chore: Update vendored sources to igraph/igraph@0f383457a13864b86a29eed4faf4efaade4c1254 #1299

krlmlr · 2024-03-12T11:17:21Z

Update to the develop branch of igraph/C. @Antonov548: Can you please pick up from here?

Closes #1296.

aviator-app · 2024-03-12T11:17:26Z

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feat: added generic, algorithm-agnostic versions of igraph_count_automorphisms(), igraph_automorphism_group() and igraph_canonical_permutation() refactor!: rename BLISS-specific isomorphism functions so they always have _bliss in the suffix - part 2 refactor!: rename BLISS-specific isomorphism functions so they always have _bliss in the suffix Merge branch 'master' into develop fix: fix segfault in GraphML reader refactor: remove unneeded include refactor: remove deprecated igraph_decompose_destroy() Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge pull request igraph/igraph#2470 from igraph/feat/is-biconnected Merge branch 'master' into develop Merge pull request igraph/igraph#2462 from igraph/feat/attribute-record-list Merge branch 'master' into develop fix: re-added missing master header in changelog Merge branch 'master' into develop Merge branch 'master' into develop refactor: consistently use ARPACK_DEFAULTS as the default arpack options chore: updated changelog feat: include Texinfo docs in source tarball fix: fix typo fix: look for either docbook2x-texi or docbook2texi fix: replace utf8 with utf-8 to prevent a warning when building texinfo docs ci: make sure that the Texinfo docs are also built Add target to build documentation in info format docs: clarify that Infomap considers edge directions fuzzer: update libxml2 to 2.12.3 fix: correct header includion in cliquer chore(deps): bump github/codeql-action from 2 to 3 chore(deps): bump actions/upload-artifact from 3 to 4 doc: clarify the effect of loop edges in igraph_similarity_inverse_log_weighted(), closes igraph/igraph#2448 refactor: rename deprecated functions in generated interfaces docs: fix typos refactor: clean up dfs/bfs and their docs refactor: replace void* with const igraph_vector_ptr_t* in attribute-related functions; more refactoring coming soon refactor!: strvector now contains pointers to const Merge branch 'master' into develop refactor: rename igraph_i_attribute_gettype() to igraph_i_attribute_get_type() for sake of consistency refactor: simplify attribute table init, copy and destroy methods chore: post-release tasks Merge branch 'master' into develop fix: fix stimulus function spec Merge branch 'master' into develop fix: community_spinglass_single() now uses igraph_real_t for output parameters that return real values, fixes igraph/igraph#2435 Merge branch 'master' into develop fix: fix jdm unit test and add rate-limited interruption to erdos_renyi_gnm_multi() fix: fix Stimulus type specs Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop fix: fix Stimulus type specs fix: allow interruption for multigaph case of G(n,m) generator Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop chore: fixed line endings and stale whitespace fix!: NCOL and LGL readers now use a default weight of 1, closes igraph/igraph#2395 fix: EDGEWEIGHTS type parameter was renamed to EDGE_WEIGHTS earlier Merge branch 'master' into develop Merge branch 'master' into develop refactor!: igraph_vector_swap() and igraph_matrix_swap() no longer return an error code Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Multi edge support for igraph_bipartite_game_gnm (igraph/igraph#2375) Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop correct number of erdos_renyi arguments in voronoi test chore: fix mismerged changelog refactor!: remove deprecated allocation macros Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop docs: clarify that usage of sub-headers is not supported closes igraph/igraph#2332 Merge branch 'master' into develop refactor: more readable variable named in similarity code Use two vertex selectors in Jaccard and Dice (igraph/igraph#2346) Merge branch 'master' into develop chore: update changelog, mentioning the the Pajek reader/writer now uses the 'name' attribute docs: update Pajek docs, mentioning that the 'name' attribute is used Merge pull request igraph/igraph#2276 from igraph/fix/pajek-names Merge pull request igraph/igraph#2265 from VRajesh7649/feat/erdos_penyi_gnm_multiedges Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop refactor: fixed singular/plural issues with abstract types in types.yaml, now they are consistent fix: fix typo in functions.yaml refactor: rename igraph_delete_vertices_idx() to igraph_delete_vertices_map(), closes igraph/igraph#2310 Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop chore: update changelog [skip ci] refactor: igraph_rng_set_default() now returns old RNG, fixes igraph/igraph#2273 Merge branch 'master' into develop Merge branch 'master' into develop move community_fastgreedy example to tests move community_edge_betweenness example to tests (igraph/igraph#2270) Revert "move community_edge_betweenness example to tests" move community_edge_betweenness example to tests Merge branch 'master' into develop refactor!: igraph_vector_shuffle() no longer returns an error code, closes igraph/igraph#2268 Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop fix: standards-complient definition for igraph_allow_interruption() refactor: replace IGRAPH_SUCCESS by false in IGRAPH_ALLOW_INTERRUPTION() refactor!: interruption handlers now return igraph_bool_t Merge branch 'master' into develop refactor!: removed void* argument of interruption handlers Merge branch 'master' into develop refactor!: igraph_induced_subgraph_map() does not offset the vertex IDs in the mapping any more refactor!: igraph_delete_vertices_idx() does not offset the vertex IDs in the mapping any more Merge branch 'master' into develop Merge branch 'master' into develop Merge branch 'master' into develop add mode parameter to distances_johnson (igraph/igraph#2218) Merge branch 'master' into develop chore: added 'develop' section to changelog Merge branch 'master' into develop Merge branch 'master' into develop refactor: remove unused 'destroy' field from heap data types; ABI-breaking change; refs igraph/igraph#2214

aviator-app · 2024-03-12T13:41:32Z

This pull request failed to merge: this PR is in draft state. Remove the blocked label to re-queue.

Additional debug info: PR was marked as draft after queueing

aviator-app · 2024-03-12T14:00:18Z

This pull request can't be queued because it's currently a draft.

Antonov548 · 2024-03-15T23:37:00Z

@krlmlr I couldn't get from where is version of igraph/C which is used in this pull request and why there so much difference with the current. For me it seems it's some old version.

Antonov548 · 2024-03-15T23:45:06Z

Was this line added on purpose?

rigraph/tools/update-cigraph.sh

Line 58 in 6eeb6e4

git cherry-pick b6f576d25dc2c02dfeb2979716ef4809e4404c99 --no-edit

krlmlr · 2024-03-16T03:21:56Z

Have you seen #1296?

See https://github.com/igraph/rigraph/blame/6eeb6e4a575a8c0f718f0606cfc8805932b9e604/tools/update-cigraph.sh#L58 for where the line in question was added. True, this should have been a comment in the code.

Antonov548 · 2024-03-21T08:54:16Z

@szhorvat @ntamas
This is what I added manually to the C/igraph. There is missmutch of definition and declaration:

rigraph/src/vendor/cigraph/src/isomorphism/bliss.cc

Lines 261 to 264 in 90bb9e9

    
           igraph_error_t igraph_canonical_permutation( 
        
               const igraph_t *graph, const igraph_vector_int_t *colors, 
        
               igraph_vector_int_t *labeling 
        
           ) {

ntamas · 2024-03-21T10:33:30Z

Thanks, fixed in igraph/igraph@44541b9ef

krlmlr · 2024-03-22T16:49:50Z

Thanks. So, now we can compile, but tests fail? Can we identify which, and then perhaps create a checklist?

Antonov548 · 2024-03-22T18:07:52Z

Thanks. So, now we can compile, but tests fail? Can we identify which, and then perhaps create a checklist?

Some tests are failing with stop of execution. Can you remind please how I can run without stop of execution? To see all failing tests.

krlmlr · 2024-03-22T18:12:45Z

TESTTHAT_PARALLEL=false R -q -e 'testthat::test_local(reporter = "location")

Antonov548 · 2024-04-16T11:35:16Z

Tests are passing 👍
Examples are failing 👎

szhorvat · 2024-04-16T12:32:31Z

To make this work well, I suggest basing the upgrade on the changelog, not on the tests. Reading the changelog is an absolute must to be able to adapt not just functions, but also their documentation, appropriately. Expect some subtle changes that will be missed if you rely on tests only.

https://github.com/igraph/igraph/blob/develop/CHANGELOG.md

szhorvat · 2024-04-20T21:57:48Z

In the meantime some more breaking changes were made on the C side.

szhorvat · 2024-04-25T10:05:41Z

src/rinterface_extra.c

@@ -2299,9 +2299,9 @@ igraph_error_t R_igraph_interrupt_handler(void *data) {
   */
  if (R_ToplevelExec(checkInterruptFn, NULL) == FALSE) {
    IGRAPH_FINALLY_FREE();
-    return IGRAPH_INTERRUPTED;
+    return 1;


It's a good idea to use true / false instead of 1 and 0. That way it's immediately clear that what's returned is a boolean, not an integer. The same goes for NULL vs 0.

krlmlr · 2024-07-18T09:13:20Z

@Antonov548: can you please refresh this PR, to see where we'll be at when upgrading the C core?

krlmlr added the mergequeue label Mar 12, 2024

krlmlr marked this pull request as draft March 12, 2024 11:18

aviator-app bot force-pushed the develop branch from cdc7f95 to 837c3c6 Compare March 12, 2024 13:41

aviator-app bot added the blocked label Mar 12, 2024

aviator-app bot removed the mergequeue label Mar 12, 2024

Antonov548 added 3 commits March 20, 2024 11:04

update vendor/cigraph

fce7ecf

compiling

90bb9e9

Merge remote-tracking branch 'origin/main' into develop

eb5314b

krlmlr self-assigned this Apr 9, 2024

Antonov548 added 5 commits April 12, 2024 11:34

Merge remote-tracking branch 'origin/main' into develop

530b9d9

fix compilation

70d9ce1

add multiple for R_igraph_bipartite_game_gnm

761f217

permute lose bliss info

65da706

update ARPACK_STORAGE

733a30b

krlmlr assigned Antonov548 and unassigned krlmlr Apr 13, 2024

fix: attribute records list

937b16c

Antonov548 added 2 commits April 24, 2024 17:36

fix return type

622acfb

fix warning

e7c1af2

szhorvat reviewed Apr 25, 2024

View reviewed changes

maelle added the hackathon-topic 📆 label May 23, 2024

krlmlr removed the hackathon-topic 📆 label Jul 18, 2024

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chore: Update vendored sources to igraph/igraph@0f383457a13864b86a29eed4faf4efaade4c1254 #1299

chore: Update vendored sources to igraph/igraph@0f383457a13864b86a29eed4faf4efaade4c1254 #1299

krlmlr commented Mar 12, 2024 •

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krlmlr commented Jul 18, 2024

chore: Update vendored sources to igraph/igraph@0f383457a13864b86a29eed4faf4efaade4c1254 #1299

Are you sure you want to change the base?

chore: Update vendored sources to igraph/igraph@0f383457a13864b86a29eed4faf4efaade4c1254 #1299

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