@mapequation/infomap 2.8.0 → 2.10.0

package/arguments.d.ts

@@ -1,28 +1,28 @@
-declare type OutputFormats = "clu" | "tree" | "ftree" | "newick" | "json" | "csv" | "network" | "states" | "flow";
-export interface Arguments extends Partial<{
-    clusterData: string;
-    noInfomap: boolean;
+type OutputFormats = "clu" | "tree" | "ftree" | "newick" | "json" | "csv" | "network" | "states" | "flow";
+export type Arguments = Partial<{
     skipAdjustBipartiteFlow: boolean;
     bipartiteTeleportation: boolean;
     weightThreshold: number;
     noSelfLinks: boolean;
     nodeLimit: number;
     matchableMultilayerIds: number;
+    clusterData: string;
     assignToNeighbouringModule: boolean;
     metaData: string;
     metaDataRate: number;
     metaDataUnweighted: boolean;
+    noInfomap: boolean;
+    outName: string;
+    noFileOutput: boolean;
     tree: boolean;
     ftree: boolean;
     clu: boolean;
-    verbose: 1 | 2 | 3;
-    silent: boolean;
-    outName: string;
-    noFileOutput: boolean;
     cluLevel: number;
     output: OutputFormats | OutputFormats[];
     hideBipartiteNodes: boolean;
     printAllTrials: boolean;
+    verbose: 1 | 2 | 3;
+    silent: boolean;
     twoLevel: boolean;
     flowModel: "undirected" | "directed" | "undirdir" | "outdirdir" | "rawdir" | "precomputed";
     directed: boolean;
@@ -37,6 +37,7 @@ export interface Arguments extends Partial<{
     markovTime: number;
     variableMarkovTime: boolean;
     variableMarkovDamping: number;
+    variableMarkovMinScale: number;
     preferredNumberOfModules: number;
     multilayerRelaxRate: number;
     multilayerRelaxLimit: number;
@@ -51,11 +52,12 @@ export interface Arguments extends Partial<{
     coreLoopCodelengthThreshold: number;
     tuneIterationRelativeThreshold: number;
     fastHierarchicalSolution: 1 | 2 | 3;
-    preferModularSolution: boolean;
     innerParallelization: boolean;
+    preferModularSolution: boolean;
+    numRandomMoves: number;
+    maxDegreeForRandomMoves: number;
     help: boolean | "advanced";
     version: boolean;
-}> {
-}
+}>;
 export default function argumentsToString(args: Arguments): string;
 export {};

package/arguments.js

@@ -0,0 +1,130 @@
+// Generated by scripts/generate_binding_options.py from ./Infomap --print-json-parameters.
+// Edit src/io/Config.cpp or interfaces/parameters/overrides.json, then run
+// make build-binding-options.
+function argumentsToString(args) {
+    let result = "";
+    if (args.skipAdjustBipartiteFlow)
+        result += " --skip-adjust-bipartite-flow";
+    if (args.bipartiteTeleportation)
+        result += " --bipartite-teleportation";
+    if (args.weightThreshold != null)
+        result += " --weight-threshold " + args.weightThreshold;
+    if (args.noSelfLinks)
+        result += " --no-self-links";
+    if (args.nodeLimit != null)
+        result += " --node-limit " + args.nodeLimit;
+    if (args.matchableMultilayerIds != null)
+        result += " --matchable-multilayer-ids " + args.matchableMultilayerIds;
+    if (args.clusterData != null)
+        result += " --cluster-data " + args.clusterData;
+    if (args.assignToNeighbouringModule)
+        result += " --assign-to-neighbouring-module";
+    if (args.metaData != null)
+        result += " --meta-data " + args.metaData;
+    if (args.metaDataRate != null)
+        result += " --meta-data-rate " + args.metaDataRate;
+    if (args.metaDataUnweighted)
+        result += " --meta-data-unweighted";
+    if (args.noInfomap)
+        result += " --no-infomap";
+    if (args.outName != null)
+        result += " --out-name " + args.outName;
+    if (args.noFileOutput)
+        result += " --no-file-output";
+    if (args.tree)
+        result += " --tree";
+    if (args.ftree)
+        result += " --ftree";
+    if (args.clu)
+        result += " --clu";
+    if (args.cluLevel != null)
+        result += " --clu-level " + args.cluLevel;
+    if (args.output != null) {
+        if (typeof args.output === "string")
+            result += " --output " + args.output;
+        else
+            result += " --output " + args.output.join(",");
+    }
+    if (args.hideBipartiteNodes)
+        result += " --hide-bipartite-nodes";
+    if (args.printAllTrials)
+        result += " --print-all-trials";
+    if (args.verbose)
+        result += " -" + "v".repeat(args.verbose);
+    if (args.silent)
+        result += " --silent";
+    if (args.twoLevel)
+        result += " --two-level";
+    if (args.flowModel != null)
+        result += " --flow-model " + args.flowModel;
+    if (args.directed)
+        result += " --directed";
+    if (args.recordedTeleportation)
+        result += " --recorded-teleportation";
+    if (args.useNodeWeightsAsFlow)
+        result += " --use-node-weights-as-flow";
+    if (args.toNodes)
+        result += " --to-nodes";
+    if (args.teleportationProbability != null)
+        result += " --teleportation-probability " + args.teleportationProbability;
+    if (args.regularized)
+        result += " --regularized";
+    if (args.regularizationStrength != null)
+        result += " --regularization-strength " + args.regularizationStrength;
+    if (args.entropyCorrected)
+        result += " --entropy-corrected";
+    if (args.entropyCorrectionStrength != null)
+        result += " --entropy-correction-strength " + args.entropyCorrectionStrength;
+    if (args.markovTime != null)
+        result += " --markov-time " + args.markovTime;
+    if (args.variableMarkovTime)
+        result += " --variable-markov-time";
+    if (args.variableMarkovDamping != null)
+        result += " --variable-markov-damping " + args.variableMarkovDamping;
+    if (args.variableMarkovMinScale != null)
+        result += " --variable-markov-min-scale " + args.variableMarkovMinScale;
+    if (args.preferredNumberOfModules != null)
+        result += " --preferred-number-of-modules " + args.preferredNumberOfModules;
+    if (args.multilayerRelaxRate != null)
+        result += " --multilayer-relax-rate " + args.multilayerRelaxRate;
+    if (args.multilayerRelaxLimit != null)
+        result += " --multilayer-relax-limit " + args.multilayerRelaxLimit;
+    if (args.multilayerRelaxLimitUp != null)
+        result += " --multilayer-relax-limit-up " + args.multilayerRelaxLimitUp;
+    if (args.multilayerRelaxLimitDown != null)
+        result += " --multilayer-relax-limit-down " + args.multilayerRelaxLimitDown;
+    if (args.multilayerRelaxByJsd)
+        result += " --multilayer-relax-by-jsd";
+    if (args.seed != null)
+        result += " --seed " + args.seed;
+    if (args.numTrials != null)
+        result += " --num-trials " + args.numTrials;
+    if (args.coreLoopLimit != null)
+        result += " --core-loop-limit " + args.coreLoopLimit;
+    if (args.coreLevelLimit != null)
+        result += " --core-level-limit " + args.coreLevelLimit;
+    if (args.tuneIterationLimit != null)
+        result += " --tune-iteration-limit " + args.tuneIterationLimit;
+    if (args.coreLoopCodelengthThreshold != null)
+        result += " --core-loop-codelength-threshold " + args.coreLoopCodelengthThreshold;
+    if (args.tuneIterationRelativeThreshold != null)
+        result += " --tune-iteration-relative-threshold " + args.tuneIterationRelativeThreshold;
+    if (args.fastHierarchicalSolution)
+        result += " -" + "F".repeat(args.fastHierarchicalSolution);
+    if (args.innerParallelization)
+        result += " --inner-parallelization";
+    if (args.preferModularSolution)
+        result += " --prefer-modular-solution";
+    if (args.numRandomMoves != null)
+        result += " --num-random-moves " + args.numRandomMoves;
+    if (args.maxDegreeForRandomMoves != null)
+        result += " --max-degree-for-random-moves " + args.maxDegreeForRandomMoves;
+    if (args.help)
+        result += args.help === "advanced" ? " -hh" : " -h";
+    if (args.version)
+        result += " --version";
+    return result;
+}
+
+export { argumentsToString as default };
+//# sourceMappingURL=arguments.js.map

package/arguments.js.map

@@ -0,0 +1 @@
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package/filetypes.cjs

@@ -0,0 +1,56 @@
+'use strict';
+
+Object.defineProperty(exports, '__esModule', { value: true });
+
+const isClu = (file) => {
+    const clu = file;
+    return clu.length > 0 && ("moduleId" in file[0] || "meta" in file[0]);
+};
+const isTree = (file) => {
+    const clu = file;
+    return clu.length > 0 && "path" in file[0];
+};
+function fileToString(file) {
+    if (file.length === 0) {
+        return "";
+    }
+    if (isClu(file)) {
+        return cluToString(file);
+    }
+    else if (isTree(file)) {
+        return treeToString(file);
+    }
+    return "";
+}
+function cluToString(clu) {
+    let result = "";
+    for (const node of clu) {
+        result += node.id;
+        if ("moduleId" in node)
+            result += ` ${node.moduleId}`;
+        else if ("meta" in node)
+            result += ` ${node.meta}`;
+        if (node.flow != null)
+            result += ` ${node.flow}`;
+        result += "\n";
+    }
+    return result;
+}
+function treeToString(tree) {
+    let result = "";
+    for (const node of tree) {
+        const flow = node.flow ?? 0;
+        const name = node.name ?? node.id;
+        result += `${node.path.join(":")} ${flow} "${name}"`;
+        if ("stateId" in node)
+            result += ` ${node.stateId}`;
+        result += ` ${node.id}`;
+        if ("layerId" in node)
+            result += ` ${node.layerId}`;
+        result += "\n";
+    }
+    return result;
+}
+
+exports.default = fileToString;
+//# sourceMappingURL=filetypes.cjs.map

package/filetypes.cjs.map

@@ -0,0 +1 @@
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package/filetypes.d.ts

@@ -1,26 +1,26 @@
-export declare type NodeBase = {
+export type NodeBase = {
     id: number;
     flow?: number;
 };
-declare type StateNodeBase = {
+type StateNodeBase = {
     stateId: number;
     layerId?: number;
 };
-export declare type CluNode<T extends string = "moduleId"> = {
+export type CluNode<T extends string = "moduleId"> = {
     [key in T]: number;
 } & NodeBase;
-export declare type CluStateNode = CluNode & StateNodeBase;
-export declare type Clu = CluNode[];
-export declare type MetaClu = CluNode<"meta">[];
-export declare type TreeNode = {
+export type CluStateNode = CluNode & StateNodeBase;
+export type Clu = CluNode[];
+export type MetaClu = CluNode<"meta">[];
+export type TreeNode = {
     path: number[];
     modules?: number[];
     mec?: number;
     name?: string;
 } & NodeBase;
-export declare type TreeStateNode = TreeNode & StateNodeBase;
-export declare type Tree = TreeNode[];
-export declare type StateTree = TreeStateNode[];
-export declare type FileTypes = Clu | MetaClu | Tree | StateTree;
+export type TreeStateNode = TreeNode & StateNodeBase;
+export type Tree = TreeNode[];
+export type StateTree = TreeStateNode[];
+export type FileTypes = Clu | MetaClu | Tree | StateTree;
 export default function fileToString(file: FileTypes): string;
 export {};

package/filetypes.js

@@ -0,0 +1,52 @@
+const isClu = (file) => {
+    const clu = file;
+    return clu.length > 0 && ("moduleId" in file[0] || "meta" in file[0]);
+};
+const isTree = (file) => {
+    const clu = file;
+    return clu.length > 0 && "path" in file[0];
+};
+function fileToString(file) {
+    if (file.length === 0) {
+        return "";
+    }
+    if (isClu(file)) {
+        return cluToString(file);
+    }
+    else if (isTree(file)) {
+        return treeToString(file);
+    }
+    return "";
+}
+function cluToString(clu) {
+    let result = "";
+    for (const node of clu) {
+        result += node.id;
+        if ("moduleId" in node)
+            result += ` ${node.moduleId}`;
+        else if ("meta" in node)
+            result += ` ${node.meta}`;
+        if (node.flow != null)
+            result += ` ${node.flow}`;
+        result += "\n";
+    }
+    return result;
+}
+function treeToString(tree) {
+    let result = "";
+    for (const node of tree) {
+        const flow = node.flow ?? 0;
+        const name = node.name ?? node.id;
+        result += `${node.path.join(":")} ${flow} "${name}"`;
+        if ("stateId" in node)
+            result += ` ${node.stateId}`;
+        result += ` ${node.id}`;
+        if ("layerId" in node)
+            result += ` ${node.layerId}`;
+        result += "\n";
+    }
+    return result;
+}
+
+export { fileToString as default };
+//# sourceMappingURL=filetypes.js.map

package/filetypes.js.map

@@ -0,0 +1 @@
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