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 5 years ago

Description changed:

--- 
+++ 
@@ -25,7 +25,7 @@
 - #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`

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

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -26,6 +26,9 @@
 - #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`
+

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

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -28,6 +28,12 @@
 - #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`

 **Done**

dcoudert commented 5 years ago

comment:51

With #26819, #27176, #27179, #27180, #27181, #27183 py3 and #27184, we fix 42 doctests in generic_graph.py !!!

The remainging issues are in relabel, is_isomorphic and graph_isom_equivalent_non_edge_labeled_graph.

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -34,6 +34,8 @@
 - #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`

 **Done**

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -14,28 +14,13 @@
 **Needs review**:
 - #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()`
-- #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`
-- #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`

 **Done**
@@ -88,9 +73,24 @@
 - #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`
+- #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`
+- #27166   remove deprecated classes `NetworkXGraphDeprecated` and `NetworkXDiGraphDeprecated`
+- #27167   py3: fix doctest in `distances_all_pairs.pyx`
+- #27180   py3: fix doctest in `generic_graph` (part 3) -- _build_flow_graph
+- #27181   py3: fix doctest in `generic_graph` (part 4)
+- #27184   py3: fix doctests in `generic_graph` (part 6) -- `graphviz_string`
+- #27203   py3: fix 8 doctests in `generators/families.py`

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -20,7 +20,7 @@
 - #27176   py3: fix doctest in `generic_graph` (part 1)
 - #27179   py3: fix doctest in `generic_graph` (part 2) -- cycle_basis
 - #27183   py3: fix doctest in `generic_graph` (part 5)
-- #27202   py3: fix doctests in random graphs generators
+- #27242   py3: strengthen a doctest in `vertex_separation.pyx`

 **Done**
@@ -91,6 +91,7 @@
 - #27180   py3: fix doctest in `generic_graph` (part 3) -- _build_flow_graph
 - #27181   py3: fix doctest in `generic_graph` (part 4)
 - #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`

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -21,6 +21,10 @@
 - #27179   py3: fix doctest in `generic_graph` (part 2) -- cycle_basis
 - #27183   py3: fix doctest in `generic_graph` (part 5)
 - #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`

 **Done**

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -9,6 +9,7 @@

 **Needs work**:
 - #26800   py3: bug with canonical_label
+- #27232   `is_permutation_of` broken for matrices over cyclotomic fields -- this is due to `is_isomorphic` in graphs.

 **Needs review**:

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -13,7 +13,6 @@

 **Needs review**:
-- #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
 - #27160   py3: fix doctests in `hyperbolicity` and `graph_coloring`
 - #27165   py3: fix doctests in `c_graph.pyx`
@@ -21,11 +20,8 @@
 - #27176   py3: fix doctest in `generic_graph` (part 1)
 - #27179   py3: fix doctest in `generic_graph` (part 2) -- cycle_basis
 - #27183   py3: fix doctest in `generic_graph` (part 5)
-- #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`

 **Done**
@@ -56,6 +52,7 @@
 - #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
 - #26680   clean generic_graph.py (part 14) - visualization
 - #26711   avoid `.vertices()` in graph_coloring.py
 - #26712   avoid `.vertices()` in independent_sets.pyx
@@ -98,5 +95,8 @@
 - #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`
+- #27242   py3: strengthen a doctest in `vertex_separation.pyx`
+- #27244   py3: fix doctests in `generic_graph` (part 8) -- `coarsest_equitable_refinement`
+- #27246   py3: fix doctests in `generic_graph` (part 10) -- `is_isomorphic`

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -13,14 +13,9 @@

 **Needs review**:
-- #26679   clean generic_graph.py (part 13) - searches and constructors
 - #27160   py3: fix doctests in `hyperbolicity` and `graph_coloring`
-- #27165   py3: fix doctests in `c_graph.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
-- #27183   py3: fix doctest in `generic_graph` (part 5)
-- #27243   py3: fix doctests in `generic_graph` (part 7) -- relabel 
 - #27245   py3: fix doctests in `generic_graph` (part 9) -- `automorphism_group`

@@ -53,6 +48,7 @@
 - #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
@@ -88,14 +84,18 @@
 - #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`
+- #27165   py3: fix doctests in `c_graph.pyx`
 - #27166   remove deprecated classes `NetworkXGraphDeprecated` and `NetworkXDiGraphDeprecated`
 - #27167   py3: fix doctest in `distances_all_pairs.pyx`
+- #27176   py3: fix doctest in `generic_graph` (part 1)
 - #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`
 - #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`
 - #27246   py3: fix doctests in `generic_graph` (part 10) -- `is_isomorphic`

dcoudert commented 5 years ago

comment:59

We have now drastically reduced the dependency to .vertices() and .edges() in the graph module (except in doctests, but we can specify sort=True/False).

We must now identify the tasks to do and schedule the work.

Some issues to take care of in the graph module:

22349 Deprecate sorting of methods .vertices() and .edges().
- methods using matrices: adjacency_matrix, distance_matrix, etc. For all these methods, we can now give as input an ordering of the vertices that will be used to order rows and columns. Currently, we use .vertices() by default. If we switch to list(G) by default, we have to check that it's not breaking algorithms using these matrices.
- methods using .relabel(). We must check that changing the default ordering of vertices/edges is safe. Should be ok, but we never know...
- methods for isomorphisms were we also have issues with labels (see e.g. #27232 although the case is certainly beyond what we should reasonably do).
Deprecate sorting of vertex labels in method iterator_edges of base/sparse_graph.pyx (so of the vertices of an edge). Deprecating this behavior is certainly a hard task. A first step could be to order the vertices according internal integer value, thus ensuring that (u, v) will always be ordered the same way.

And of course, changes done here will certainly break many methods in other modules...

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -2,17 +2,22 @@

 **Major issues**
-- methods `.vertices()` and `.edges()` use sort by default
+- #22349 Deprecate sorting of methods `.vertices()` and `.edges()`
 - 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 - #26940 is attempt to stop sorting returned list of edges
+- methods using matrices: `adjacency_matrix`, `distance_matrix`, etc. For all these methods, we can now give as input an ordering of the vertices that will be used to order rows and columns. Currently, we use `.vertices()` by default. If we switch to `list(G)` by default, we have to check that it's not breaking algorithms using these matrices.
+- sort used in methods for checking isomorphisms w/wo edge labels

 **Needs work**:
-- #26800   py3: bug with canonical_label
+- #22349   Deprecate sorting of Graph vertices and edges by default
+- #26800   py3: bug with `canonical_label`
 - #27232   `is_permutation_of` broken for matrices over cyclotomic fields -- this is due to `is_isomorphic` in graphs.

 **Needs review**:
+- #27135   pep8 in `digraph_generators.py` (part 2)
+- #27137   pep8 in `digraph_generators.py` (part 4)
+- #27138   pep8 in `digraph_generators.py` (part 5)
 - #27160   py3: fix doctests in `hyperbolicity` and `graph_coloring`
 - #27170   py3: fix 14 doctests in `digraph.py`
 - #27179   py3: fix doctest in `generic_graph` (part 2) -- cycle_basis

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -12,15 +12,14 @@
 - #22349   Deprecate sorting of Graph vertices and edges by default
 - #26800   py3: bug with `canonical_label`
 - #27232   `is_permutation_of` broken for matrices over cyclotomic fields -- this is due to `is_isomorphic` in graphs.
+- `sage.graphs.graph_database`: there is a failing doctest in py3 with `interactive_query`...

 **Needs review**:
 - #27135   pep8 in `digraph_generators.py` (part 2)
 - #27137   pep8 in `digraph_generators.py` (part 4)
 - #27138   pep8 in `digraph_generators.py` (part 5)
-- #27160   py3: fix doctests in `hyperbolicity` and `graph_coloring`
 - #27170   py3: fix 14 doctests in `digraph.py`
-- #27179   py3: fix doctest in `generic_graph` (part 2) -- cycle_basis
 - #27245   py3: fix doctests in `generic_graph` (part 9) -- `automorphism_group`

@@ -89,10 +88,12 @@
 - #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`
 - #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)

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -19,8 +19,7 @@
 - #27135   pep8 in `digraph_generators.py` (part 2)
 - #27137   pep8 in `digraph_generators.py` (part 4)
 - #27138   pep8 in `digraph_generators.py` (part 5)
-- #27170   py3: fix 14 doctests in `digraph.py`
-- #27245   py3: fix doctests in `generic_graph` (part 9) -- `automorphism_group`
+- #27408   Edge view for graphs

 **Done**
@@ -92,6 +91,7 @@
 - #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
@@ -103,6 +103,7 @@
 - #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`

dcoudert commented 5 years ago

comment:62

Proposal for an EdgeView for graphs in #27408.

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -5,21 +5,20 @@
 - #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 that will be used to order rows and columns. Currently, we use `.vertices()` by default. If we switch to `list(G)` by default, we have to check that it's not breaking algorithms using these matrices.
-- sort used in methods for checking isomorphisms w/wo edge labels
+- sort used in methods for checking isomorphisms w/wo edge labels (see also #27232 and #26800). Sorting of lists of possibly unhashable objects is needed here, or may be  a method for checking that there is a permutation from one list to the other could be enough ?

 **Needs work**:
 - #22349   Deprecate sorting of Graph vertices and edges by default
 - #26800   py3: bug with `canonical_label`
 - #27232   `is_permutation_of` broken for matrices over cyclotomic fields -- this is due to `is_isomorphic` in graphs.
-- `sage.graphs.graph_database`: there is a failing doctest in py3 with `interactive_query`...
-
+- #27435   py3: failing doctest in `graph_database.py` with `interactive_query`

 **Needs review**:
 - #27135   pep8 in `digraph_generators.py` (part 2)
 - #27137   pep8 in `digraph_generators.py` (part 4)
 - #27138   pep8 in `digraph_generators.py` (part 5)
-- #27408   Edge view for graphs
+- #27408   Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.

 **Done**

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -11,13 +11,13 @@
 **Needs work**:
 - #22349   Deprecate sorting of Graph vertices and edges by default
 - #26800   py3: bug with `canonical_label`
-- #27232   `is_permutation_of` broken for matrices over cyclotomic fields -- this is due to `is_isomorphic` in graphs.
 - #27435   py3: failing doctest in `graph_database.py` with `interactive_query`

 **Needs review**:
 - #27135   pep8 in `digraph_generators.py` (part 2)
 - #27137   pep8 in `digraph_generators.py` (part 4)
 - #27138   pep8 in `digraph_generators.py` (part 5)
+- #27232   is_isomorphic broken with keyword edge_labels=True
 - #27408   Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.

jhpalmieri commented 5 years ago

comment:65

I don't know if this is a good idea or not, but see #27452 for a branch which fixes the last doctest failures in src/homology. This bypasses an issue with graphs, as mentioned above:

sage: S1 = simplicial_complexes.Sphere(1)
sage: g = S1.wedge(S1).graph()
sage: g
Graph on 5 vertices
sage: g.vertices()
...
TypeError: '<' not supported between instances of 'int' and 'str'

The branch at #27452 relabels the graph of a simplicial complex so that the vertices are sortable, before trying to compute its minimal spanning tree. Is this just sweeping things under the rug, or is it okay?

tscrim commented 5 years ago

comment:66

I think it is one way forward. It does suffer in large cases because you have to make a full copy of the simplicial complex's graph, but I don't think it is simply sweeping it under the rug. Perhaps for that a user should know better than to have complicated labels for such tests?

dcoudert commented 5 years ago

comment:67

An alternative is to (optionally) make spanning tree methods return a Graph, in which case there is no need to sort end vertices.

tscrim commented 5 years ago

comment:68

Replying to @dcoudert:

An alternative is to (optionally) make spanning tree methods return a Graph, in which case there is no need to sort end vertices.

My gut reaction was that seems heavy handed. It would make sense, but I suspect the reason we don't is because it would be too expensive (relatively) to return a (Di)Graph. I haven't looked into this (it is too late for me to do so tonight), but just a thought.

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -14,12 +14,11 @@
 - #27435   py3: failing doctest in `graph_database.py` with `interactive_query`

 **Needs review**:
-- #27135   pep8 in `digraph_generators.py` (part 2)
 - #27137   pep8 in `digraph_generators.py` (part 4)
 - #27138   pep8 in `digraph_generators.py` (part 5)
 - #27232   is_isomorphic broken with keyword edge_labels=True
 - #27408   Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.
-
+- #27571   some changes in `automorphism_group` and fix one doctest in `MathonPseudocyclicStronglyRegularGraph`

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

dcoudert commented 5 years ago

comment:70

Some doctests are failing with bliss (not related to #27571)

sage -t src/sage/graphs/generators/families.py
**********************************************************************
File "src/sage/graphs/generators/families.py", line 3191, in sage.graphs.generators.families.MathonPseudocyclicStronglyRegularGraph
Failed example:
    G3x3.automorphism_group(algorithm="bliss").order() # optional - bliss
Expected:
    27
Got:
    3
**********************************************************************
File "src/sage/graphs/generators/families.py", line 3196, in sage.graphs.generators.families.MathonPseudocyclicStronglyRegularGraph
Failed example:
    G9.automorphism_group(algorithm="bliss").order() # optional - bliss
Expected:
    9
Got:
    3

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -19,6 +19,7 @@
 - #27232   is_isomorphic broken with keyword edge_labels=True
 - #27408   Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.
 - #27571   some changes in `automorphism_group` and fix one doctest in `MathonPseudocyclicStronglyRegularGraph`
+- #27695   try to sort vertices to produce consistent graph6 and dig6 strings in Python3

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

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -10,11 +10,9 @@

 **Needs work**:
 - #22349   Deprecate sorting of Graph vertices and edges by default
-- #26800   py3: bug with `canonical_label`
 - #27435   py3: failing doctest in `graph_database.py` with `interactive_query`

 **Needs review**:
-- #27137   pep8 in `digraph_generators.py` (part 4)
 - #27138   pep8 in `digraph_generators.py` (part 5)
 - #27232   is_isomorphic broken with keyword edge_labels=True
 - #27408   Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.
@@ -59,6 +57,7 @@
 - #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
@@ -79,6 +78,7 @@
 - #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)
 - #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`

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -12,12 +12,12 @@
 - #22349   Deprecate sorting of Graph vertices and edges by default
 - #27435   py3: failing doctest in `graph_database.py` with `interactive_query`

+
 **Needs review**:
-- #27138   pep8 in `digraph_generators.py` (part 5)
 - #27232   is_isomorphic broken with keyword edge_labels=True
 - #27408   Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.
 - #27571   some changes in `automorphism_group` and fix one doctest in `MathonPseudocyclicStronglyRegularGraph`
-- #27695   try to sort vertices to produce consistent graph6 and dig6 strings in Python3
+

 **Done**
 - #26274   avoid comparison of vertex labels in MIP - graph_coloring.py
@@ -79,6 +79,7 @@
 - #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`
@@ -104,5 +105,6 @@
 - #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`
+- #27695   try to sort vertices to produce consistent graph6 and dig6 strings in Python3

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -11,12 +11,12 @@
 **Needs work**:
 - #22349   Deprecate sorting of Graph vertices and edges by default
 - #27435   py3: failing doctest in `graph_database.py` with `interactive_query`
-
+- #28108   py3: ValueError in graph_generators doctests with plantri optional package (follow up of #27948)

 **Needs review**:
 - #27232   is_isomorphic broken with keyword edge_labels=True
 - #27408   Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.
-- #27571   some changes in `automorphism_group` and fix one doctest in `MathonPseudocyclicStronglyRegularGraph`
+- #27948   py3: fix doctests with optional package plantri 

 **Done**
@@ -106,5 +106,6 @@
 - #27245   py3: fix doctests in `generic_graph` (part 9) -- `automorphism_group`
 - #27246   py3: fix doctests in `generic_graph` (part 10) -- `is_isomorphic`
 - #27695   try to sort vertices to produce consistent graph6 and dig6 strings in Python3
+- #27571   some changes in `automorphism_group` and fix one doctest in `MathonPseudocyclicStronglyRegularGraph`

dcoudert commented 5 years ago

comment:75

We are almost done. We have currently 3 open tickets for the remaining failing doctests.

Needs work (contributors are more than welcome):

27435: failing doctest in graph_database.py with interactive_query.
28108: 2 ValueError? in graph_generators.py doctests with plantri optional package (follow up of #27948)

Needs review / help / comment:

27232: fix failing doctests in is_isomorphic, which are the last 8 remaining failing doctests in generic_graph.py

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -16,7 +16,6 @@
 **Needs review**:
 - #27232   is_isomorphic broken with keyword edge_labels=True
 - #27408   Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.
-- #27948   py3: fix doctests with optional package plantri 

 **Done**
@@ -105,7 +104,8 @@
 - #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`
+- #27571   some changes in `automorphism_group` and fix one doctest in `MathonPseudocyclicStronglyRegularGraph`
 - #27695   try to sort vertices to produce consistent graph6 and dig6 strings in Python3
-- #27571   some changes in `automorphism_group` and fix one doctest in `MathonPseudocyclicStronglyRegularGraph`
+- #27948   py3: fix doctests with optional package plantri

jhpalmieri commented 5 years ago

comment:76

Replying to @dcoudert:

We are almost done. We have currently 3 open tickets for the remaining failing doctests.

Needs work (contributors are more than welcome):

27435: failing doctest in graph_database.py with interactive_query.

For this one, I would be tempted to label it # py2 since it seems to rely on the legacy Sage notebook. I can open a ticket if that sounds like a valid approach.

dcoudert commented 5 years ago

comment:77

27435: failing doctest in graph_database.py with interactive_query.

For this one, I would be tempted to label it # py2 since it seems to rely on the legacy Sage notebook. I can open a ticket if that sounds like a valid approach.

It is related to sage notebook, but doctests are failing only with py3... So I don't know which is the best approach. Should we try to make a little change to sagenb to make #27435 fixing the issue, although sagenb will be removed in the future (but when?) ?

jhpalmieri commented 5 years ago

comment:78

I apologize, my comments really belong on #27435. I'll continue the discussion there.

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -10,11 +10,9 @@

 **Needs work**:
 - #22349   Deprecate sorting of Graph vertices and edges by default
-- #27435   py3: failing doctest in `graph_database.py` with `interactive_query`
 - #28108   py3: ValueError in graph_generators doctests with plantri optional package (follow up of #27948)

 **Needs review**:
-- #27232   is_isomorphic broken with keyword edge_labels=True
 - #27408   Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.

@@ -99,11 +97,13 @@
 - #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`
 - #27695   try to sort vertices to produce consistent graph6 and dig6 strings in Python3
 - #27948   py3: fix doctests with optional package plantri

dcoudert commented 5 years ago

comment:79

All doctests in the standard graphs module are now fixed ! Thanks to all of you for your great help.

We can now check all optional packages. For instance, plantri has 2 failing doctests (#28108).

dcoudert commented 5 years ago

comment:80

The last failing doctests of the optional packages (benzene, bliss, buckygen, csdp, dot2tex and graphviz, gap_packages, igraph and python_igraph, mcqd, plantri, tdlib) are fixed with #27948, #28108 and #28371.

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -5,15 +5,14 @@
 - #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 that will be used to order rows and columns. Currently, we use `.vertices()` by default. If we switch to `list(G)` by default, we have to check that it's not breaking algorithms using these matrices.
-- sort used in methods for checking isomorphisms w/wo edge labels (see also #27232 and #26800). Sorting of lists of possibly unhashable objects is needed here, or may be  a method for checking that there is a permutation from one list to the other could be enough ?

 **Needs work**:
 - #22349   Deprecate sorting of Graph vertices and edges by default
-- #28108   py3: ValueError in graph_generators doctests with plantri optional package (follow up of #27948)

 **Needs review**:
 - #27408   Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.
+- #28371   py3: errors with optional package CSDP

 **Done**
@@ -105,7 +104,16 @@
 - #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)

+**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
+
+
+

dcoudert commented 5 years ago

Description changed:

--- 
+++ 
@@ -4,7 +4,7 @@
 **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 that will be used to order rows and columns. Currently, we use `.vertices()` by default. If we switch to `list(G)` by default, we have to check that it's not breaking algorithms using these matrices.
+- 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**:
@@ -12,7 +12,7 @@

 **Needs review**:
 - #27408   Edge view for graphs -- introduce deprecation warning for `sort=None` as the plan is to set `sort=False` by default.
-- #28371   py3: errors with optional package CSDP
+- #27513   Allow custom order for edges as well as vertices for incidence matrix

 **Done**
@@ -109,6 +109,7 @@
 - #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:**
@@ -116,4 +117,3 @@
 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

-

dcoudert commented 4 years ago

comment:82

it's time to close this ticket.

dcoudert commented 4 years ago

Author: David Coudert

jhpalmieri commented 4 years ago

comment:83

Yes, I agree.

jhpalmieri commented 4 years ago

Reviewer: John Palmieri

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`

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

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

28108: 2 `ValueError?` in `graph_generators.py` doctests with `plantri` optional package (follow up of #27948)

27232: fix failing doctests in `is_isomorphic`, which are the last 8 remaining failing doctests in `generic_graph.py`

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

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