Update prettier to 3.9.x

.prettierrc

@@ -2,7 +2,7 @@
   "overrides": [
     {
       "files": [".prettierrc", ".babelrc", ".eslintrc", ".stylelintrc"],
-        "options": {
+      "options": {
         "parser": "json"
       }
     }

e2e/helpers/cleanupOutput.js

@@ -22,9 +22,9 @@ async function cleanupOutputFiles(outputDir, outputId) {
       .filter(
         (entry) =>
           entry.includes(outputId) ||
-          entry.startsWith('RAxML_GUI_ModelTest_nucleotide')
+          entry.startsWith('RAxML_GUI_ModelTest_nucleotide'),
       )
-      .map((entry) => fs.rm(path.join(outputDir, entry), { force: true }))
+      .map((entry) => fs.rm(path.join(outputDir, entry), { force: true })),
   );
 }
 

e2e/helpers/waitForOutput.js

@@ -24,7 +24,9 @@ async function waitForOutputFile(filePaths, { timeout = 10 * 60 * 1000 } = {}) {
     await new Promise((resolve) => setTimeout(resolve, 1000));
   }
 
-  throw new Error(`Timed out waiting for output file: ${candidates.join(' or ')}`);
+  throw new Error(
+    `Timed out waiting for output file: ${candidates.join(' or ')}`,
+  );
 }
 
 module.exports = {

e2e/modeltest-then-raxml-ng.spec.js

@@ -61,7 +61,7 @@ test.describe('ModelTest then raxml-ng', () => {
     expect(commandText).not.toMatch(/--model GTR(\s|$)/);
 
     const modeltestFiles = (await fs.readdir(outputDir)).filter((filename) =>
-      filename.startsWith('RAxML_GUI_ModelTest_nucleotide')
+      filename.startsWith('RAxML_GUI_ModelTest_nucleotide'),
     );
     expect(modeltestFiles.length).toBeGreaterThan(0);
 
@@ -74,33 +74,84 @@ test.describe('ModelTest then raxml-ng', () => {
     });
     await expect(page.locator('#error-dialog-title')).toHaveCount(0);
 
-    await expect(page.getByText(`Result for output id '${outputId}'`)).toBeVisible();
-    await expect(page.getByText(`${outputId}.raxml.bestTree.tre`)).toBeVisible();
+    await expect(
+      page.getByText(`Result for output id '${outputId}'`),
+    ).toBeVisible();
+    await expect(
+      page.getByText(`${outputId}.raxml.bestTree.tre`),
+    ).toBeVisible();
     await expect(page.getByText(`${outputId}.raxml.support.tre`)).toBeVisible();
-    await expect(page.getByText(`${outputId}.raxml.bootstraps.tre`)).toBeVisible();
+    await expect(
+      page.getByText(`${outputId}.raxml.bootstraps.tre`),
+    ).toBeVisible();
 
     const bestTreePath = path.join(outputDir, `${outputId}.raxml.bestTree.tre`);
     const supportTreePath = path.join(
       outputDir,
-      `${outputId}.raxml.support.tre`
+      `${outputId}.raxml.support.tre`,
     );
     const bootstrapsTreePath = path.join(
       outputDir,
-      `${outputId}.raxml.bootstraps.tre`
+      `${outputId}.raxml.bootstraps.tre`,
     );
     const logPath = path.join(outputDir, `${outputId}.raxml.log.txt`);
-    const bestModelPath = path.join(outputDir, `${outputId}.raxml.bestModel.txt`);
+    const bestModelPath = path.join(
+      outputDir,
+      `${outputId}.raxml.bestModel.txt`,
+    );
     const settingsPath = path.join(
       outputDir,
-      `RAxML_GUI_Settings_${outputId}.txt`
+      `RAxML_GUI_Settings_${outputId}.txt`,
     );
 
-    await expect.poll(async () => fs.stat(bestTreePath).then(() => true).catch(() => false)).toBe(true);
-    await expect.poll(async () => fs.stat(supportTreePath).then(() => true).catch(() => false)).toBe(true);
-    await expect.poll(async () => fs.stat(bootstrapsTreePath).then(() => true).catch(() => false)).toBe(true);
-    await expect.poll(async () => fs.stat(logPath).then(() => true).catch(() => false)).toBe(true);
-    await expect.poll(async () => fs.stat(bestModelPath).then(() => true).catch(() => false)).toBe(true);
-    await expect.poll(async () => fs.stat(settingsPath).then(() => true).catch(() => false)).toBe(true);
+    await expect
+      .poll(async () =>
+        fs
+          .stat(bestTreePath)
+          .then(() => true)
+          .catch(() => false),
+      )
+      .toBe(true);
+    await expect
+      .poll(async () =>
+        fs
+          .stat(supportTreePath)
+          .then(() => true)
+          .catch(() => false),
+      )
+      .toBe(true);
+    await expect
+      .poll(async () =>
+        fs
+          .stat(bootstrapsTreePath)
+          .then(() => true)
+          .catch(() => false),
+      )
+      .toBe(true);
+    await expect
+      .poll(async () =>
+        fs
+          .stat(logPath)
+          .then(() => true)
+          .catch(() => false),
+      )
+      .toBe(true);
+    await expect
+      .poll(async () =>
+        fs
+          .stat(bestModelPath)
+          .then(() => true)
+          .catch(() => false),
+      )
+      .toBe(true);
+    await expect
+      .poll(async () =>
+        fs
+          .stat(settingsPath)
+          .then(() => true)
+          .catch(() => false),
+      )
+      .toBe(true);
 
     const bestTree = await fs.readFile(bestTreePath, 'utf8');
     expect(bestTree).toContain('TAXON_');

e2e/raxmlHPC.spec.js

@@ -60,13 +60,13 @@ test.describe('raxmlHPC', () => {
     const outputFilename = `${outputId}.tre`;
     const bestTreePath = path.join(
       outputDir,
-      `RAxML_bestTree.${outputFilename}`
+      `RAxML_bestTree.${outputFilename}`,
     );
     const infoPathTxt = path.join(outputDir, `RAxML_info.${outputId}.txt`);
     const infoPathTre = path.join(outputDir, `RAxML_info.${outputFilename}`);
     const settingsPath = path.join(
       outputDir,
-      `RAxML_GUI_Settings_${outputId}.txt`
+      `RAxML_GUI_Settings_${outputId}.txt`,
     );
 
     const runButton = page.getByTestId('run-analysis');
@@ -82,7 +82,10 @@ test.describe('raxmlHPC', () => {
     expect(bestTree).toContain('TAXON_');
     expect(bestTree).toMatch(/[()]/);
 
-    const infoPath = (await fs.stat(infoPathTxt).then(() => infoPathTxt).catch(() => infoPathTre));
+    const infoPath = await fs
+      .stat(infoPathTxt)
+      .then(() => infoPathTxt)
+      .catch(() => infoPathTre);
     const infoText = await fs.readFile(infoPath, 'utf8');
     expect(infoText.length).toBeGreaterThan(0);
   });

package.json

@@ -113,7 +113,7 @@
     "electron-webpack": "^2.8.2",
     "nodemon": "^3.1.10",
     "npm-run-all": "^4.1.5",
-    "prettier": "^3.6.2",
+    "prettier": "^3.9.6",
     "shx": "^0.4.0",
     "typescript": "^5.8.3",
     "wait-on": "^9.1.0"

src/app/AlignmentCard.js

@@ -172,12 +172,10 @@ function AlignmentCard({ alignment }) {
                   ...alignment.modelExtra,
                   setValue: alignment.modelExtra.onChange,
                   title: alignment.modelExtra.label,
-                  options: alignment.modelExtra.options.map((model) => (
-                    {
-                      value: model,
-                      title: model,
-                    }
-                  )),
+                  options: alignment.modelExtra.options.map((model) => ({
+                    value: model,
+                    title: model,
+                  })),
                 }}
               />
             ) : null}
@@ -207,10 +205,7 @@ function AlignmentCard({ alignment }) {
         avatar={Type}
         action={
           <div>
-            <Tooltip
-              aria-label="remove-alignment"
-              title="Remove alignment"
-            >
+            <Tooltip aria-label="remove-alignment" title="Remove alignment">
               <IconButton onClick={alignment.remove} size="large">
                 <DeleteForeverIcon />
               </IconButton>
@@ -220,7 +215,8 @@ function AlignmentCard({ alignment }) {
               aria-owns={anchorEl ? 'alignment-menu' : undefined}
               aria-haspopup="true"
               onClick={handleMenuClick}
-              size="large">
+              size="large"
+            >
               <MoreVertIcon />
             </IconButton>
 
@@ -342,7 +338,8 @@ function FinalAlignmentCard({ sx, alignment }) {
               aria-owns={anchorEl ? 'alignment-menu' : undefined}
               aria-haspopup="true"
               onClick={handleMenuClick}
-              size="large">
+              size="large"
+            >
               <MoreVertIcon />
             </IconButton>
 
@@ -376,7 +373,7 @@ function FinalAlignmentCard({ sx, alignment }) {
               checked={alignment.fillTaxonGapsWithEmptySeqeunces}
               onChange={(event) => {
                 alignment.setFillTaxonGapsWithEmptySeqeunces(
-                  event.target.checked
+                  event.target.checked,
                 );
               }}
               value="fillTaxonGapsWithEmptySeqeunces"
@@ -406,7 +403,8 @@ function FinalAlignmentCard({ sx, alignment }) {
             component="code"
             sx={{
               color: (theme) => theme.palette.primary.contrastText,
-              fontFamily: 'Consolas, "Liberation Mono", Menlo, Courier, monospace',
+              fontFamily:
+                'Consolas, "Liberation Mono", Menlo, Courier, monospace',
               fontSize: '10px',
               height: '100%',
               overflowWrap: 'break-word',

src/app/App.js

@@ -44,7 +44,6 @@ const VerticalHeading = styled(Typography)(({ theme }) => ({
 }));
 
 const App = () => {
-
   const TabItems = store.runs.map((run) => (
     <Tab
       key={run.id}
@@ -270,7 +269,7 @@ const App = () => {
                 height: '100%',
                 overflowY: 'auto',
                 paddingBottom: '20px',
-                borderLeft: '1px solid #ccc'
+                borderLeft: '1px solid #ccc',
               }}
             >
               <Box
@@ -401,9 +400,7 @@ const App = () => {
             </IconButton>
             <Box display="flex">
               {/* In dev mode the app version shown is from electron, in production it is ours */}
-              <Box sx={{ marginRight: '20px' }}>
-                raxmlGUI {store.version}
-              </Box>
+              <Box sx={{ marginRight: '20px' }}>raxmlGUI {store.version}</Box>
               <Box sx={{ marginRight: '20px' }}>
                 {binary.value} {binary.version}
               </Box>

src/app/AstralTreeCard.js

@@ -16,7 +16,7 @@ import CardActions from '@mui/material/CardActions';
 import Box from '@mui/material/Box';
 
 function AstralTreeCard({ astralTree }) {
-  const { } = astralTree;
+  const {} = astralTree;
 
   const [anchorEl, setAnchorEl] = React.useState(null);
 
@@ -44,9 +44,7 @@ function AstralTreeCard({ astralTree }) {
       }}
     >
       <Box>
-        <Box display="flex" flexWrap="wrap" alignItems="center">
-
-        </Box>
+        <Box display="flex" flexWrap="wrap" alignItems="center"></Box>
       </Box>
     </Box>
   );
@@ -91,7 +89,8 @@ function AstralTreeCard({ astralTree }) {
               aria-owns={anchorEl ? 'astralTree-menu' : undefined}
               aria-haspopup="true"
               onClick={handleMenuClick}
-              size="large">
+              size="large"
+            >
               <MoreVertIcon />
             </IconButton>
 

src/app/CitationModal.js

@@ -13,7 +13,6 @@ import ToggleButtonGroup from '@mui/material/ToggleButtonGroup';
 import CodeHighlight from './components/CodeHighlight';
 
 function CitationModal({ citation }) {
-
   return (
     <Card
       elevation={0}
@@ -22,13 +21,13 @@ function CitationModal({ citation }) {
         display: 'flex',
         flexDirection: 'column',
         alignItems: 'center',
-        maxWidth: '700px'
+        maxWidth: '700px',
       }}
     >
       <CardContent
         sx={{
           maxHeight: '600px',
-          overflowY: 'auto'
+          overflowY: 'auto',
         }}
       >
         <Typography variant="h4">How to cite?</Typography>
@@ -43,7 +42,7 @@ function CitationModal({ citation }) {
             aria-label="text format"
             size="small"
           >
-            {citation.formats.map(format => (
+            {citation.formats.map((format) => (
               <ToggleButton
                 key={format.value}
                 value={format.value}
@@ -54,7 +53,7 @@ function CitationModal({ citation }) {
             ))}
           </ToggleButtonGroup>
         </Box>
-        {citation.content.map(article => (
+        {citation.content.map((article) => (
           <Box key={article.name} mt={2}>
             <Typography variant="subtitle2">{article.name}</Typography>
             <CodeHighlight
@@ -63,7 +62,7 @@ function CitationModal({ citation }) {
               sx={{
                 backgroundColor: (theme) => theme.palette.output.background,
                 borderRadius: '4px',
-                padding: '4px'
+                padding: '4px',
               }}
             />
           </Box>
@@ -90,7 +89,7 @@ function CitationModal({ citation }) {
 }
 
 CitationModal.propTypes = {
-  citation: PropTypes.object.isRequired
+  citation: PropTypes.object.isRequired,
 };
 
 export default observer(CitationModal);

src/app/Console.js

@@ -38,7 +38,8 @@ const Console = ({ run }) => {
             component="code"
             sx={{
               color: (theme) => theme.palette.console.contrastText,
-              fontFamily: 'Consolas, "Liberation Mono", Menlo, Courier, monospace',
+              fontFamily:
+                'Consolas, "Liberation Mono", Menlo, Courier, monospace',
               fontSize: '12px',
               height: '100%',
               position: 'absolute',
@@ -55,7 +56,8 @@ const Console = ({ run }) => {
             component="code"
             sx={{
               color: (theme) => theme.palette.console.contrastText,
-              fontFamily: 'Consolas, "Liberation Mono", Menlo, Courier, monospace',
+              fontFamily:
+                'Consolas, "Liberation Mono", Menlo, Courier, monospace',
               fontSize: '12px',
               height: '100%',
               position: 'absolute',
@@ -73,7 +75,7 @@ const Console = ({ run }) => {
 };
 
 Console.propTypes = {
-  run: PropTypes.object.isRequired
+  run: PropTypes.object.isRequired,
 };
 
 export default observer(Console);