/build/pkgs/python_igraph/checksums.ini
index 2e820f171fd..d7247b21a30 100644
--- a/build/pkgs/python_igraph/checksums.ini
+++ b/build/pkgs/python_igraph/checksums.ini
@@ -1,5 +1,4 @@
 tarball=python-igraph-VERSION.tar.gz
-sha1=ab9e19b43b598b15c8cd671f73efa0bbce98395f
-md5=909d1b330e317d5b8cc9ac37096c94c1
-cksum=1231908814
+sha1=da963213ab22c60938d4e77ffab811875ee43a8a
+sha256=2d71d645a4c3344c5910543fabbae10d3163f46a3e824ba7753c14b9036b8233
 upstream_url=https://pypi.io/packages/source/i/igraph/igraph-VERSION.tar.gz
diff --git a/build/pkgs/python_igraph/package-version.txt b/build/pkgs/python_igraph/package-version.txt
index 35ad34429be..62d5dbdf3c7 100644
--- a/build/pkgs/python_igraph/package-version.txt
+++ b/build/pkgs/python_igraph/package-version.txt
@@ -1 +1 @@
-0.11.4
+0.11.5

From 254adacea70cbebc1540302cd4c1dc041b0edd9a Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 4 Jun 2024 19:04:14 -0700
Subject: [PATCH 40/51] build/pkgs/igraph/spkg-configure.m4: Only accept igraph
 0.10.12

---
 build/pkgs/igraph/spkg-configure.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/pkgs/igraph/spkg-configure.m4 b/build/pkgs/igraph/spkg-configure.m4
index 22823f5ae8d..0072f6ea6bc 100644
--- a/build/pkgs/igraph/spkg-configure.m4
+++ b/build/pkgs/igraph/spkg-configure.m4
@@ -3,7 +3,7 @@ SAGE_SPKG_CONFIGURE([igraph], [
     dnl check for igraph with pkg-config
     dnl Per upstream in https://github.com/sagemath/sage/pull/36750#issuecomment-1826998762:
     dnl each python-igraph release is only guaranteed to be compatible with the same C/igraph that it bundles
-    PKG_CHECK_MODULES([IGRAPH], [igraph >= 0.10.8 igraph < 0.10.12], [], [
+    PKG_CHECK_MODULES([IGRAPH], [igraph >= 0.10.12 igraph < 0.10.13], [], [
         sage_spkg_install_igraph=yes])
   ])
 ])

From e7d34311fed20ff320f77002103649570b091a87 Mon Sep 17 00:00:00 2001
From: Travis Scrimshaw <tcscrims@gmail.com>
Date: Tue, 9 Apr 2024 10:57:53 +0900
Subject: [PATCH 41/51] Implementation of faithful repr of a Lie algebra in
 char p > 0.

---
 .../algebras/lie_algebras/representation.py   | 239 ++++++++++++++++++
 ...ite_dimensional_lie_algebras_with_basis.py |  17 +-
 2 files changed, 252 insertions(+), 4 deletions(-)

diff --git a/src/sage/algebras/lie_algebras/representation.py b/src/sage/algebras/lie_algebras/representation.py
index b283bf3e694..069eecef004 100644
--- a/src/sage/algebras/lie_algebras/representation.py
+++ b/src/sage/algebras/lie_algebras/representation.py
@@ -788,3 +788,242 @@ def _acted_upon_(self, scalar, self_on_left=False):
                 return P._project(P._to_pbw(scalar) * self._lift_pbw())
 
             return super()._acted_upon_(scalar, self_on_left)
+
+
+class FaithfulRepresentationPBWPosChar(CombinatorialFreeModule, Representation_abstract):
+    r"""
+    A faithful representation of a finite dimensional Lie algebra
+    in positive characteristic.
+
+    .. WARNING::
+
+        This is often a very large dimensional representation relative
+        to the dimension of the Lie algebra.
+
+    ALGORITHM:
+
+    We implement the algorithm given in [deG2000] Section 6.6. Let `L`
+    be a finite dimensional Lie algebra over a ring of characteristic `p`
+    with basis `(b_1, \ldots, b_n)`. We compute (monic) `p`-polynomials
+    `f_i` such that `A = \mathrm{ad}(b_i)` solves `f_i(A) = 0` by using
+    minimal polynomial of `A`. The `(f_1, \ldots, f_n)` is a Gröbner basis
+    for an ideal `I` of the universal enveloping algebra `U(L)` such that
+    the quotient `U(L) / I` is a faithful representation of `L`.
+
+    EXAMPLES::
+
+        sage: sl2 = LieAlgebra(GF(3), cartan_type=['A',1])
+        sage: F = sl2.faithful_representation()
+        sage: F
+        Faithful representation with p-multiplicies (1, 3, 1) of Lie algebra
+         of ['A', 1] in the Chevalley basis
+        sage: F.dimension()
+        243
+    """
+    def __init__(self, L):
+        r"""
+        Initialize ``self``.
+
+        EXAMPLES::
+
+            sage: sl2 = LieAlgebra(GF(3), cartan_type=['A',1])
+            sage: F = sl2.faithful_representation()
+            sage: TestSuite(F).run()
+        """
+        R = L.base_ring()
+        self._p = R.characteristic()
+        if self._p == 0:
+            raise ValueError("the Lie algebra must be over a ring of positive characteristic")
+
+        self._pbw = L.pbw_basis()
+        self._key_order = tuple(self._pbw.algebra_generators().keys())
+
+        # calculate the Gröbner basis and p-exponents
+        gb = []
+        p_exp = []
+        B = L.basis()
+        for k in self._key_order:
+            b = B[k]
+            ad = b.adjoint_matrix()
+            g = ad.minpoly()
+            d = g.degree()
+            # TODO: Use the sparse polynomial ring?
+            x = g.parent().gen()
+            r = [x**(self._p**i) % g for i in range(d+1)]
+            deg = max(ri.degree() for ri in r)
+            mat = matrix(R, [[ri[j] for ri in r] for j in range(deg+1)])
+            la = mat.right_kernel_matrix()[0]
+            if la:
+                mongen = self._pbw._indices.monoid_generators()[k]
+                gb.append(self._pbw._from_dict({mongen ** (self._p ** i): val
+                                                for i, val in enumerate(la) if val},
+                                               remove_zeros=False))
+                p_exp.append(max(la.support()))
+
+        self._groebner_basis = gb
+        self._p_exp = tuple(p_exp)
+        self._degrees = [self._p ** m for m in self._p_exp]
+
+        from sage.groups.abelian_gps.abelian_group import AbelianGroup
+        indices = AbelianGroup(self._degrees)
+
+        Representation_abstract.__init__(self, L)
+        CombinatorialFreeModule.__init__(self, R, indices, prefix='', bracket=False)
+
+    def _repr_(self):
+        r"""
+        Return a string representation of ``self``.
+
+        EXAMPLES::
+
+            sage: sl3 = LieAlgebra(GF(3), cartan_type=['A',2])
+            sage: sl3.faithful_representation()
+            Faithful representation with p-multiplicies (1, 1, 1, 3, 3, 1, 1, 1)
+             of Lie algebra of ['A', 2] in the Chevalley basis
+        """
+        return "Faithful representation with p-multiplicies {} of {}".format(self.p_exponents(), self._lie_algebra)
+
+    def _latex_(self):
+        r"""
+        Return a string representation of ``self``.
+
+        EXAMPLES::
+
+            sage: sl2 = LieAlgebra(GF(3), cartan_type=['A',1])
+            sage: latex(sl2.faithful_representation())
+            U(\mathfrak{g}(A_{1})_{\Bold{F}_{3}}) / \langle PBW_{\alpha_{1}}^{3},
+             2 PBW_{\alpha^\vee_{1}}^{27} + PBW_{\alpha^\vee_{1}},
+             PBW_{-\alpha_{1}}^{3} \rangle
+        """
+        from sage.misc.latex import latex
+        g = latex(self._lie_algebra)
+        data = ', '.join(latex(f) for f in self._groebner_basis)
+        return "U({}) / \\langle {} \\rangle".format(g, data)
+
+    @cached_method
+    def p_exponents(self):
+        """
+        Return the `p`-exponents of ``self``.
+
+        Let `p` be the characteristic of the base ring of ``self`.
+        The `p`-*exponents* are the exponents `m_i` such that the `i`-th
+        `p`-polynomial `f_i` is of degree `p^{m_i}`.
+
+        EXAMPLES::
+
+            sage: sp4 = LieAlgebra(GF(3), cartan_type=['C',2])
+            sage: F = sp4.faithful_representation()
+            sage: F.p_exponents()
+            (1, 1, 1, 1, 3, 3, 1, 1, 1, 1)
+        """
+        return self._p_exp
+
+    def groebner_basis(self):
+        """
+        Return the defining Gröbner basis of ``self``.
+
+        EXAMPLES::
+
+            sage: sp4 = LieAlgebra(GF(3), cartan_type=['C',2])
+            sage: F = sp4.faithful_representation()
+            sage: F.groebner_basis()
+            [PBW[alpha[2]]^3,
+             PBW[alpha[1]]^3,
+             PBW[alpha[1] + alpha[2]]^3,
+             PBW[2*alpha[1] + alpha[2]]^3,
+             2*PBW[alphacheck[1]]^27 + PBW[alphacheck[1]],
+             2*PBW[alphacheck[2]]^27 + PBW[alphacheck[2]],
+             PBW[-alpha[2]]^3,
+             PBW[-alpha[1]]^3,
+             PBW[-alpha[1] - alpha[2]]^3,
+             PBW[-2*alpha[1] - alpha[2]]^3]
+        """
+        return self._groebner_basis
+
+    def _project(self, x):
+        r"""
+        The projection to ``self`` from the PBW basis.
+
+        EXAMPLES::
+
+            sage: sl2 = LieAlgebra(GF(3), cartan_type=['A',1])
+            sage: F = sl2.faithful_representation()
+            sage: PBW = F._pbw
+            sage: elt = PBW.an_element(); elt
+            PBW[alpha[1]]^2*PBW[alphacheck[1]]^2*PBW[-alpha[1]]^3
+             + 2*PBW[alpha[1]] + 1
+            sage: F._project(elt)
+            1 + 2*f0
+            sage: F._project(elt^2)
+            1 + f0 + f0^2
+            sage: F._project(elt^3)
+            1
+
+            sage: elt = PBW(sum(sl2.basis())); elt
+            PBW[alpha[1]] + PBW[alphacheck[1]] + PBW[-alpha[1]]
+            sage: F._project(elt)
+            f2 + f1 + f0
+            sage: F._project(elt^2)
+            2*f2 + f2^2 + 2*f1 + 2*f1*f2 + f1^2 + 2*f0 + 2*f0*f2 + 2*f0*f1 + f0^2
+            sage: F._project(elt^3)
+            2*f2 + f1 + f1^3 + 2*f0
+            sage: F._project(elt^4)
+            f2 + 2*f2^2 + f1 + f1^2 + f1^3*f2 + f1^4 + f0 + f0*f2 + f0*f1^3 + 2*f0^2
+        """
+        reduction = True
+        while reduction:
+            reduction = False
+            mc = x._monomial_coefficients
+            for m, c in mc.items():
+                d = m.dict()
+                for k, e, g in zip(self._key_order, self._degrees, self._groebner_basis):
+                    if k not in d:
+                        continue
+                    if d[k] >= e:
+                        d[k] -= e
+                        x -= self._pbw.monomial(self._pbw._indices(d)) * g
+                        reduction = True
+                        break
+        data = {}
+        for m, c in x._monomial_coefficients.items():
+            d = m.dict()
+            data[self._indices([d.get(k, 0) for k in self._key_order])] = c
+        return self.element_class(self, data)
+
+    class Element(CombinatorialFreeModule.Element):
+        def _acted_upon_(self, scalar, self_on_left=False):
+            r"""
+            Return the action of ``scalar`` on ``self``.
+
+            EXAMPLES::
+
+                sage: sl2 = LieAlgebra(GF(3), cartan_type=['A',1])
+                sage: F = sl2.faithful_representation()
+                sage: v = F.an_element(); v
+                1 + 2*f2 + f0*f1*f2
+                sage: sl2.an_element() * v
+                f2 + 2*f2^2 + f1 + 2*f1*f2 + 2*f1^2*f2 + f0 + 2*f0*f2 + 2*f0*f2^2
+                 + 2*f0*f1*f2 + f0*f1*f2^2 + f0*f1^2*f2 + f0^2*f1*f2
+                sage: sl2.pbw_basis().an_element() * v
+                1 + 2*f2 + 2*f0 + f0*f2 + f0*f1*f2 + 2*f0^2*f1*f2
+                sage: 5 * v
+                2 + f2 + 2*f0*f1*f2
+                sage: v * 5
+                2 + f2 + 2*f0*f1*f2
+                sage: v._acted_upon_(sl2.an_element(), True) is None
+                True
+            """
+            P = self.parent()
+            if scalar in P._lie_algebra or scalar in P._pbw:
+                if self_on_left:
+                    return None
+                if not self:  # we are (already) the zero vector
+                    return self
+                scalar = P._pbw(scalar)
+                monoid = P._pbw._indices
+                I = P._key_order
+                lift = P._pbw.element_class(P._pbw, {monoid(list(zip(I, m.exponents()))): coeff
+                                                     for m, coeff in self._monomial_coefficients.items()})
+                return P._project(scalar * lift)
+
+            return super()._acted_upon_(scalar, self_on_left)
diff --git a/src/sage/categories/finite_dimensional_lie_algebras_with_basis.py b/src/sage/categories/finite_dimensional_lie_algebras_with_basis.py
index 4477401a909..7e66c6f6f4e 100644
--- a/src/sage/categories/finite_dimensional_lie_algebras_with_basis.py
+++ b/src/sage/categories/finite_dimensional_lie_algebras_with_basis.py
@@ -2139,7 +2139,7 @@ def faithful_representation(self, algorithm=None):
             - ``algorithm`` -- one of the following depending on the
               classification of the Lie algebra:
 
-              Nilpotent Lie algebras:
+              Nilpotent:
 
               * ``'regular'`` -- use the universal enveloping algebra quotient
                 :class:`~sage.algebras.lie_algebras.representation.FaithfulRepresentationNilpotentPBW`
@@ -2147,7 +2147,7 @@ def faithful_representation(self, algorithm=None):
                 precise details, see the documentation of
                 :class:`~sage.algebras.lie_algebras.representation.FaithfulRepresentationNilpotentPBW`)
 
-              Solvable but not nilpotent:
+              Solvable:
 
               * Not implemented
 
@@ -2157,7 +2157,13 @@ def faithful_representation(self, algorithm=None):
 
               General case
 
-              * Not implemented
+              * ``'generic'`` -- generic algortihm (only implemented currently
+                for positive characteristic)
+
+            Note that the algorithm for any more generic cases can be used
+            in the specialized cases. For instance, using ``'generic'`` for
+            any Lie algebra (e.g., even if nilpotent) will use the generic
+            implementation.
 
             EXAMPLES::
 
@@ -2207,7 +2213,10 @@ def faithful_representation(self, algorithm=None):
                 if algorithm == "minimal":
                     from sage.algebras.lie_algebras.representation import FaithfulRepresentationNilpotentPBW
                     return FaithfulRepresentationNilpotentPBW(self, minimal=True)
-            else:
+            if algorithm is None or algorithm == "generic":
+                if self.base_ring().characteristic() > 0:
+                    from sage.algebras.lie_algebras.representation import FaithfulRepresentationPBWPosChar
+                    return FaithfulRepresentationPBWPosChar(self)
                 raise NotImplementedError("only implemented for nilpotent Lie algebras")
             raise ValueError("invalid algorithm '{}'".format(algorithm))
 

From 67637264db0cca4f346b80984a74f0d755c1b371 Mon Sep 17 00:00:00 2001
From: Travis Scrimshaw <tcscrims@gmail.com>
Date: Thu, 11 Apr 2024 14:39:41 +0900
Subject: [PATCH 42/51] Fixing lint/doc issue.

---
 src/sage/algebras/lie_algebras/representation.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/sage/algebras/lie_algebras/representation.py b/src/sage/algebras/lie_algebras/representation.py
index 069eecef004..e6494806d26 100644
--- a/src/sage/algebras/lie_algebras/representation.py
+++ b/src/sage/algebras/lie_algebras/representation.py
@@ -905,7 +905,7 @@ def p_exponents(self):
         """
         Return the `p`-exponents of ``self``.
 
-        Let `p` be the characteristic of the base ring of ``self`.
+        Let `p` be the characteristic of the base ring of ``self``.
         The `p`-*exponents* are the exponents `m_i` such that the `i`-th
         `p`-polynomial `f_i` is of degree `p^{m_i}`.
 

From 6149b978a57f7b51ca7ba2fe4c62501d1903792d Mon Sep 17 00:00:00 2001
From: Travis Scrimshaw <tcscrims@gmail.com>
Date: Tue, 4 Jun 2024 16:13:48 +0900
Subject: [PATCH 43/51] Implementing reviewer changes.

---
 src/sage/algebras/lie_algebras/representation.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/sage/algebras/lie_algebras/representation.py b/src/sage/algebras/lie_algebras/representation.py
index e6494806d26..6594c9d1148 100644
--- a/src/sage/algebras/lie_algebras/representation.py
+++ b/src/sage/algebras/lie_algebras/representation.py
@@ -805,17 +805,18 @@ class FaithfulRepresentationPBWPosChar(CombinatorialFreeModule, Representation_a
     We implement the algorithm given in [deG2000] Section 6.6. Let `L`
     be a finite dimensional Lie algebra over a ring of characteristic `p`
     with basis `(b_1, \ldots, b_n)`. We compute (monic) `p`-polynomials
-    `f_i` such that `A = \mathrm{ad}(b_i)` solves `f_i(A) = 0` by using
-    minimal polynomial of `A`. The `(f_1, \ldots, f_n)` is a Gröbner basis
-    for an ideal `I` of the universal enveloping algebra `U(L)` such that
-    the quotient `U(L) / I` is a faithful representation of `L`.
+    `f_i` such that `A = \mathrm{ad}(b_i)` (the adjoint action of `b_i`)
+    solves `f_i(A) = 0` by using minimal polynomial of `A`. The
+    `(f_1, \ldots, f_n)` is a Gröbner basis for an ideal `I` of the
+    universal enveloping algebra `U(L)` such that the quotient `U(L) / I`
+    is a faithful representation of `L`.
 
     EXAMPLES::
 
         sage: sl2 = LieAlgebra(GF(3), cartan_type=['A',1])
         sage: F = sl2.faithful_representation()
         sage: F
-        Faithful representation with p-multiplicies (1, 3, 1) of Lie algebra
+        Faithful representation with p-multiplicities (1, 3, 1) of Lie algebra
          of ['A', 1] in the Chevalley basis
         sage: F.dimension()
         243
@@ -878,10 +879,10 @@ def _repr_(self):
 
             sage: sl3 = LieAlgebra(GF(3), cartan_type=['A',2])
             sage: sl3.faithful_representation()
-            Faithful representation with p-multiplicies (1, 1, 1, 3, 3, 1, 1, 1)
+            Faithful representation with p-multiplicities (1, 1, 1, 3, 3, 1, 1, 1)
              of Lie algebra of ['A', 2] in the Chevalley basis
         """
-        return "Faithful representation with p-multiplicies {} of {}".format(self.p_exponents(), self._lie_algebra)
+        return "Faithful representation with p-multiplicities {} of {}".format(self.p_exponents(), self._lie_algebra)
 
     def _latex_(self):
         r"""

From 46d125c080f36fddac064b0689193c324927aa71 Mon Sep 17 00:00:00 2001
From: Travis Scrimshaw <tcscrims@gmail.com>
Date: Wed, 5 Jun 2024 11:16:23 +0900
Subject: [PATCH 44/51] Adding back in import that was there in previous
 version.

---
 src/sage/algebras/lie_algebras/representation.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/sage/algebras/lie_algebras/representation.py b/src/sage/algebras/lie_algebras/representation.py
index 6594c9d1148..bedcb869867 100644
--- a/src/sage/algebras/lie_algebras/representation.py
+++ b/src/sage/algebras/lie_algebras/representation.py
@@ -16,6 +16,7 @@
 #                  https://www.gnu.org/licenses/
 # ****************************************************************************
 
+from sage.misc.cachefunc import cached_method
 from sage.sets.family import Family, AbstractFamily
 from sage.matrix.constructor import matrix
 from sage.combinat.free_module import CombinatorialFreeModule

From 57260136c4f655c85ba6027fe5a966da4a6821b7 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 4 Jun 2024 22:17:00 -0700
Subject: [PATCH 45/51] .github/workflows/*build*.yml: Survive GHA cache upload
 timeouts

---
 .github/workflows/build.yml         | 17 ++++++++++++++---
 .github/workflows/doc-build-pdf.yml |  6 ++++++
 .github/workflows/doc-build.yml     |  5 +++++
 3 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 605707ffd9e..c7200f847d8 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -198,7 +198,9 @@ jobs:
             TARGETS=${{ steps.build-targets.outputs.build_targets }}
 
       - name: Start container
-        if: steps.changed-files.outputs.doctests_all_changed_files
+        id: container
+        # Try to continue when "exporting to GitHub Actions Cache" failed with timeout
+        if: (success() || failure()) && steps.changed-files.outputs.doctests_all_changed_files
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -208,7 +210,7 @@ jobs:
       # Testing
 
       - name: Check that all modules can be imported
-        if: steps.changed-files.outputs.doctests_all_changed_files
+        if: (success() || failure()) && steps.container.outcome == 'success' && steps.changed-files.outputs.doctests_all_changed_files
         run: |
           # Increase the length of the lines in the "short summary"
           export COLUMNS=120
@@ -220,7 +222,7 @@ jobs:
         shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
 
       - name: Test changed files (sage -t --new)
-        if: steps.changed-files.outputs.doctests_all_changed_files
+        if: (success() || failure()) && steps.container.outcome == 'success' && steps.changed-files.outputs.doctests_all_changed_files
         run: |
           export MAKE="make -j2 --output-sync=recurse" SAGE_NUM_THREADS=4
           # https://github.com/tj-actions/changed-files?tab=readme-ov-file#outputs-
@@ -305,6 +307,8 @@ jobs:
             TARGETS=${{ needs.test-new.outputs.build_targets }}
 
       - name: Start container
+        id: container
+        if: (success() || failure())
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -314,6 +318,7 @@ jobs:
       # Testing
 
       - name: Test modularized distributions
+        if: (success() || failure()) && steps.container.outcome == 'success'
         run: |
           export MAKE="make -j2 --output-sync=recurse" SAGE_NUM_THREADS=4
           make V=0 tox-ensure && make ${{ matrix.targets }}
@@ -401,6 +406,7 @@ jobs:
 
       - name: Start container
         id: container
+        if: (success() || failure())
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -410,6 +416,7 @@ jobs:
       # Testing
 
       - name: Test all files (sage -t --long ${{ matrix.tests }})
+        if: (success() || failure()) && steps.container.outcome == 'success'
         run: |
           mkdir .coverage
           rm -rf /sage/.coverage
@@ -513,6 +520,7 @@ jobs:
 
       - name: Start container
         id: container
+        if: (success() || failure())
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -526,8 +534,10 @@ jobs:
         with:
           path: .coverage
           pattern: coverage-*
+        if: (success() || failure()) && steps.container.outcome == 'success'
 
       - name: Coverage report
+        if: (success() || failure()) && steps.container.outcome == 'success'
         # Using --omit to avoid "CoverageWarning: Couldn't parse '/tmp/tmp06qizzie/tmp_ldpu46ob.py': No source for code"
         run: |
           rm -rf /sage/.coverage
@@ -541,6 +551,7 @@ jobs:
         shell: sh .ci/docker-exec-script.sh BUILD . {0}
 
       - name: Upload coverage to codecov
+        if: (success() || failure()) && steps.container.outcome == 'success'
         uses: codecov/codecov-action@v4
         with:
           directory: .coverage/coverage-report
diff --git a/.github/workflows/doc-build-pdf.yml b/.github/workflows/doc-build-pdf.yml
index d4cc6ebc6ca..2eac8e17ffc 100644
--- a/.github/workflows/doc-build-pdf.yml
+++ b/.github/workflows/doc-build-pdf.yml
@@ -101,6 +101,9 @@ jobs:
             TARGETS=ci-build-with-fallback
 
       - name: Start container
+        id: container
+        # Try to continue when "exporting to GitHub Actions Cache" failed with timeout
+        if: (success() || failure())
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -110,6 +113,8 @@ jobs:
       # Docs
 
       - name: Update system packages
+        id: packages
+        if: (success() || failure()) && steps.container.outcome == 'success'
         run: |
           export PATH="build/bin:$PATH"
           eval $(sage-print-system-package-command auto update)
@@ -119,6 +124,7 @@ jobs:
 
       - name: Build docs (PDF)
         id: docbuild
+        if: (success() || failure()) && steps.packages.outcome == 'success'
         run: |
           export MAKE="make -j5 --output-sync=recurse" SAGE_NUM_THREADS=5
           make doc-clean doc-uninstall; make sagemath_doc_html-build-deps sagemath_doc_pdf-no-deps
diff --git a/.github/workflows/doc-build.yml b/.github/workflows/doc-build.yml
index 4d0420874b8..f47dac38d57 100644
--- a/.github/workflows/doc-build.yml
+++ b/.github/workflows/doc-build.yml
@@ -105,6 +105,9 @@ jobs:
             TARGETS=ci-build-with-fallback
 
       - name: Start container
+        id: container
+        # Try to continue when "exporting to GitHub Actions Cache" failed with timeout
+        if: (success() || failure())
         run: |
           docker run --name BUILD -dit \
                      --mount type=bind,src=$(pwd),dst=$(pwd) \
@@ -115,6 +118,7 @@ jobs:
 
       - name: Store old docs
         id: worktree
+        if: (success() || failure()) && steps.container.outcome == 'success'
         run: |
           git config --global --add safe.directory $(pwd)
           git config --global user.email "ci-sage@example.com"
@@ -140,6 +144,7 @@ jobs:
 
       - name: Build docs
         id: docbuild
+        if: (success() || failure()) && steps.worktree.outcome == 'success'
         # Always non-incremental because of the concern that
         # incremental docbuild may introduce broken links (inter-file references) though build succeeds
         run: |

From 6d3a2336c39f088c43da6718f342f8fd66436c48 Mon Sep 17 00:00:00 2001
From: Giacomo Pope <44242839+GiacomoPope@users.noreply.github.com>
Date: Wed, 5 Jun 2024 14:58:43 +0100
Subject: [PATCH 46/51] Apply suggestions from code review

Add reviewer suggestions

Co-authored-by: grhkm21 <83517584+grhkm21@users.noreply.github.com>
---
 src/sage/matrix/matrix_mod2_dense.pyx | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/sage/matrix/matrix_mod2_dense.pyx b/src/sage/matrix/matrix_mod2_dense.pyx
index 14eb6f02539..5eb71dc252a 100644
--- a/src/sage/matrix/matrix_mod2_dense.pyx
+++ b/src/sage/matrix/matrix_mod2_dense.pyx
@@ -532,7 +532,7 @@ cdef class Matrix_mod2_dense(matrix_dense.Matrix_dense):   # dense or sparse
 
         INPUT:
 
-        - ``copy`` - (default: True) if True, return a copy so you can
+        - ``copy`` -- (default: ``True``) if True, return a copy so you can
           modify it safely
 
         EXAMPLES:
@@ -542,7 +542,6 @@ cdef class Matrix_mod2_dense(matrix_dense.Matrix_dense):   # dense or sparse
             sage: M2 = Matrix(GF(2), [[1, 0, 0], [0, 1, 0], [0, 1, 1]])
             sage: M2.columns()
             [(1, 0, 0), (0, 1, 1), (0, 0, 1)]
-
         """
         x = self.fetch('columns')
         if x is not None:
@@ -564,8 +563,7 @@ cdef class Matrix_mod2_dense(matrix_dense.Matrix_dense):   # dense or sparse
         self.cache('columns', C)
         if copy:
             return list(C)
-        else:
-            return C
+        return C
 
     ########################################################################
     # LEVEL 2 functionality

From 2693e1cd3964b9084fb02545869bf3b46fe50dfb Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Tue, 4 Jun 2024 19:34:03 -0700
Subject: [PATCH 47/51] build/bin/sage-dist-helpers (sdh_pip_install): Pass
 config-settings which begin with a hyphen correctly

---
 build/bin/sage-dist-helpers | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/build/bin/sage-dist-helpers b/build/bin/sage-dist-helpers
index d7ef0a81a8b..d55ac539837 100644
--- a/build/bin/sage-dist-helpers
+++ b/build/bin/sage-dist-helpers
@@ -247,9 +247,10 @@ sdh_pip_install() {
                 install_options="$install_options $1"
                 ;;
             -C|--config-settings)
-                build_options="$build_options --config-setting"
                 shift
-                build_options="$build_options $1"
+                # Per 'python -m build --help', options which begin with a hyphen
+                # must be in the form of "--config-setting=--opt(=value)" or "-C--opt(=value)"
+                build_options="$build_options --config-setting=$1"
                 ;;
             *)
                 break

From 0996d9509ae27a2526625b68edb9f49789d5749e Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Wed, 5 Jun 2024 10:29:41 -0700
Subject: [PATCH 48/51] build/pkgs/cmake/spkg-configure.m4: Require at least
 3.18 (for igraph)

---
 build/pkgs/cmake/spkg-configure.m4 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/build/pkgs/cmake/spkg-configure.m4 b/build/pkgs/cmake/spkg-configure.m4
index 4210442c44c..6149f49a7c5 100644
--- a/build/pkgs/cmake/spkg-configure.m4
+++ b/build/pkgs/cmake/spkg-configure.m4
@@ -1,5 +1,5 @@
 SAGE_SPKG_CONFIGURE([cmake], [dnl
-        AC_CACHE_CHECK([for cmake >= 3.11], [ac_cv_path_CMAKE], [dnl
+        AC_CACHE_CHECK([for cmake >= 3.18], [ac_cv_path_CMAKE], [dnl
         dnl Do not accept cmake installed via https://pypi.org/project/cmake/
         dnl in the default user scheme; it will not work in our venv because
         dnl we set PYTHONUSERBASE in sage-env.
@@ -8,7 +8,7 @@ SAGE_SPKG_CONFIGURE([cmake], [dnl
                 cmake_version=`$ac_path_CMAKE --version 2>&1 \
                     | $SED -n -e 's/cmake version *\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\)/\1/p'`
                 AS_IF([test -n "$cmake_version"], [dnl
-                    AX_COMPARE_VERSION([$cmake_version], [ge], [3.11], [dnl
+                    AX_COMPARE_VERSION([$cmake_version], [ge], [3.18], [dnl
                         ac_cv_path_CMAKE="$ac_path_CMAKE"
                         ac_path_CMAKE_found=:
                     ])

From 9cf43cf3fb6fdfa839b62df2c9f6e202a9be2227 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Chapoton?= <chapoton@unistra.fr>
Date: Wed, 5 Jun 2024 20:59:40 +0200
Subject: [PATCH 49/51] just a few details in permutation.py

---
 src/sage/combinat/permutation.py | 145 ++++++++++++++++---------------
 1 file changed, 73 insertions(+), 72 deletions(-)

diff --git a/src/sage/combinat/permutation.py b/src/sage/combinat/permutation.py
index b4e93a80b60..79e68a0a8bf 100644
--- a/src/sage/combinat/permutation.py
+++ b/src/sage/combinat/permutation.py
@@ -463,17 +463,17 @@ def __classcall_private__(cls, l, check=True):
 
         # if l is a pair of standard tableaux or a pair of lists
         elif isinstance(l, (tuple, list)) and len(l) == 2 and \
-            all(isinstance(x, Tableau) for x in l):
+                all(isinstance(x, Tableau) for x in l):
             return RSK_inverse(*l, output='permutation')
         elif isinstance(l, (tuple, list)) and len(l) == 2 and \
-            all(isinstance(x, list) for x in l):
-            P,Q = (Tableau(_) for _ in l)
+                all(isinstance(x, list) for x in l):
+            P, Q = (Tableau(_) for _ in l)
             return RSK_inverse(P, Q, 'permutation')
         # if it's a tuple or nonempty list of tuples, also assume cycle
         # notation
         elif isinstance(l, tuple) or \
              (isinstance(l, list) and l and
-             all(isinstance(x, tuple) for x in l)):
+              all(isinstance(x, tuple) for x in l)):
             if l and (isinstance(l[0], (int, Integer)) or len(l[0]) > 0):
                 if isinstance(l[0], tuple):
                     n = max(max(x) for x in l)
@@ -683,8 +683,8 @@ def _latex_(self):
             return " ".join(f"{let}_{{{i}}}" for i in redword)
         if display == "twoline":
             return r"\begin{{pmatrix}} {} \\ {} \end{{pmatrix}}".format(
-                    " & ".join("%s" % i for i in range(1, len(self._list)+1)),
-                    " & ".join("%s" % i for i in self._list))
+                " & ".join("%s" % i for i in range(1, len(self._list)+1)),
+                " & ".join("%s" % i for i in self._list))
         if display == "list":
             return repr(self._list)
         if display == "cycle":
@@ -1068,20 +1068,20 @@ def _to_cycles_set(self, singletons=True):
 
         if not singletons:
             # remove the fixed points
-            L = {i+1 for i,pi in enumerate(p) if pi != i+1}
+            L = {i for i, pi in enumerate(p, start=1) if pi != i}
         else:
-            L = set(range(1,len(p)+1))
+            L = set(range(1, len(p) + 1))
 
         # Go through until we've considered every remaining number
         while L:
             # take the first remaining element
             cycleFirst = L.pop()
-            next = p[cycleFirst-1]
+            next = p[cycleFirst - 1]
             cycle = [cycleFirst]
             while next != cycleFirst:
                 cycle.append(next)
                 L.remove(next)
-                next = p[next-1]
+                next = p[next - 1]
             # add the cycle
             cycles.append(tuple(cycle))
 
@@ -1109,7 +1109,7 @@ def _to_cycles_list(self, singletons=True):
 
         if not singletons:
             # remove the fixed points
-            L = [i + 1 for i, pi in enumerate(p) if pi != i + 1]
+            L = [i for i, pi in enumerate(p, start=1) if pi != i]
         else:
             L = list(range(1, len(p) + 1))
 
@@ -1125,7 +1125,7 @@ def _to_cycles_list(self, singletons=True):
                 cycle.append(next)
                 # remove next from L
                 # we use a binary search to find it
-                L.pop(bisect_left(L,next))
+                L.pop(bisect_left(L, next))
                 next = p[next-1]
             # add the cycle
             cycles.append(tuple(cycle))
@@ -1164,7 +1164,7 @@ def signature(self) -> Integer:
             sage: Permutation([]).sign()
             1
         """
-        return (-1)**(len(self)-len(self.to_cycles()))
+        return (-1)**(len(self) - len(self.to_cycles()))
 
     # one can also use sign as an alias for signature
     sign = signature
@@ -1592,7 +1592,7 @@ def merge_and_countv(ivA_A, ivB_B):
             else:
                 C.extend(B[j:])
                 ivC.extend(ivB[j:])
-            return ivC,C
+            return ivC, C
 
         def base_case(L):
             s = sorted(L)
@@ -1628,7 +1628,7 @@ def inversions(self) -> list:
         """
         p = self[:]
         n = len(p)
-        return [(i+1,j+1) for i in range(n-1) for j in range(i+1,n)
+        return [(i+1, j+1) for i in range(n-1) for j in range(i+1, n)
                 if p[i] > p[j]]
 
     def stack_sort(self) -> Permutation:
@@ -1917,7 +1917,7 @@ def absolute_length(self) -> Integer:
         """
         return self.size() - len(self.cycle_type())
 
-    @combinatorial_map(order=2,name='inverse')
+    @combinatorial_map(order=2, name='inverse')
     def inverse(self) -> Permutation:
         r"""
         Return the inverse of ``self``.
@@ -1932,8 +1932,8 @@ def inverse(self) -> Permutation:
             [3, 1, 5, 2, 4]
         """
         w = list(range(len(self)))
-        for i, j in enumerate(self):
-            w[j - 1] = i + 1
+        for i, j in enumerate(self, start=1):
+            w[j - 1] = i
         return Permutations()(w)
 
     __invert__ = inverse
@@ -3081,7 +3081,6 @@ def number_of_fixed_points(self) -> Integer:
             sage: Permutation([1,2,3,4]).number_of_fixed_points()
             4
         """
-
         return len(self.fixed_points())
 
     def is_derangement(self) -> bool:
@@ -3778,7 +3777,7 @@ def weak_excedences(self) -> list:
             sage: Permutation([1,4,3,2,5]).weak_excedences()
             [1, 4, 3, 5]
         """
-        return [pi for i, pi in enumerate(self) if pi >= i + 1]
+        return [pi for i, pi in enumerate(self, start=1) if pi >= i]
 
     def bruhat_inversions(self) -> list:
         r"""
@@ -5370,7 +5369,7 @@ def shifted_shuffle(self, other):
             True
         """
         return self.shifted_concatenation(other, "right").\
-        right_permutohedron_interval(self.shifted_concatenation(other, "left"))
+            right_permutohedron_interval(self.shifted_concatenation(other, "left"))
 
     def nth_roots(self, n):
         r"""
@@ -5480,8 +5479,8 @@ def rewind(L, n):
                     b = True
                     poss = [P.identity()]
                     for pa in partition:
-                            poss = [p*q for p in poss
-                                    for q in merging_cycles([rewind(cycles[m][i-1], n//len(pa)) for i in pa])]
+                        poss = [p*q for p in poss
+                                for q in merging_cycles([rewind(cycles[m][i-1], n//len(pa)) for i in pa])]
                     possibilities[i] += poss
             if not b:
                 return
@@ -5613,6 +5612,7 @@ def number_of_nth_roots(self, n):
 
         return result
 
+
 def _tableau_contribution(T):
     r"""
     Get the number of SYT of shape(``T``).
@@ -5856,21 +5856,21 @@ def __classcall_private__(cls, n=None, k=None, **kwargs):
                         if len(a) == 1 and a[0] != 1:
                             a = a[0]
                         if a in StandardPermutations_all():
-                            if a == [1,2]:
+                            if a == [1, 2]:
                                 return StandardPermutations_avoiding_12(n)
-                            elif a == [2,1]:
+                            elif a == [2, 1]:
                                 return StandardPermutations_avoiding_21(n)
-                            elif a == [1,2,3]:
+                            elif a == [1, 2, 3]:
                                 return StandardPermutations_avoiding_123(n)
-                            elif a == [1,3,2]:
+                            elif a == [1, 3, 2]:
                                 return StandardPermutations_avoiding_132(n)
-                            elif a == [2,1,3]:
+                            elif a == [2, 1, 3]:
                                 return StandardPermutations_avoiding_213(n)
-                            elif a == [2,3,1]:
+                            elif a == [2, 3, 1]:
                                 return StandardPermutations_avoiding_231(n)
-                            elif a == [3,1,2]:
+                            elif a == [3, 1, 2]:
                                 return StandardPermutations_avoiding_312(n)
-                            elif a == [3,2,1]:
+                            elif a == [3, 2, 1]:
                                 return StandardPermutations_avoiding_321(n)
                             else:
                                 return StandardPermutations_avoiding_generic(n, (a,))
@@ -5970,36 +5970,36 @@ class options(GlobalOptions):
         NAME = 'Permutations'
         module = 'sage.combinat.permutation'
         display = {'default': "list",
-                     'description': "Specifies how the permutations should be printed",
-                     'values': {'list': "the permutations are displayed in list notation"
-                                      " (aka 1-line notation)",
-                                 'cycle': "the permutations are displayed in cycle notation"
-                                      " (i. e., as products of disjoint cycles)",
-                                 'singleton': "the permutations are displayed in cycle notation"
-                                           " with singleton cycles shown as well",
-                                 'reduced_word': "the permutations are displayed as reduced words"},
-                     'alias': {'word': "reduced_word", 'reduced_expression': "reduced_word"},
-                     'case_sensitive': False}
-        latex = {'default': "list",
-                   'description': "Specifies how the permutations should be latexed",
-                   'values': {'list': "latex as a list in one-line notation",
-                               'twoline': "latex in two-line notation",
-                               'cycle': "latex in cycle notation",
-                               'singleton': "latex in cycle notation with singleton cycles shown as well",
-                               'reduced_word': "latex as reduced words"},
-                   'alias': {'word': "reduced_word", 'reduced_expression': "reduced_word", 'oneline': "list"},
+                   'description': "Specifies how the permutations should be printed",
+                   'values': {'list': "the permutations are displayed in list notation"
+                              " (aka 1-line notation)",
+                            'cycle': "the permutations are displayed in cycle notation"
+                              " (i. e., as products of disjoint cycles)",
+                              'singleton': "the permutations are displayed in cycle notation"
+                              " with singleton cycles shown as well",
+                              'reduced_word': "the permutations are displayed as reduced words"},
+                   'alias': {'word': "reduced_word", 'reduced_expression': "reduced_word"},
                    'case_sensitive': False}
+        latex = {'default': "list",
+                 'description': "Specifies how the permutations should be latexed",
+                 'values': {'list': "latex as a list in one-line notation",
+                            'twoline': "latex in two-line notation",
+                            'cycle': "latex in cycle notation",
+                            'singleton': "latex in cycle notation with singleton cycles shown as well",
+                            'reduced_word': "latex as reduced words"},
+                 'alias': {'word': "reduced_word", 'reduced_expression': "reduced_word", 'oneline': "list"},
+                 'case_sensitive': False}
         latex_empty_str = {'default': "1",
-                             'description': 'The LaTeX representation of a reduced word when said word is empty',
-                             'checker': lambda char: isinstance(char,str)}
+                           'description': 'The LaTeX representation of a reduced word when said word is empty',
+                           'checker': lambda char: isinstance(char, str)}
         generator_name = {'default': "s",
-                            'description': "the letter used in latexing the reduced word",
-                            'checker': lambda char: isinstance(char,str)}
+                          'description': "the letter used in latexing the reduced word",
+                            'checker': lambda char: isinstance(char, str)}
         mult = {'default': "l2r",
-                  'description': "The multiplication of permutations",
-                  'values': {'l2r': r"left to right: `(p_1 \cdot p_2)(x) = p_2(p_1(x))`",
-                              'r2l': r"right to left: `(p_1 \cdot p_2)(x) = p_1(p_2(x))`"},
-                  'case_sensitive': False}
+                'description': "The multiplication of permutations",
+                'values': {'l2r': r"left to right: `(p_1 \cdot p_2)(x) = p_2(p_1(x))`",
+                           'r2l': r"right to left: `(p_1 \cdot p_2)(x) = p_1(p_2(x))`"},
+                'case_sensitive': False}
 
 
 class Permutations_nk(Permutations):
@@ -6082,7 +6082,8 @@ def __iter__(self) -> Iterator[Permutation]:
             sage: [p for p in Permutations(3,4)]
             []
         """
-        for x in itertools.permutations(range(1,self.n+1), int(self._k)):
+        for x in itertools.permutations(range(1, self.n + 1),
+                                        int(self._k)):
             yield self.element_class(self, x, check=False)
 
     def cardinality(self) -> Integer:
@@ -7751,8 +7752,8 @@ def inverse(self):
                 [4, 2, 1, 3]
             """
             w = list(range(len(self)))
-            for i, j in enumerate(self):
-                w[j - 1] = i + 1
+            for i, j in enumerate(self, start=1):
+                w[j - 1] = i
             return self.__class__(self.parent(), w)
 
         __invert__ = inverse
@@ -7868,8 +7869,8 @@ def from_rank(n, rank):
     """
     # Find the factoradic of rank
     factoradic = [None] * n
-    for j in range(1,n+1):
-        factoradic[n-j] = Integer(rank % j)
+    for j in range(1, n + 1):
+        factoradic[n - j] = Integer(rank % j)
         rank = int(rank) // j
 
     return from_lehmer_code(factoradic, Permutations(n))
@@ -7896,8 +7897,8 @@ def from_inversion_vector(iv, parent=None):
     """
     p = iv[:]
     open_spots = list(range(len(iv)))
-    for i, ivi in enumerate(iv):
-        p[open_spots.pop(ivi)] = i + 1
+    for i, ivi in enumerate(iv, start=1):
+        p[open_spots.pop(ivi)] = i
 
     if parent is None:
         parent = Permutations()
@@ -8182,16 +8183,16 @@ def bistochastic_as_sum_of_permutations(M, check=True):
 
     while G.size() > 0:
         matching = G.matching(use_edge_labels=True)
-        matching = [(min(u,v), max(u, v), w) for u,v,w in matching]
+        matching = [(min(u, v), max(u, v), w) for u, v, w in matching]
 
         # This minimum is strictly larger than 0
         minimum = min([x[2] for x in matching])
 
-        for (u,v,l) in matching:
+        for u, v, l in matching:
             if minimum == l:
-                G.delete_edge((u,v,l))
+                G.delete_edge((u, v, l))
             else:
-                G.set_edge_label(u,v,l-minimum)
+                G.set_edge_label(u, v, l - minimum)
 
         matching.sort(key=lambda x: x[0])
         value += minimum * CFM(P([x[1]-n+1 for x in matching]))
@@ -8481,9 +8482,9 @@ def descents_composition_last(dc):
             raise TypeError("The argument must be of type Composition")
     s = 0
     res = []
-    for i in reversed(range(len(dc))):
-        res = list(range(s+1,s+dc[i]+1)) + res
-        s += dc[i]
+    for dci in reversed(dc):
+        res = list(range(s + 1, s + dci + 1)) + res
+        s += dci
 
     return Permutations()(res)
 
@@ -8756,7 +8757,7 @@ def from_major_code(mc, final_descent=False):
     # the letter i into the word w^(i+1) in such a way that
     # maj(w^i)-maj(w^(i+1)) = mc[i]
 
-    for i in reversed(range(1,len(mc))):
+    for i in reversed(range(1, len(mc))):
         # Lemma 2.2 in Skandera
 
         # Get the descents of w and place them in reverse order

From 35587cb6d0753c9de2c94fdcc193a84944ee7d71 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Wed, 5 Jun 2024 22:03:13 -0700
Subject: [PATCH 50/51] build/pkgs/openssl: Update to 3.2.2

---
 build/pkgs/openssl/checksums.ini       | 4 ++--
 build/pkgs/openssl/package-version.txt | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/build/pkgs/openssl/checksums.ini b/build/pkgs/openssl/checksums.ini
index 6e2b7e18955..eac86dcdd87 100644
--- a/build/pkgs/openssl/checksums.ini
+++ b/build/pkgs/openssl/checksums.ini
@@ -1,4 +1,4 @@
 tarball=openssl-VERSION.tar.gz
-sha1=b48e20c07facfdf6da9ad43a6c5126d51897699b
-sha256=f93c9e8edde5e9166119de31755fc87b4aa34863662f67ddfcba14d0b6b69b61
+sha1=b12311372a0277ca0eb218a68a7fd9f5ce66d162
+sha256=197149c18d9e9f292c43f0400acaba12e5f52cacfe050f3d199277ea738ec2e7
 upstream_url=https://www.openssl.org/source/openssl-VERSION.tar.gz
diff --git a/build/pkgs/openssl/package-version.txt b/build/pkgs/openssl/package-version.txt
index f93fc9f42ea..be94e6f53db 100644
--- a/build/pkgs/openssl/package-version.txt
+++ b/build/pkgs/openssl/package-version.txt
@@ -1 +1 @@
-3.0.12
+3.2.2

From 31e216689afea5bc4e0daaee0122c546f42d1da5 Mon Sep 17 00:00:00 2001
From: Release Manager <release@sagemath.org>
Date: Sun, 9 Jun 2024 12:05:34 +0200
Subject: [PATCH 51/51] Updated SageMath version to 10.4.beta9

---
 CITATION.cff                                             | 4 ++--
 VERSION.txt                                              | 2 +-
 build/pkgs/configure/checksums.ini                       | 4 ++--
 build/pkgs/configure/package-version.txt                 | 2 +-
 build/pkgs/sage_conf/version_requirements.txt            | 2 +-
 build/pkgs/sage_docbuild/version_requirements.txt        | 2 +-
 build/pkgs/sage_setup/version_requirements.txt           | 2 +-
 build/pkgs/sage_sws2rst/version_requirements.txt         | 2 +-
 build/pkgs/sagelib/version_requirements.txt              | 2 +-
 build/pkgs/sagemath_bliss/version_requirements.txt       | 2 +-
 build/pkgs/sagemath_categories/version_requirements.txt  | 2 +-
 build/pkgs/sagemath_coxeter3/version_requirements.txt    | 2 +-
 build/pkgs/sagemath_environment/version_requirements.txt | 2 +-
 build/pkgs/sagemath_mcqd/version_requirements.txt        | 2 +-
 build/pkgs/sagemath_meataxe/version_requirements.txt     | 2 +-
 build/pkgs/sagemath_objects/version_requirements.txt     | 2 +-
 build/pkgs/sagemath_repl/version_requirements.txt        | 2 +-
 build/pkgs/sagemath_sirocco/version_requirements.txt     | 2 +-
 build/pkgs/sagemath_tdlib/version_requirements.txt       | 2 +-
 pkgs/sage-conf/VERSION.txt                               | 2 +-
 pkgs/sage-conf_conda/VERSION.txt                         | 2 +-
 pkgs/sage-conf_pypi/VERSION.txt                          | 2 +-
 pkgs/sage-docbuild/VERSION.txt                           | 2 +-
 pkgs/sage-setup/VERSION.txt                              | 2 +-
 pkgs/sage-sws2rst/VERSION.txt                            | 2 +-
 pkgs/sagemath-bliss/VERSION.txt                          | 2 +-
 pkgs/sagemath-categories/VERSION.txt                     | 2 +-
 pkgs/sagemath-coxeter3/VERSION.txt                       | 2 +-
 pkgs/sagemath-environment/VERSION.txt                    | 2 +-
 pkgs/sagemath-mcqd/VERSION.txt                           | 2 +-
 pkgs/sagemath-meataxe/VERSION.txt                        | 2 +-
 pkgs/sagemath-objects/VERSION.txt                        | 2 +-
 pkgs/sagemath-repl/VERSION.txt                           | 2 +-
 pkgs/sagemath-sirocco/VERSION.txt                        | 2 +-
 pkgs/sagemath-tdlib/VERSION.txt                          | 2 +-
 src/VERSION.txt                                          | 2 +-
 src/bin/sage-version.sh                                  | 6 +++---
 src/sage/version.py                                      | 7 +++----
 38 files changed, 44 insertions(+), 45 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 6a6902fc831..0d43a526e62 100644
--- 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: 10.4.beta8
+version: 10.4.beta9
 doi: 10.5281/zenodo.8042260
-date-released: 2024-06-01
+date-released: 2024-06-09
 repository-code: "https://github.com/sagemath/sage"
 url: "https://www.sagemath.org/"
diff --git a/VERSION.txt b/VERSION.txt
index 5d451269673..76bb72f1560 100644
--- a/VERSION.txt
+++ b/VERSION.txt
@@ -1 +1 @@
-SageMath version 10.4.beta8, Release Date: 2024-06-01
+SageMath version 10.4.beta9, Release Date: 2024-06-09
diff --git a/build/pkgs/configure/checksums.ini b/build/pkgs/configure/checksums.ini
index c85cd40f8b1..da9cfbb1ff9 100644
--- a/build/pkgs/configure/checksums.ini
+++ b/build/pkgs/configure/checksums.ini
@@ -1,3 +1,3 @@
 tarball=configure-VERSION.tar.gz
-sha1=350c449fd9df824dcb6a12b4a0cd50fca58df01b
-sha256=113e10f9ffbb9c4b9e372efd5de3321122472f5dfb4dafddda1fadd4f03caf6f
+sha1=f3e560bbf33add8504ba9f7ba93fff9e82e3e445
+sha256=bef93be1bb978fa34cd5aaa9c041d1a97a33ff35f88c9df2f9c25e6764770c56
diff --git a/build/pkgs/configure/package-version.txt b/build/pkgs/configure/package-version.txt
index 784c733b28c..ca5926f5634 100644
--- a/build/pkgs/configure/package-version.txt
+++ b/build/pkgs/configure/package-version.txt
@@ -1 +1 @@
-5d54f4073fe10ee7578952774c799363fda8939d
+5c12765f7e585b58ab0cd99f7998cfa615f85247
diff --git a/build/pkgs/sage_conf/version_requirements.txt b/build/pkgs/sage_conf/version_requirements.txt
index bc253d58444..bf5142c02e5 100644
--- 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 ~= 10.4b8
+sage-conf ~= 10.4b9
diff --git a/build/pkgs/sage_docbuild/version_requirements.txt b/build/pkgs/sage_docbuild/version_requirements.txt
index 88c4d5b252f..3bc4e773ff1 100644
--- 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 ~= 10.4b8
+sage-docbuild ~= 10.4b9
diff --git a/build/pkgs/sage_setup/version_requirements.txt b/build/pkgs/sage_setup/version_requirements.txt
index 8431cb882ad..d04bde41fdd 100644
--- 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 ~= 10.4b8
+sage-setup ~= 10.4b9
diff --git a/build/pkgs/sage_sws2rst/version_requirements.txt b/build/pkgs/sage_sws2rst/version_requirements.txt
index 45259114676..d3698b0a9ae 100644
--- 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 ~= 10.4b8
+sage-sws2rst ~= 10.4b9
diff --git a/build/pkgs/sagelib/version_requirements.txt b/build/pkgs/sagelib/version_requirements.txt
index fbefd68c27a..1dd1a4f846b 100644
--- 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 ~= 10.4b8
+sagemath-standard ~= 10.4b9
diff --git a/build/pkgs/sagemath_bliss/version_requirements.txt b/build/pkgs/sagemath_bliss/version_requirements.txt
index 9831109152b..bc95834828a 100644
--- 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 ~= 10.4b8
+sagemath-bliss ~= 10.4b9
diff --git a/build/pkgs/sagemath_categories/version_requirements.txt b/build/pkgs/sagemath_categories/version_requirements.txt
index e22c57defcd..08fa02e2044 100644
--- 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 ~= 10.4b8
+sagemath-categories ~= 10.4b9
diff --git a/build/pkgs/sagemath_coxeter3/version_requirements.txt b/build/pkgs/sagemath_coxeter3/version_requirements.txt
index a16d1a99bd4..13e0b652f36 100644
--- 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 ~= 10.4b8
+sagemath-coxeter3 ~= 10.4b9
diff --git a/build/pkgs/sagemath_environment/version_requirements.txt b/build/pkgs/sagemath_environment/version_requirements.txt
index c265b92492a..72433ad30cd 100644
--- 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 ~= 10.4b8
+sagemath-environment ~= 10.4b9
diff --git a/build/pkgs/sagemath_mcqd/version_requirements.txt b/build/pkgs/sagemath_mcqd/version_requirements.txt
index 026c86366d5..76e1fd5907c 100644
--- 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 ~= 10.4b8
+sagemath-mcqd ~= 10.4b9
diff --git a/build/pkgs/sagemath_meataxe/version_requirements.txt b/build/pkgs/sagemath_meataxe/version_requirements.txt
index d92e7b1741a..db6dcee5827 100644
--- 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 ~= 10.4b8
+sagemath-meataxe ~= 10.4b9
diff --git a/build/pkgs/sagemath_objects/version_requirements.txt b/build/pkgs/sagemath_objects/version_requirements.txt
index 22c106b51ab..a48fb049cb7 100644
--- 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 ~= 10.4b8
+sagemath-objects ~= 10.4b9
diff --git a/build/pkgs/sagemath_repl/version_requirements.txt b/build/pkgs/sagemath_repl/version_requirements.txt
index 60f6680492b..661b369f395 100644
--- 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 ~= 10.4b8
+sagemath-repl ~= 10.4b9
diff --git a/build/pkgs/sagemath_sirocco/version_requirements.txt b/build/pkgs/sagemath_sirocco/version_requirements.txt
index 4910ccf4f54..af89ffdd30f 100644
--- 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 ~= 10.4b8
+sagemath-sirocco ~= 10.4b9
diff --git a/build/pkgs/sagemath_tdlib/version_requirements.txt b/build/pkgs/sagemath_tdlib/version_requirements.txt
index 919126f9b00..13e940295b6 100644
--- 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 ~= 10.4b8
+sagemath-tdlib ~= 10.4b9
diff --git a/pkgs/sage-conf/VERSION.txt b/pkgs/sage-conf/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sage-conf/VERSION.txt
+++ b/pkgs/sage-conf/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sage-conf_conda/VERSION.txt b/pkgs/sage-conf_conda/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sage-conf_conda/VERSION.txt
+++ b/pkgs/sage-conf_conda/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sage-conf_pypi/VERSION.txt b/pkgs/sage-conf_pypi/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sage-conf_pypi/VERSION.txt
+++ b/pkgs/sage-conf_pypi/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sage-docbuild/VERSION.txt b/pkgs/sage-docbuild/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sage-docbuild/VERSION.txt
+++ b/pkgs/sage-docbuild/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sage-setup/VERSION.txt b/pkgs/sage-setup/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sage-setup/VERSION.txt
+++ b/pkgs/sage-setup/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sage-sws2rst/VERSION.txt b/pkgs/sage-sws2rst/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sage-sws2rst/VERSION.txt
+++ b/pkgs/sage-sws2rst/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sagemath-bliss/VERSION.txt b/pkgs/sagemath-bliss/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sagemath-bliss/VERSION.txt
+++ b/pkgs/sagemath-bliss/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sagemath-categories/VERSION.txt b/pkgs/sagemath-categories/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sagemath-categories/VERSION.txt
+++ b/pkgs/sagemath-categories/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sagemath-coxeter3/VERSION.txt b/pkgs/sagemath-coxeter3/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sagemath-coxeter3/VERSION.txt
+++ b/pkgs/sagemath-coxeter3/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sagemath-environment/VERSION.txt b/pkgs/sagemath-environment/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sagemath-environment/VERSION.txt
+++ b/pkgs/sagemath-environment/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sagemath-mcqd/VERSION.txt b/pkgs/sagemath-mcqd/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sagemath-mcqd/VERSION.txt
+++ b/pkgs/sagemath-mcqd/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sagemath-meataxe/VERSION.txt b/pkgs/sagemath-meataxe/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sagemath-meataxe/VERSION.txt
+++ b/pkgs/sagemath-meataxe/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sagemath-objects/VERSION.txt b/pkgs/sagemath-objects/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sagemath-objects/VERSION.txt
+++ b/pkgs/sagemath-objects/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sagemath-repl/VERSION.txt b/pkgs/sagemath-repl/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sagemath-repl/VERSION.txt
+++ b/pkgs/sagemath-repl/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sagemath-sirocco/VERSION.txt b/pkgs/sagemath-sirocco/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sagemath-sirocco/VERSION.txt
+++ b/pkgs/sagemath-sirocco/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/pkgs/sagemath-tdlib/VERSION.txt b/pkgs/sagemath-tdlib/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/pkgs/sagemath-tdlib/VERSION.txt
+++ b/pkgs/sagemath-tdlib/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/src/VERSION.txt b/src/VERSION.txt
index 3ed4d9d5bfe..88de6ab407c 100644
--- a/src/VERSION.txt
+++ b/src/VERSION.txt
@@ -1 +1 @@
-10.4.beta8
+10.4.beta9
diff --git a/src/bin/sage-version.sh b/src/bin/sage-version.sh
index 1cf2fdb230e..e07f9f4e32b 100644
--- 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='10.4.beta8'
-SAGE_RELEASE_DATE='2024-06-01'
-SAGE_VERSION_BANNER='SageMath version 10.4.beta8, Release Date: 2024-06-01'
+SAGE_VERSION='10.4.beta9'
+SAGE_RELEASE_DATE='2024-06-09'
+SAGE_VERSION_BANNER='SageMath version 10.4.beta9, Release Date: 2024-06-09'
diff --git a/src/sage/version.py b/src/sage/version.py
index 19902d4869d..7aa5469a8ce 100644
--- a/src/sage/version.py
+++ b/src/sage/version.py
@@ -1,6 +1,5 @@
-# sage_setup: distribution = sagemath-environment
 # Sage version information for Python scripts
 # This file is auto-generated by the sage-update-version script, do not edit!
-version = '10.4.beta8'
-date = '2024-06-01'
-banner = 'SageMath version 10.4.beta8, Release Date: 2024-06-01'
+version = '10.4.beta9'
+date = '2024-06-09'
+banner = 'SageMath version 10.4.beta9, Release Date: 2024-06-09'