docs: link to replacements of deprecated functions #1823
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Would you like to share the code that did the search+replace? We might run into conflicts, I'd also like to tweak a detail. |
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There's no code. I did it with a text editor, and regex find/replace, so that I could review at least a subset of replacements before proceeding. |
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I now see you asked, |
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I can fix this without too much trouble. |
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@krlmlr, this is done now. Replacement across all files in
I didn't notice anything going wrong. But I did notice an unusual way to refer to a class (use of parentheses), which is also fixed now. |
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Thanks! |
schochastics
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Co-authored-by: Kirill Müller <krlmlr@users.noreply.github.com>
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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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This is a simple find-and-replace job to actually link to replacements of deprecated functions instead of simply mentioning them.
Is there a reason it wasn't done this way? Perhaps it is not standard in the R world?
Do we want
[`some_fun()`](inline code) or simply[some_fun()](not in code style)? I see both styles used at the moment.I am hoping this encourages people to upgrade to the non-deprecated alternative more quickly. I still see tutorials published with the old names ...
The search pattern was: