From 03e2a6b086b364029f3bdb87c37e1ef294d599d0 Mon Sep 17 00:00:00 2001
From: jonbrenas <jb52@sanger.ac.uk>
Date: Tue, 14 May 2024 05:02:38 -0500
Subject: [PATCH] Removed the code setting the project id and added some text
 about ignoring the warning

---
 docs/workshop-6/module-4-primers.ipynb | 701 ++-----------------------
 1 file changed, 35 insertions(+), 666 deletions(-)

diff --git a/docs/workshop-6/module-4-primers.ipynb b/docs/workshop-6/module-4-primers.ipynb
index 4d30789..df054c3 100644
--- a/docs/workshop-6/module-4-primers.ipynb
+++ b/docs/workshop-6/module-4-primers.ipynb
@@ -338,664 +338,26 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "5fd538ef",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "os.environ[\"GOOGLE_CLOUD_PROJECT\"] = \"PAMCA-W6M7-AnoPrimer\""
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "id": "528ae85d",
-   "metadata": {
-    "id": "528ae85d",
-    "tags": []
-   },
-   "outputs": [
-    {
-     "data": {
-      "application/javascript": [
-       "'use strict';\n",
-       "(function(root) {\n",
-       "  function now() {\n",
-       "    return new Date();\n",
-       "  }\n",
-       "\n",
-       "  const force = true;\n",
-       "\n",
-       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
-       "    root._bokeh_onload_callbacks = [];\n",
-       "    root._bokeh_is_loading = undefined;\n",
-       "  }\n",
-       "\n",
-       "const JS_MIME_TYPE = 'application/javascript';\n",
-       "  const HTML_MIME_TYPE = 'text/html';\n",
-       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
-       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
-       "\n",
-       "  /**\n",
-       "   * Render data to the DOM node\n",
-       "   */\n",
-       "  function render(props, node) {\n",
-       "    const script = document.createElement(\"script\");\n",
-       "    node.appendChild(script);\n",
-       "  }\n",
-       "\n",
-       "  /**\n",
-       "   * Handle when an output is cleared or removed\n",
-       "   */\n",
-       "  function handleClearOutput(event, handle) {\n",
-       "    function drop(id) {\n",
-       "      const view = Bokeh.index.get_by_id(id)\n",
-       "      if (view != null) {\n",
-       "        view.model.document.clear()\n",
-       "        Bokeh.index.delete(view)\n",
-       "      }\n",
-       "    }\n",
-       "\n",
-       "    const cell = handle.cell;\n",
-       "\n",
-       "    const id = cell.output_area._bokeh_element_id;\n",
-       "    const server_id = cell.output_area._bokeh_server_id;\n",
-       "\n",
-       "    // Clean up Bokeh references\n",
-       "    if (id != null) {\n",
-       "      drop(id)\n",
-       "    }\n",
-       "\n",
-       "    if (server_id !== undefined) {\n",
-       "      // Clean up Bokeh references\n",
-       "      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
-       "      cell.notebook.kernel.execute(cmd_clean, {\n",
-       "        iopub: {\n",
-       "          output: function(msg) {\n",
-       "            const id = msg.content.text.trim()\n",
-       "            drop(id)\n",
-       "          }\n",
-       "        }\n",
-       "      });\n",
-       "      // Destroy server and session\n",
-       "      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
-       "      cell.notebook.kernel.execute(cmd_destroy);\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  /**\n",
-       "   * Handle when a new output is added\n",
-       "   */\n",
-       "  function handleAddOutput(event, handle) {\n",
-       "    const output_area = handle.output_area;\n",
-       "    const output = handle.output;\n",
-       "\n",
-       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
-       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
-       "      return\n",
-       "    }\n",
-       "\n",
-       "    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
-       "\n",
-       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
-       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
-       "      // store reference to embed id on output_area\n",
-       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
-       "    }\n",
-       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
-       "      const bk_div = document.createElement(\"div\");\n",
-       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
-       "      const script_attrs = bk_div.children[0].attributes;\n",
-       "      for (let i = 0; i < script_attrs.length; i++) {\n",
-       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
-       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
-       "      }\n",
-       "      // store reference to server id on output_area\n",
-       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  function register_renderer(events, OutputArea) {\n",
-       "\n",
-       "    function append_mime(data, metadata, element) {\n",
-       "      // create a DOM node to render to\n",
-       "      const toinsert = this.create_output_subarea(\n",
-       "        metadata,\n",
-       "        CLASS_NAME,\n",
-       "        EXEC_MIME_TYPE\n",
-       "      );\n",
-       "      this.keyboard_manager.register_events(toinsert);\n",
-       "      // Render to node\n",
-       "      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
-       "      render(props, toinsert[toinsert.length - 1]);\n",
-       "      element.append(toinsert);\n",
-       "      return toinsert\n",
-       "    }\n",
-       "\n",
-       "    /* Handle when an output is cleared or removed */\n",
-       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
-       "    events.on('delete.Cell', handleClearOutput);\n",
-       "\n",
-       "    /* Handle when a new output is added */\n",
-       "    events.on('output_added.OutputArea', handleAddOutput);\n",
-       "\n",
-       "    /**\n",
-       "     * Register the mime type and append_mime function with output_area\n",
-       "     */\n",
-       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
-       "      /* Is output safe? */\n",
-       "      safe: true,\n",
-       "      /* Index of renderer in `output_area.display_order` */\n",
-       "      index: 0\n",
-       "    });\n",
-       "  }\n",
-       "\n",
-       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
-       "  if (root.Jupyter !== undefined) {\n",
-       "    const events = require('base/js/events');\n",
-       "    const OutputArea = require('notebook/js/outputarea').OutputArea;\n",
-       "\n",
-       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
-       "      register_renderer(events, OutputArea);\n",
-       "    }\n",
-       "  }\n",
-       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
-       "    root._bokeh_timeout = Date.now() + 5000;\n",
-       "    root._bokeh_failed_load = false;\n",
-       "  }\n",
-       "\n",
-       "  const NB_LOAD_WARNING = {'data': {'text/html':\n",
-       "     \"<div style='background-color: #fdd'>\\n\"+\n",
-       "     \"<p>\\n\"+\n",
-       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
-       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
-       "     \"</p>\\n\"+\n",
-       "     \"<ul>\\n\"+\n",
-       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
-       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
-       "     \"</ul>\\n\"+\n",
-       "     \"<code>\\n\"+\n",
-       "     \"from bokeh.resources import INLINE\\n\"+\n",
-       "     \"output_notebook(resources=INLINE)\\n\"+\n",
-       "     \"</code>\\n\"+\n",
-       "     \"</div>\"}};\n",
-       "\n",
-       "  function display_loaded(error = null) {\n",
-       "    const el = document.getElementById(null);\n",
-       "    if (el != null) {\n",
-       "      const html = (() => {\n",
-       "        if (typeof root.Bokeh === \"undefined\") {\n",
-       "          if (error == null) {\n",
-       "            return \"BokehJS is loading ...\";\n",
-       "          } else {\n",
-       "            return \"BokehJS failed to load.\";\n",
-       "          }\n",
-       "        } else {\n",
-       "          const prefix = `BokehJS ${root.Bokeh.version}`;\n",
-       "          if (error == null) {\n",
-       "            return `${prefix} successfully loaded.`;\n",
-       "          } else {\n",
-       "            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n",
-       "          }\n",
-       "        }\n",
-       "      })();\n",
-       "      el.innerHTML = html;\n",
-       "\n",
-       "      if (error != null) {\n",
-       "        const wrapper = document.createElement(\"div\");\n",
-       "        wrapper.style.overflow = \"auto\";\n",
-       "        wrapper.style.height = \"5em\";\n",
-       "        wrapper.style.resize = \"vertical\";\n",
-       "        const content = document.createElement(\"div\");\n",
-       "        content.style.fontFamily = \"monospace\";\n",
-       "        content.style.whiteSpace = \"pre-wrap\";\n",
-       "        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n",
-       "        content.textContent = error.stack ?? error.toString();\n",
-       "        wrapper.append(content);\n",
-       "        el.append(wrapper);\n",
-       "      }\n",
-       "    } else if (Date.now() < root._bokeh_timeout) {\n",
-       "      setTimeout(() => display_loaded(error), 100);\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  function run_callbacks() {\n",
-       "    try {\n",
-       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
-       "        if (callback != null)\n",
-       "          callback();\n",
-       "      });\n",
-       "    } finally {\n",
-       "      delete root._bokeh_onload_callbacks\n",
-       "    }\n",
-       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
-       "  }\n",
-       "\n",
-       "  function load_libs(css_urls, js_urls, callback) {\n",
-       "    if (css_urls == null) css_urls = [];\n",
-       "    if (js_urls == null) js_urls = [];\n",
-       "\n",
-       "    root._bokeh_onload_callbacks.push(callback);\n",
-       "    if (root._bokeh_is_loading > 0) {\n",
-       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
-       "      return null;\n",
-       "    }\n",
-       "    if (js_urls == null || js_urls.length === 0) {\n",
-       "      run_callbacks();\n",
-       "      return null;\n",
-       "    }\n",
-       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
-       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
-       "\n",
-       "    function on_load() {\n",
-       "      root._bokeh_is_loading--;\n",
-       "      if (root._bokeh_is_loading === 0) {\n",
-       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
-       "        run_callbacks()\n",
-       "      }\n",
-       "    }\n",
-       "\n",
-       "    function on_error(url) {\n",
-       "      console.error(\"failed to load \" + url);\n",
-       "    }\n",
-       "\n",
-       "    for (let i = 0; i < css_urls.length; i++) {\n",
-       "      const url = css_urls[i];\n",
-       "      const element = document.createElement(\"link\");\n",
-       "      element.onload = on_load;\n",
-       "      element.onerror = on_error.bind(null, url);\n",
-       "      element.rel = \"stylesheet\";\n",
-       "      element.type = \"text/css\";\n",
-       "      element.href = url;\n",
-       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
-       "      document.body.appendChild(element);\n",
-       "    }\n",
-       "\n",
-       "    for (let i = 0; i < js_urls.length; i++) {\n",
-       "      const url = js_urls[i];\n",
-       "      const element = document.createElement('script');\n",
-       "      element.onload = on_load;\n",
-       "      element.onerror = on_error.bind(null, url);\n",
-       "      element.async = false;\n",
-       "      element.src = url;\n",
-       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
-       "      document.head.appendChild(element);\n",
-       "    }\n",
-       "  };\n",
-       "\n",
-       "  function inject_raw_css(css) {\n",
-       "    const element = document.createElement(\"style\");\n",
-       "    element.appendChild(document.createTextNode(css));\n",
-       "    document.body.appendChild(element);\n",
-       "  }\n",
-       "\n",
-       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.1.min.js\"];\n",
-       "  const css_urls = [];\n",
-       "\n",
-       "  const inline_js = [    function(Bokeh) {\n",
-       "      Bokeh.set_log_level(\"info\");\n",
-       "    },\n",
-       "function(Bokeh) {\n",
-       "    }\n",
-       "  ];\n",
-       "\n",
-       "  function run_inline_js() {\n",
-       "    if (root.Bokeh !== undefined || force === true) {\n",
-       "      try {\n",
-       "            for (let i = 0; i < inline_js.length; i++) {\n",
-       "      inline_js[i].call(root, root.Bokeh);\n",
-       "    }\n",
-       "\n",
-       "      } catch (error) {throw error;\n",
-       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
-       "      setTimeout(run_inline_js, 100);\n",
-       "    } else if (!root._bokeh_failed_load) {\n",
-       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
-       "      root._bokeh_failed_load = true;\n",
-       "    } else if (force !== true) {\n",
-       "      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n",
-       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  if (root._bokeh_is_loading === 0) {\n",
-       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
-       "    run_inline_js();\n",
-       "  } else {\n",
-       "    load_libs(css_urls, js_urls, function() {\n",
-       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
-       "      run_inline_js();\n",
-       "    });\n",
-       "  }\n",
-       "}(window));"
-      ],
-      "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded(error = null) {\n    const el = document.getElementById(null);\n    if (el != null) {\n      const html = (() => {\n        if (typeof root.Bokeh === \"undefined\") {\n          if (error == null) {\n            return \"BokehJS is loading ...\";\n          } else {\n            return \"BokehJS failed to load.\";\n          }\n        } else {\n          const prefix = `BokehJS ${root.Bokeh.version}`;\n          if (error == null) {\n            return `${prefix} successfully loaded.`;\n          } else {\n            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n          }\n        }\n      })();\n      el.innerHTML = html;\n\n      if (error != null) {\n        const wrapper = document.createElement(\"div\");\n        wrapper.style.overflow = \"auto\";\n        wrapper.style.height = \"5em\";\n        wrapper.style.resize = \"vertical\";\n        const content = document.createElement(\"div\");\n        content.style.fontFamily = \"monospace\";\n        content.style.whiteSpace = \"pre-wrap\";\n        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n        content.textContent = error.stack ?? error.toString();\n        wrapper.append(content);\n        el.append(wrapper);\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(() => display_loaded(error), 100);\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.1.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n      try {\n            for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n\n      } catch (error) {throw error;\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "'use strict';\n",
-       "(function(root) {\n",
-       "  function now() {\n",
-       "    return new Date();\n",
-       "  }\n",
-       "\n",
-       "  const force = true;\n",
-       "\n",
-       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
-       "    root._bokeh_onload_callbacks = [];\n",
-       "    root._bokeh_is_loading = undefined;\n",
-       "  }\n",
-       "\n",
-       "const JS_MIME_TYPE = 'application/javascript';\n",
-       "  const HTML_MIME_TYPE = 'text/html';\n",
-       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
-       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
-       "\n",
-       "  /**\n",
-       "   * Render data to the DOM node\n",
-       "   */\n",
-       "  function render(props, node) {\n",
-       "    const script = document.createElement(\"script\");\n",
-       "    node.appendChild(script);\n",
-       "  }\n",
-       "\n",
-       "  /**\n",
-       "   * Handle when an output is cleared or removed\n",
-       "   */\n",
-       "  function handleClearOutput(event, handle) {\n",
-       "    function drop(id) {\n",
-       "      const view = Bokeh.index.get_by_id(id)\n",
-       "      if (view != null) {\n",
-       "        view.model.document.clear()\n",
-       "        Bokeh.index.delete(view)\n",
-       "      }\n",
-       "    }\n",
-       "\n",
-       "    const cell = handle.cell;\n",
-       "\n",
-       "    const id = cell.output_area._bokeh_element_id;\n",
-       "    const server_id = cell.output_area._bokeh_server_id;\n",
-       "\n",
-       "    // Clean up Bokeh references\n",
-       "    if (id != null) {\n",
-       "      drop(id)\n",
-       "    }\n",
-       "\n",
-       "    if (server_id !== undefined) {\n",
-       "      // Clean up Bokeh references\n",
-       "      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
-       "      cell.notebook.kernel.execute(cmd_clean, {\n",
-       "        iopub: {\n",
-       "          output: function(msg) {\n",
-       "            const id = msg.content.text.trim()\n",
-       "            drop(id)\n",
-       "          }\n",
-       "        }\n",
-       "      });\n",
-       "      // Destroy server and session\n",
-       "      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
-       "      cell.notebook.kernel.execute(cmd_destroy);\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  /**\n",
-       "   * Handle when a new output is added\n",
-       "   */\n",
-       "  function handleAddOutput(event, handle) {\n",
-       "    const output_area = handle.output_area;\n",
-       "    const output = handle.output;\n",
-       "\n",
-       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
-       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
-       "      return\n",
-       "    }\n",
-       "\n",
-       "    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
-       "\n",
-       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
-       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
-       "      // store reference to embed id on output_area\n",
-       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
-       "    }\n",
-       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
-       "      const bk_div = document.createElement(\"div\");\n",
-       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
-       "      const script_attrs = bk_div.children[0].attributes;\n",
-       "      for (let i = 0; i < script_attrs.length; i++) {\n",
-       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
-       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
-       "      }\n",
-       "      // store reference to server id on output_area\n",
-       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  function register_renderer(events, OutputArea) {\n",
-       "\n",
-       "    function append_mime(data, metadata, element) {\n",
-       "      // create a DOM node to render to\n",
-       "      const toinsert = this.create_output_subarea(\n",
-       "        metadata,\n",
-       "        CLASS_NAME,\n",
-       "        EXEC_MIME_TYPE\n",
-       "      );\n",
-       "      this.keyboard_manager.register_events(toinsert);\n",
-       "      // Render to node\n",
-       "      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
-       "      render(props, toinsert[toinsert.length - 1]);\n",
-       "      element.append(toinsert);\n",
-       "      return toinsert\n",
-       "    }\n",
-       "\n",
-       "    /* Handle when an output is cleared or removed */\n",
-       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
-       "    events.on('delete.Cell', handleClearOutput);\n",
-       "\n",
-       "    /* Handle when a new output is added */\n",
-       "    events.on('output_added.OutputArea', handleAddOutput);\n",
-       "\n",
-       "    /**\n",
-       "     * Register the mime type and append_mime function with output_area\n",
-       "     */\n",
-       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
-       "      /* Is output safe? */\n",
-       "      safe: true,\n",
-       "      /* Index of renderer in `output_area.display_order` */\n",
-       "      index: 0\n",
-       "    });\n",
-       "  }\n",
-       "\n",
-       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
-       "  if (root.Jupyter !== undefined) {\n",
-       "    const events = require('base/js/events');\n",
-       "    const OutputArea = require('notebook/js/outputarea').OutputArea;\n",
-       "\n",
-       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
-       "      register_renderer(events, OutputArea);\n",
-       "    }\n",
-       "  }\n",
-       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
-       "    root._bokeh_timeout = Date.now() + 5000;\n",
-       "    root._bokeh_failed_load = false;\n",
-       "  }\n",
-       "\n",
-       "  const NB_LOAD_WARNING = {'data': {'text/html':\n",
-       "     \"<div style='background-color: #fdd'>\\n\"+\n",
-       "     \"<p>\\n\"+\n",
-       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
-       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
-       "     \"</p>\\n\"+\n",
-       "     \"<ul>\\n\"+\n",
-       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
-       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
-       "     \"</ul>\\n\"+\n",
-       "     \"<code>\\n\"+\n",
-       "     \"from bokeh.resources import INLINE\\n\"+\n",
-       "     \"output_notebook(resources=INLINE)\\n\"+\n",
-       "     \"</code>\\n\"+\n",
-       "     \"</div>\"}};\n",
-       "\n",
-       "  function display_loaded(error = null) {\n",
-       "    const el = document.getElementById(null);\n",
-       "    if (el != null) {\n",
-       "      const html = (() => {\n",
-       "        if (typeof root.Bokeh === \"undefined\") {\n",
-       "          if (error == null) {\n",
-       "            return \"BokehJS is loading ...\";\n",
-       "          } else {\n",
-       "            return \"BokehJS failed to load.\";\n",
-       "          }\n",
-       "        } else {\n",
-       "          const prefix = `BokehJS ${root.Bokeh.version}`;\n",
-       "          if (error == null) {\n",
-       "            return `${prefix} successfully loaded.`;\n",
-       "          } else {\n",
-       "            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n",
-       "          }\n",
-       "        }\n",
-       "      })();\n",
-       "      el.innerHTML = html;\n",
-       "\n",
-       "      if (error != null) {\n",
-       "        const wrapper = document.createElement(\"div\");\n",
-       "        wrapper.style.overflow = \"auto\";\n",
-       "        wrapper.style.height = \"5em\";\n",
-       "        wrapper.style.resize = \"vertical\";\n",
-       "        const content = document.createElement(\"div\");\n",
-       "        content.style.fontFamily = \"monospace\";\n",
-       "        content.style.whiteSpace = \"pre-wrap\";\n",
-       "        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n",
-       "        content.textContent = error.stack ?? error.toString();\n",
-       "        wrapper.append(content);\n",
-       "        el.append(wrapper);\n",
-       "      }\n",
-       "    } else if (Date.now() < root._bokeh_timeout) {\n",
-       "      setTimeout(() => display_loaded(error), 100);\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  function run_callbacks() {\n",
-       "    try {\n",
-       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
-       "        if (callback != null)\n",
-       "          callback();\n",
-       "      });\n",
-       "    } finally {\n",
-       "      delete root._bokeh_onload_callbacks\n",
-       "    }\n",
-       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
-       "  }\n",
-       "\n",
-       "  function load_libs(css_urls, js_urls, callback) {\n",
-       "    if (css_urls == null) css_urls = [];\n",
-       "    if (js_urls == null) js_urls = [];\n",
-       "\n",
-       "    root._bokeh_onload_callbacks.push(callback);\n",
-       "    if (root._bokeh_is_loading > 0) {\n",
-       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
-       "      return null;\n",
-       "    }\n",
-       "    if (js_urls == null || js_urls.length === 0) {\n",
-       "      run_callbacks();\n",
-       "      return null;\n",
-       "    }\n",
-       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
-       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
-       "\n",
-       "    function on_load() {\n",
-       "      root._bokeh_is_loading--;\n",
-       "      if (root._bokeh_is_loading === 0) {\n",
-       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
-       "        run_callbacks()\n",
-       "      }\n",
-       "    }\n",
-       "\n",
-       "    function on_error(url) {\n",
-       "      console.error(\"failed to load \" + url);\n",
-       "    }\n",
-       "\n",
-       "    for (let i = 0; i < css_urls.length; i++) {\n",
-       "      const url = css_urls[i];\n",
-       "      const element = document.createElement(\"link\");\n",
-       "      element.onload = on_load;\n",
-       "      element.onerror = on_error.bind(null, url);\n",
-       "      element.rel = \"stylesheet\";\n",
-       "      element.type = \"text/css\";\n",
-       "      element.href = url;\n",
-       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
-       "      document.body.appendChild(element);\n",
-       "    }\n",
-       "\n",
-       "    for (let i = 0; i < js_urls.length; i++) {\n",
-       "      const url = js_urls[i];\n",
-       "      const element = document.createElement('script');\n",
-       "      element.onload = on_load;\n",
-       "      element.onerror = on_error.bind(null, url);\n",
-       "      element.async = false;\n",
-       "      element.src = url;\n",
-       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
-       "      document.head.appendChild(element);\n",
-       "    }\n",
-       "  };\n",
-       "\n",
-       "  function inject_raw_css(css) {\n",
-       "    const element = document.createElement(\"style\");\n",
-       "    element.appendChild(document.createTextNode(css));\n",
-       "    document.body.appendChild(element);\n",
-       "  }\n",
-       "\n",
-       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.1.min.js\"];\n",
-       "  const css_urls = [];\n",
-       "\n",
-       "  const inline_js = [    function(Bokeh) {\n",
-       "      Bokeh.set_log_level(\"info\");\n",
-       "    },\n",
-       "function(Bokeh) {\n",
-       "    }\n",
-       "  ];\n",
-       "\n",
-       "  function run_inline_js() {\n",
-       "    if (root.Bokeh !== undefined || force === true) {\n",
-       "      try {\n",
-       "            for (let i = 0; i < inline_js.length; i++) {\n",
-       "      inline_js[i].call(root, root.Bokeh);\n",
-       "    }\n",
-       "\n",
-       "      } catch (error) {throw error;\n",
-       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
-       "      setTimeout(run_inline_js, 100);\n",
-       "    } else if (!root._bokeh_failed_load) {\n",
-       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
-       "      root._bokeh_failed_load = true;\n",
-       "    } else if (force !== true) {\n",
-       "      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n",
-       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  if (root._bokeh_is_loading === 0) {\n",
-       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
-       "    run_inline_js();\n",
-       "  } else {\n",
-       "    load_libs(css_urls, js_urls, function() {\n",
-       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
-       "      run_inline_js();\n",
-       "    });\n",
-       "  }\n",
-       "}(window));"
-      ],
-      "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded(error = null) {\n    const el = document.getElementById(null);\n    if (el != null) {\n      const html = (() => {\n        if (typeof root.Bokeh === \"undefined\") {\n          if (error == null) {\n            return \"BokehJS is loading ...\";\n          } else {\n            return \"BokehJS failed to load.\";\n          }\n        } else {\n          const prefix = `BokehJS ${root.Bokeh.version}`;\n          if (error == null) {\n            return `${prefix} successfully loaded.`;\n          } else {\n            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n          }\n        }\n      })();\n      el.innerHTML = html;\n\n      if (error != null) {\n        const wrapper = document.createElement(\"div\");\n        wrapper.style.overflow = \"auto\";\n        wrapper.style.height = \"5em\";\n        wrapper.style.resize = \"vertical\";\n        const content = document.createElement(\"div\");\n        content.style.fontFamily = \"monospace\";\n        content.style.whiteSpace = \"pre-wrap\";\n        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n        content.textContent = error.stack ?? error.toString();\n        wrapper.append(content);\n        el.append(wrapper);\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(() => display_loaded(error), 100);\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.4.1.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n      try {\n            for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n\n      } catch (error) {throw error;\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "cell_type": "markdown",
+   "id": "bdf2903a",
+   "metadata": {},
+   "source": [
+    "You might see a warning message looking something like:\n",
+    "\n",
+    "`Tue May 14 04:41:51 2024 WARNING No project ID could be determined. Consider running 'gcloud config set project' or setting the GOOGLE_CLOUD_PROJECT environment variable`\n",
+    "\n",
+    "This can safely be ignored."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "528ae85d",
+   "metadata": {
+    "id": "528ae85d",
+    "tags": []
+   },
+   "outputs": [],
    "source": [
     "# Import libraries \n",
     "import malariagen_data\n",
@@ -1093,6 +455,13 @@
     "tags": []
    },
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Tue May 14 04:48:39 2024 WARNING No project ID could be determined. Consider running `gcloud config set project` or setting the GOOGLE_CLOUD_PROJECT environment variable\n"
+     ]
+    },
     {
      "data": {
       "application/javascript": [
@@ -10044,9 +9413,9 @@
        }
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@@ -10176,7 +9545,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Mon May 13 10:50:51 2024 INFO No DNA BLAT matches were found for this sequence in genome anoGam3.\n"
+      "Tue May 14 04:49:16 2024 INFO No DNA BLAT matches were found for this sequence in genome anoGam3.\n"
      ]
     },
     {
@@ -15213,9 +14582,9 @@
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-      "Mon May 13 10:52:18 2024 INFO No DNA BLAT matches were found for this sequence in genome anoGam3.\n"
+      "Tue May 14 04:50:39 2024 INFO No DNA BLAT matches were found for this sequence in genome anoGam3.\n"
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-      "Mon May 13 10:52:18 2024 INFO No DNA BLAT matches were found for this sequence in genome anoGam3.\n"
+      "Tue May 14 04:50:40 2024 INFO No DNA BLAT matches were found for this sequence in genome anoGam3.\n"
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-      "Mon May 13 10:52:19 2024 INFO No DNA BLAT matches were found for this sequence in genome anoGam3.\n"
+      "Tue May 14 04:50:40 2024 INFO No DNA BLAT matches were found for this sequence in genome anoGam3.\n"
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