Replace ESLint with Biome

.gitignore

@@ -1,3 +1,6 @@
+# Don't include Claude config.
+.claude
+
 # Don't save any JPhyloRef files into GitHub.
 /test/jphyloref-*.jar
 

bin/phyx2owl.js

@@ -1,7 +1,7 @@
 #!/usr/bin/env node
 
-const fs = require('fs');
-const path = require('path');
+const fs = require('node:fs');
+const path = require('node:path');
 const phyx = require('..');
 
 /*
@@ -10,21 +10,29 @@ const phyx = require('..');
 
 // Read command line arguments.
 const argv = require('yargs')
-  .usage("$0 [files or directories to convert into OWL ontologies]")
-  .describe('max-internal-specifiers', 'The maximum number of internal specifiers (phylorefs with more than this number will be ignored)')
+  .usage('$0 [files or directories to convert into OWL ontologies]')
+  .describe(
+    'max-internal-specifiers',
+    'The maximum number of internal specifiers (phylorefs with more than this number will be ignored)',
+  )
   .default('max-internal-specifiers', 8)
-  .describe('max-external-specifiers', 'The maximum number of external specifiers (phylorefs with more than this number will be ignored)')
+  .describe(
+    'max-external-specifiers',
+    'The maximum number of external specifiers (phylorefs with more than this number will be ignored)',
+  )
   .default('max-external-specifiers', 8)
   .describe('base-iri', 'The base IRI to use for the input files')
   .help()
-  .alias('h', 'help')
-  .argv
+  .alias('h', 'help').argv;
 
 /*
  * Get a list of all files in a directory. We will recurse into directories and choose
  * files that meet the criteria in the function `check(filename) => boolean`.
  */
-function getFilesInDir(filePath, check = (filename => filename.toLowerCase().endsWith(".json"))) {
+function getFilesInDir(
+  filePath,
+  check = filename => filename.toLowerCase().endsWith('.json'),
+) {
   // console.debug(`Processing file: ${filePath}`)
   if (!fs.existsSync(filePath)) return [];
 
@@ -41,7 +49,8 @@ function getFilesInDir(filePath, check = (filename => filename.toLowerCase().end
   } else if (lsync.isDirectory()) {
     // If `path` is a directory, recurse into every file in that directory.
     const files = fs.readdirSync(filePath);
-    return files.map(file => getFilesInDir(path.join(filePath, file), check))
+    return files
+      .map(file => getFilesInDir(path.join(filePath, file), check))
       .reduce((acc, curr) => acc.concat(curr), []);
   } else {
     // console.debug(`${filePath} is neither a file nor a directory; skipping.`);
@@ -53,7 +62,7 @@ function getFilesInDir(filePath, check = (filename => filename.toLowerCase().end
 // At this point, we convert directories into lists of files.
 const filenames = argv._;
 if (filenames.length === 0) {
-  console.error("No input files provided.");
+  console.error('No input files provided.');
   process.exit(1);
 }
 
@@ -63,7 +72,9 @@ const files = filenames
 // console.debug(`Files to process: ${files.join(", ")}`);
 
 if (files.length === 0) {
-  console.error(`Input files do not exist or consist of directories that do not contain JSON files: ${filenames.join(', ')}`);
+  console.error(
+    `Input files do not exist or consist of directories that do not contain JSON files: ${filenames.join(', ')}`,
+  );
   process.exit(1);
 }
 
@@ -73,20 +84,20 @@ if (files.length === 0) {
  * filename: either by replacing '.json' with '.owl', or by concatenating
  * '.owl' at the end.
  */
-function convertFileToOWL(filename, argOutputFilename = "") {
+function convertFileToOWL(filename, argOutputFilename = '') {
   // console.debug(`Starting with ${filename}.`);
   let outputFilename;
-  if (argOutputFilename != "") {
+  if (argOutputFilename !== '') {
     outputFilename = argOutputFilename;
-  } else if (filename.toLowerCase().endsWith(".json")) {
-    outputFilename = filename.substring(0, filename.length - 5) + ".owl";
+  } else if (filename.toLowerCase().endsWith('.json')) {
+    outputFilename = `${filename.substring(0, filename.length - 5)}.owl`;
   } else {
-    outputFilename = filename + ".owl";
+    outputFilename = `${filename}.owl`;
   }
 
   try {
     // Parse the input file into JSON.
-    let phyxContent = JSON.parse(fs.readFileSync(filename));
+    const phyxContent = JSON.parse(fs.readFileSync(filename));
 
     // Remove any phylorefs that have too many specifiers.
     const phylorefCount = (phyxContent.phylorefs || []).length;
@@ -95,10 +106,14 @@ function convertFileToOWL(filename, argOutputFilename = "") {
       const internalSpecifiersCount = wrappedPhyloref.internalSpecifiers.length;
       const externalSpecifiersCount = wrappedPhyloref.externalSpecifiers.length;
       if (internalSpecifiersCount > argv.maxInternalSpecifiers) {
-        console.warn(`Phyloreference ${wrappedPhyloref.label} was skipped, since it has ${internalSpecifiersCount} internal specifiers.`);
+        console.warn(
+          `Phyloreference ${wrappedPhyloref.label} was skipped, since it has ${internalSpecifiersCount} internal specifiers.`,
+        );
         return false;
       } else if (externalSpecifiersCount > argv.maxExternalSpecifiers) {
-        console.warn(`Phyloreference ${wrappedPhyloref.label} was skipped, since it has ${externalSpecifiersCount} external specifiers.`);
+        console.warn(
+          `Phyloreference ${wrappedPhyloref.label} was skipped, since it has ${externalSpecifiersCount} external specifiers.`,
+        );
         return false;
       }
       return true;
@@ -107,41 +122,45 @@ function convertFileToOWL(filename, argOutputFilename = "") {
 
     // Convert the Phyx file into JSON-LD.
     const wrappedPhyx = new phyx.PhyxWrapper(phyxContent);
-    wrappedPhyx.toRDF(argv.baseIri, path.dirname(filename))
+    wrappedPhyx
+      .toRDF(argv.baseIri, path.dirname(filename))
       .then(nquads => {
-        fs.writeFileSync(
-          outputFilename,
-          nquads
-        );
+        fs.writeFileSync(outputFilename, nquads);
       })
       .catch(err => {
         throw err;
       });
 
     // Report on whether any phyloreferences were converted.
-    if (filteredPhylorefs.length == 0) {
-        console.warn(`No phyloreferences in ${filename} were converted to ${outputFilename}, as they were all filtered out.`);
-        return false;
+    if (filteredPhylorefs.length === 0) {
+      console.warn(
+        `No phyloreferences in ${filename} were converted to ${outputFilename}, as they were all filtered out.`,
+      );
+      return false;
     } else if (phylorefCount > filteredPhylorefs.length) {
-        console.warn(`Only ${filteredPhylorefs.length} out of ${phylorefCount} were converted from ${filename} to ${outputFilename}.`);
-        return true;
+      console.warn(
+        `Only ${filteredPhylorefs.length} out of ${phylorefCount} were converted from ${filename} to ${outputFilename}.`,
+      );
+      return true;
     } else {
-        console.info(`Converted ${filename} to ${outputFilename}.`);
-        return true;
+      console.info(`Converted ${filename} to ${outputFilename}.`);
+      return true;
     }
-
-    return true;
-  } catch(e) {
-    console.error(`Could not convert ${filename} to ${outputFilename}: ${e} at ${e.stack}`);
-    console.error(``)
+  } catch (e) {
+    console.error(
+      `Could not convert ${filename} to ${outputFilename}: ${e} at ${e.stack}`,
+    );
+    console.error(``);
   }
   return false;
 }
 
 // Count and report all the successes in converting files to OWL.
 const successes = files.map(file => convertFileToOWL(file));
-if(successes.every(x => x)) {
+if (successes.every(x => x)) {
   console.log(`${successes.length} files converted successfully.`);
 } else {
-  console.log(`Errors occurred; ${successes.filter(x => x).length} files converted successfully, ${successes.filter(x => !x).length} files failed.`);
+  console.log(
+    `Errors occurred; ${successes.filter(x => x).length} files converted successfully, ${successes.filter(x => !x).length} files failed.`,
+  );
 }