Meta-ticket: make graphs compatible with Python 3

dcoudert commented 6 years ago

This ticket is used to keep track of the progress towards python3 in graphs.

Major issues

22349 Deprecate sorting of methods .vertices() and .edges()
direct comparison of vertex labels (e.g., in method iterator_edges of base/sparse_graph.pyx)
methods using matrices: adjacency_matrix, distance_matrix, etc. For all these methods, we can now give as input an ordering of the vertices (and edges) that will be used to order rows and columns. Currently, we use .vertices() and .edges() by default. If we switch to list(G) by default, we have to check that it's not breaking algorithms using these matrices.

Needs work:

22349 Deprecate sorting of Graph vertices and edges by default

Needs review:

27408 Edge view for graphs -- introduce deprecation warning for sort=None as the plan is to set sort=False by default.
27513 Allow custom order for edges as well as vertices for incidence matrix

Done

26274 avoid comparison of vertex labels in MIP - graph_coloring.py
26282 avoid comparison of vertex labels in MIP - graph.py
26284 avoid comparison of vertex labels in MIP - connectivity.pyx
26285 avoid comparison of vertex labels in MIP - generic_graph.py
26469 avoid sorting vertex labels in graph_plot.py
26478 clean graph_plot_js.py, graph_list.py and graph_input.py
26480 clean graph_latex.py
26484 clean graph_coloring.py and avoid comparison of vertex labels
26520 Meta-ticket for methods in src/sage/graphs/graph_decomposition/ - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834
26528 avoid using .vertices() in comparability, hyperbolicity and distances_all_pairs
26531 avoid using .vertices() in asteroidal_triples
26534 avoid using .vertices() in weakly_chordal.pyx
26554 improve the boost graph interface to avoid using .vertices()
26618 avoid using .vertices() in centrality.pyx
26621 avoid using .vertices() and .edges() in bliss.pyx
26622 avoid using .vertices() in convexity_properties.pyx
26624 clean generic_graph.py (part 1)
26627 clean generic_graph.py (part 2)
26630 clean generic_graph.py (part 3)
26633 clean generic_graph.py (part 4)
26634 clean generic_graph.py (part 5)
26637 clean generic_graph.py (part 6)
26658 clean generic_graph.py (part 7) - planarity
26663 clean generic_graph.py (part 8) - connectivity
26666 clean generic_graph.py (part 9) - edge and vertex handlers
26672 clean generic_graph.py (part 10) - degree
26675 clean generic_graph.py (part 11) - substructures
26678 clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
26679 clean generic_graph.py (part 13) - searches and constructors
26680 clean generic_graph.py (part 14) - visualization
26711 avoid .vertices() in graph_coloring.py
26712 avoid .vertices() in independent_sets.pyx
26757 py3: fixing round in graph_latex.py
26761 py3: fix BlanusaSecondSnarkGraph
26762 py3: fix HortonGraph generator
26763 py3: fix SzekeresSnarkGraph generator
26779 py3: fix graph_input.py and hypergraph_generators.py
26800 py3: bug with canonical_label fixed by #27695
26801 py3: change sorting of neighbors labels in static_sparse_graph.pyx
26812 py3: fix doctest in graph_generators.py
26846 for graph isomorphism
26851 py3: avoid .vertices() and .edges() in union of graphs
26869 py3: improve is_aperiodic to fix doctests (due to deprecation warning in networkx)
26870 py3: fix error with map in strongly_regular_db.pyx
26871 py3: fix doctests in digraph_generators.py
26940 stop sorting returned list of edges in spanning tree methods
26971 py3: some minor fix for traveling salesman
26973 py3: avoid .vertices() in graph_plot.py
27007 py3: avoid .vertices() in planarity.pyx
27008 py3: avoid .vertices() in method apex_vertices
27009 py3: avoid sorting vertices and edges in method treewidth
27010 py3: avoid .vertices() in methods _ford_fulkerson, edge_cut, bounded_outdegree_orientation and gomory_hu_tree
27029 Avoid calling .vertices() in graph_isom_equivalent_non_edge_labeled_graph()
27059 py3: improve doctests in spanning_tree.pyx
27123 bliss automorphism_group() shouldn't sort vertices
27125 py3: fix some doctests in graph.py
27127 py3: avoid .vertices() in method ear_decomposition
27129 py3: fix other doctests in graph.py
27137 pep8 in digraph_generators.py (part 4)
27138 pep8 in digraph_generators.py (part 5)
27144 py3: fix doctests in connectivity.pyx
27147 py3: fix doctests in dense_graph.pyx, sparse_graph.pyx, static_sparse_graph.pyx
27148 py3: fix doctests in centrality.pyx
27149 py3: fix doctests in comparability.pyx
27151 py3: fix doctests in vertex_separation.pyx
27158 py3: fix doctests in boost_graph.pyx
27159 py3: fix doctests in strongly_regular_db.pyx
27160 py3: fix doctests in hyperbolicity and graph_coloring
27165 py3: fix doctests in c_graph.pyx
27166 remove deprecated classes NetworkXGraphDeprecated and NetworkXDiGraphDeprecated
27167 py3: fix doctest in distances_all_pairs.pyx
27170 py3: fix 14 doctests in digraph.py
27176 py3: fix doctest in generic_graph (part 1)
27179 py3: fix doctest in generic_graph (part 2) -- cycle_basis
27180 py3: fix doctest in generic_graph (part 3) -- _build_flow_graph
27181 py3: fix doctest in generic_graph (part 4)
27183 py3: fix doctest in generic_graph (part 5)
27184 py3: fix doctests in generic_graph (part 6) -- graphviz_string
27202 py3: fix doctests in random graphs generators
27203 py3: fix 8 doctests in generators/families.py
27232 is_isomorphic broken with keyword edge_labels=True
27242 py3: strengthen a doctest in vertex_separation.pyx
27243 py3: fix doctests in generic_graph (part 7) -- relabel
27244 py3: fix doctests in generic_graph (part 8) -- coarsest_equitable_refinement
27245 py3: fix doctests in generic_graph (part 9) -- automorphism_group
27246 py3: fix doctests in generic_graph (part 10) -- is_isomorphic
27435 py3: failing doctest in graph_database.py with interactive_query
27571 some changes in automorphism_group and fix one doctest in MathonPseudocyclicStronglyRegularGraph
27628 py3: fix doctest with igraph
27695 try to sort vertices to produce consistent graph6 and dig6 strings in Python3
27811 fix doctest with igraph
27948 py3: fix doctests with optional package plantri
28108 py3: ValueError in graph_generators doctests with plantri optional package (follow up of #27948)
28371 py3: errors with optional package CSDP

Optional packages:

With #27628, #27811, #27948, #28108 and #28371 all failing doctests of the optional packages used in the graph module are fixed: benzene, bliss, buckygen, csdp, dot2tex and graphviz, gap_packages, igraph and python_igraph, mcqd, plantri, tdlib

CC: @tscrim @fchapoton @jhpalmieri @jfraymond

Component: graph theory

Author: David Coudert

Reviewer: John Palmieri

Issue created by migration from https://trac.sagemath.org/ticket/26640

dcoudert commented 6 years ago

Description changed:

--- 
+++ 
@@ -7,6 +7,7 @@

 **Done**
+- #26618 avoid using `.vertices()` in `centrality.pyx`
 - #26621 avoid using `.vertices()` and `.edges()` in `bliss.pyx`

dcoudert commented 6 years ago

Description changed:

--- 
+++ 
@@ -4,9 +4,11 @@
 **Major issues**
 - methods `.vertices()` and `.edges()` use sort by default
 - direct comparison of vertex labels (e.g., in method `iterator_edges` of `base/sparse_graph.pyx`)
-
+- all `min_spanning_tree` methods sort edges before returning the result

 **Done**
+- #26469 avoid sorting vertex labels in `graph_plot.py` 
+- #26531 avoid using `.vertices()` in asteroidal_triples
 - #26618 avoid using `.vertices()` in `centrality.pyx`
 - #26621 avoid using `.vertices()` and `.edges()` in `bliss.pyx`

dcoudert commented 5 years ago

comment:4

I'm answering here the question of #26567#comment:9 about how to make iterator_edges of sparse_graph.pyx py3 compatible, and if something similar to #26567 for dense_graph.pyx can be done for sparse_graph.pyx.

So far, I don't know what's the best option.

just stop ordering end vertices of edges as well as vertices in general, but it shall break many algorithms
change the way we use graphs to ensure that internally vertices are all integers, and then use method get_vertex_label (that we already have but rarely use) only when the user wants to display lists of vertices/edges. I think networkx is now doing something like that.
try to mimic the py2 sorting using try... except statements, but this might induce some slowdown.
maintain an ordering of the vertices and a mapping from vertices to integers used when sorting list of vertices and the end vertices of edges. This ordering could be updated at vertex insertion/deletion time.

All these options have pros and cons, and each of them will require a significant amount of work to fix doctests and algorithms.

In the last months, we did significant progresses on reducing the dependency on ordering, but this is not enough and this central issue is very complex to fix. Which is the best option in the short/long term ?

fchapoton commented 5 years ago

Description changed:

--- 
+++ 
@@ -12,4 +12,13 @@
 - #26618 avoid using `.vertices()` in `centrality.pyx`
 - #26621 avoid using `.vertices()` and `.edges()` in `bliss.pyx`

+**Needs review**:

+- #26520   clean graph decompositions
+- #26633   clean generic_graph.py (part 4) 
+- #26634   clean generic_graph.py (part 5)
+- #26663   clean generic_graph.py (part 8) - connectivity  
+- #26675   clean generic_graph.py (part 11) - substructures
+- #26678   clean generic_graph.py (part 12) - centrality and distances
+- #26679   clean generic_graph.py (part 13) - searches and constructors
+- #26680   clean generic_graph.py (part 14) - visualization

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -6,19 +6,44 @@
 - direct comparison of vertex labels (e.g., in method `iterator_edges` of `base/sparse_graph.pyx`)
 - all `min_spanning_tree` methods sort edges before returning the result

-**Done**
-- #26469 avoid sorting vertex labels in `graph_plot.py` 
-- #26531 avoid using `.vertices()` in asteroidal_triples
-- #26618 avoid using `.vertices()` in `centrality.pyx`
-- #26621 avoid using `.vertices()` and `.edges()` in `bliss.pyx`
+
+**Needs work**:
+- #26800   py3: bug with canonical_label
+

 **Needs review**:
-
 - #26520   clean graph decompositions
-- #26633   clean generic_graph.py (part 4) 
 - #26634   clean generic_graph.py (part 5)
 - #26663   clean generic_graph.py (part 8) - connectivity  
 - #26675   clean generic_graph.py (part 11) - substructures
 - #26678   clean generic_graph.py (part 12) - centrality and distances
 - #26679   clean generic_graph.py (part 13) - searches and constructors
+- #26779   py3: fix `graph_input.py` and `hypergraph_generators.py`
+- #26812   py3: fix doctest in `graph_generators.py`
+
+
+**Done**
+- #26274   avoid comparison of vertex labels in MIP - graph_coloring.py
+- #26282   avoid comparison of vertex labels in MIP - graph.py
+- #26284   avoid comparison of vertex labels in MIP - connectivity.pyx
+- #26285   avoid comparison of vertex labels in MIP - generic_graph.py
+- #26469   avoid sorting vertex labels in `graph_plot.py`
+- #26484   clean graph_coloring.py and avoid comparison of vertex labels
+- #26528   avoid using `.vertices()` in comparability, hyperbolicity and distances_all_pairs
+- #26531   avoid using `.vertices()` in asteroidal_triples
+- #26534   avoid using `.vertices()` in weakly_chordal.pyx
+- #26554   improve the boost graph interface to avoid using `.vertices()` 
+- #26618   avoid using `.vertices()` in `centrality.pyx`
+- #26621   avoid using `.vertices()` and `.edges()` in `bliss.pyx`
+- #26622   avoid using `.vertices()` in convexity_properties.pyx
+- #26633   clean generic_graph.py (part 4) 
 - #26680   clean generic_graph.py (part 14) - visualization
+- #26711   avoid `.vertices()` in graph_coloring.py
+- #26712   avoid `.vertices()` in independent_sets.pyx
+- #26757   py3: fixing round in graph_latex.py
+- #26761   py3: fix `BlanusaSecondSnarkGraph`
+- #26762   py3: fix `HortonGraph` generator
+- #26763   py3: fix `SzekeresSnarkGraph` generator
+- #26801   py3: change sorting of neighbors labels in `static_sparse_graph.pyx`
+
+

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -16,7 +16,7 @@
 - #26634   clean generic_graph.py (part 5)
 - #26663   clean generic_graph.py (part 8) - connectivity  
 - #26675   clean generic_graph.py (part 11) - substructures
-- #26678   clean generic_graph.py (part 12) - centrality and distances
+- #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
 - #26779   py3: fix `graph_input.py` and `hypergraph_generators.py`
 - #26812   py3: fix doctest in `graph_generators.py`

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -12,7 +12,7 @@

 **Needs review**:
-- #26520   clean graph decompositions
+- #26520   Meta-ticket for methods in `src/sage/graphs/graph_decomposition/` - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834
 - #26634   clean generic_graph.py (part 5)
 - #26663   clean generic_graph.py (part 8) - connectivity  
 - #26675   clean generic_graph.py (part 11) - substructures

fchapoton commented 5 years ago

comment:9

May I ask in which ticket, if any, you do touch the "is_isomorphic" method ?

I would really like this to work with python 3:

sage: G = Graph()
sage: G.add_edge((1,'a'))
sage: G
Graph on 2 vertices
sage: G.is_isomorphic(G)

dcoudert commented 5 years ago

comment:10

I have not touched any method related to isomorphism. I have only opened a ticket to show a bug with canonical_label #26800.

fchapoton commented 5 years ago

comment:11

ok.. Then either we wait for all these tickets to be closed (and this may take a lot of time) or we can try to fix this isomorphism problem now..

dcoudert commented 5 years ago

comment:12

We can start working on it. In the worst case, I will have to fix some merge conflicts.

fchapoton commented 5 years ago

comment:13

I have made a first tentative at u/chapoton/graphe_iso

dcoudert commented 5 years ago

comment:14

I'm not good enough with git to know what you have changed, except the first 2 calls to .vertices(). It seems ok. Note that the function has 2 more calls to .vertices() that are clearly useless. I think the proposed change fix some doctests, so you should open a ticket.

fchapoton commented 5 years ago

comment:15

I made #26846 for graph isomorphism

fchapoton commented 5 years ago

Description changed:

--- 
+++ 
@@ -20,7 +20,7 @@
 - #26679   clean generic_graph.py (part 13) - searches and constructors
 - #26779   py3: fix `graph_input.py` and `hypergraph_generators.py`
 - #26812   py3: fix doctest in `graph_generators.py`
-
+- #26846        for graph isomorphism

 **Done**
 - #26274   avoid comparison of vertex labels in MIP - graph_coloring.py

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -21,6 +21,8 @@
 - #26779   py3: fix `graph_input.py` and `hypergraph_generators.py`
 - #26812   py3: fix doctest in `graph_generators.py`
 - #26846        for graph isomorphism
+- #26851   py3: avoid `.vertices()` and `.edges()` in `union` of graphs 
+

 **Done**
 - #26274   avoid comparison of vertex labels in MIP - graph_coloring.py

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -14,12 +14,10 @@
 **Needs review**:
 - #26520   Meta-ticket for methods in `src/sage/graphs/graph_decomposition/` - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834
 - #26634   clean generic_graph.py (part 5)
-- #26663   clean generic_graph.py (part 8) - connectivity  
 - #26675   clean generic_graph.py (part 11) - substructures
 - #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
 - #26779   py3: fix `graph_input.py` and `hypergraph_generators.py`
-- #26812   py3: fix doctest in `graph_generators.py`
 - #26846        for graph isomorphism
 - #26851   py3: avoid `.vertices()` and `.edges()` in `union` of graphs 

@@ -38,7 +36,15 @@
 - #26618   avoid using `.vertices()` in `centrality.pyx`
 - #26621   avoid using `.vertices()` and `.edges()` in `bliss.pyx`
 - #26622   avoid using `.vertices()` in convexity_properties.pyx
-- #26633   clean generic_graph.py (part 4) 
+- #26624   clean generic_graph.py (part 1)
+- #26627   clean generic_graph.py (part 2)
+- #26630   clean generic_graph.py (part 3)
+- #26633   clean generic_graph.py (part 4)
+- #26637   clean generic_graph.py (part 6)
+- #26658   clean generic_graph.py (part 7) - planarity
+- #26663   clean generic_graph.py (part 8) - connectivity  
+- #26666   clean generic_graph.py (part 9) - edge and vertex handlers
+- #26672   clean generic_graph.py (part 10) - degree
 - #26680   clean generic_graph.py (part 14) - visualization
 - #26711   avoid `.vertices()` in graph_coloring.py
 - #26712   avoid `.vertices()` in independent_sets.pyx
@@ -47,5 +53,6 @@
 - #26762   py3: fix `HortonGraph` generator
 - #26763   py3: fix `SzekeresSnarkGraph` generator
 - #26801   py3: change sorting of neighbors labels in `static_sparse_graph.pyx`
+- #26812   py3: fix doctest in `graph_generators.py`

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -13,11 +13,8 @@

 **Needs review**:
 - #26520   Meta-ticket for methods in `src/sage/graphs/graph_decomposition/` - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834
-- #26634   clean generic_graph.py (part 5)
-- #26675   clean generic_graph.py (part 11) - substructures
 - #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
-- #26779   py3: fix `graph_input.py` and `hypergraph_generators.py`
 - #26846        for graph isomorphism
 - #26851   py3: avoid `.vertices()` and `.edges()` in `union` of graphs 

@@ -40,11 +37,13 @@
 - #26627   clean generic_graph.py (part 2)
 - #26630   clean generic_graph.py (part 3)
 - #26633   clean generic_graph.py (part 4)
+- #26634   clean generic_graph.py (part 5)
 - #26637   clean generic_graph.py (part 6)
 - #26658   clean generic_graph.py (part 7) - planarity
 - #26663   clean generic_graph.py (part 8) - connectivity  
 - #26666   clean generic_graph.py (part 9) - edge and vertex handlers
 - #26672   clean generic_graph.py (part 10) - degree
+- #26675   clean generic_graph.py (part 11) - substructures
 - #26680   clean generic_graph.py (part 14) - visualization
 - #26711   avoid `.vertices()` in graph_coloring.py
 - #26712   avoid `.vertices()` in independent_sets.pyx
@@ -52,6 +51,7 @@
 - #26761   py3: fix `BlanusaSecondSnarkGraph`
 - #26762   py3: fix `HortonGraph` generator
 - #26763   py3: fix `SzekeresSnarkGraph` generator
+- #26779   py3: fix `graph_input.py` and `hypergraph_generators.py`
 - #26801   py3: change sorting of neighbors labels in `static_sparse_graph.pyx`
 - #26812   py3: fix doctest in `graph_generators.py`

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -17,6 +17,7 @@
 - #26679   clean generic_graph.py (part 13) - searches and constructors
 - #26846        for graph isomorphism
 - #26851   py3: avoid `.vertices()` and `.edges()` in `union` of graphs 
+- #26869   py3: improve `is_aperiodic` to fix doctests (due to deprecation warning in networkx)

 **Done**

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -18,6 +18,7 @@
 - #26846        for graph isomorphism
 - #26851   py3: avoid `.vertices()` and `.edges()` in `union` of graphs 
 - #26869   py3: improve `is_aperiodic` to fix doctests (due to deprecation warning in networkx)
+- #26870   py3: fix error with `map` in `strongly_regular_db.pyx`

 **Done**

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -19,6 +19,7 @@
 - #26851   py3: avoid `.vertices()` and `.edges()` in `union` of graphs 
 - #26869   py3: improve `is_aperiodic` to fix doctests (due to deprecation warning in networkx)
 - #26870   py3: fix error with `map` in `strongly_regular_db.pyx`
+- #26871   py3: fix doctests in `digraph_generators.py`

 **Done**

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -4,7 +4,7 @@
 **Major issues**
 - methods `.vertices()` and `.edges()` use sort by default
 - direct comparison of vertex labels (e.g., in method `iterator_edges` of `base/sparse_graph.pyx`)
-- all `min_spanning_tree` methods sort edges before returning the result
+- all `min_spanning_tree` methods sort edges before returning the result - #26940 is attempt to stop sorting returned list of edges

 **Needs work**:
@@ -20,7 +20,7 @@
 - #26869   py3: improve `is_aperiodic` to fix doctests (due to deprecation warning in networkx)
 - #26870   py3: fix error with `map` in `strongly_regular_db.pyx`
 - #26871   py3: fix doctests in `digraph_generators.py`
-
+- #26940   stop sorting returned list of edges in spanning tree methods 

 **Done**
 - #26274   avoid comparison of vertex labels in MIP - graph_coloring.py

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -15,11 +15,6 @@
 - #26520   Meta-ticket for methods in `src/sage/graphs/graph_decomposition/` - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834
 - #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
-- #26846        for graph isomorphism
-- #26851   py3: avoid `.vertices()` and `.edges()` in `union` of graphs 
-- #26869   py3: improve `is_aperiodic` to fix doctests (due to deprecation warning in networkx)
-- #26870   py3: fix error with `map` in `strongly_regular_db.pyx`
-- #26871   py3: fix doctests in `digraph_generators.py`
 - #26940   stop sorting returned list of edges in spanning tree methods 

 **Done**
@@ -57,5 +52,10 @@
 - #26779   py3: fix `graph_input.py` and `hypergraph_generators.py`
 - #26801   py3: change sorting of neighbors labels in `static_sparse_graph.pyx`
 - #26812   py3: fix doctest in `graph_generators.py`
+- #26846        for graph isomorphism
+- #26851   py3: avoid `.vertices()` and `.edges()` in `union` of graphs 
+- #26869   py3: improve `is_aperiodic` to fix doctests (due to deprecation warning in networkx)
+- #26870   py3: fix error with `map` in `strongly_regular_db.pyx`
+- #26871   py3: fix doctests in `digraph_generators.py`

fchapoton commented 5 years ago

comment:24

Salut !

we should probably add #26971 somewhere
where are the plot methods handled ?

dcoudert commented 5 years ago

comment:25

See #26469, #26478, #26480, #26484.

I will check #26971 soon.

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -16,6 +16,8 @@
 - #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
 - #26940   stop sorting returned list of edges in spanning tree methods 
+- #26971   py3: some minor fix for traveling salesman
+

 **Done**
 - #26274   avoid comparison of vertex labels in MIP - graph_coloring.py
@@ -23,7 +25,9 @@
 - #26284   avoid comparison of vertex labels in MIP - connectivity.pyx
 - #26285   avoid comparison of vertex labels in MIP - generic_graph.py
 - #26469   avoid sorting vertex labels in `graph_plot.py`
-- #26484   clean graph_coloring.py and avoid comparison of vertex labels
+- #26478   clean `graph_plot_js.py`, `graph_list.py` and `graph_input.py`
+- #26480   clean graph_latex.py
+- #26484   clean `graph_coloring.py` and avoid comparison of vertex labels
 - #26528   avoid using `.vertices()` in comparability, hyperbolicity and distances_all_pairs
 - #26531   avoid using `.vertices()` in asteroidal_triples
 - #26534   avoid using `.vertices()` in weakly_chordal.pyx

fchapoton commented 5 years ago

comment:26

Concerning plot, there are still problems in py3 when plotting posets. This point to the remaining

File "/home/u1/chapoton/sage3/local/lib/python3.6/site-packages/sage/graphs/graph_plot.py", line 255, in __init__
        self._nodelist = graph.vertices()

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -17,6 +17,7 @@
 - #26679   clean generic_graph.py (part 13) - searches and constructors
 - #26940   stop sorting returned list of edges in spanning tree methods 
 - #26971   py3: some minor fix for traveling salesman
+- #26973   py3: avoid `.vertices()` in `graph_plot.py`

 **Done**

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -15,9 +15,6 @@
 - #26520   Meta-ticket for methods in `src/sage/graphs/graph_decomposition/` - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834
 - #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
-- #26940   stop sorting returned list of edges in spanning tree methods 
-- #26971   py3: some minor fix for traveling salesman
-- #26973   py3: avoid `.vertices()` in `graph_plot.py`

 **Done**
@@ -62,5 +59,8 @@
 - #26869   py3: improve `is_aperiodic` to fix doctests (due to deprecation warning in networkx)
 - #26870   py3: fix error with `map` in `strongly_regular_db.pyx`
 - #26871   py3: fix doctests in `digraph_generators.py`
+- #26940   stop sorting returned list of edges in spanning tree methods 
+- #26971   py3: some minor fix for traveling salesman
+- #26973   py3: avoid `.vertices()` in `graph_plot.py`

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -15,7 +15,7 @@
 - #26520   Meta-ticket for methods in `src/sage/graphs/graph_decomposition/` - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834
 - #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
-
+- #27007   py3: avoid `.vertices()` in `planarity.pyx`

 **Done**
 - #26274   avoid comparison of vertex labels in MIP - graph_coloring.py

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -16,6 +16,8 @@
 - #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
 - #27007   py3: avoid `.vertices()` in `planarity.pyx`
+- #27008   py3: avoid `.vertices()` in method `apex_vertices`$
+

 **Done**
 - #26274   avoid comparison of vertex labels in MIP - graph_coloring.py

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -17,6 +17,7 @@
 - #26679   clean generic_graph.py (part 13) - searches and constructors
 - #27007   py3: avoid `.vertices()` in `planarity.pyx`
 - #27008   py3: avoid `.vertices()` in method `apex_vertices`$
+- #27009   py3: avoid sorting vertices and edges in method treewidth

 **Done**

dcoudert commented 5 years ago

comment:32

With #27008, #27009 and #27010, all remaining doctest errors in graph.py concern the order in which solutions are displayed (not always the same in py2 and py3).

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -18,7 +18,7 @@
 - #27007   py3: avoid `.vertices()` in `planarity.pyx`
 - #27008   py3: avoid `.vertices()` in method `apex_vertices`$
 - #27009   py3: avoid sorting vertices and edges in method treewidth
-
+- #27010   py3: avoid `.vertices()` in methods `_ford_fulkerson`, `edge_cut`, `bounded_outdegree_orientation` and `gomory_hu_tree`

 **Done**
 - #26274   avoid comparison of vertex labels in MIP - graph_coloring.py

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -19,6 +19,7 @@
 - #27008   py3: avoid `.vertices()` in method `apex_vertices`$
 - #27009   py3: avoid sorting vertices and edges in method treewidth
 - #27010   py3: avoid `.vertices()` in methods `_ford_fulkerson`, `edge_cut`, `bounded_outdegree_orientation` and `gomory_hu_tree`
+- #27059   py3: improve doctests in `spanning_tree.pyx`

 **Done**
 - #26274   avoid comparison of vertex labels in MIP - graph_coloring.py

embray commented 5 years ago

comment:34

Retarging tickets optimistically to the next milestone. If you are responsible for this ticket (either its reporter or owner) and don't believe you are likely to complete this ticket before the next release (8.7) please retarget this ticket's milestone to sage-pending or sage-wishlist.

jhpalmieri commented 5 years ago

comment:35

I would like to ask some questions about how to deal with simplicial complexes.

The is_isomorphic method for simplicial complexes translates each complex to a graph and then asks whether they are isomorphic, preserving edge labels. Some edges are labeled and some are not: the edge labels look like

sage: g.edge_labels()
[None,
 None,
 'special_edge',
 'special_edge']

This fails in Python 3 because it tries to sort edges, and it can't sort str and NoneType. It is easy enough to provide labels in this case, but should the graph is_isomorphic method deal well with graphs where some edges have labels and some don't? (I don't have an opinion and I will fix the simplicial complex code separately.)

Again with the is_isomorphic method for simplicial complexes: it defines a graph with vertices labeled by the vertices of the complex and its facets, and it adds an edge between a vertex v and a facet f if v is in f. The graph code tries to sort the vertices, and since the vertices in a simplicial complex can be integers, strings, whatever, the sorting goes badly. Again, I think I can handle this for simplicial complexes by translating everything to something sortable, then sorting, and then translating back at the end, but should the graph is_isomorphic method handle these sorts of cases better?
Consider this:

sage: S1 = simplicial_complexes.Sphere(1)
sage: g = S1.wedge(S1).graph()
sage: g
Graph on 5 vertices
sage: g.vertices()
[0, 'L1', 'L2', 'R1', 'R2']

In Python 3, the last line instead raises an error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-4-b2087dfc7b91> in <module>()
----> 1 g.vertices()

/Users/jpalmier/Desktop/Sage/sage_builds/PYTHON3/sage-8.6.rc1/local/lib/python3.6/site-packages/sage/graphs/generic_graph.py in vertices(self, sort, key)
  10053             raise ValueError('sort keyword is False, yet a key function is given')
  10054         if sort:
> 10055             return sorted(list(self.vertex_iterator()), key=key)
  10056         return list(self.vertex_iterator())
  10057 

TypeError: '<' not supported between instances of 'int' and 'str'
sage: g.min_spanning_tree()
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-5-8a025bbcbd58> in <module>()
----> 1 g.min_spanning_tree()

/Users/jpalmier/Desktop/Sage/sage_builds/PYTHON3/sage-8.6.rc1/local/lib/python3.6/site-packages/sage/graphs/generic_graph.py in min_spanning_tree(self, weight_function, algorithm, starting_vertex, check)
   4231                 return min_spanning_tree(g,
   4232                                          weight_function=wfunction_float,
-> 4233                                          algorithm=algorithm.split("_")[0])
   4234 
   4235         if algorithm == "Prim_fringe":

/Users/jpalmier/Desktop/Sage/sage_builds/PYTHON3/sage-8.6.rc1/local/lib/python3.6/site-packages/sage/graphs/base/boost_graph.pyx in sage.graphs.base.boost_graph.min_spanning_tree (build/cythonized/sage/graphs/base/boost_graph.cpp:9345)()
    604 
    605 
--> 606 cpdef min_spanning_tree(g,
    607                         weight_function=None,
    608                         algorithm='Kruskal'):

/Users/jpalmier/Desktop/Sage/sage_builds/PYTHON3/sage-8.6.rc1/local/lib/python3.6/site-packages/sage/graphs/base/boost_graph.pyx in sage.graphs.base.boost_graph.min_spanning_tree (build/cythonized/sage/graphs/base/boost_graph.cpp:9100)()
    719     else:
    720         edges = [(int_to_vertex[<int> result[2*i]], int_to_vertex[<int> result[2*i+1]]) for i in range(n-1)]
--> 721         return [(min(e[0],e[1]), max(e[0],e[1]), g.edge_label(e[0], e[1])) for e in edges]
    722 
    723 

TypeError: '<' not supported between instances of 'int' and 'str'

In Python 2, g.min_spanning_tree() works, while in Python 3, it raises a similar TypeError:

sage: g.min_spanning_tree()
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-5-8a025bbcbd58> in <module>()
----> 1 g.min_spanning_tree()

/Users/jpalmier/Desktop/Sage/sage_builds/PYTHON3/sage-8.6.rc1/local/lib/python3.6/site-packages/sage/graphs/generic_graph.py in min_spanning_tree(self, weight_function, algorithm, starting_vertex, check)
   4231                 return min_spanning_tree(g,
   4232                                          weight_function=wfunction_float,
-> 4233                                          algorithm=algorithm.split("_")[0])
   4234 
   4235         if algorithm == "Prim_fringe":

/Users/jpalmier/Desktop/Sage/sage_builds/PYTHON3/sage-8.6.rc1/local/lib/python3.6/site-packages/sage/graphs/base/boost_graph.pyx in sage.graphs.base.boost_graph.min_spanning_tree (build/cythonized/sage/graphs/base/boost_graph.cpp:9345)()
    604 
    605 
--> 606 cpdef min_spanning_tree(g,
    607                         weight_function=None,
    608                         algorithm='Kruskal'):

/Users/jpalmier/Desktop/Sage/sage_builds/PYTHON3/sage-8.6.rc1/local/lib/python3.6/site-packages/sage/graphs/base/boost_graph.pyx in sage.graphs.base.boost_graph.min_spanning_tree (build/cythonized/sage/graphs/base/boost_graph.cpp:9100)()
    719     else:
    720         edges = [(int_to_vertex[<int> result[2*i]], int_to_vertex[<int> result[2*i+1]]) for i in range(n-1)]
--> 721         return [(min(e[0],e[1]), max(e[0],e[1]), g.edge_label(e[0], e[1])) for e in edges]
    722 
    723 

TypeError: '<' not supported between instances of 'int' and 'str'

Once again, I could probably get around this by translating all of the vertices to something sortable and then translating back, but I do think that the graph theory code should be able to handle graphs whose vertices are a combination of int and str and anything else. I would like to put in a request for fixing this particular problem.

jhpalmieri commented 5 years ago

comment:36

Maybe one of these (the second one, I think) was taken care of by #27027.

jhpalmieri commented 5 years ago

comment:37

See #27067 for simplicial complexes fixes for the first two items.

dcoudert commented 5 years ago

comment:38

I fully agree that the graph theory code should be able to handle vertices of different types. We have done significant progresses recently, and many methods are no longer sorting vertices. But a lot remains to be done since a huge part of the code uses vertex ids instead of internal int labels. We have to find solutions for instance for listing edges as end points are currently sorted...

Note that I'm not able to try your example with py3 as this S1.wedge(S1).graph() already raises an error.

jhpalmieri commented 5 years ago

comment:39

First, you have all done great work with graphs, and you've made a tremendous amount of progress. Partly my questions were because I don't know whether some of these things have been done in tickets which have not yet been merged, but I think that's not the case.

Speaking of things which have not yet been merged, you need #26966 to be able to do S1.wedge(S1).graph(). Sorry, I hadn't realized that when I posted my example.

jhpalmieri commented 5 years ago

comment:40

Also, as I hope was clear in my questions, the first two are not critiques but honest questions: I don't know how Sage should handle those situations. The fact that things happen to work in Python 2 does not mean that they should automatically work in Python 3. For example, if you explicitly ask for isomorphisms preserving edge labels, an argument could be made that you should actually label all of the edges. The last item on my list was an explicit request, which it sounds like you agree with but also sounds like it take some work.

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -15,10 +15,6 @@
 - #26520   Meta-ticket for methods in `src/sage/graphs/graph_decomposition/` - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834
 - #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
-- #27007   py3: avoid `.vertices()` in `planarity.pyx`
-- #27008   py3: avoid `.vertices()` in method `apex_vertices`$
-- #27009   py3: avoid sorting vertices and edges in method treewidth
-- #27010   py3: avoid `.vertices()` in methods `_ford_fulkerson`, `edge_cut`, `bounded_outdegree_orientation` and `gomory_hu_tree`
 - #27059   py3: improve doctests in `spanning_tree.pyx`

 **Done**
@@ -66,5 +62,9 @@
 - #26940   stop sorting returned list of edges in spanning tree methods 
 - #26971   py3: some minor fix for traveling salesman
 - #26973   py3: avoid `.vertices()` in `graph_plot.py`
+- #27007   py3: avoid `.vertices()` in `planarity.pyx`
+- #27008   py3: avoid `.vertices()` in method `apex_vertices`
+- #27009   py3: avoid sorting vertices and edges in method treewidth
+- #27010   py3: avoid `.vertices()` in methods `_ford_fulkerson`, `edge_cut`, `bounded_outdegree_orientation` and `gomory_hu_tree`

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -16,6 +16,10 @@
 - #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
 - #27059   py3: improve doctests in `spanning_tree.pyx`
+- #27123   bliss `automorphism_group()` shouldn't sort vertices 
+- #27125   py3: fix some doctests in `graph.py`
+- #27127   py3: avoid `.vertices()` in method `ear_decomposition`
+

 **Done**
 - #26274   avoid comparison of vertex labels in MIP - graph_coloring.py

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -19,6 +19,7 @@
 - #27123   bliss `automorphism_group()` shouldn't sort vertices 
 - #27125   py3: fix some doctests in `graph.py`
 - #27127   py3: avoid `.vertices()` in method `ear_decomposition`
+- #27129   py3: fix other doctests in `graph.py`

 **Done**

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -12,13 +12,10 @@

 **Needs review**:
-- #26520   Meta-ticket for methods in `src/sage/graphs/graph_decomposition/` - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834
 - #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
-- #27059   py3: improve doctests in `spanning_tree.pyx`
-- #27123   bliss `automorphism_group()` shouldn't sort vertices 
-- #27125   py3: fix some doctests in `graph.py`
-- #27127   py3: avoid `.vertices()` in method `ear_decomposition`
+- #27029   Avoid calling `.vertices()` in `graph_isom_equivalent_non_edge_labeled_graph()`
+- #27123   bliss `automorphism_group()` shouldn't sort vertices
 - #27129   py3: fix other doctests in `graph.py`

@@ -31,6 +28,7 @@
 - #26478   clean `graph_plot_js.py`, `graph_list.py` and `graph_input.py`
 - #26480   clean graph_latex.py
 - #26484   clean `graph_coloring.py` and avoid comparison of vertex labels
+- #26520   Meta-ticket for methods in `src/sage/graphs/graph_decomposition/` - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834
 - #26528   avoid using `.vertices()` in comparability, hyperbolicity and distances_all_pairs
 - #26531   avoid using `.vertices()` in asteroidal_triples
 - #26534   avoid using `.vertices()` in weakly_chordal.pyx
@@ -71,5 +69,8 @@
 - #27008   py3: avoid `.vertices()` in method `apex_vertices`
 - #27009   py3: avoid sorting vertices and edges in method treewidth
 - #27010   py3: avoid `.vertices()` in methods `_ford_fulkerson`, `edge_cut`, `bounded_outdegree_orientation` and `gomory_hu_tree`
+- #27059   py3: improve doctests in `spanning_tree.pyx`
+- #27125   py3: fix some doctests in `graph.py`
+- #27127   py3: avoid `.vertices()` in method `ear_decomposition`

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -17,6 +17,7 @@
 - #27029   Avoid calling `.vertices()` in `graph_isom_equivalent_non_edge_labeled_graph()`
 - #27123   bliss `automorphism_group()` shouldn't sort vertices
 - #27129   py3: fix other doctests in `graph.py`
+- #27144   py3: fix doctests in `connectivity.pyx`

 **Done**

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -18,6 +18,10 @@
 - #27123   bliss `automorphism_group()` shouldn't sort vertices
 - #27129   py3: fix other doctests in `graph.py`
 - #27144   py3: fix doctests in `connectivity.pyx`
+- #27147   py3: fix doctests in `dense_graph.pyx`, `sparse_graph.pyx`, `static_sparse_graph.pyx`
+- #27148   py3: fix doctests in `centrality.pyx`
+- #27149   py3: fix doctests in `comparability.pyx`
+- #27151   py3: fix doctests in `vertex_separation.pyx`

 **Done**

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -22,6 +22,9 @@
 - #27148   py3: fix doctests in `centrality.pyx`
 - #27149   py3: fix doctests in `comparability.pyx`
 - #27151   py3: fix doctests in `vertex_separation.pyx`
+- #27158   py3: fix doctests in `boost_graph.pyx`
+- #27159   py3: fix doctests in `strongly_regular_db.pyx`
+- #27160   py3: fix doctests in `hyperbolicity` and `graph_coloring`

 **Done**

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -15,7 +15,6 @@
 - #26678   clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826
 - #26679   clean generic_graph.py (part 13) - searches and constructors
 - #27029   Avoid calling `.vertices()` in `graph_isom_equivalent_non_edge_labeled_graph()`
-- #27123   bliss `automorphism_group()` shouldn't sort vertices
 - #27129   py3: fix other doctests in `graph.py`
 - #27144   py3: fix doctests in `connectivity.pyx`
 - #27147   py3: fix doctests in `dense_graph.pyx`, `sparse_graph.pyx`, `static_sparse_graph.pyx`
@@ -25,6 +24,7 @@
 - #27158   py3: fix doctests in `boost_graph.pyx`
 - #27159   py3: fix doctests in `strongly_regular_db.pyx`
 - #27160   py3: fix doctests in `hyperbolicity` and `graph_coloring`
+- #27165   py3: fix doctests in `c_graph.pyx`

 **Done**
@@ -78,6 +78,7 @@
 - #27009   py3: avoid sorting vertices and edges in method treewidth
 - #27010   py3: avoid `.vertices()` in methods `_ford_fulkerson`, `edge_cut`, `bounded_outdegree_orientation` and `gomory_hu_tree`
 - #27059   py3: improve doctests in `spanning_tree.pyx`
+- #27123   bliss `automorphism_group()` shouldn't sort vertices
 - #27125   py3: fix some doctests in `graph.py`
 - #27127   py3: avoid `.vertices()` in method `ear_decomposition`

sagemath / sage

Meta-ticket: make graphs compatible with Python 3 #26640

22349 Deprecate sorting of methods .vertices() and .edges()

22349 Deprecate sorting of Graph vertices and edges by default

27408 Edge view for graphs -- introduce deprecation warning for sort=None as the plan is to set sort=False by default.

27513 Allow custom order for edges as well as vertices for incidence matrix

26274 avoid comparison of vertex labels in MIP - graph_coloring.py

26282 avoid comparison of vertex labels in MIP - graph.py

26284 avoid comparison of vertex labels in MIP - connectivity.pyx

26285 avoid comparison of vertex labels in MIP - generic_graph.py

26469 avoid sorting vertex labels in graph_plot.py

26478 clean graph_plot_js.py, graph_list.py and graph_input.py

26480 clean graph_latex.py

26484 clean graph_coloring.py and avoid comparison of vertex labels

26520 Meta-ticket for methods in src/sage/graphs/graph_decomposition/ - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834

26528 avoid using .vertices() in comparability, hyperbolicity and distances_all_pairs

26531 avoid using .vertices() in asteroidal_triples

26534 avoid using .vertices() in weakly_chordal.pyx

26554 improve the boost graph interface to avoid using .vertices()

26618 avoid using .vertices() in centrality.pyx

26621 avoid using .vertices() and .edges() in bliss.pyx

26622 avoid using .vertices() in convexity_properties.pyx

26624 clean generic_graph.py (part 1)

26627 clean generic_graph.py (part 2)

26630 clean generic_graph.py (part 3)

26633 clean generic_graph.py (part 4)

26634 clean generic_graph.py (part 5)

26637 clean generic_graph.py (part 6)

26658 clean generic_graph.py (part 7) - planarity

26663 clean generic_graph.py (part 8) - connectivity

26666 clean generic_graph.py (part 9) - edge and vertex handlers

26672 clean generic_graph.py (part 10) - degree

26675 clean generic_graph.py (part 11) - substructures

26678 clean generic_graph.py (part 12) - meta-ticket for methods related to clustering, centrality and distances. Tickets are #26803, #26813, #26814, #26815, #26819, #26820, #26821, #26822, #26823, #26824, #26825, #26826

26679 clean generic_graph.py (part 13) - searches and constructors

26680 clean generic_graph.py (part 14) - visualization

26711 avoid .vertices() in graph_coloring.py

26712 avoid .vertices() in independent_sets.pyx

26757 py3: fixing round in graph_latex.py

26761 py3: fix BlanusaSecondSnarkGraph

26762 py3: fix HortonGraph generator

26763 py3: fix SzekeresSnarkGraph generator

26779 py3: fix graph_input.py and hypergraph_generators.py

26800 py3: bug with canonical_label fixed by #27695

26801 py3: change sorting of neighbors labels in static_sparse_graph.pyx

26812 py3: fix doctest in graph_generators.py

26846 for graph isomorphism

26851 py3: avoid .vertices() and .edges() in union of graphs

26869 py3: improve is_aperiodic to fix doctests (due to deprecation warning in networkx)

26870 py3: fix error with map in strongly_regular_db.pyx

26871 py3: fix doctests in digraph_generators.py

26940 stop sorting returned list of edges in spanning tree methods

26971 py3: some minor fix for traveling salesman

26973 py3: avoid .vertices() in graph_plot.py

27007 py3: avoid .vertices() in planarity.pyx

27008 py3: avoid .vertices() in method apex_vertices

27009 py3: avoid sorting vertices and edges in method treewidth

27010 py3: avoid .vertices() in methods _ford_fulkerson, edge_cut, bounded_outdegree_orientation and gomory_hu_tree

27029 Avoid calling .vertices() in graph_isom_equivalent_non_edge_labeled_graph()

27059 py3: improve doctests in spanning_tree.pyx

27123 bliss automorphism_group() shouldn't sort vertices

27125 py3: fix some doctests in graph.py

27127 py3: avoid .vertices() in method ear_decomposition

27129 py3: fix other doctests in graph.py

27137 pep8 in digraph_generators.py (part 4)

27138 pep8 in digraph_generators.py (part 5)

27144 py3: fix doctests in connectivity.pyx

27147 py3: fix doctests in dense_graph.pyx, sparse_graph.pyx, static_sparse_graph.pyx

27148 py3: fix doctests in centrality.pyx

27149 py3: fix doctests in comparability.pyx

27151 py3: fix doctests in vertex_separation.pyx

27158 py3: fix doctests in boost_graph.pyx

27159 py3: fix doctests in strongly_regular_db.pyx

27160 py3: fix doctests in hyperbolicity and graph_coloring

27165 py3: fix doctests in c_graph.pyx

27166 remove deprecated classes NetworkXGraphDeprecated and NetworkXDiGraphDeprecated

27167 py3: fix doctest in distances_all_pairs.pyx

27170 py3: fix 14 doctests in digraph.py

27176 py3: fix doctest in generic_graph (part 1)

27179 py3: fix doctest in generic_graph (part 2) -- cycle_basis

22349 Deprecate sorting of methods `.vertices()` and `.edges()`

27408 Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.

26469 avoid sorting vertex labels in `graph_plot.py`

26478 clean `graph_plot_js.py`, `graph_list.py` and `graph_input.py`

26484 clean `graph_coloring.py` and avoid comparison of vertex labels

26520 Meta-ticket for methods in `src/sage/graphs/graph_decomposition/` - #26827, #26828, #26829, #26830, #26831, #26832, #26833, #26834

26528 avoid using `.vertices()` in comparability, hyperbolicity and distances_all_pairs

26531 avoid using `.vertices()` in asteroidal_triples

26534 avoid using `.vertices()` in weakly_chordal.pyx

26554 improve the boost graph interface to avoid using `.vertices()`

26618 avoid using `.vertices()` in `centrality.pyx`

26621 avoid using `.vertices()` and `.edges()` in `bliss.pyx`

26622 avoid using `.vertices()` in convexity_properties.pyx

26711 avoid `.vertices()` in graph_coloring.py

26712 avoid `.vertices()` in independent_sets.pyx

26761 py3: fix `BlanusaSecondSnarkGraph`

26762 py3: fix `HortonGraph` generator

26763 py3: fix `SzekeresSnarkGraph` generator

26779 py3: fix `graph_input.py` and `hypergraph_generators.py`

26800 py3: bug with `canonical_label` fixed by #27695

26801 py3: change sorting of neighbors labels in `static_sparse_graph.pyx`

26812 py3: fix doctest in `graph_generators.py`

26851 py3: avoid `.vertices()` and `.edges()` in `union` of graphs

26869 py3: improve `is_aperiodic` to fix doctests (due to deprecation warning in networkx)

26870 py3: fix error with `map` in `strongly_regular_db.pyx`

26871 py3: fix doctests in `digraph_generators.py`

26973 py3: avoid `.vertices()` in `graph_plot.py`

27007 py3: avoid `.vertices()` in `planarity.pyx`

27008 py3: avoid `.vertices()` in method `apex_vertices`

27010 py3: avoid `.vertices()` in methods `_ford_fulkerson`, `edge_cut`, `bounded_outdegree_orientation` and `gomory_hu_tree`

27029 Avoid calling `.vertices()` in `graph_isom_equivalent_non_edge_labeled_graph()`

27059 py3: improve doctests in `spanning_tree.pyx`

27123 bliss `automorphism_group()` shouldn't sort vertices

27125 py3: fix some doctests in `graph.py`

27127 py3: avoid `.vertices()` in method `ear_decomposition`

27129 py3: fix other doctests in `graph.py`

27137 pep8 in `digraph_generators.py` (part 4)

27138 pep8 in `digraph_generators.py` (part 5)

27144 py3: fix doctests in `connectivity.pyx`

27147 py3: fix doctests in `dense_graph.pyx`, `sparse_graph.pyx`, `static_sparse_graph.pyx`

27148 py3: fix doctests in `centrality.pyx`

27149 py3: fix doctests in `comparability.pyx`

27151 py3: fix doctests in `vertex_separation.pyx`

27158 py3: fix doctests in `boost_graph.pyx`

27159 py3: fix doctests in `strongly_regular_db.pyx`

27160 py3: fix doctests in `hyperbolicity` and `graph_coloring`

27165 py3: fix doctests in `c_graph.pyx`

27166 remove deprecated classes `NetworkXGraphDeprecated` and `NetworkXDiGraphDeprecated`

27167 py3: fix doctest in `distances_all_pairs.pyx`

27170 py3: fix 14 doctests in `digraph.py`

27176 py3: fix doctest in `generic_graph` (part 1)

27179 py3: fix doctest in `generic_graph` (part 2) -- cycle_basis

27180 py3: fix doctest in `generic_graph` (part 3) -- _build_flow_graph

27181 py3: fix doctest in `generic_graph` (part 4)

27183 py3: fix doctest in `generic_graph` (part 5)

27184 py3: fix doctests in `generic_graph` (part 6) -- `graphviz_string`

27203 py3: fix 8 doctests in `generators/families.py`

27242 py3: strengthen a doctest in `vertex_separation.pyx`

27243 py3: fix doctests in `generic_graph` (part 7) -- relabel

27244 py3: fix doctests in `generic_graph` (part 8) -- `coarsest_equitable_refinement`

27245 py3: fix doctests in `generic_graph` (part 9) -- `automorphism_group`

27246 py3: fix doctests in `generic_graph` (part 10) -- `is_isomorphic`

27435 py3: failing doctest in `graph_database.py` with `interactive_query`

27571 some changes in `automorphism_group` and fix one doctest in `MathonPseudocyclicStronglyRegularGraph`