@mapequation/infomap 2.7.0 → 2.8.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (6) hide show
  1. package/{LICENSE_AGPLv3.txt → LICENSE_GPLv3.txt} +83 -70
  2. package/README.md +2 -2
  3. package/README.rst +3 -3
  4. package/index.js +1 -1
  5. package/package.json +4 -4
  6. package/CHANGELOG.md +0 -538
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@mapequation/infomap",
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- "version": "2.7.0",
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+ "version": "2.8.0",
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  "description": "Infomap network clustering algorithm",
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  "browser": "index.js",
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  "publishConfig": {
@@ -12,7 +12,7 @@
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  "arguments.d.ts",
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  "filetypes.d.ts",
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  "network.d.ts",
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- "LICENSE_AGPLv3.txt"
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+ "LICENSE_GPLv3.txt"
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  ],
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  "main": "index.js",
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  "types": "index.d.ts",
@@ -47,7 +47,7 @@
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  "name": "Martin Rosvall"
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  }
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  ],
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- "license": "AGPL-3.0-or-later",
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+ "license": "GPL-3.0-or-later",
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  "bugs": {
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  "url": "https://github.com/mapequation/infomap/issues"
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  },
@@ -85,7 +85,7 @@
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  "Development Status :: 5 - Production/Stable",
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  "Intended Audience :: Science/Research",
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  "Topic :: Scientific/Engineering :: Information Analysis",
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- "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
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+ "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
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  "Programming Language :: Python :: 3"
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  ]
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  }
package/CHANGELOG.md DELETED
@@ -1,538 +0,0 @@
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- # Changelog
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-
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- All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines.
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-
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- ## [2.7.0](https://github.com/mapequation/infomap/compare/v2.6.1...v2.7.0) (2023-04-04)
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-
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-
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- ### Features
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-
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- * Add flow model "precomputed" ([407dbe9](https://github.com/mapequation/infomap/commit/407dbe9592641bea7a4cac292a7d25df308644ca))
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-
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-
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- ### Bug Fixes
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-
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- * Do not add links with zero weight ([cc61b61](https://github.com/mapequation/infomap/commit/cc61b61db228e8a0b433d5bc55f0fedc540e1c0d)), closes [#324](https://github.com/mapequation/infomap/issues/324)
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- * **python:** Typo in assign_to_neighbouring_module ([c644e80](https://github.com/mapequation/infomap/commit/c644e80d1717cc28c6247b470e4f1c6eb2d4a420))
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-
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- ### [2.6.1](https://github.com/mapequation/infomap/compare/v2.6.0...v2.6.1) (2022-10-31)
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-
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- ### Bug Fixes
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-
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- * Scale variable Markov time logarithmic as default ([#320](https://github.com/mapequation/infomap/issues/320)) ([3f40134](https://github.com/mapequation/infomap/commit/3f40134b0346586b9d051c3a2996a77500ba10d6))
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- * Set num trials to 1 if no infomap ([be60a09](https://github.com/mapequation/infomap/commit/be60a09c785d8bee9ac885ebc92473494db368c1))
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-
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- ## [2.6.0](https://github.com/mapequation/infomap/compare/v2.5.0...v2.6.0) (2022-08-09)
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- ### Features
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-
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- * **python:** Add entropy_rate property ([a243dfc](https://github.com/mapequation/infomap/commit/a243dfcdf4629aff85b425d11aa7317b1fc6b80c))
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- * Variable Markov time ([#315](https://github.com/mapequation/infomap/issues/315)) ([cd7b25b](https://github.com/mapequation/infomap/commit/cd7b25b8aded24f85034ddc0d2d3bbacb881b24c))
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-
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- ### Bug Fixes
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-
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- * Adjust entropy correction to Miller-Madow ([324c9f7](https://github.com/mapequation/infomap/commit/324c9f757d94b2d045ec77d14b53491ef30aba17))
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- * Don't write multilevel json output for aggregated higher-order networks ([1f5e7ea](https://github.com/mapequation/infomap/commit/1f5e7eab31b865fd2208cecbd0ed50642b9ca199))
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- * Fix calc entropy rate for undirected networks ([ccd6b6c](https://github.com/mapequation/infomap/commit/ccd6b6cbdb8b322a5e457355a214801301351d4a))
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- * **py:** Fix ignored variable_markov_time argument ([eedc777](https://github.com/mapequation/infomap/commit/eedc77705e44255c580d973c9403d1062a6e1712))
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- * **py:** Fix test for entropy rate ([78772b5](https://github.com/mapequation/infomap/commit/78772b5b81323d65456220e23456210c48fc0871))
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- * **python:** Fix physical leaf node iterator on state networks ([#312](https://github.com/mapequation/infomap/issues/312)) ([4e2918c](https://github.com/mapequation/infomap/commit/4e2918c131beeda4187012e8c9672e3635f77df4)), closes [#313](https://github.com/mapequation/infomap/issues/313)
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- * **python:** Only aggregate states into physical nodes when we have a higher-order network ([7e3277c](https://github.com/mapequation/infomap/commit/7e3277c97881057b36756f6328089ed7252234eb))
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- * **python:** Segfault when accessing physical_nodes ([cc5c95e](https://github.com/mapequation/infomap/commit/cc5c95e302e5093ee168a9952bbb70dc1e5b74ce)), closes [#300](https://github.com/mapequation/infomap/issues/300)
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-
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- ## [2.5.0](https://github.com/mapequation/infomap/compare/v2.4.1...v2.5.0) (2022-06-07)
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- ### Features
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-
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- * Output per-module codelength in json ([eae6650](https://github.com/mapequation/infomap/commit/eae6650c48dbf90a938d011f1c736794a786d7ef))
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- * Print all trials using --print-all-trials ([e65bea8](https://github.com/mapequation/infomap/commit/e65bea86c21ebcabafb053e79306049e92429ca1)), closes [#298](https://github.com/mapequation/infomap/issues/298)
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- * Write node metadata to json ([472b791](https://github.com/mapequation/infomap/commit/472b791742f0f692a0a4b06262b33165245f6f36))
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-
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- ### Bug Fixes
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- * Constrain numerical arguments to sensible values ([174c99f](https://github.com/mapequation/infomap/commit/174c99fb56c4a50a2e11c37208bcec3e98ba4ab4))
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- * Don't allow less than 1 trial ([18e97e2](https://github.com/mapequation/infomap/commit/18e97e21d76e7d27520eb2625c281031d72376d3))
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- * Json multilevel modules for higher-order networks ([d020c7c](https://github.com/mapequation/infomap/commit/d020c7c444d1227cb26aa249f7cae5e7de5ecaa4)), closes [#266](https://github.com/mapequation/infomap/issues/266)
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- * Only print all trials when running with more than 1 trial ([5f9d8b5](https://github.com/mapequation/infomap/commit/5f9d8b5e56ae348b142404f3f775ad526d396c55))
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- * **python:** Fix elapsed running time ([1131e84](https://github.com/mapequation/infomap/commit/1131e845243d3053cceae5bdf069569b2856bc4a))
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- * **python:** Replace MersenneTwister implementation with stdlib ([be3effd](https://github.com/mapequation/infomap/commit/be3effd9813a00892437c806b62cb8ee15387d3d))
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- ### [2.4.1](https://github.com/mapequation/infomap/compare/v2.4.0...v2.4.1) (2022-05-27)
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- ### Bug Fixes
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- * Json output causes segfault ([78e80c5](https://github.com/mapequation/infomap/commit/78e80c581edd92001818abdf50066b798251c604))
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- ## [2.4.0](https://github.com/mapequation/infomap/compare/v2.3.0...v2.4.0) (2022-05-24)
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- ### Features
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- * **js:** React hook ([c19a819](https://github.com/mapequation/infomap/commit/c19a81917849e27298d00bc1b7c6bde2d66f46c5))
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- ### Bug Fixes
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- * **js-parser:** Parse module level from clu files ([bb91066](https://github.com/mapequation/infomap/commit/bb9106625761716dfabbb240ba39702c110f011a))
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- * **js:** Correctly parse clu-files without header ([04c39ea](https://github.com/mapequation/infomap/commit/04c39ea46b716fb10af987a568d5ab226e6ad69d))
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- * **python:** Don't allow adding multilayer intra-inter links and ordinary nodes. ([8c3d09c](https://github.com/mapequation/infomap/commit/8c3d09c5c5188c1c94d691beff2c519100b939f9)), closes [#287](https://github.com/mapequation/infomap/issues/287)
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- * **python:** Improve constructor and run signatures ([6852e14](https://github.com/mapequation/infomap/commit/6852e142343c91e61a9affe9bcff2897375cf70c)), closes [#286](https://github.com/mapequation/infomap/issues/286)
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- * **python:** no_self_links was always set unless include_self_links=True ([9afe5fa](https://github.com/mapequation/infomap/commit/9afe5fa7afbf3f143dd2b8d293be59f572a14c79))
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- * **python:** Prevent infinite loop in getMultilevelModules ([1174b66](https://github.com/mapequation/infomap/commit/1174b6658ed5c0bbc2c976223524f5f58e4d6c35)), closes [#284](https://github.com/mapequation/infomap/issues/284)
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- * Using deprecated option --include-self-links references missing option --no-loops ([1497bf7](https://github.com/mapequation/infomap/commit/1497bf71fe7a6f5dad725742db8c36a49171eb4d))
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- ## [2.3.0](https://github.com/mapequation/infomap/compare/v2.2.0...v2.3.0) (2022-04-13)
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- ### Features
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- * Matchable multilayer ids ([c9d28b6](https://github.com/mapequation/infomap/commit/c9d28b6e739731043e0dd6b82d0ae9898f686618)), closes [#279](https://github.com/mapequation/infomap/issues/279)
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- ### Bug Fixes
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- * **js:** Don't call error on worker terminate ([cc57c8c](https://github.com/mapequation/infomap/commit/cc57c8cbafa3ec313426e1356a8140fa6d09c9b5))
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- * **js:** More robust heuristic to parse output format type ([33bde00](https://github.com/mapequation/infomap/commit/33bde00775c2fd41fb03b7592ae80633f09e8263))
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- * Match multilayer nodes by node and layer ids when using --cluster-data ([b5f6eb3](https://github.com/mapequation/infomap/commit/b5f6eb38d1740559ae93591e659ff8f2f53b7927))
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- * **python:** Add no_self_links to api ([b3d903d](https://github.com/mapequation/infomap/commit/b3d903d16e7619edebabe58a9004f40c88ea3614)), closes [#285](https://github.com/mapequation/infomap/issues/285)
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- * **python:** Add recorded teleportation keyword argument ([839e1e0](https://github.com/mapequation/infomap/commit/839e1e057b2f7181a87d77758ae00c20aa368891)), closes [#270](https://github.com/mapequation/infomap/issues/270)
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- * **python:** Fix matchable multilayer id option ([8377e07](https://github.com/mapequation/infomap/commit/8377e077832eafba1cb989dcad6e24b7a8f87edf))
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- ## [2.2.0](https://github.com/mapequation/infomap/compare/v2.1.0...v2.2.0) (2022-03-07)
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- ### Features
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- * Add flow-model, higher-order, and state-level fields to json, tree and clu output ([24125e5](https://github.com/mapequation/infomap/commit/24125e5874cd0599e7274e08a2691855f212186b))
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- ### Bug Fixes
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- * **js:** More forgiving clu and tree parsing ([4764946](https://github.com/mapequation/infomap/commit/47649466a0ef2a200dc766b1442c7f33a8fec20f))
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- * Write json output with --no-infomap ([c0cec87](https://github.com/mapequation/infomap/commit/c0cec8715981f53dd53c3134c8f16e5b4d644717)), closes [#268](https://github.com/mapequation/infomap/issues/268)
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- ## [2.1.0](https://github.com/mapequation/infomap/compare/v2.0.2...v2.1.0) (2022-02-11)
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- ### Features
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- * **js:** Add progress event callback ([0fab95b](https://github.com/mapequation/infomap/commit/0fab95bd59717aaf2f36792f2be5a54223e38fab))
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- ### Bug Fixes
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- * **js:** Change Typescript types to use mec instead of modularCentrality ([298eed3](https://github.com/mapequation/infomap/commit/298eed32d977758b07af058327775c234340b7b5))
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- * **js:** Parse node path as string instead of array of number ([51feb73](https://github.com/mapequation/infomap/commit/51feb73254b17857e4feb27197d4bb8c8157db05))
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- * **js:** Validate parsed results and throw instead of returning null on failure ([5f56b94](https://github.com/mapequation/infomap/commit/5f56b94fe0f956483f61a03ef07e94d8def2205e))
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- ### [2.0.2](https://github.com/mapequation/infomap/compare/v2.0.1...v2.0.2) (2022-01-31)
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- ### Bug Fixes
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- * Change json key modularCentrality to mec ([78c7a57](https://github.com/mapequation/infomap/commit/78c7a573914e127bda03a2b8001df321e5bffd04))
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- * **js:** Parse directed field in ftree files ([916f54a](https://github.com/mapequation/infomap/commit/916f54a05fb2ffd86ddf0ba297952e85ccfaa5b8))
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- * **js:** Pass parseLinks to main parse function and correctly detect multilayer tree files ([0a40ca6](https://github.com/mapequation/infomap/commit/0a40ca6c1606c189f02e691a2fdb74a4494ffbe7))
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- * Minify json output ([123c2b1](https://github.com/mapequation/infomap/commit/123c2b10f1e6486135346f8cd546ca0e72fb4d2e)), closes [#260](https://github.com/mapequation/infomap/issues/260)
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- ### [2.0.1](https://github.com/mapequation/infomap/compare/v2.0.0...v2.0.1) (2022-01-26)
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- ### Bug Fixes
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- * Bug in write state network to json ([50f8de2](https://github.com/mapequation/infomap/commit/50f8de2008cf6422693a74279b347d043735200d)), closes [#262](https://github.com/mapequation/infomap/issues/262)
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- * **js:** Broken parser due to duplicate variable name ([f437e13](https://github.com/mapequation/infomap/commit/f437e138f7b24140732831e63fac8c28e44e44bf))
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- * Use min mass for dangling nodes when regularized ([f741d07](https://github.com/mapequation/infomap/commit/f741d079b04558102130cbbbd742a0ddc3c1c366))
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- ## [2.0.0](https://github.com/mapequation/infomap/compare/v1.9.0...v2.0.0) (2022-01-13)
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- ### ⚠ BREAKING CHANGES
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- ### Features
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- * Entropy bias correction ([#258](https://github.com/mapequation/infomap/issues/258)) ([8ea235c](https://github.com/mapequation/infomap/commit/8ea235cf9159fc1a672a0470798ab7e443590fde))
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- * Regularized map equation ([#181](https://github.com/mapequation/infomap/issues/181)) ([0673000](https://github.com/mapequation/infomap/commit/06730005329acb4ba781d647e7009d4ff2510ae7)), closes [#256](https://github.com/mapequation/infomap/issues/256)
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- ### Bug Fixes
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- * Add new feature flags to python and js api ([48245a7](https://github.com/mapequation/infomap/commit/48245a795f87675b62b94b2f8bd8251b71e5f62e))
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- * Include self links by default ([#255](https://github.com/mapequation/infomap/issues/255)) ([1f68940](https://github.com/mapequation/infomap/commit/1f68940a90633405f696efa93471ca8cbb25f14c))
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- * **example:** Fix building c++ examples ([0d5c063](https://github.com/mapequation/infomap/commit/0d5c0639cb76b9b275388c1a45873496f675aeea)), closes [#252](https://github.com/mapequation/infomap/issues/252)
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- * Remove superfluous --input-format flag ([2dd77c4](https://github.com/mapequation/infomap/commit/2dd77c4689c67485454478d739c22c8deb44eda0))
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- ## [1.9.0](https://github.com/mapequation/infomap/compare/v1.8.0...v1.9.0) (2021-11-17)
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- ### Features
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- * **python:** Add API for intra/inter-layer links ([#245](https://github.com/mapequation/infomap/issues/245)) ([aa31ab2](https://github.com/mapequation/infomap/commit/aa31ab22ff8a706f7b1e5bbf75740d35ef5716bf)), closes [#244](https://github.com/mapequation/infomap/issues/244)
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- * Incorrect one-level codelength for higher-order input ([5a6d1a1](https://github.com/mapequation/infomap/commit/5a6d1a10657c568f0fddf3afd6729a63e3543081)), closes [#182](https://github.com/mapequation/infomap/issues/182)
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- ## [1.8.0](https://github.com/mapequation/infomap/compare/v1.7.3...v1.8.0) (2021-11-05)
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- ### Features
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- * **js:** Add clu and tree javascript parser ([f0c738c](https://github.com/mapequation/infomap/commit/f0c738c2ebbd4d1f43d14b75f82767b30dbfb02f))
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- * Add modular centrality score ([31cdd7f](https://github.com/mapequation/infomap/commit/31cdd7fa7a12add63f5b8818e503fe81b3f48555))
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- ### [1.7.3](https://github.com/mapequation/infomap/compare/v1.7.2...v1.7.3) (2021-10-26)
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- * **js:** Don't run error callback on finish ([13a21f0](https://github.com/mapequation/infomap/commit/13a21f00f445e8a378ca287e080085b47df4653f))
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- ### [1.7.2](https://github.com/mapequation/infomap/compare/v1.7.1...v1.7.2) (2021-10-26)
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- * **js:** Run error callback on terminate ([e83e897](https://github.com/mapequation/infomap/commit/e83e8970656e654aee353705a85bd7f97aae3f71))
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- ### [1.7.1](https://github.com/mapequation/infomap/compare/v1.7.0...v1.7.1) (2021-10-14)
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- ## [1.7.0](https://github.com/mapequation/infomap/compare/v1.6.0...v1.7.0) (2021-10-04)
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- ### Features
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- * **python:** Add multilevel_modules property ([0d4cc37](https://github.com/mapequation/infomap/commit/0d4cc375cebe8477ea2e0073f9e7056411c3091e))
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- * **python:** Add num_levels property ([abd4f7f](https://github.com/mapequation/infomap/commit/abd4f7f8cc272cc20e4996b03a10dd2411a46260))
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- * **python:** Pass dict to add_nodes ([e30870f](https://github.com/mapequation/infomap/commit/e30870f28366676e105b189980a2c5eb921b9481))
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- * **python:** Pass dict to add_state_nodes ([5cd9ba2](https://github.com/mapequation/infomap/commit/5cd9ba25db758d2cb1a928c32adfdea21dda87d0))
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- * **python:** Pass dict to set_names ([0ed79e8](https://github.com/mapequation/infomap/commit/0ed79e8b08ab1ae410a3fdbb4dd59ddb2ecf149a))
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- * Add directed field to json output ([7db19f2](https://github.com/mapequation/infomap/commit/7db19f216b3d7f825a7eb90c89e0a0696c3a3e95))
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- * Write json multilevel modules and module information ([e6796c8](https://github.com/mapequation/infomap/commit/e6796c8d91499c1287278ab818c7e62d7426c303))
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- ### Bug Fixes
228
-
229
- * **python:** Adding a networkx DiGraph should set the directed flag ([a60a404](https://github.com/mapequation/infomap/commit/a60a404eac88d04a3bb6beb1b130452b28a99d83))
230
- * **python:** Using directed=False should use undirected flow ([be0f6e2](https://github.com/mapequation/infomap/commit/be0f6e2f9ffc80ee58305709ebc6b801187e21bb))
231
- * Metadata codelength works after multiple runs ([ec00ccd](https://github.com/mapequation/infomap/commit/ec00ccd7d14bdff54e6757b4cd1fd84e93dd4e58)), closes [#167](https://github.com/mapequation/infomap/issues/167)
232
- * Module ids wrong for uneven depth and chosen level > 1 ([c3a0c90](https://github.com/mapequation/infomap/commit/c3a0c9025ae82a84f05e929f105b88d1d28f8be1)), closes [#221](https://github.com/mapequation/infomap/issues/221)
233
-
234
- ## [1.6.0](https://github.com/mapequation/infomap/compare/v1.5.1...v1.6.0) (2021-07-08)
235
-
236
-
237
- ### Features
238
-
239
- * **python:** Add get_dataframe ([13066b3](https://github.com/mapequation/infomap/commit/13066b3300c921dcb18b46be2a633153ecf0ffa8))
240
- * **python:** Add write method ([fdb3ce1](https://github.com/mapequation/infomap/commit/fdb3ce13a96c77b46b064fcda5fdcaf0f0a3c753))
241
- * **python:** Add write_state_network and write_pajek ([da715a9](https://github.com/mapequation/infomap/commit/da715a9ccfc27b6dd2a079bd9f4e3ef6501a95a1))
242
-
243
-
244
- ### Bug Fixes
245
-
246
- * Intra-module links missing from ftree output ([b347e24](https://github.com/mapequation/infomap/commit/b347e2491f343f2a541e6a3e4b7ac8837d0ae507))
247
- * **js:** Add type to files parameter ([269b426](https://github.com/mapequation/infomap/commit/269b426326e7eca02b53dcbddf3ae0925a4b5a23))
248
- * **js:** Output arguments should not be required to be an array ([a292318](https://github.com/mapequation/infomap/commit/a29231853e4d900e5f99dee962b1f44a20fc4e93))
249
- * **js:** Worker should accept extra files as objects ([524a0e7](https://github.com/mapequation/infomap/commit/524a0e7e80c2bef897dab85cd60473a3e06408c9))
250
- * **python:** get_multilevel_modules should return a dict ([f050fb5](https://github.com/mapequation/infomap/commit/f050fb568df4fb678e6c4689bef85cf18a6d93f2))
251
-
252
- ### [1.5.1](https://github.com/mapequation/infomap/compare/v1.5.0...v1.5.1) (2021-06-23)
253
-
254
-
255
- ### Bug Fixes
256
-
257
- * **js:** Add missing flow network file output ([6b8ddb8](https://github.com/mapequation/infomap/commit/6b8ddb820bc48eaed27a4e66d2810151b65b8bb9))
258
- * **js:** Handle json parse exceptions in worker ([a8a127b](https://github.com/mapequation/infomap/commit/a8a127b02e81b1bbd2a919edbc7952724b2e8682))
259
- * **js:** Pass arguments as object ([13e71a0](https://github.com/mapequation/infomap/commit/13e71a0b1a7465e5f59bb3d05ef1bbdef7b5f65f))
260
- * **js:** Worker should accept network as object ([d7184b8](https://github.com/mapequation/infomap/commit/d7184b840e7aae3b7d59b9b8bb2fa432d8d4c616))
261
- * Avoid nan values for relative codelength savings ([e6a429e](https://github.com/mapequation/infomap/commit/e6a429e6bd463fc405161f6b4e981439979fc5c3))
262
-
263
- ## [1.5.0](https://github.com/mapequation/infomap/compare/v1.4.4...v1.5.0) (2021-06-22)
264
-
265
-
266
- ### Features
267
-
268
- * **js:** Add Typescript types to JS worker ([f2fecf4](https://github.com/mapequation/infomap/commit/f2fecf4898dd0200709def0da11bea1883e70eaa))
269
- * **python:** Add get_links, links and flow_links ([a4c2611](https://github.com/mapequation/infomap/commit/a4c26112821abc05185442b1eb27fd1bf83fdbc9))
270
- * Write tree to CSV file ([5d0d36a](https://github.com/mapequation/infomap/commit/5d0d36a58413c0755f97d93dd00d8f6db7b2b785))
271
-
272
- ### [1.4.4](https://github.com/mapequation/infomap/compare/v1.4.3...v1.4.4) (2021-06-14)
273
-
274
-
275
- ### Bug Fixes
276
-
277
- * **python:** Fix OpenMP detection ([27f9070](https://github.com/mapequation/infomap/commit/27f9070d4676aee859f14bbf0ba2e1de6a417636))
278
-
279
- ### [1.4.3](https://github.com/mapequation/infomap/compare/v1.4.2...v1.4.3) (2021-06-14)
280
-
281
- ### [1.4.2](https://github.com/mapequation/infomap/compare/v1.4.1...v1.4.2) (2021-06-14)
282
-
283
-
284
- ### Bug Fixes
285
-
286
- * **build:** Fix building Python package with OpenMP if available ([cfaade5](https://github.com/mapequation/infomap/commit/cfaade5bb699980954fc6d618ef1eb211bb2a63e))
287
-
288
- ### [1.4.1](https://github.com/mapequation/infomap/compare/v1.4.0...v1.4.1) (2021-06-10)
289
-
290
-
291
- ### Bug Fixes
292
-
293
- * **js:** Add newick and json to output from JS worker ([549ee84](https://github.com/mapequation/infomap/commit/549ee84858860680d2b9ed93e2d79a419c24e7d1))
294
- * **python:** Add missing write_newick and write_json methods ([62c2736](https://github.com/mapequation/infomap/commit/62c2736dfb048de432093313e19b3d67869d3138))
295
- * Change Newick output extention to .nwk ([f0e2e8e](https://github.com/mapequation/infomap/commit/f0e2e8ef8b6f5da6985c548b2f2b00521177cad8))
296
-
297
- ## [1.4.0](https://github.com/mapequation/infomap/compare/v1.3.0...v1.4.0) (2021-06-10)
298
-
299
-
300
- ### Features
301
-
302
- * Support printing JSON tree ([22116d6](https://github.com/mapequation/infomap/commit/22116d6a9077909c2e5eb2160feea913022752e8))
303
- * **python:** Accept named arguments ([5dabf4a](https://github.com/mapequation/infomap/commit/5dabf4abbaa90512d5a1ffd11c8986f8623ccb13))
304
- * **python:** Add 'add_networkx_graph' method to API ([4067d40](https://github.com/mapequation/infomap/commit/4067d40268c4b2726652b5ef47358ca049c58edd))
305
- * **python:** Add effective number of modules ([0f9a516](https://github.com/mapequation/infomap/commit/0f9a5169cacde5c9106bb6cf7dfa3b726a1c28d5))
306
- * **python:** Add shorthand for accessing number of nodes and links ([8808045](https://github.com/mapequation/infomap/commit/88080454e054c51516ee7047975baf480ce1bd42))
307
- * Add 'flow' to output options for node/edge flow ([d74a773](https://github.com/mapequation/infomap/commit/d74a773dd33102b85ff444158c958a8048c8cb02))
308
-
309
-
310
- ### Bug Fixes
311
-
312
- * **python:** Also add nodes in networkx example ([3a88878](https://github.com/mapequation/infomap/commit/3a888789cc229521cffdf6da62fd0c239a5607eb))
313
- * **python:** Fix effective_num_modules ([f41827f](https://github.com/mapequation/infomap/commit/f41827fde6f30e914e73d8a141992c4363f14adc))
314
- * **R:** Expose base class methods to avoid c stack usage error ([47bdec0](https://github.com/mapequation/infomap/commit/47bdec0ab9a3d0e80cd7a77a7629ad9d9b400183))
315
- * **R:** Fix swig build by hiding python specifics ([6b8a67e](https://github.com/mapequation/infomap/commit/6b8a67e6f09a02daad8e85c8b9fcec0f632526e3))
316
- * **R:** Replace enum class with struct for R ([73c702f](https://github.com/mapequation/infomap/commit/73c702fd23e7a02ae8ccc3630f5713181cb842a9))
317
- * **R:** Update R example and build to Infomap v1 ([17e1cc0](https://github.com/mapequation/infomap/commit/17e1cc00bd789c8798bd0633a39285a4160854a4))
318
- * **R:** Update swig version in docker build ([74c4e86](https://github.com/mapequation/infomap/commit/74c4e86cfdd395ec1b335fc34dd5e0b34d7f6c1e))
319
-
320
- ## [1.3.0](https://github.com/mapequation/infomap/compare/v1.2.1...v1.3.0) (2020-12-03)
321
-
322
-
323
- ### Features
324
-
325
- * Add --hide-bipartite-nodes ([#156](https://github.com/mapequation/infomap/issues/156)) ([f5e673c](https://github.com/mapequation/infomap/commit/f5e673c64efaf5ae825ee6b303e78389b8d594f9))
326
- * New optional flow model for bipartite input ([91f35fe](https://github.com/mapequation/infomap/commit/91f35fef9b1246b87cde46d8e36ad7a992291a28))
327
- * Support Newick tree format in output ([9749a05](https://github.com/mapequation/infomap/commit/9749a0535b9db47826c198b6f98b8fe2510eadc4))
328
-
329
-
330
- ### Bug Fixes
331
-
332
- * Continue searching from input tree ([2199921](https://github.com/mapequation/infomap/commit/21999211ed822a8e46a8f1cd158185ce79b3075e))
333
- * Fine-tune bottom modules in input tree with -F ([c187718](https://github.com/mapequation/infomap/commit/c187718e49618e2dac6c060233c844ff9a40893f))
334
- * Implement missing multilayer relax by JSD ([95141bf](https://github.com/mapequation/infomap/commit/95141bf89452053a5f8f7bb2afbfc4048f066ee3)), closes [#154](https://github.com/mapequation/infomap/issues/154)
335
- * Use correct objective in coarse tune for memory and multilevel networks ([97db558](https://github.com/mapequation/infomap/commit/97db558f27a81994a09aa6834bff5d8810a93130)), closes [#174](https://github.com/mapequation/infomap/issues/174)
336
-
337
- ### [1.2.1](https://github.com/mapequation/infomap/compare/v1.2.0...v1.2.1) (2020-11-10)
338
-
339
-
340
- ### Bug Fixes
341
-
342
- * --clu-level was not respected in command line usage ([b82a0b1](https://github.com/mapequation/infomap/commit/b82a0b1a0582583b4552887650b0a6b92aba14fc)), closes [#153](https://github.com/mapequation/infomap/issues/153)
343
- * Allow ftree cluster data ([bfe3601](https://github.com/mapequation/infomap/commit/bfe3601a50675cf353379efdb940b184773fb2b2))
344
- * Apply weight-threshold also to multilayer nodes ([db2d781](https://github.com/mapequation/infomap/commit/db2d781c5257932ad5a4e5fe1976498b01985a39))
345
- * Remove ClusterReader/BipartiteClusterReader ([8e08309](https://github.com/mapequation/infomap/commit/8e0830915f47bd4460a1b1b4f3794d60919a429a)), closes [#162](https://github.com/mapequation/infomap/issues/162)
346
- * **windows:** Include algorithm header ([4f9ef88](https://github.com/mapequation/infomap/commit/4f9ef88409012ff00457291fc0ad8d0f33063c59)), closes [#150](https://github.com/mapequation/infomap/issues/150)
347
-
348
- ## [1.2.0](https://github.com/mapequation/infomap/compare/v1.1.4...v1.2.0) (2020-09-30)
349
-
350
-
351
- ### Features
352
-
353
- * Add option to --use-node-weights-as-flow ([0d75174](https://github.com/mapequation/infomap/commit/0d751745ba565e06f93dfad6feb79ac9c6794e1e))
354
- * Show bipartite start id in bipartite output ([f6e9233](https://github.com/mapequation/infomap/commit/f6e9233932f39f2dbe72b842fe2ddb259b725e08))
355
-
356
-
357
- ### Bug Fixes
358
-
359
- * Fix flow calculator for bipartite networks ([b725b27](https://github.com/mapequation/infomap/commit/b725b27563e84092438839606aba294d7b993de5))
360
- * **python:** Fix bipartite_start_id getter ([d326298](https://github.com/mapequation/infomap/commit/d326298c22570ded7002a8ee9cc361a448d8e4c5))
361
-
362
- ### [1.1.4](https://github.com/mapequation/infomap/compare/v1.1.3...v1.1.4) (2020-09-13)
363
-
364
-
365
- ### Bug Fixes
366
-
367
- * Clarify that the algorithm searches for multi-level solutions by default ([47be4de](https://github.com/mapequation/infomap/commit/47be4defa349e3be99851105aff290cd488b9282))
368
- * **python:** Fix color indices in networkx example ([dcf5888](https://github.com/mapequation/infomap/commit/dcf588800faf7f5d1f9be13d0bcc5528a2c2cf18))
369
-
370
- ### [1.1.3](https://github.com/mapequation/infomap/compare/v1.1.2...v1.1.3) (2020-05-09)
371
-
372
-
373
- ### Bug Fixes
374
-
375
- * **python:** Correct codelength terms after N > 1 ([146cee6](https://github.com/mapequation/infomap/commit/146cee6246e55fb9c4a711c1278bdc251b54fced))
376
- * **python:** Define module_codelength as L - L_index ([fa6eb94](https://github.com/mapequation/infomap/commit/fa6eb946acb22d808cd286bcfad6d76d3f2d4293))
377
- * **python:** Don't create empty node names if they didn't already exist ([#126](https://github.com/mapequation/infomap/issues/126)) ([4d1cd56](https://github.com/mapequation/infomap/commit/4d1cd565e356f5c4ac4e8ce1620ae128a0f9ad4c))
378
- * **python:** Expose num_non_trivial_top_modules ([6b91184](https://github.com/mapequation/infomap/commit/6b911842693f46546fdc89beb145394ed74dacdf))
379
-
380
- ### [1.1.2](https://github.com/mapequation/infomap/compare/v1.1.1...v1.1.2) (2020-04-08)
381
-
382
-
383
- ### Bug Fixes
384
-
385
- * **python:** Expose node names with get_name and get_names ([#125](https://github.com/mapequation/infomap/issues/125)) ([b8cb409](https://github.com/mapequation/infomap/commit/b8cb409eec171d63f60634ce3a19cc01bc3a6eef)), closes [#52](https://github.com/mapequation/infomap/issues/52)
386
-
387
- ### [1.1.1](https://github.com/mapequation/infomap/compare/v1.1.0...v1.1.1) (2020-04-08)
388
-
389
-
390
- ### Bug Fixes
391
-
392
- * Remove implied link direction from --skip-adjust-bipartite-flow ([05c3eba](https://github.com/mapequation/infomap/commit/05c3eba891521e6833292802c9c9671dee1303f7))
393
-
394
- ## [1.1.0](https://github.com/mapequation/infomap/compare/v1.0.11...v1.1.0) (2020-03-31)
395
-
396
-
397
- ### Features
398
-
399
- * Show num levels and modules in file output ([0b70cd8](https://github.com/mapequation/infomap/commit/0b70cd82030693faaf24a318d45b7e929dc61c77))
400
- * **python:** Expose codelengths for all trials ([eab7ae8](https://github.com/mapequation/infomap/commit/eab7ae861b2d93a9aea640994b53a80f4a52030c))
401
-
402
-
403
- ### Bug Fixes
404
-
405
- * Don't use physical names in _states_as_physical.net ([5889fb1](https://github.com/mapequation/infomap/commit/5889fb17b13a38b1ce7a3b5ae714810bba1406c2))
406
-
407
- ### [1.0.11](https://github.com/mapequation/infomap/compare/v1.0.10...v1.0.11) (2020-03-31)
408
-
409
-
410
- ### Bug Fixes
411
-
412
- * Handle zero weights in intra-layer links ([ddc5a3d](https://github.com/mapequation/infomap/commit/ddc5a3d827013cc006bdfa4b3518c32aef2ec722))
413
-
414
- ### [1.0.10](https://github.com/mapequation/infomap/compare/v1.0.9...v1.0.10) (2020-03-17)
415
-
416
-
417
- ### Bug Fixes
418
-
419
- * Handle unassigned nodes after input tree ([d337535](https://github.com/mapequation/infomap/commit/d33753500939912035e30db4b4dfaf38beeb3eb1)), closes [#119](https://github.com/mapequation/infomap/issues/119)
420
-
421
- ### [1.0.9](https://github.com/mapequation/infomap/compare/v1.0.8...v1.0.9) (2020-03-14)
422
-
423
-
424
- ### Bug Fixes
425
-
426
- * **windows:** compilation error on std::min ([b6c1a41](https://github.com/mapequation/infomap/commit/b6c1a419ad7f732520723a5df621eaed4bb5d2da))
427
-
428
- ### [1.0.8](https://github.com/mapequation/infomap/compare/v1.0.7...v1.0.8) (2020-03-12)
429
-
430
-
431
- ### Bug Fixes
432
-
433
- * Fix reconstruct physically merged state nodes ([dc91e1a](https://github.com/mapequation/infomap/commit/dc91e1ad93fe150c58994c9dd2ab3aebefd84ef8)), closes [#118](https://github.com/mapequation/infomap/issues/118)
434
- * Remove debug output ([#117](https://github.com/mapequation/infomap/issues/117)) ([60e7ab3](https://github.com/mapequation/infomap/commit/60e7ab346f50d3cedff06a6b7a12ef106b296f5a))
435
-
436
- ### [1.0.7](https://github.com/mapequation/infomap/compare/v1.0.6...v1.0.7) (2020-03-09)
437
-
438
-
439
- ### Bug Fixes
440
-
441
- * Add header in network and states output ([c415a4b](https://github.com/mapequation/infomap/commit/c415a4bf05625eaa2330e6e9e3c9b1e2797895c5))
442
- * Use *Edges/*Arcs instead of *Links in pajek output ([ff3a98e](https://github.com/mapequation/infomap/commit/ff3a98e18c119a64b8324018920452b6611b77d2))
443
- * Use node_id instead of id in clu output ([39cd4e4](https://github.com/mapequation/infomap/commit/39cd4e4d866ee03c1d701946225a2bd76a0a9790))
444
- * **js:** Fix support for all file io in Infomap.js ([ea9d899](https://github.com/mapequation/infomap/commit/ea9d899bdebdd361f0ff90e673471f92bc46cfaa))
445
-
446
- ### [1.0.6](https://github.com/mapequation/infomap/compare/v1.0.5...v1.0.6) (2020-03-03)
447
-
448
-
449
- ### Bug Fixes
450
-
451
- * **python:** Enable numpy.int64 in link weights ([8d91206](https://github.com/mapequation/infomap/commit/8d9120681f932bd0cfad37cc4740f719f2acb358)), closes [#107](https://github.com/mapequation/infomap/issues/107)
452
- * **python:** Print tree by default with python cli ([1565cab](https://github.com/mapequation/infomap/commit/1565cab1f3afec8c555180dd620379557709d3d0)), closes [#106](https://github.com/mapequation/infomap/issues/106)
453
-
454
- ### [1.0.5](https://github.com/mapequation/infomap/compare/v1.0.4...v1.0.5) (2020-03-02)
455
-
456
-
457
- ### Bug Fixes
458
-
459
- * Common parameters should not be advanced ([#101](https://github.com/mapequation/infomap/issues/101)) ([2907c86](https://github.com/mapequation/infomap/commit/2907c8605313d60fc7c74e36d7a841b2f96c7b1d)), closes [#100](https://github.com/mapequation/infomap/issues/100)
460
- * consistently use 1-based indexing for paths and 0 for indexes ([f283818](https://github.com/mapequation/infomap/commit/f2838189771cfc118ee20152d96694b438168ca8)), closes [#103](https://github.com/mapequation/infomap/issues/103)
461
- * Fix ftree links since remapping path from 1 ([f447b48](https://github.com/mapequation/infomap/commit/f447b4872cb29b651747c08cd919e837353b4354)), closes [#102](https://github.com/mapequation/infomap/issues/102)
462
-
463
- ### [1.0.4](https://github.com/mapequation/infomap/compare/v1.0.3...v1.0.4) (2020-02-28)
464
-
465
-
466
- ### Bug Fixes
467
-
468
- * **js:** Revert attempted worker blob optimization ([c521373](https://github.com/mapequation/infomap/commit/c521373fadaf741a34792ea27cd2efba6813cff9))
469
-
470
- ### [1.0.3](https://github.com/mapequation/infomap/compare/v1.0.2...v1.0.3) (2020-02-28)
471
-
472
-
473
- ### Bug Fixes
474
-
475
- * **js:** Handle Infomap exceptions in js ([7a641f9](https://github.com/mapequation/infomap/commit/7a641f94ddae3df99c2065e77e3a1bc78922e174)), closes [#99](https://github.com/mapequation/infomap/issues/99)
476
- * **python:** Start module id from 1 in get_[multilevel_]modules ([9419798](https://github.com/mapequation/infomap/commit/94197982597df86ae315dd9520ae24c27f67c552))
477
-
478
- ### [1.0.2](https://github.com/mapequation/infomap/compare/v1.0.1...v1.0.2) (2020-02-28)
479
-
480
-
481
- ### Bug Fixes
482
-
483
- * **windows:** Fix compilation error on std::min ([3b000dc](https://github.com/mapequation/infomap/commit/3b000dcea45875e222d69b63ae0c289bcc6efcdc)), closes [#97](https://github.com/mapequation/infomap/issues/97)
484
-
485
- ### [1.0.1](https://github.com/mapequation/infomap/compare/v1.0.0...v1.0.1) (2020-02-27)
486
-
487
-
488
- ### Bug Fixes
489
-
490
- * **python:** Fix missing package_meta on pip install ([dd24b1d](https://github.com/mapequation/infomap/commit/dd24b1d8fa7aa0c0b276dd611c57ef8a110002b8)), closes [#95](https://github.com/mapequation/infomap/issues/95)
491
-
492
- ## 1.0.0 (2020-02-26)
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-
494
-
495
- ### ⚠ BREAKING CHANGES
496
-
497
- * **python:** Drop support for python 2
498
- * **python:** Rename physicalId to node_id.
499
- Remove initial partition as first argument to run, use initial_partition argument.
500
- Start InfomapIterator.path indexing from one.
501
- * Output header format has changed
502
- * Ftree output format has changed to include enter flow
503
- * Clu output now contains top modules instead of leaf modules
504
- * Tree output is sorted on flow
505
- * Clu module ids starts from 1 instead of 0
506
- * Output contains name of the physical node instead of state id
507
- * Full multilayer format require the *multilayer heading
508
- * 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.
509
- * Removed --print-state-network, use -o states
510
- * Renamed --set-unidentified-nodes-to-closest-module to
511
- --assing-to-neighbouring-module
512
- * No support for *path input
513
-
514
- ### Features
515
-
516
- * **python:** Add meta info to infomap package ([a2caaf4](https://github.com/mapequation/infomap/commit/a2caaf4ff7f368c237c2752207b097028bacb900)), closes [#63](https://github.com/mapequation/infomap/issues/63)
517
- * Add enter flow to ftree output ([bd3255e](https://github.com/mapequation/infomap/commit/bd3255e61977ce8f1d9e0babb95ec8158710e3a8)), closes [#82](https://github.com/mapequation/infomap/issues/82)
518
- * Show entropy rate in the beginning ([f61692c](https://github.com/mapequation/infomap/commit/f61692c60c681d532f7a45b980f5041199b088b5))
519
- * **python:** Improve Python API ([#87](https://github.com/mapequation/infomap/issues/87)) ([c39cd9f](https://github.com/mapequation/infomap/commit/c39cd9f2a310a10a30e0de83dab95902e8c6aa91))
520
- * Add -o/--output option for comma-separated formats ([a255a18](https://github.com/mapequation/infomap/commit/a255a181f109b51eed3e1cbb82bb5f73f1894dd0))
521
- * Add meta data in output file header ([66ccc64](https://github.com/mapequation/infomap/commit/66ccc64fec74a47a92b053642d7ad5fb63b74df2))
522
- * Add option to print parameters in json ([3a2509d](https://github.com/mapequation/infomap/commit/3a2509d28dec022d5bdd2c8b8a4a5fd87448edab))
523
- * Allow multilayer formats without specifying -i. ([08e09f1](https://github.com/mapequation/infomap/commit/08e09f136321dcf917d0d131d57041d32c923e64))
524
- * Allow one-sided multilayer relax limit ([a116b83](https://github.com/mapequation/infomap/commit/a116b83bcf1240a17aca12a576fe634fd3db91dd)), closes [#68](https://github.com/mapequation/infomap/issues/68)
525
- * Begin module id from 1 instead of 0 in clu output ([2bbea5d](https://github.com/mapequation/infomap/commit/2bbea5d537ef0e68ac167d1f84acbf0888d22fb8))
526
- * Create npm package with Infomap worker, changelog and parameters ([44dae36](https://github.com/mapequation/infomap/commit/44dae36d65e9dccd2462db330298887318bc2463))
527
- * Output name of physical node instead of state id ([dda3277](https://github.com/mapequation/infomap/commit/dda3277a2f97152a5b5011c94e440f9bb5ee9b9b))
528
- * Remove --skip-complete-dangling-memory-nodes ([6909f21](https://github.com/mapequation/infomap/commit/6909f21a3ebc6eb84c5bc10f6f43c1839020ba41))
529
- * Remove support for *path input ([e7be175](https://github.com/mapequation/infomap/commit/e7be175378838b294d64390bd6f59cdc6b8a42f1))
530
- * Rename --set-unidentified-nodes-to-closest-module ([16fdc15](https://github.com/mapequation/infomap/commit/16fdc155d2d1fefbb22af1305f7ae7efcd1f06f4))
531
- * Simplify command line interface ([f537132](https://github.com/mapequation/infomap/commit/f5371328e63d761ccaf6ee1cdce543ced80fe25c))
532
- * Sort tree on flow ([6e27858](https://github.com/mapequation/infomap/commit/6e278584c45367145f57ce6323f6a8a9c2d64ffe)), closes [#71](https://github.com/mapequation/infomap/issues/71)
533
- * Write top modules to .clu, not bottom level ([1e16a3c](https://github.com/mapequation/infomap/commit/1e16a3ccdf15ee6155a22d8d0cd4bc6ebfdeb94f))
534
-
535
-
536
- ### Bug Fixes
537
-
538
- * **js:** Add missing this in error handler ([7345cdf](https://github.com/mapequation/infomap/commit/7345cdff8aa2b362df9d6522960fb992f5634f6e))