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igraph 1.6.0

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@github-actions github-actions released this 13 Dec 01:40
· 1837 commits to main since this release
## Breaking changes

- New `arpack_defaults()` replaces `igraph.arpack.default` and `arpack_defaults` lists (#800), with consistent usage checks (#966).

- Define methods for `ape::as.phylo()` instead of own `as_phylo()` generic, remove deprecated `asPhylo()` (#763).

- `bfs()` with unreachable nodes returns zero instead of `NaN` as `rank` (#956), and negative instead of `NaN` for `dist` (#926).

- `random_walk()` adds one more step, the resulting list of vertices is of length `steps + 1` (#934).

- `girth()` returns `Inf` for acyclic graphs (#931).

- Remove some behaviour / parameters that were deprecated in 1.3 (#842).

- Remove `scg_eps()`, `scg_group()` and `scg_semi_proj()`, broken and no longer maintained (#946).

## Bug fixes

- Fix `printf()` warning (#975).

- Fix calls to `isSymmetric()` for matrix objects with a class (#965).

- Reduce frequency of interruption checks (#957).

## Features

- Change "incidence matrix" naming to "biadjacency matrix" (#962).

- Add aliases using the neighborhood terminology for all ego functions: (#950).

- Rename arguments to `assortativity(values, values.in)` from `types1` and `types2` (#952).

- Add ellipsis to `cluster_label_prop()` (#954).

- Placeholders for `is_acyclic()` and `is_forest()`, to be implemented in igraph 2.0.0 (#945).

- `is_tree(details = TRUE)` designates the first vertex as root for non-trees (#935).

- `all_shortest_paths()` returns the vertex list in both `res` and `vpaths` components (#930).

- Improve symmetry check for adjacency matrices on input (#911).

- Warn if non-symmetric undirected adjacency matrix (#904).

## Documentation

- Remove duplicate `\seealso{}` (#948).

- Update `knnk()` and `sir()` docs.

- Fix formula in `reciprocity()` docs.

- `strength()` does not give a warning when no weights are given.

- Update `sample_smallworld()` manual page (#895).

- Correct documentation for weighted cliques.

- Update Erdos-Renyi model docs.

## Testing

- Clean up tests (#967).

- Stabilize tests for `cluster_label_prop()` (#932), `sample_pa()` (#927), `cluster_louvain()` (#933), SIR (#936), `sample_forestfire()` (#929).

- Hard-code graph used in test (#928).

- Update GML test file (#925).

- Improve test for sampling from Dirichlet distribution (#923).

- Omit test that no longer holds with igraph 0.10 (#922).

- Stabilize test in preparation for upgrade (#920).

- Stabilize plot test (#919).

- Fix checks.