diff --git a/docs/as1/as1.0.ipynb b/docs/as1/as1.0.ipynb index d0ec6d0..e3bca20 100644 --- a/docs/as1/as1.0.ipynb +++ b/docs/as1/as1.0.ipynb @@ -172,28 +172,13 @@ "colab": { "base_uri": "https://localhost:8080/" }, - "execution": { - "iopub.execute_input": "2026-04-05T04:05:09.844381Z", - "iopub.status.busy": "2026-04-05T04:05:09.844101Z", - "iopub.status.idle": "2026-04-05T04:05:11.705969Z", - "shell.execute_reply": "2026-04-05T04:05:11.704899Z", - "shell.execute_reply.started": "2026-04-05T04:05:09.844351Z" - }, "id": "hGA4d7Yrpk8m", "outputId": "c29827c1-0361-4926-c227-8f6e76c2a497", "tags": [ "remove-input" ] }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Note: you may need to restart the kernel to use updated packages.\n" - ] - } - ], + "outputs": [], "source": [ "%pip install -qq malariagen_data" ] @@ -202,13 +187,6 @@ "cell_type": "code", "execution_count": 2, "metadata": { - "execution": { - "iopub.execute_input": "2026-04-05T04:05:11.706973Z", - "iopub.status.busy": "2026-04-05T04:05:11.706697Z", - "iopub.status.idle": "2026-04-05T04:05:17.371545Z", - "shell.execute_reply": "2026-04-05T04:05:17.370432Z", - "shell.execute_reply.started": "2026-04-05T04:05:11.706939Z" - }, "id": "AnmzLmEgpk8n", "tags": [ "remove-input" @@ -489,7 +467,7 @@ " document.body.appendChild(element);\n", " }\n", "\n", - " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.8.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.8.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.8.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.8.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.8.2.min.js\"];\n", + " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.7.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.7.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.7.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.7.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.7.0.min.js\"];\n", " const css_urls = [];\n", "\n", " const inline_js = [ function(Bokeh) {\n", @@ -529,7 +507,7 @@ " }\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 \"
\\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 \"\\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-3.8.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.8.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.8.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.8.2.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.8.2.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/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 \"
\\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 \"\\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-3.7.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.7.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.7.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.7.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.7.0.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" @@ -542,19 +520,12 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 3, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 927 }, - "execution": { - "iopub.execute_input": "2026-04-05T04:05:29.540570Z", - "iopub.status.busy": "2026-04-05T04:05:29.540132Z", - "iopub.status.idle": "2026-04-05T04:05:29.640314Z", - "shell.execute_reply": "2026-04-05T04:05:29.639173Z", - "shell.execute_reply.started": "2026-04-05T04:05:29.540540Z" - }, "id": "qsElasBepk8n", "outputId": "4bf80a06-c2e8-4d2d-b4a6-99c8c66da7db", "tags": [ @@ -680,7 +651,7 @@ "thakare-2022 thakare-2022 15" ] }, - "execution_count": 4, + "execution_count": 3, "metadata": {}, "output_type": "execute_result" } @@ -701,19 +672,12 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 4, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 1000 }, - "execution": { - "iopub.execute_input": "2026-04-05T04:05:34.859189Z", - "iopub.status.busy": "2026-04-05T04:05:34.858770Z", - "iopub.status.idle": "2026-04-05T04:05:35.892325Z", - "shell.execute_reply": "2026-04-05T04:05:35.890422Z", - "shell.execute_reply.started": "2026-04-05T04:05:34.859156Z" - }, "id": "a1OMvuTxUWpJ", "outputId": "9f872334-fd50-4649-990a-df60ea71c12c", "tags": [ @@ -725,46 +689,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Load sample metadata: ⠏ (0:00:00.76) " - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1363-VO-ET-GADISA-VMF00316\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1364-VO-SD-KAFY-VMF00317\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1365-VO-DJ-ADBI-VMF00318\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1366-VO-YE-ALLAN-VMF00319\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1367-VO-AF-DONNELLY-VMF00320\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1368-VO-PK-DONNELLY-VMF00321\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1369-VO-SA-AL-NAZAWI-VMF00322\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1370-VO-IR-ENAYATI-VMF00323\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1385-VO-DJ-WEETMAN-VMF00338\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1386-VO-KE-OCHOMO-VMF00339\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1458-VO-ET-YEWHALAW-VMF00340\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set 1459-VO-SD-AHMED-VMF00342\n", - " warnings.warn(\n", - "/home/jupyter/malariagen-data-python/malariagen_data/anoph/sample_metadata.py:417: UserWarning: WARNING: The surveillance flags data is missing for sample set thakare-2022\n", - " warnings.warn(\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - " " + " \r" ] }, { @@ -877,7 +802,7 @@ " \n", " 1385-VO-DJ-WEETMAN\n", " 1385-VO-DJ-WEETMAN-VMF00338\n", - " Colony\n", + " Lab Cross\n", " 2025\n", " 14\n", " \n", @@ -932,7 +857,7 @@ "1368-VO-PK-DONNELLY 1368-VO-PK-DONNELLY-VMF00321 Pakistan 2005 15\n", "1369-VO-SA-AL-NAZAWI 1369-VO-SA-AL-NAZAWI-VMF00322 Saudi Arabia 2023 42\n", "1370-VO-IR-ENAYATI 1370-VO-IR-ENAYATI-VMF00323 Iran 2023 72\n", - "1385-VO-DJ-WEETMAN 1385-VO-DJ-WEETMAN-VMF00338 Colony 2025 14\n", + "1385-VO-DJ-WEETMAN 1385-VO-DJ-WEETMAN-VMF00338 Lab Cross 2025 14\n", "1386-VO-KE-OCHOMO 1386-VO-KE-OCHOMO-VMF00339 Kenya 2022 1\n", " 2024 28\n", "1458-VO-ET-YEWHALAW 1458-VO-ET-YEWHALAW-VMF00340 Ethiopia 2023 23\n", @@ -940,7 +865,7 @@ "thakare-2022 thakare-2022 India 2021 15" ] }, - "execution_count": 6, + "execution_count": 4, "metadata": {}, "output_type": "execute_result" } @@ -976,6 +901,13 @@ "We hope this page has provided a useful introduction to the `As1.0` data resource. If you would like to start working with these data, please visit the [cloud data access guide](https://malariagen.github.io/vector-data/as1/cloud.html) or the [data download guide](https://malariagen.github.io/vector-data/as1/download.html) or continue browsing the other documentation on this site.\n", "\n" ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { @@ -985,15 +917,15 @@ "provenance": [] }, "environment": { - "kernel": "malariagen-dev-as1", - "name": "workbench-notebooks.m138", + "kernel": "mgenv_7.3.0", + "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)", + "display_name": "mgenv_7.3.0", "language": "python", - "name": "malariagen-dev-as1" + "name": "mgenv_7.3.0" }, "language_info": { "codemirror_mode": { @@ -1005,7 +937,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.13" + "version": "3.12.11" } }, "nbformat": 4,