Added access to server files from python using open

book/_config.yml

@@ -22,6 +22,3 @@ bibtex_bibfiles:
 launch_buttons:
   thebe: true
   
-repository:
-  url: https://gitlab.tudelft.nl/mude/book  # Online location of your book
-  branch: main  # Which branch of the repository should be used when creating links (optional)

book/_toc.yml

@@ -45,6 +45,9 @@ parts:
       - file: sandbox/SanPart/premath/00_01c_PreMath.md
       - file: sandbox/SanPart/premath/00_02_PreMath.md
       - file: sandbox/SanPart/premath/00_03_PreMath.md
+    - file: sandbox/it
+      sections:
+      - file: sandbox/it-benchmark_dont_execute.ipynb
   - caption: MUDE Cookbook
     chapters:
     - file: cookbook/blank
@@ -176,4 +179,4 @@ parts:
         - file: old/coding/2-2/1_1_dont_execute.ipynb
         - file: old/coding/2-2/1_2_dont_execute.ipynb
       - file: old/coding/2-2/1-part-2.md
-      - file: old/coding/2-2/1-part-3.md
\ No newline at end of file
+      - file: old/coding/2-2/1-part-3.md

book/sandbox/it-benchmark_dont_execute.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Benchmarks"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with open(\"reading_test.txt\") as f:\n",
+    "    print(f.read())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.9"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "a67e065d7bac6c9a1464b57d1c6c9ee143117011e86b73963744a6c83e2c9c0b"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

book/sandbox/it.md

+# IT Benchmarks
+
+Some benchmarks for any IT stuff going on in here.
+
+```{tableofcontents}
+```
\ No newline at end of file

book/sandbox/reading_test.txt

+Hopefully we can read this!

book/thebe_lite/sphinx-thebe.js

@@ -130,19 +130,71 @@ const loadStyleAsync = async (styleSource) => {
   });
 };
 
+function override_pyodide_open(fs, home, server_path) {
+  const old_open = fs.open;
+  function new_open(path, flags, mode) {
+    console.log(`Params: ${path}, ${flags}, ${mode}`);
+    // Being called from writeFile, or in write mode, we don't want to load in that case
+    // This catches any errors caused by things like missing directories
+    if (flags === 577) {
+      console.log("Running old open");
+      return old_open(path, flags, mode);
+    }
+
+    console.log(`Params: ${path}, ${flags}, ${mode}`);
+    try {
+      return old_open(path, flags, mode);
+    } catch {
+      const fullPath = path;
+      // Remove '/home/pyodide' or '/home/drive' etc.
+      if (path.startsWith(home)) {
+        path = path.slice(home.length);
+      }
+
+      // Last entry is the file itself
+      let directories = fullPath.split("/").slice(0, -1);
+      let currentDirectory = "/";
+
+      for (const directory of directories) {
+        if (directory === "") continue;
+        currentDirectory += directory + "/";
+        try {
+          fs.mkdir(currentDirectory);
+          console.log(`Made up to: ${currentDirectory}`);
+        } catch {}
+      }
+
+      let request = new XMLHttpRequest();
+      // Fetch relative to where we are in the server, to simulate how it works in notebooks
+      // We will still put it in the directory requested by pyodide however, so the next call to open succeeds without tampering
+      const requestFrom = path[0] === "/" ? path : server_path + path;
+      console.log(`Requesting from: ${requestFrom}`);
+      request.open("GET", requestFrom, false);
+      request.send();
+
+      if (request.status !== 200) {
+        throw new fs.ErrnoError(44);
+      }
+      fs.writeFile(fullPath, request.response);
+
+      return old_open(fullPath, flags, mode);
+    }
+  }
+  fs.open = new_open;
+}
 
 var initThebe = async () => {
   // Load thebe dynamically if it's not already loaded
   if (typeof thebelab === "undefined") {
     console.log("[sphinx-thebe]: Loading thebe...");
     $(".thebe-launch-button ").css("display", "none");
-    
+
     // Provides nice things like a running animation and some padding
     {
       await loadStyleAsync("/thebe.css");
       await loadStyleAsync("/_static/code.css");
     }
-    
+
     $(".thebe-launch-button ").css("display", "block");
     $(".thebe-launch-button ").text("Loading thebe...");
 
@@ -153,7 +205,12 @@ var initThebe = async () => {
     console.log("[sphinx-thebe]: Finished loading thebe...");
     configureThebe();
     modifyDOMForThebe();
-    thebelab.bootstrap(thebeLiteConfig);
+    await thebelab.bootstrap(thebeLiteConfig);
+    await thebelab.session.kernel.requestExecute({
+      code: `import js; from os import getcwd; import pyodide_js; js.fs = pyodide_js.FS; js.eval("""${override_pyodide_open.toString()}"""); js.eval(f"override_pyodide_open(fs, '{getcwd()}/', ${
+        location.pathname.split("/").slice(0, -1).join("/") + "/"
+      })")`,
+    });
   } else {
     console.log("[sphinx-thebe]: thebe already loaded...");
   }
@@ -168,4 +225,3 @@ var detectLanguage = (language) => {
   }
   return language;
 };
-

build-lite.sh

@@ -17,4 +17,8 @@ else
 	fi
 fi
 
+# Copy all non notebook, markdown or build files into the build for local access in pyodide etc.
+find book/ | grep -v "^book/_.*\|.*\.\(md\|ipynb\)\|thebe_lite" | grep "\." | cut -c 6- | xargs -i sh -c 'echo "book/_build/html/{}" | grep -o "^.*/" | xargs -d "\n" mkdir -p; cp book/"{}" book/_build/html/"{}"'
+
 $python_command -m http.server 8000 --directory book/_build/html &
+