Fix pyodide runner (#106)

* Install pydantic separately

* Install earlier

* Underscore

* Update pyodite

* Install pinned pydantic

* Remove pin

* Pin

* Lower Pydantic pin

* Add pygments

* Fix multiqc.run

* Import ClConfig

* Suppress warning

* Better comments

* Remove warning supresion in favour of MultiQC update

* No version check

* Clean up

public/run_deps/pyodideWorker.js

@@ -1,4 +1,4 @@
-importScripts("https://cdn.jsdelivr.net/pyodide/v0.24.1/full/pyodide.js");
+importScripts("https://cdn.jsdelivr.net/pyodide/v0.26.2/full/pyodide.js");
 
 async function loadAndRunPython() {
   self.pyodide = await loadPyodide();
@@ -9,6 +9,11 @@ async function loadAndRunPython() {
     console.log("colormath installed successfully");
     await micropip.install("/run_deps/spectra-0.0.11-py3-none-any.whl");
     console.log("spectra installed successfully");
+    await micropip.install("pygments");  // for some reason it needs to be installed separately
+    console.log("pygments installed successfully");
+    // MultiQC pins 2.7.1, and Pyodide only has 2.7.0, so we need to override here:
+    await micropip.install("pydantic==2.7.*");  // pyodide only has 2.7.0, not 2.7.1
+    console.log("pydantic installed successfully");
 
     // Now we want to install multiqc with all other dependencies _except_ kaleido,
     // which is not needed for the browser-based setup, and it doesn't have 
@@ -17,14 +22,14 @@ async function loadAndRunPython() {
     const response = await fetch(`https://pypi.org/pypi/multiqc/json`);
     const packageData = await response.json();
     let dependencies = packageData.info["requires_dist"];
-    // And excluding 'kaleido' (and 'Pillow', also needed only for flat plot export)
-    dependencies = dependencies.filter(dep => !dep.includes("kaleido") && !dep.includes("Pillow"));
     // Removing all "extras" dependencies:
     dependencies = dependencies.filter(dep => !dep.includes("; extra =="));
     // Removing any other possible environment markers:
     dependencies = dependencies.map(dep => dep.split(";")[0].trim());
     // And installing the remaining dependencies one by one:
     for (const dep of dependencies) {
+      if (dep.includes("pydantic")) continue  // pydantic was already installed above
+      if (dep.includes("kaleido") || dep.includes("Pillow")) continue  // only needed only for the flat plot export
       console.log("Installing " + dep);
       await micropip.install(dep);
     }

src/components/run/Runner.svelte

@@ -42,7 +42,8 @@
     pyodideWorker.postMessage({
       code: `
 import multiqc
-multiqc.run('/data', no_ansi=True, force=True)
+from multiqc.core.update_config import ClConfig
+multiqc.run('/data', cfg=ClConfig(no_ansi=True, no_version_check=True, force=True))
         `,
     });
   }
@@ -55,7 +56,7 @@ multiqc.run('/data', no_ansi=True, force=True)
   function clean_stdout(line: string) {
     line = line.replace(
       /^  \/\/\/ MultiQC 🔍 (.+)/,
-      '\n<span class="slashes">///</span> <a href="https://multiqc.info/" target="_blank" >MultiQC</a> 🔍 <span>$1</span>\n'
+      '\n<span class="slashes">///</span> <a href="https://multiqc.info/" target="_blank" >MultiQC</a> 🔍 <span>$1</span>\n',
     );
     line = line.replace(/^(\| +.+ \|)/, "<span>$1</span>");
     return line;

src/multiqc_releases.json

@@ -1 +1 @@
-{"latest":"v1.23","latest_published_at":"2024-07-09T18:04:00Z"}
+{"latest":"v1.24.1","latest_published_at":"2024-08-21T11:27:14Z"}