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Changelog

All notable changes to this project will be documented in this file. See standard-version for commit guidelines.

2.5.0 (2022-06-07)

Features

  • Output per-module codelength in json (eae6650)
  • Print all trials using --print-all-trials (e65bea8), closes #298
  • Write node metadata to json (472b791)

Bug Fixes

  • Constrain numerical arguments to sensible values (174c99f)
  • Don't allow less than 1 trial (18e97e2)
  • Json multilevel modules for higher-order networks (d020c7c), closes #266
  • Only print all trials when running with more than 1 trial (5f9d8b5)
  • python: Fix elapsed running time (1131e84)
  • python: Replace MersenneTwister implementation with stdlib (be3effd)

2.4.1 (2022-05-27)

Bug Fixes

  • Json output causes segfault (78e80c5)

2.4.0 (2022-05-24)

Features

Bug Fixes

  • js-parser: Parse module level from clu files (bb91066)
  • js: Correctly parse clu-files without header (04c39ea)
  • python: Don't allow adding multilayer intra-inter links and ordinary nodes. (8c3d09c), closes #287
  • python: Improve constructor and run signatures (6852e14), closes #286
  • python: no_self_links was always set unless include_self_links=True (9afe5fa)
  • python: Prevent infinite loop in getMultilevelModules (1174b66), closes #284
  • Using deprecated option --include-self-links references missing option --no-loops (1497bf7)

2.3.0 (2022-04-13)

Features

Bug Fixes

  • js: Don't call error on worker terminate (cc57c8c)
  • js: More robust heuristic to parse output format type (33bde00)
  • Match multilayer nodes by node and layer ids when using --cluster-data (b5f6eb3)
  • python: Add no_self_links to api (b3d903d), closes #285
  • python: Add recorded teleportation keyword argument (839e1e0), closes #270
  • python: Fix matchable multilayer id option (8377e07)

2.2.0 (2022-03-07)

Features

  • Add flow-model, higher-order, and state-level fields to json, tree and clu output (24125e5)

Bug Fixes

  • js: More forgiving clu and tree parsing (4764946)
  • Write json output with --no-infomap (c0cec87), closes #268

2.1.0 (2022-02-11)

Features

  • js: Add progress event callback (0fab95b)

Bug Fixes

  • js: Change Typescript types to use mec instead of modularCentrality (298eed3)
  • js: Parse node path as string instead of array of number (51feb73)
  • js: Validate parsed results and throw instead of returning null on failure (5f56b94)

2.0.2 (2022-01-31)

Bug Fixes

  • Change json key modularCentrality to mec (78c7a57)
  • js: Parse directed field in ftree files (916f54a)
  • js: Pass parseLinks to main parse function and correctly detect multilayer tree files (0a40ca6)
  • Minify json output (123c2b1), closes #260

2.0.1 (2022-01-26)

Bug Fixes

  • Bug in write state network to json (50f8de2), closes #262
  • js: Broken parser due to duplicate variable name (f437e13)
  • Use min mass for dangling nodes when regularized (f741d07)

2.0.0 (2022-01-13)

BREAKING CHANGES

  • Removes --input-format.
  • Removes --include-self-links.

Features

Bug Fixes

  • Add new feature flags to python and js api (48245a7)

  • Include self links by default (#255) (1f68940)

  • example: Fix building c++ examples (0d5c063), closes #252

  • Remove superfluous --input-format flag (2dd77c4)

1.9.0 (2021-11-17)

Features

  • python: Add API for intra/inter-layer links (#245) (aa31ab2), closes #244

Bug Fixes

  • Incorrect one-level codelength for higher-order input (5a6d1a1), closes #182
  • Write "directed", not "1", in cli output notice (f0a9dc7)

1.8.0 (2021-11-05)

Features

  • js: Add clu and tree javascript parser (f0c738c)
  • Add modular centrality score (31cdd7f)

1.7.3 (2021-10-26)

Bug Fixes

  • js: Don't run error callback on finish (13a21f0)

1.7.2 (2021-10-26)

Bug Fixes

  • js: Run error callback on terminate (e83e897)

1.7.1 (2021-10-14)

1.7.0 (2021-10-04)

Features

  • python: Add multilevel_modules property (0d4cc37)
  • python: Add num_levels property (abd4f7f)
  • python: Pass dict to add_nodes (e30870f)
  • python: Pass dict to add_state_nodes (5cd9ba2)
  • python: Pass dict to set_names (0ed79e8)
  • Add directed field to json output (7db19f2)
  • Write json multilevel modules and module information (e6796c8)

Bug Fixes

  • python: Adding a networkx DiGraph should set the directed flag (a60a404)
  • python: Using directed=False should use undirected flow (be0f6e2)
  • Metadata codelength works after multiple runs (ec00ccd), closes #167
  • Module ids wrong for uneven depth and chosen level > 1 (c3a0c90), closes #221

1.6.0 (2021-07-08)

Features

  • python: Add get_dataframe (13066b3)
  • python: Add write method (fdb3ce1)
  • python: Add write_state_network and write_pajek (da715a9)

Bug Fixes

  • Intra-module links missing from ftree output (b347e24)
  • js: Add type to files parameter (269b426)
  • js: Output arguments should not be required to be an array (a292318)
  • js: Worker should accept extra files as objects (524a0e7)
  • python: get_multilevel_modules should return a dict (f050fb5)

1.5.1 (2021-06-23)

Bug Fixes

  • js: Add missing flow network file output (6b8ddb8)
  • js: Handle json parse exceptions in worker (a8a127b)
  • js: Pass arguments as object (13e71a0)
  • js: Worker should accept network as object (d7184b8)
  • Avoid nan values for relative codelength savings (e6a429e)

1.5.0 (2021-06-22)

Features

  • js: Add Typescript types to JS worker (f2fecf4)
  • python: Add get_links, links and flow_links (a4c2611)
  • Write tree to CSV file (5d0d36a)

1.4.4 (2021-06-14)

Bug Fixes

  • python: Fix OpenMP detection (27f9070)

1.4.3 (2021-06-14)

1.4.2 (2021-06-14)

Bug Fixes

  • build: Fix building Python package with OpenMP if available (cfaade5)

1.4.1 (2021-06-10)

Bug Fixes

  • js: Add newick and json to output from JS worker (549ee84)
  • python: Add missing write_newick and write_json methods (62c2736)
  • Change Newick output extention to .nwk (f0e2e8e)

1.4.0 (2021-06-10)

Features

  • Support printing JSON tree (22116d6)
  • python: Accept named arguments (5dabf4a)
  • python: Add 'add_networkx_graph' method to API (4067d40)
  • python: Add effective number of modules (0f9a516)
  • python: Add shorthand for accessing number of nodes and links (8808045)
  • Add 'flow' to output options for node/edge flow (d74a773)

Bug Fixes

  • python: Also add nodes in networkx example (3a88878)
  • python: Fix effective_num_modules (f41827f)
  • R: Expose base class methods to avoid c stack usage error (47bdec0)
  • R: Fix swig build by hiding python specifics (6b8a67e)
  • R: Replace enum class with struct for R (73c702f)
  • R: Update R example and build to Infomap v1 (17e1cc0)
  • R: Update swig version in docker build (74c4e86)

1.3.0 (2020-12-03)

Features

  • Add --hide-bipartite-nodes (#156) (f5e673c)
  • New optional flow model for bipartite input (91f35fe)
  • Support Newick tree format in output (9749a05)

Bug Fixes

  • Continue searching from input tree (2199921)
  • Fine-tune bottom modules in input tree with -F (c187718)
  • Implement missing multilayer relax by JSD (95141bf), closes #154
  • Use correct objective in coarse tune for memory and multilevel networks (97db558), closes #174

1.2.1 (2020-11-10)

Bug Fixes

  • --clu-level was not respected in command line usage (b82a0b1), closes #153
  • Allow ftree cluster data (bfe3601)
  • Apply weight-threshold also to multilayer nodes (db2d781)
  • Remove ClusterReader/BipartiteClusterReader (8e08309), closes #162
  • windows: Include algorithm header (4f9ef88), closes #150

1.2.0 (2020-09-30)

Features

  • Add option to --use-node-weights-as-flow (0d75174)
  • Show bipartite start id in bipartite output (f6e9233)

Bug Fixes

  • Fix flow calculator for bipartite networks (b725b27)
  • python: Fix bipartite_start_id getter (d326298)

1.1.4 (2020-09-13)

Bug Fixes

  • Clarify that the algorithm searches for multi-level solutions by default (47be4de)
  • python: Fix color indices in networkx example (dcf5888)

1.1.3 (2020-05-09)

Bug Fixes

  • python: Correct codelength terms after N > 1 (146cee6)
  • python: Define module_codelength as L - L_index (fa6eb94)
  • python: Don't create empty node names if they didn't already exist (#126) (4d1cd56)
  • python: Expose num_non_trivial_top_modules (6b91184)

1.1.2 (2020-04-08)

Bug Fixes

  • python: Expose node names with get_name and get_names (#125) (b8cb409), closes #52

1.1.1 (2020-04-08)

Bug Fixes

  • Remove implied link direction from --skip-adjust-bipartite-flow (05c3eba)

1.1.0 (2020-03-31)

Features

  • Show num levels and modules in file output (0b70cd8)
  • python: Expose codelengths for all trials (eab7ae8)

Bug Fixes

  • Don't use physical names in _states_as_physical.net (5889fb1)

1.0.11 (2020-03-31)

Bug Fixes

  • Handle zero weights in intra-layer links (ddc5a3d)

1.0.10 (2020-03-17)

Bug Fixes

  • Handle unassigned nodes after input tree (d337535), closes #119

1.0.9 (2020-03-14)

Bug Fixes

  • windows: compilation error on std::min (b6c1a41)

1.0.8 (2020-03-12)

Bug Fixes

1.0.7 (2020-03-09)

Bug Fixes

  • Add header in network and states output (c415a4b)
  • Use *Edges/*Arcs instead of *Links in pajek output (ff3a98e)
  • Use node_id instead of id in clu output (39cd4e4)
  • js: Fix support for all file io in Infomap.js (ea9d899)

1.0.6 (2020-03-03)

Bug Fixes

  • python: Enable numpy.int64 in link weights (8d91206), closes #107
  • python: Print tree by default with python cli (1565cab), closes #106

1.0.5 (2020-03-02)

Bug Fixes

  • Common parameters should not be advanced (#101) (2907c86), closes #100
  • consistently use 1-based indexing for paths and 0 for indexes (f283818), closes #103
  • Fix ftree links since remapping path from 1 (f447b48), closes #102

1.0.4 (2020-02-28)

Bug Fixes

  • js: Revert attempted worker blob optimization (c521373)

1.0.3 (2020-02-28)

Bug Fixes

  • js: Handle Infomap exceptions in js (7a641f9), closes #99
  • python: Start module id from 1 in get_[multilevel_]modules (9419798)

1.0.2 (2020-02-28)

Bug Fixes

  • windows: Fix compilation error on std::min (3b000dc), closes #97

1.0.1 (2020-02-27)

Bug Fixes

  • python: Fix missing package_meta on pip install (dd24b1d), closes #95

1.0.0 (2020-02-26)

BREAKING CHANGES

  • python: Drop support for python 2
  • python: Rename physicalId to node_id. Remove initial partition as first argument to run, use initial_partition argument. Start InfomapIterator.path indexing from one.
  • Output header format has changed
  • Ftree output format has changed to include enter flow
  • Clu output now contains top modules instead of leaf modules
  • Tree output is sorted on flow
  • Clu module ids starts from 1 instead of 0
  • Output contains name of the physical node instead of state id
  • Full multilayer format require the *multilayer heading
  • Remove undirdir and outdirdir, use --flow-model. Rename min-improment to --core-loop-codelength-thresh. Remove random-loop-limit. Rename tune-iteration-threshold to --tune-iteration-relative-threshold. Rename skip-replace-to-one-module to --prefer-modular-solution.
  • Removed --print-state-network, use -o states
  • Renamed --set-unidentified-nodes-to-closest-module to --assing-to-neighbouring-module
  • No support for *path input

Features

  • python: Add meta info to infomap package (a2caaf4), closes #63
  • Add enter flow to ftree output (bd3255e), closes #82
  • Show entropy rate in the beginning (f61692c)
  • python: Improve Python API (#87) (c39cd9f)
  • Add -o/--output option for comma-separated formats (a255a18)
  • Add meta data in output file header (66ccc64)
  • Add option to print parameters in json (3a2509d)
  • Allow multilayer formats without specifying -i. (08e09f1)
  • Allow one-sided multilayer relax limit (a116b83), closes #68
  • Begin module id from 1 instead of 0 in clu output (2bbea5d)
  • Create npm package with Infomap worker, changelog and parameters (44dae36)
  • Output name of physical node instead of state id (dda3277)
  • Remove --skip-complete-dangling-memory-nodes (6909f21)
  • Remove support for *path input (e7be175)
  • Rename --set-unidentified-nodes-to-closest-module (16fdc15)
  • Simplify command line interface (f537132)
  • Sort tree on flow (6e27858), closes #71
  • Write top modules to .clu, not bottom level (1e16a3c)

Bug Fixes

  • js: Add missing this in error handler (7345cdf)