Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add the flag specs to the cloud guide #69

Merged
merged 2 commits into from
Jun 17, 2024
Merged

Add the flag specs to the cloud guide #69

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
cc2af6c
fix code on cloud example
ahernank Jun 17, 2024
52b0176
fix flag
ahernank Jun 17, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
76 changes: 56 additions & 20 deletions docs/af1/af1.1.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -119,14 +119,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"**Note:** To access the `Af1.1` release, you need to use the `pre=True` flag as shown in the line below. \n",
"**Note:** To access the `Af1.1` release, you need to use the `pre=True` flag. \n",
"\n",
"This flag is used when more data will be added to this release, for the case of `Af1.1`, CNV data for the sample sets on this release will be included at a future date."
]
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 1,
"metadata": {
"id": "AnmzLmEgpk8n",
"tags": [
Expand All @@ -137,6 +137,7 @@
{
"data": {
"application/javascript": [
"'use strict';\n",
"(function(root) {\n",
" function now() {\n",
" return new Date();\n",
Expand Down Expand Up @@ -298,17 +299,42 @@
" \"</code>\\n\"+\n",
" \"</div>\"}};\n",
"\n",
" function display_loaded() {\n",
" function display_loaded(error = null) {\n",
" const el = document.getElementById(null);\n",
" if (el != null) {\n",
" el.textContent = \"BokehJS is loading...\";\n",
" }\n",
" if (root.Bokeh !== undefined) {\n",
" if (el != null) {\n",
" el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\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, 100)\n",
" setTimeout(() => display_loaded(error), 100);\n",
" }\n",
" }\n",
"\n",
Expand Down Expand Up @@ -382,7 +408,7 @@
" document.body.appendChild(element);\n",
" }\n",
"\n",
" const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.3.0.min.js\"];\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",
Expand All @@ -394,10 +420,13 @@
"\n",
" function run_inline_js() {\n",
" if (root.Bokeh !== undefined || force === true) {\n",
" for (let i = 0; i < inline_js.length; i++) {\n",
" try {\n",
" for (let i = 0; i < inline_js.length; i++) {\n",
" inline_js[i].call(root, root.Bokeh);\n",
" }\n",
"} else if (Date.now() < root._bokeh_timeout) {\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",
Expand All @@ -419,7 +448,7 @@
" }\n",
"}(window));"
],
"application/vnd.bokehjs_load.v0+json": ""
"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"
Expand All @@ -432,7 +461,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 2,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
Expand Down Expand Up @@ -593,7 +622,7 @@
"small-2020-af small-2020-af 50"
]
},
"execution_count": 4,
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -614,7 +643,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 3,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
Expand All @@ -627,6 +656,13 @@
]
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" \r"
]
},
{
"data": {
"text/html": [
Expand Down Expand Up @@ -1175,7 +1211,7 @@
" 2011 0 "
]
},
"execution_count": 5,
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -1228,9 +1264,9 @@
"provenance": []
},
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "global-global-binder-5.0.0",
"language": "python",
"name": "python3"
"name": "conda-env-global-global-binder-5.0.0-py"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -1242,7 +1278,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.11"
"version": "3.10.14"
}
},
"nbformat": 4,
Expand Down
4 changes: 2 additions & 2 deletions docs/af1/af1.2.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -108,14 +108,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"**Note:** To access the `Af1.2` release, you need to use the `pre=True` flag as shown in the line below. \n",
"**Note:** To access the `Af1.2` release, you need to use the `pre=True` flag. \n",
"\n",
"This flag is used when more data will be added to this release, for the case of `Af1.2`, CNV data for the sample sets on this release will be included at a future date."
]
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"metadata": {
"id": "AnmzLmEgpk8n",
"tags": [
Expand Down
2 changes: 1 addition & 1 deletion docs/af1/af1.3.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"**Note:** To access the `Af1.3` release, you need to use the `pre=True` flag as shown in the line below. \n",
"**Note:** To access the `Af1.3` release, you need to use the `pre=True` flag. \n",
"\n",
"This flag is used when more data will be added to this release, for the case of `Af1.3`, CNV data for the sample sets on this release will be included at a future date."
]
Expand Down
9 changes: 9 additions & 0 deletions docs/af1/cloud.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -516,6 +516,15 @@
"af1"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**Note:** To access the `Af1.1`, `Af1.2` & `Af1.3` releases, you need to use the `pre=True` flag in code above. \n",
"\n",
"This flag is used when more data will be added to this release. In the case of `Af1.1`, `Af1.2` & `Af1.3`; CNV data for the sample sets on these releases will be included at a future date."
]
},
{
"cell_type": "markdown",
"metadata": {
Expand Down
Loading