fix: changed base location for graph_from_graphdb and added tests #1732
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maelle
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maelle
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good idea!
I see a typo in the file "algothitms", it could be fixed at the same time.
I wonder whether the database should be cached in an user dir. Should the argument of where to save it be exposed?
I suggest hosting it under the igraph organization for the purposes of allowing the function to work. In our own copy, we should mention the license and list the original authors, in addition to linking to Zenodo. I'm really glads to see that this is on Zenodo given that the MIVIA website is gone now.
This dataset is way too large for the igraphdata package. I suggest using a separate repo, exactly what @schochastics did, but under the igraph organization. I believe you should be able to create a new repo, but if not let me know and I'll see if I can fix that. Can this function operate with a local copy of the database? Would this be easy to implement, and if yes, can we include an explanation of how to do it? Other than the comments above, this LGTM. |
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I will try to host it under the igraph org and put all the necessary information into the README. The files have a CC license so that should all be fine. I also checked that it works with a local copy. You simply need to provide the path to the database. I will also update the docs so that this is clear |
krlmlr
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Do these actually work and look better? Please merge when good and green.
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Co-authored-by: Maëlle Salmon <maelle.salmon@yahoo.se>
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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Fix #1712
Downloaded the database from here: https://zenodo.org/records/11204020
and hosted it here: https://github.com/schochastics/graphsdb/
General question: should we host it somewhere else?