Tags: maelle/rigraph
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igraph 1.3.5.9101 ## Bug fixes - Handle the default NULL value of frame.plot properly. - Do not use 'frame' partial argument when calling plot.default(). - `NULL` means empty vertex or edge list again in all functions (igraph#625). * NULL remains an alias for an empty vertex or edge list Reverts d05ac31. * Special case * Revert igraph#608 * Style * doc: fix docs - Fix builds with some `make` variants (igraph#617). - Fix syntax error in new unit test. - Fixed indexing of result vertices in convex_hull(), closes igraph#613. - Avoid defining PACKAGE_VERSION at all in Makevars (igraph#600). * Avoid defining PACKAGE_VERSION at all in Makevars * Fix test * don't try to tweak igraph_version.h.in now that we don't pass PACKAGE_VERSION from the compiler CLI - PACKAGE_VERSION is now quoted dynamically in igraph_version.h to avoid quoting in the Windows shell. - Try alternative escaping of PACKAGE_VERSION in the Windows build. - Try not to escape PACKAGE_VERSION in the Windows build. - Do not use sprintf in C code. - Fix detection of already-applied patches in tools/apply-patch.sh for newer versions of macOS. - Dfs()$root index should be 1-based, fixes igraph#589. - Fix a bug in graph_from_incidence_matrix() for directed=T, mode='all' from sparse matrices, fixes igraph#354. - Fix a bug in graph_from_incidence_matrix() for directed=T, mode='all' when the graph also had weights, fixes igraph#353. - Trivial speedup in get.adjacency.dense() when using attributes. - Fix typon in previous commit. - Fix as.dendrogram.communities() for large dendrograms, closes igraph#292. - Fix documentation of graph_from_adj_list, closes igraph#170. - Use on.exit() to restore par(xpd=...). - Remove unimplemented pie.border from docs, refs igraph#132. - Restore par(xpd=...) after plotting. - Eliminate Clang 15 warnings. - Bump max iteration count of eigenvector centrality to 3000. - Defer resolution of IGRAPH_VERSION in igraph_version.h to make it harder to publish igraph on CRAN with an invalid version number. - Fix typo in name of test file. - Distances(algorithm='johnson') now throws an error if mode != 'out' for directed graphs. - Removed ARPACK homepage reference now that the homepage is gone. ## Features - Support `index = NULL` when setting attributes (igraph#608). - New id argument to print(), with new option print.id (igraph#605). - Tkplot() now has a palette, also fixes igraph#159. ## Chore - Fix make from a clean repository. - Track revdepcheck results (igraph#621). - Move to single branch setup (igraph#620). - Stabilize vs-es tests (igraph#631). - Add fledge workflow. - Prepare for using fledge for managing NEWS.md (igraph#615). - Style remaining files (igraph#614). - Clarify changelog item [skip ci]. - Apply styler (igraph#612). * Attach code to roxygen2 blocks * Remove space at EOL * Turn off styler in generated code * none * spaces * indention * line_breaks * line_breaks, strict = TRUE * Manual * tokens * tokens, strict = TRUE * Document - Store generated files (@krlmlr, igraph#597). - Remove or replace `\dontrun{}` (igraph#593). * Remove or replace \dontrun * Qualify * Unexported * Make has_glpk() and has_graphml() available in package - Updated changelog. - Extract is_single_index() and get_single_index() (igraph#596). - Update vendored igraph. - Updated changelog. - Update issue template. - Updated vendored igraph. - Update vendored igraph. - Update vendored igraph. - Correct misstatement in NEWS. - Updated vendored igraph. - Update NEWS [skip ci]. - Updated vendored igraph. ## Documentation - Further polish print_all() docs. - Clarify print_all() output. - Polish sample_fitness_pl() docs. - Wrap README badges for detection by pkgdown (igraph#637). - Clarify documentation of alpha_centrality. - Update Erdős-Rényi sampler docs, change an incorrect G(n,p) to G(n,m) in sample_bipartite(). - Use Markdown in documentation (igraph#624). * Enable Markdown, mostly whitespace changes * Indent * Parentheses * as.dendrogram() * print() * plot() * summary() * Pipe * simple * full - Fix typo [skip ci]. - Fix minor typo [skip ci]. - Improve PageRank docs. - Clarify edge_density docs. - Add references to realize_degseq() docs. ## Refactoring - Renamed automorphisms() to count_automorphisms(). ## Testing - Add an example for a plot test (igraph#598). * Add an example for a plot test * Fix random seed - Skip unstable leading eigenvector stress test on R 3.4 and 3.5. ## doc - Switch to https in a URL that CRAN check was complaining about. ## WIP - Add coverage reporting (igraph#592). * Micro-tweaks to smoke test * Tweaks to main test * Add coverage workflow * Install dependencies once * Create source package first * Make DESCRIPTION first * Avoid installing R * Try stable without needs * Move to Config/Needs * Use RSPM * setwd() first * Configure codecov * Fix name * Fix shell call * Add coverage needs * Fix codecov() call * Use numbered oldrel ## Uncategorized - PLACEHOLDER https://github.com/maelle/rigraph/pull/642 (igraph#642). - Added igraph extended tutorial as R vignette (@ntamas, igraph#587). - Update igraph_extended_tutorial_R_vignette_english.Rmd (@ntamas, igraph#587). - Bump version to 1.3.5.9095 (@ntamas, igraph#587). - A bunch of fixes after review and rename (@ntamas, igraph#587). - Adapt one line suggested by @szhorvat (@ntamas, igraph#587). - R vignette compiles into html and PDF using rmarkdown (@ntamas, igraph#587). - Remove methods since R is not very much OO (@ntamas, igraph#587). - Bump version to 1.3.5.9096 (@ntamas, igraph#587). - Corrections throughout (@ntamas, igraph#587). - Bump version to 1.3.5.9097 (@ntamas, igraph#587). - Fix: fix deprecation warnings about 'from' and 'to' in edge selectors (@ntamas, igraph#587). - Read/write files corrected (@ntamas, igraph#587). - Remove Spanish version, will be a separate PR (@ntamas, igraph#587). - NEWS.md went for a spin, bring it back (@ntamas, igraph#587). - Minor tweaks, adjusted figure sizes, work in progress (@ntamas, igraph#587). - Title, notes, first paragraph (@ntamas, igraph#587). - Starting igraph (@ntamas, igraph#587). - More corrections (@ntamas, igraph#587). - Clean up a bunch of Python-isms in the second half (@ntamas, igraph#587). - Session info, headers down a notch, some wording (@ntamas, igraph#587). - Bump version to 1.3.5.9098 (@ntamas, igraph#587). - Doc: more updates to the vignette (@ntamas, igraph#587). - Bump version to 1.3.5.9099 (@ntamas, igraph#587). - Doc: vignette cleanup finished (@ntamas, igraph#587). - Revert changes to DESCRIPTION (@ntamas, igraph#587). - Revert changes to NEWS.md (@ntamas, igraph#587). - Ignore. - Update instructions. - Ignore. - Automated changes. - Run autoconf on 22.04. - Automated changes. - PLACEHOLDER https://github.com/maelle/rigraph/pull/634 (igraph#634). - PLACEHOLDER https://github.com/maelle/rigraph/pull/632 (igraph#632). - Fix: distances() with algorithm='johnson' now handles all mode parameter values correctly. - Docs: better explain use cases of Johnson's shortest path length algorithm. - PLACEHOLDER https://github.com/maelle/rigraph/pull/619 (igraph#619). - Man to repository (@krlmlr, igraph#602). - Src to repository (@krlmlr, igraph#602). - Unignore src (@krlmlr, igraph#602). - Update makefile (@krlmlr, igraph#602). - Delete config.h.in from src (@krlmlr, igraph#602). - Add validation after make igraph (@krlmlr, igraph#602). - Typo (@krlmlr, igraph#602). - Remove duplicates (@krlmlr, igraph#602). - Add loops and multiple argument (@krlmlr, igraph#602). - Update man (@krlmlr, igraph#602). - Fix tests and printing (@krlmlr, igraph#602). - Add `ignore` option for `loops` (@krlmlr, igraph#602). - Remove default argument (@krlmlr, igraph#602). - Document arguments (@krlmlr, igraph#602). - Document arguments (@krlmlr, igraph#602). - Consistent default arguments (@krlmlr, igraph#602). - Hide new arguments for now, revert tests (@krlmlr, igraph#602). - Document (@krlmlr, igraph#602). - Fix: don't expose 'multiple' argument of igraph_i_incident (@krlmlr, igraph#602). - Fix: disallow multiple edges in as_graphnel() (@krlmlr, igraph#602). - Chore: update changelog (@krlmlr, igraph#602). - Fix: cleaning up, get_adjedgelist() should not expose multiple=..., only loops, but it's okay for get_adjlist() (@krlmlr, igraph#602). - Test: add unit test for loop edge duplication in as_graphnel() (@krlmlr, igraph#602). - PLACEHOLDER https://github.com/maelle/rigraph/pull/607 (igraph#607). - PLACEHOLDER https://github.com/maelle/rigraph/pull/606 (igraph#606). - PLACEHOLDER https://github.com/maelle/rigraph/pull/603 (igraph#603). - PLACEHOLDER https://github.com/maelle/rigraph/pull/298 (igraph#298). - PLACEHOLDER https://github.com/maelle/rigraph/pull/599 (igraph#599). - PLACEHOLDER https://github.com/maelle/rigraph/pull/595 (igraph#595). - PLACEHOLDER https://github.com/maelle/rigraph/pull/594 (igraph#594). - 9L -> igraph_t_idx_attr. - 3L and 4L. - Igraph_attr_idx. - Fix: element 10 of the igraph data structure is an R env. - Faster build process. - Avoid @include. - Use new target. - Update contributing guide. - Remove auto.R. - Aaa-auto.R. - Remove remaining @ include tags. - Remove more library(igraph) and library(Matrix). - Avoid require(digest). - Avoid require(Matrix) in tests. - PLACEHOLDER https://github.com/maelle/rigraph/pull/580 (igraph#580). - PLACEHOLDER https://github.com/maelle/rigraph/pull/576 (igraph#576). - Remove spaces at EOL. - Remove blank lines at EOF.
igraph 1.3.5.9097 ## Bug fixes - `NULL` means empty vertex or edge list again in all functions (igraph#625). * NULL remains an alias for an empty vertex or edge list Reverts d05ac31. * Special case * Revert igraph#608 * Style * doc: fix docs - Fix builds with some `make` variants (igraph#617). - Fix syntax error in new unit test. - Fixed indexing of result vertices in convex_hull(), closes igraph#613. - Avoid defining PACKAGE_VERSION at all in Makevars (igraph#600). * Avoid defining PACKAGE_VERSION at all in Makevars * Fix test * don't try to tweak igraph_version.h.in now that we don't pass PACKAGE_VERSION from the compiler CLI - PACKAGE_VERSION is now quoted dynamically in igraph_version.h to avoid quoting in the Windows shell. - Try alternative escaping of PACKAGE_VERSION in the Windows build. - Try not to escape PACKAGE_VERSION in the Windows build. - Do not use sprintf in C code. - Fix detection of already-applied patches in tools/apply-patch.sh for newer versions of macOS. - Dfs()$root index should be 1-based, fixes igraph#589. - Fix a bug in graph_from_incidence_matrix() for directed=T, mode='all' from sparse matrices, fixes igraph#354. - Fix a bug in graph_from_incidence_matrix() for directed=T, mode='all' when the graph also had weights, fixes igraph#353. - Trivial speedup in get.adjacency.dense() when using attributes. - Fix typon in previous commit. - Fix as.dendrogram.communities() for large dendrograms, closes igraph#292. - Fix documentation of graph_from_adj_list, closes igraph#170. - Use on.exit() to restore par(xpd=...). - Remove unimplemented pie.border from docs, refs igraph#132. - Restore par(xpd=...) after plotting. - Eliminate Clang 15 warnings. - Bump max iteration count of eigenvector centrality to 3000. - Defer resolution of IGRAPH_VERSION in igraph_version.h to make it harder to publish igraph on CRAN with an invalid version number. - Fix typo in name of test file. - Distances(algorithm='johnson') now throws an error if mode != 'out' for directed graphs. - Removed ARPACK homepage reference now that the homepage is gone. ## Features - Support `index = NULL` when setting attributes (igraph#608). - New id argument to print(), with new option print.id (igraph#605). - Tkplot() now has a palette, also fixes igraph#159. ## Chore - Track revdepcheck results (igraph#621). - Move to single branch setup (igraph#620). - Stabilize vs-es tests (igraph#631). - Add fledge workflow. - Prepare for using fledge for managing NEWS.md (igraph#615). - Style remaining files (igraph#614). - Clarify changelog item [skip ci]. - Apply styler (igraph#612). * Attach code to roxygen2 blocks * Remove space at EOL * Turn off styler in generated code * none * spaces * indention * line_breaks * line_breaks, strict = TRUE * Manual * tokens * tokens, strict = TRUE * Document - Store generated files (@krlmlr, igraph#597). - Remove or replace `\dontrun{}` (igraph#593). * Remove or replace \dontrun * Qualify * Unexported * Make has_glpk() and has_graphml() available in package - Updated changelog. - Extract is_single_index() and get_single_index() (igraph#596). - Update vendored igraph. - Updated changelog. - Update issue template. - Updated vendored igraph. - Update vendored igraph. - Update vendored igraph. - Correct misstatement in NEWS. - Updated vendored igraph. - Update NEWS [skip ci]. - Updated vendored igraph. ## Documentation - Clarify documentation of alpha_centrality. - Update Erdős-Rényi sampler docs, change an incorrect G(n,p) to G(n,m) in sample_bipartite(). - Use Markdown in documentation (igraph#624). * Enable Markdown, mostly whitespace changes * Indent * Parentheses * as.dendrogram() * print() * plot() * summary() * Pipe * simple * full - Fix typo [skip ci]. - Fix minor typo [skip ci]. - Improve PageRank docs. - Clarify edge_density docs. - Add references to realize_degseq() docs. ## Refactoring - Renamed automorphisms() to count_automorphisms(). ## Testing - Add an example for a plot test (igraph#598). * Add an example for a plot test * Fix random seed - Skip unstable leading eigenvector stress test on R 3.4 and 3.5. ## doc - Switch to https in a URL that CRAN check was complaining about. ## WIP - Add coverage reporting (igraph#592). * Micro-tweaks to smoke test * Tweaks to main test * Add coverage workflow * Install dependencies once * Create source package first * Make DESCRIPTION first * Avoid installing R * Try stable without needs * Move to Config/Needs * Use RSPM * setwd() first * Configure codecov * Fix name * Fix shell call * Add coverage needs * Fix codecov() call * Use numbered oldrel ## Uncategorized - Ignore. - Update instructions. - Ignore. - Automated changes. - Run autoconf on 22.04. - Automated changes. - PLACEHOLDER https://github.com/maelle/rigraph/pull/634 (igraph#634). - PLACEHOLDER https://github.com/maelle/rigraph/pull/632 (igraph#632). - Fix: distances() with algorithm='johnson' now handles all mode parameter values correctly. - Docs: better explain use cases of Johnson's shortest path length algorithm. - PLACEHOLDER https://github.com/maelle/rigraph/pull/619 (igraph#619). - Man to repository (@krlmlr, igraph#602). - Src to repository (@krlmlr, igraph#602). - Unignore src (@krlmlr, igraph#602). - Update makefile (@krlmlr, igraph#602). - Delete config.h.in from src (@krlmlr, igraph#602). - Add validation after make igraph (@krlmlr, igraph#602). - Typo (@krlmlr, igraph#602). - Remove duplicates (@krlmlr, igraph#602). - Add loops and multiple argument (@krlmlr, igraph#602). - Update man (@krlmlr, igraph#602). - Fix tests and printing (@krlmlr, igraph#602). - Add `ignore` option for `loops` (@krlmlr, igraph#602). - Remove default argument (@krlmlr, igraph#602). - Document arguments (@krlmlr, igraph#602). - Document arguments (@krlmlr, igraph#602). - Consistent default arguments (@krlmlr, igraph#602). - Hide new arguments for now, revert tests (@krlmlr, igraph#602). - Document (@krlmlr, igraph#602). - Fix: don't expose 'multiple' argument of igraph_i_incident (@krlmlr, igraph#602). - Fix: disallow multiple edges in as_graphnel() (@krlmlr, igraph#602). - Chore: update changelog (@krlmlr, igraph#602). - Fix: cleaning up, get_adjedgelist() should not expose multiple=..., only loops, but it's okay for get_adjlist() (@krlmlr, igraph#602). - Test: add unit test for loop edge duplication in as_graphnel() (@krlmlr, igraph#602). - PLACEHOLDER https://github.com/maelle/rigraph/pull/607 (igraph#607). - PLACEHOLDER https://github.com/maelle/rigraph/pull/606 (igraph#606). - PLACEHOLDER https://github.com/maelle/rigraph/pull/603 (igraph#603). - PLACEHOLDER https://github.com/maelle/rigraph/pull/298 (igraph#298). - PLACEHOLDER https://github.com/maelle/rigraph/pull/599 (igraph#599). - PLACEHOLDER https://github.com/maelle/rigraph/pull/595 (igraph#595). - PLACEHOLDER https://github.com/maelle/rigraph/pull/594 (igraph#594). - 9L -> igraph_t_idx_attr. - 3L and 4L. - Igraph_attr_idx. - Fix: element 10 of the igraph data structure is an R env. - Faster build process. - Avoid @include. - Use new target. - Update contributing guide. - Remove auto.R. - Aaa-auto.R. - Remove remaining @ include tags. - Remove more library(igraph) and library(Matrix). - Avoid require(digest). - Avoid require(Matrix) in tests. - PLACEHOLDER https://github.com/maelle/rigraph/pull/580 (igraph#580). - PLACEHOLDER https://github.com/maelle/rigraph/pull/576 (igraph#576). - Remove spaces at EOL. - Remove blank lines at EOF.
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