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@szhorvat szhorvat commented Mar 12, 2025

This PR makes the necessary doc updates after this C core PR: igraph/igraph#2720

Merge this only after:

  • the vendoring script is fixed and the C core change is lifted into R
  • the auto-formatter is fixed and docs can be properly regenerated
  • document() must first be run for the changes in this PR

@szhorvat szhorvat force-pushed the docs/infinite-nei branch from 565d064 to 7de97dd Compare March 13, 2025 12:05
…unctions

after negative/infinite values became allowed in the C core
@szhorvat szhorvat force-pushed the docs/infinite-nei branch from 7de97dd to 0ab93f4 Compare March 17, 2025 19:43
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@krlmlr krlmlr merged commit 6e13dde into main Mar 20, 2025
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@krlmlr krlmlr deleted the docs/infinite-nei branch March 20, 2025 09:39
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krlmlr commented Mar 20, 2025

Thanks!

krlmlr added a commit that referenced this pull request Oct 13, 2025
igraph 2.2.0

Update C core to version 0.10.17. See <https://github.com/igraph/rigraph/blob/20552ef94aed6ae4b23465ae8c7e4d3b0e558c71/src/vendor/cigraph/CHANGELOG.md> for a complete changelog, in particular the section "Breaking changes".

- Generate almost all R implementations (#2047).

- Expose `align_layout()` and add to `layout_nicely()` to align layout with axis automatically (#1907, #1957, #1958).

- Expose `simple_cycles()` which lists all simple cycles (#1573, #1580).

- Expose `is_complete()`, `is_clique()` and `is_ivs()` (#1316, #1388, #1581).

- Expose `find_cycle()` (#1471, #1571).

- Expose `feedback_vertex_set()` to find a minimum feedback vertex set in a graph (#1446, #1447, #1560).

- Add `weights` parameter to `local_scan()` (#1082, #1448, #1982).

- Add more layouts to `tkplot()` (#160, #1967).

- Add `plot(mark.lwd = )` to change line width of mark.groups (#306, #1898).

- Add `plot(vertex.label.angle = , vertex.label.adj = )` arguments to rotate vertex labels (#106, #1899).

- Add relative size scaling to vertices in `plot()` (@gvegayon, #172).

- Split `sample_bipartite()` into two functions for the G(n, m) and G(n, p) case (#630, #1692).

- Implement multi attribute assignment (#55, #1916) and adding attributes via data frames (#1373, #1669, #1716). Support factors in `graph_from_data_frame()` (#34, #1829).

- All `_hrg()` functions check their argument (#1074, #1699).

- HRG printing with `type = "auto"` uses `"plain"` for large trees (#1879).

- `get_edge_ids()` accepts data frames and matrices (#1663).

- `igraph_version()` returns version of C core in an attribute (#1208, #1781).

- Breaking change: change arguments default and order for `graph_from_lcf()` (#1858, #1872).

- Breaking change: Subset assignment of a graph avoids addition of double edges and ignores loops unless the new `loops` argument is set to `TRUE` (#1662, #1661).

- Breaking change: remove deprecated `neimode` parameter from `bfs()` and `dfs()` (#1105, #1526).

- Breaking change: stricter deprecation of non-functional parameters of `layout_with_kk()` and `layout_with_fr()` (#1108, #1628).

- `NA` attribute values are replaced with default values in `plot()` (#293, #1707).

- `NA` checking only in from/to columns of edge data frame (#1906).

- Keep vertex attribute type for `disjoint_union()` (#1640, #1909).

- Error in bipartite projection if `type` is not a vertex attribute (#898, #1889).

- Do not try to destroy non-initialized SIR objects upon error (#1888).

- Added proper `NA` handling for matrix inputs (#917, #918, #1828).

- Remove string matrix support from functions operating on biadjacency matrices (#1540, #1542, #1803).

- Integer vectors are validated before transferring them to the C library (#1434, #1582).

- Changed base location for `graph_from_graphdb()` and added tests (#1712, #1732).

- Recycling of logical vectors when indexing into edge/vertex selectors now throws an error (#848, #1731).

- Use `function()` instead of `(x)` in `arrow.mode` (#1722).

- Temporarily disable generating an interface for `igraph_simple_cycles_callback()` as the framework for handling callback functions is not yet present.

- Adjust loop position to vertex size in `plot()` (#1980).

- Don't rescale plot coordinates to `[-1,1] x [-1,1]` by default (#1492, #1956, #1962).

- Fail if `"layout"` attribute doesn't match the number of vertices (#1880).

- Automatically arrange loops in `plot()` (#407, #556, #1881).

- Vectorized drawing of arrows in `plot()` (#257, #1904).

- Allow more than one edge label font family in `plot()` (#37, #1896).

- Pie shapes now work as intended (#1882, #1883).

- Loops not plotted on canvas (#1799, #1800).

- Replace `NA` values in `label` attributes in `plot()` with default values (#1796, #1797).

- Removed duplicated plotting of arrow heads (#640, #1709).

- Correct mapping of edge label properties in plots when loops are present (#157, #1706).

- Welcome Maëlle Salmon and David Schoch as authors (#1733), add author links (#1821).

- Remove demos (#2008).

- Add 2023 preprint (#1240, #1984).

- Update allcontributors info (#1975).

- Link to replacements of deprecated functions (#1823).

- Add documentation of all file formats to `read_graph()` and `write_graph()` (#777, #1969). Recommend `saveRDS()` and `readRDS()` for saving and loading graphs (#1242, #1700).

- Document return value of `make_clusters()` (#1794).

- Clarify that `girth()` returns `Inf` for acyclic graphs (@eqmooring, #1831).

- Clarify the use of weights in `layout_with_kk()`.

- Refer to current latest version of R in troubleshooting page.

- Fix typos in `laplacian_matrix()` documentation.

- Document ellipsis in `cohesion()` (#971, #1985).

- Correct the description of the `weights` parameter of `hits_scores()`.

- Better describe output of `all_shortest_paths()` (#1029, #1778).

- `make_graph()` now supports `"Groetzsch"` as an alias of `"Grotzsch"`. This change was implemented in the C core.

- Update description of `order` parameter of `ego()` and related functions (#1746).

- Added lifecycle table (#1525).

- Add more about igraph.r2cdocs in the contributing guide (#1686, #1697).

- Accelerate check if an index sequence corresponds to the entire list of vertices (#1427, #1818).

- Faster single bracket querying of a graph (#1465, #1658).
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3 participants