@mapequation/infomap 2.10.1 → 2.12.0
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.
- package/README.md +30 -0
- package/README.rst +76 -18
- package/arguments.cjs +22 -6
- package/arguments.cjs.map +1 -1
- package/arguments.d.ts +7 -1
- package/arguments.js +22 -6
- package/arguments.js.map +1 -1
- package/index.cjs +210 -4081
- package/index.cjs.map +1 -1
- package/index.d.ts +4 -17
- package/index.js +210 -4083
- package/index.js.map +1 -1
- package/index.umd.js +539 -4090
- package/index.umd.js.map +1 -1
- package/network.cjs +2 -2
- package/network.cjs.map +1 -1
- package/network.d.ts +1 -1
- package/network.js +2 -2
- package/network.js.map +1 -1
- package/package.json +7 -1
- package/react.cjs +133 -21
- package/react.cjs.map +1 -1
- package/react.d.ts +17 -6
- package/react.js +134 -22
- package/react.js.map +1 -1
- package/result.cjs +311 -0
- package/result.cjs.map +1 -0
- package/result.d.ts +21 -0
- package/result.js +307 -0
- package/result.js.map +1 -0
package/README.md
CHANGED
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@@ -56,6 +56,36 @@ React users can import the hook entrypoint directly from the main package:
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import { useInfomap } from "@mapequation/infomap/react";
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```
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The hook exposes `run`, `runAsync`, `running`, `progress`, `output`,
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`outputText`, `clearOutput`, and `on`. It keeps `running` set until the worker
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finishes or errors, and it terminates active workers when the component
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unmounts. Console output collection is opt-in.
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```js
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const { outputText, run, running } = useInfomap(
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{ silent: true },
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{
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collectOutput: true,
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events: {
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finished: (result) => console.log(result),
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error: (message) => console.warn(message),
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},
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},
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);
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run({ network, args: { clu: true, tree: true } });
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```
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Result helpers are available from `@mapequation/infomap/result` for common UI
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tasks such as metadata display and file downloads:
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```js
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import { getResultFiles, getResultMetadata } from "@mapequation/infomap/result";
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const metadata = getResultMetadata(result);
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const files = getResultFiles(result, "network");
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```
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## Use from a CDN
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With JSDelivr, the package is available as `window.infomap.default`.
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package/README.rst
CHANGED
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@@ -1,14 +1,15 @@
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-
|ci|
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|ci|
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Infomap
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=======
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Infomap is a network clustering algorithm based on the `Map equation`_.
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This repository contains the native CLI, the Python package, the R package,
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the JavaScript web worker, the Docker images,
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published Python documentation.
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the JavaScript web worker, the Docker images, the tutorial notebooks, and the
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source for the published Python documentation.
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Start with `mapequation.org/infomap/`_ for the user guide
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Start with `mapequation.org/infomap/`_ for the user guide, the
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`Infomap Python API`_ for Python examples and tutorial notebooks, and
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`CHANGELOG.md`_ for release notes.
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For contributing, security reporting, and maintainer workflows, see
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:target: https://github.com/mapequation/infomap/actions/workflows/ci.yml
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:alt: CI
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..
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:alt: Docs
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.. |docker| image:: https://github.com/mapequation/infomap/actions/workflows/docker-smoke.yml/badge.svg
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:target: https://github.com/mapequation/infomap/actions/workflows/docker-smoke.yml
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:alt: Docker smoke
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.. _Map equation: https://www.mapequation.org/publications.html#Rosvall-Axelsson-Bergstrom-2009-Map-equation
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.. _`mapequation.org/infomap/`: https://www.mapequation.org/infomap/
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.. _Map equation: https://www.mapequation.org/publications.html#Rosvall-Axelsson-Bergstrom-2009-Map-equation?utm_source=infomap&utm_medium=readme&utm_campaign=infomap
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.. _`mapequation.org/infomap/`: https://www.mapequation.org/infomap/?utm_source=infomap&utm_medium=readme&utm_campaign=infomap
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.. _`CHANGELOG.md`: https://github.com/mapequation/infomap/blob/master/CHANGELOG.md
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.. _`CONTRIBUTING.md`: https://github.com/mapequation/infomap/blob/master/CONTRIBUTING.md
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.. _`SECURITY.md`: https://github.com/mapequation/infomap/blob/master/SECURITY.md
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@@ -48,6 +41,14 @@ Install from `PyPI`_:
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pip install infomap
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Install optional integrations for common Python graph and analysis workflows:
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.. code-block:: bash
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pip install "infomap[networkx]"
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pip install "infomap[igraph]"
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pip install "infomap[pandas]"
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Upgrades use the usual `pip` flow:
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.. code-block:: bash
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Quick start with Python:
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.. code-block:: python
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import networkx as nx
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import infomap
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graph = nx.karate_club_graph()
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communities = infomap.find_communities(
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graph,
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seed=123,
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num_trials=20,
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)
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print(communities)
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For Jupyter, start with the
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`quickstart notebook <https://github.com/mapequation/infomap/blob/master/examples/notebooks/quickstart.ipynb>`_.
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It shows the notebook-native Infomap result summary, dataframe inspection, a
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copyable static network partition helper, and export paths for further
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analysis.
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For direct control over Infomap-specific options and result access:
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.. code-block:: python
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from infomap import Infomap, InfomapOptions
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options = InfomapOptions(two_level=True, silent=True, num_trials=20)
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options = InfomapOptions(two_level=True, silent=True, num_trials=20, seed=123)
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im = Infomap.from_options(options)
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im.add_link(0, 1)
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im.add_link(1, 2)
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im.run()
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print(im.num_top_modules, im.codelength)
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print(im.to_dataframe(columns=["node_id", "module_id", "flow"], index="node_id"))
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.. _PyPI: https://pypi.org/project/infomap/
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.. _`Infomap Python API`: https://mapequation.
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.. _`Infomap Python API`: https://mapequation.org/infomap-python-docs/
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R package
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^^^^^^^^^
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brew upgrade infomap
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The Homebrew formula installs Bash and Zsh completion files into Homebrew's
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standard completion directories.
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JavaScript package
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^^^^^^^^^^^^^^^^^^
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.. code-block:: bash
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docker run \
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docker run --rm \
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-p 8888:8888 \
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ghcr.io/mapequation/infomap:notebook \
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start.sh jupyter lab
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The notebook image includes the survey companion notebooks from
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``examples/notebooks`` and opens in that workspace by default. To keep local
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copies or outputs, mount a host directory as a separate workspace path:
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.. code-block:: bash
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docker run --rm \
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-v "$(pwd)":/home/jovyan/work/local \
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-p 8888:8888 \
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ghcr.io/mapequation/infomap:notebook \
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start.sh jupyter lab
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./Infomap --help
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Install shell completion scripts manually with:
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.. code-block:: bash
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./Infomap --completion zsh > ~/.zfunc/_Infomap
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mkdir -p ~/.local/share/bash-completion/completions
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./Infomap --completion bash > ~/.local/share/bash-completion/completions/infomap
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For Zsh, make sure ``~/.zfunc`` is in ``fpath`` and ``compinit`` is loaded from
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``~/.zshrc``. For Bash, make sure ``bash-completion`` is sourced from
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``~/.bashrc``.
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See ``BUILD.md`` for platform-specific maintainer build details.
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Maintainers should use:
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- ``CONTRIBUTING.md`` for pull request and contributor guidance
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- ``SECURITY.md`` for vulnerability reporting
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Agent skill
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-----------
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This repository includes an Infomap agent skill in ``skills/infomap/`` for
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reproducible CLI, Python, R, and notebook research workflows.
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Feedback
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--------
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package/arguments.cjs
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// Generated by scripts/generate_binding_options.py from ./Infomap --print-json-parameters.
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// Edit src/io/ParameterCatalog.cpp or interfaces/parameters/overrides.json, then run
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function argumentsToString(args) {
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result += " --hide-bipartite-nodes";
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if (args.printAllTrials)
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result += " --print-all-trials";
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if (args.noOverwrite)
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result += " --no-overwrite";
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result += " --timing-json " + args.timingJson;
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result += " --summary-json " + args.summaryJson;
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result += " --manifest-json " + args.manifestJson;
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result += " --memory-report";
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result += " --silent";
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result +=
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result +=
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package/arguments.cjs.map
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{"version":3,"file":"arguments.cjs","sources":["../../../interfaces/js/src/arguments.ts"],"sourcesContent":[null],"names":[],"mappings":";;;;AAAA;AACA;AACA;
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|
+
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|
package/arguments.d.ts
CHANGED
|
@@ -21,8 +21,15 @@ export type Arguments = Partial<{
|
|
|
21
21
|
output: OutputFormats | OutputFormats[];
|
|
22
22
|
hideBipartiteNodes: boolean;
|
|
23
23
|
printAllTrials: boolean;
|
|
24
|
+
noOverwrite: boolean;
|
|
25
|
+
printConfigFingerprint: boolean;
|
|
26
|
+
timingJson: string;
|
|
27
|
+
summaryJson: string;
|
|
28
|
+
manifestJson: string;
|
|
29
|
+
memoryReport: boolean;
|
|
24
30
|
verbose: 1 | 2 | 3;
|
|
25
31
|
silent: boolean;
|
|
32
|
+
pretty: boolean;
|
|
26
33
|
twoLevel: boolean;
|
|
27
34
|
flowModel: "undirected" | "directed" | "undirdir" | "outdirdir" | "rawdir" | "precomputed";
|
|
28
35
|
directed: boolean;
|
|
@@ -52,7 +59,6 @@ export type Arguments = Partial<{
|
|
|
52
59
|
coreLoopCodelengthThreshold: number;
|
|
53
60
|
tuneIterationRelativeThreshold: number;
|
|
54
61
|
fastHierarchicalSolution: 1 | 2 | 3;
|
|
55
|
-
innerParallelization: boolean;
|
|
56
62
|
preferModularSolution: boolean;
|
|
57
63
|
numRandomMoves: number;
|
|
58
64
|
maxDegreeForRandomMoves: number;
|
package/arguments.js
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
// Generated by scripts/generate_binding_options.py from ./Infomap --print-json-parameters.
|
|
2
|
-
// Edit src/io/
|
|
2
|
+
// Edit src/io/ParameterCatalog.cpp or interfaces/parameters/overrides.json, then run
|
|
3
3
|
// make build-binding-options.
|
|
4
4
|
function argumentsToString(args) {
|
|
5
5
|
let result = "";
|
|
@@ -49,10 +49,24 @@ function argumentsToString(args) {
|
|
|
49
49
|
result += " --hide-bipartite-nodes";
|
|
50
50
|
if (args.printAllTrials)
|
|
51
51
|
result += " --print-all-trials";
|
|
52
|
+
if (args.noOverwrite)
|
|
53
|
+
result += " --no-overwrite";
|
|
54
|
+
if (args.printConfigFingerprint)
|
|
55
|
+
result += " --print-config-fingerprint";
|
|
56
|
+
if (args.timingJson != null)
|
|
57
|
+
result += " --timing-json " + args.timingJson;
|
|
58
|
+
if (args.summaryJson != null)
|
|
59
|
+
result += " --summary-json " + args.summaryJson;
|
|
60
|
+
if (args.manifestJson != null)
|
|
61
|
+
result += " --manifest-json " + args.manifestJson;
|
|
62
|
+
if (args.memoryReport)
|
|
63
|
+
result += " --memory-report";
|
|
52
64
|
if (args.verbose)
|
|
53
65
|
result += " -" + "v".repeat(args.verbose);
|
|
54
66
|
if (args.silent)
|
|
55
67
|
result += " --silent";
|
|
68
|
+
if (args.pretty)
|
|
69
|
+
result += " --pretty";
|
|
56
70
|
if (args.twoLevel)
|
|
57
71
|
result += " --two-level";
|
|
58
72
|
if (args.flowModel != null)
|
|
@@ -74,7 +88,8 @@ function argumentsToString(args) {
|
|
|
74
88
|
if (args.entropyCorrected)
|
|
75
89
|
result += " --entropy-corrected";
|
|
76
90
|
if (args.entropyCorrectionStrength != null)
|
|
77
|
-
result +=
|
|
91
|
+
result +=
|
|
92
|
+
" --entropy-correction-strength " + args.entropyCorrectionStrength;
|
|
78
93
|
if (args.markovTime != null)
|
|
79
94
|
result += " --markov-time " + args.markovTime;
|
|
80
95
|
if (args.variableMarkovTime)
|
|
@@ -106,13 +121,14 @@ function argumentsToString(args) {
|
|
|
106
121
|
if (args.tuneIterationLimit != null)
|
|
107
122
|
result += " --tune-iteration-limit " + args.tuneIterationLimit;
|
|
108
123
|
if (args.coreLoopCodelengthThreshold != null)
|
|
109
|
-
result +=
|
|
124
|
+
result +=
|
|
125
|
+
" --core-loop-codelength-threshold " + args.coreLoopCodelengthThreshold;
|
|
110
126
|
if (args.tuneIterationRelativeThreshold != null)
|
|
111
|
-
result +=
|
|
127
|
+
result +=
|
|
128
|
+
" --tune-iteration-relative-threshold " +
|
|
129
|
+
args.tuneIterationRelativeThreshold;
|
|
112
130
|
if (args.fastHierarchicalSolution)
|
|
113
131
|
result += " -" + "F".repeat(args.fastHierarchicalSolution);
|
|
114
|
-
if (args.innerParallelization)
|
|
115
|
-
result += " --inner-parallelization";
|
|
116
132
|
if (args.preferModularSolution)
|
|
117
133
|
result += " --prefer-modular-solution";
|
|
118
134
|
if (args.numRandomMoves != null)
|
package/arguments.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"arguments.js","sources":["../../../interfaces/js/src/arguments.ts"],"sourcesContent":[null],"names":[],"mappings":"AAAA;AACA;AACA;
|
|
1
|
+
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