diff --git a/docs/adar1/cloud.ipynb b/docs/adar1/cloud.ipynb
index 486e6f5..b884e13 100644
--- a/docs/adar1/cloud.ipynb
+++ b/docs/adar1/cloud.ipynb
@@ -16,7 +16,7 @@
"\n",
"## Data hosting\n",
"\n",
- "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_adar_release_master_us_central1` bucket, which is a single-region bucket located in the United States. All data hosted in GCS are publicly accessible and do not require any authentication to access. "
+ "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_adar_release_master_us_central1` bucket, which is a single-region bucket located in the United States. All data hosted on GCS are publicly accessible but do require an authentication step, please see details on the [Vector Observatory Data Access page](https://malariagen.github.io/vector-data/vobs/vobs-data-access.html)."
]
},
{
@@ -5122,9 +5122,9 @@
},
"environment": {
"kernel": "mgenv_7.3.0",
- "name": "workbench-notebooks.m141",
+ "name": "workbench-notebooks.m142",
"type": "gcloud",
- "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m141"
+ "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m142"
},
"kernelspec": {
"display_name": "mgenv_7.3.0",
diff --git a/docs/adir1/cloud.ipynb b/docs/adir1/cloud.ipynb
index 5ffc729..08c5d7a 100644
--- a/docs/adir1/cloud.ipynb
+++ b/docs/adir1/cloud.ipynb
@@ -16,7 +16,7 @@
"\n",
"## Data hosting\n",
"\n",
- "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_adir_release_master_us_central1` bucket, which is a single-region bucket located in the United States. All data hosted in GCS are publicly accessible and do not require any authentication to access. "
+ "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_adir_release_master_us_central1` bucket, which is a single-region bucket located in the United States. All data hosted on GCS are publicly accessible but do require an authentication step, please see details on the [Vector Observatory Data Access page](https://malariagen.github.io/vector-data/vobs/vobs-data-access.html)."
]
},
{
@@ -115,7 +115,318 @@
"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\nconst 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 \"
\\n\"+\n \"
\\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 \"
\\n\"+\n \"
\\n\"+\n \"- re-rerun `output_notebook()` to attempt to load from CDN again, or
\\n\"+\n \"- use INLINE resources instead, as so:
\\n\"+\n \"
\\n\"+\n \"
\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\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} encountered errors 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-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.3.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));",
+ "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",
+ " \"\\n\"+\n",
+ " \"
\\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",
+ " \"
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"- re-rerun `output_notebook()` to attempt to load from CDN again, or
\\n\"+\n",
+ " \"- use INLINE resources instead, as so:
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"from bokeh.resources import INLINE\\n\"+\n",
+ " \"output_notebook(resources=INLINE)\\n\"+\n",
+ " \"\\n\"+\n",
+ " \"
\"}};\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} encountered errors 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-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.3.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": ""
},
"metadata": {},
@@ -4572,6 +4883,12 @@
"name": "Ag3.0 cloud data access 2022-03-14.ipynb",
"provenance": []
},
+ "environment": {
+ "kernel": "adir1.0-dev-env",
+ "name": "workbench-notebooks.m142",
+ "type": "gcloud",
+ "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m142"
+ },
"kernelspec": {
"display_name": "Adir1.0 Dev",
"language": "python",
diff --git a/docs/af1/cloud.ipynb b/docs/af1/cloud.ipynb
index 2ee86d3..cbad5cf 100644
--- a/docs/af1/cloud.ipynb
+++ b/docs/af1/cloud.ipynb
@@ -16,7 +16,7 @@
"\n",
"## Data hosting\n",
"\n",
- "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_afun_release_master_us_central1` bucket, which is a single-region bucket located in the United States. All data hosted in GCS are publicly accessible and do not require any authentication to access. "
+ "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_afun_release_master_us_central1` bucket, which is a single-region bucket located in the United States. All data hosted on GCS are publicly accessible but do require an authentication step, please see details on the [Vector Observatory Data Access page](https://malariagen.github.io/vector-data/vobs/vobs-data-access.html)."
]
},
{
@@ -9929,6 +9929,12 @@
"name": "Ag3.0 cloud data access 2022-03-14.ipynb",
"provenance": []
},
+ "environment": {
+ "kernel": "conda-env-global-global-mgenv-6.0.6-py",
+ "name": "workbench-notebooks.m142",
+ "type": "gcloud",
+ "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m142"
+ },
"kernelspec": {
"display_name": "global-global-mgenv-6.0.6",
"language": "python",
diff --git a/docs/ag3/cloud.ipynb b/docs/ag3/cloud.ipynb
index a22000a..fae5a92 100644
--- a/docs/ag3/cloud.ipynb
+++ b/docs/ag3/cloud.ipynb
@@ -16,7 +16,7 @@
"\n",
"## Data hosting\n",
"\n",
- "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_agam_release_master_us_central1` bucket, which is a single-region bucket located in the United States. All data hosted in GCS are publicly accessible and do not require any authentication to access. "
+ "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_agam_release_master_us_central1` bucket, which is a single-region bucket located in the United States. All data hosted on GCS are publicly accessible but do require an authentication step, please see details on the [Vector Observatory Data Access page](https://malariagen.github.io/vector-data/vobs/vobs-data-access.html)."
]
},
{
@@ -17441,6 +17441,12 @@
"name": "Ag3.0 cloud data access 2022-03-14.ipynb",
"provenance": []
},
+ "environment": {
+ "kernel": "conda-env-global-global-mgenv-6.0.6-py",
+ "name": "workbench-notebooks.m142",
+ "type": "gcloud",
+ "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m142"
+ },
"kernelspec": {
"display_name": "global-global-mgenv-6.0.6",
"language": "python",
diff --git a/docs/amin1/cloud.ipynb b/docs/amin1/cloud.ipynb
index ec5daa3..b718f27 100644
--- a/docs/amin1/cloud.ipynb
+++ b/docs/amin1/cloud.ipynb
@@ -16,7 +16,7 @@
"\n",
"## Data hosting\n",
"\n",
- "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_amin_release` bucket, which is a multi-region bucket located in the United States. All data hosted in GCS are publicly accessible and do not require any authentication to access. "
+ "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_amin_release` bucket, which is a multi-region bucket located in the United States. All data hosted on GCS are publicly accessible but do require an authentication step, please see details on the [Vector Observatory Data Access page](https://malariagen.github.io/vector-data/vobs/vobs-data-access.html)."
]
},
{
@@ -6156,6 +6156,12 @@
"name": "Amin1.0-cloud-data-access.ipynb",
"provenance": []
},
+ "environment": {
+ "kernel": "conda-env-global-global-mgenv-6.0.6-py",
+ "name": "workbench-notebooks.m142",
+ "type": "gcloud",
+ "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m142"
+ },
"kernelspec": {
"display_name": "global-global-mgenv-6.0.6",
"language": "python",
diff --git a/docs/as1/cloud.ipynb b/docs/as1/cloud.ipynb
index f1b6880..0b51438 100644
--- a/docs/as1/cloud.ipynb
+++ b/docs/as1/cloud.ipynb
@@ -16,7 +16,7 @@
"\n",
"## Data hosting\n",
"\n",
- "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_aste_release_master_us_central1` bucket, which is a single-region bucket located in the United States. All data hosted in GCS are publicly accessible and do not require any authentication to access. "
+ "All data required for this notebook is hosted on Google Cloud Storage (GCS). Data are hosted in the `vo_aste_release_master_us_central1` bucket, which is a single-region bucket located in the United States. All data hosted on GCS are publicly accessible but do require an authentication step, please see details on the [Vector Observatory Data Access page](https://malariagen.github.io/vector-data/vobs/vobs-data-access.html)."
]
},
{
@@ -5292,9 +5292,9 @@
},
"environment": {
"kernel": "malariagen-dev-as1",
- "name": "workbench-notebooks.m138",
+ "name": "workbench-notebooks.m142",
"type": "gcloud",
- "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138"
+ "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m142"
},
"kernelspec": {
"display_name": "malariagen-dev-as1 (Local)",