From 75e34f59870813c24598ed7e95c56803c7cd5907 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rok=20Ro=C5=A1kar?= <rok.roskar@sdsc.ethz.ch>
Date: Mon, 30 Mar 2020 15:47:04 +0000
Subject: [PATCH] renku run papermill notebooks/examples/italy-covid-19.ipynb
runs/italy-covid-19.ipynb -p data_folder ./data/covid-19-italy/
---
...55fbcb87444ea80501341f0b7f1a_papermill.cwl | 67 ++++
runs/italy-covid-19.ipynb | 302 +++++++++++-------
2 files changed, 261 insertions(+), 108 deletions(-)
create mode 100644 .renku/workflow/f2c255fbcb87444ea80501341f0b7f1a_papermill.cwl
diff --git a/.renku/workflow/f2c255fbcb87444ea80501341f0b7f1a_papermill.cwl b/.renku/workflow/f2c255fbcb87444ea80501341f0b7f1a_papermill.cwl
new file mode 100644
index 0000000..a0f3059
--- /dev/null
+++ b/.renku/workflow/f2c255fbcb87444ea80501341f0b7f1a_papermill.cwl
@@ -0,0 +1,67 @@
+arguments: []
+baseCommand:
+- papermill
+class: CommandLineTool
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default:
+ class: File
+ path: ../../notebooks/examples/italy-covid-19.ipynb
+ inputBinding:
+ position: 1
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_2:
+ default: runs/italy-covid-19.ipynb
+ inputBinding:
+ position: 2
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_3:
+ default: data_folder
+ inputBinding:
+ position: 3
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19-italy
+ inputBinding:
+ position: 4
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: Directory
+outputs:
+ output_0:
+ outputBinding:
+ glob: $(inputs.input_2)
+ streamable: false
+ type: File
+permanentFailCodes: []
+requirements:
+- class: InlineJavascriptRequirement
+- class: InitialWorkDirRequirement
+ listing:
+ - entry: '$({"listing": [], "class": "Directory"})'
+ entryname: runs
+ writable: true
+ - entry: $(inputs.input_1)
+ entryname: notebooks/examples/italy-covid-19.ipynb
+ writable: false
+ - entry: $(inputs.input_4)
+ entryname: data/covid-19-italy
+ writable: false
+successCodes: []
+temporaryFailCodes: []
diff --git a/runs/italy-covid-19.ipynb b/runs/italy-covid-19.ipynb
index 156f53c..073621f 100644
--- a/runs/italy-covid-19.ipynb
+++ b/runs/italy-covid-19.ipynb
@@ -4,10 +4,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.016838,
- "end_time": "2020-03-30T15:01:07.532187",
+ "duration": 0.017573,
+ "end_time": "2020-03-30T15:47:00.902430",
"exception": false,
- "start_time": "2020-03-30T15:01:07.515349",
+ "start_time": "2020-03-30T15:47:00.884857",
"status": "completed"
},
"tags": []
@@ -23,10 +23,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.029402,
- "end_time": "2020-03-30T15:01:07.571765",
+ "duration": 0.042314,
+ "end_time": "2020-03-30T15:47:00.956999",
"exception": false,
- "start_time": "2020-03-30T15:01:07.542363",
+ "start_time": "2020-03-30T15:47:00.914685",
"status": "completed"
},
"tags": []
@@ -42,10 +42,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.590434,
- "end_time": "2020-03-30T15:01:08.171053",
+ "duration": 0.574034,
+ "end_time": "2020-03-30T15:47:01.544605",
"exception": false,
- "start_time": "2020-03-30T15:01:07.580619",
+ "start_time": "2020-03-30T15:47:00.970571",
"status": "completed"
},
"tags": []
@@ -57,6 +57,8 @@
"import pandas as pd\n",
"import altair as alt\n",
"\n",
+ "from IPython.display import display, HTML\n",
+ "\n",
"from covid_19_dashboard.italy_utils import get_region_populations, prepare_dataframe"
]
},
@@ -65,10 +67,34 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.029052,
- "end_time": "2020-03-30T15:01:08.208621",
+ "duration": 0.038937,
+ "end_time": "2020-03-30T15:47:01.597549",
+ "exception": false,
+ "start_time": "2020-03-30T15:47:01.558612",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "html_credits=HTML('''\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</a>\n",
+ "<br>\n",
+ "Analysis and Visualization:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
+ "</p>''')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "papermill": {
+ "duration": 0.033582,
+ "end_time": "2020-03-30T15:47:01.645232",
"exception": false,
- "start_time": "2020-03-30T15:01:08.179569",
+ "start_time": "2020-03-30T15:47:01.611650",
"status": "completed"
},
"tags": [
@@ -82,13 +108,13 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.027658,
- "end_time": "2020-03-30T15:01:08.244634",
+ "duration": 0.041421,
+ "end_time": "2020-03-30T15:47:01.700886",
"exception": false,
- "start_time": "2020-03-30T15:01:08.216976",
+ "start_time": "2020-03-30T15:47:01.659465",
"status": "completed"
},
"tags": [
@@ -103,13 +129,13 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.036949,
- "end_time": "2020-03-30T15:01:08.290501",
+ "duration": 0.045634,
+ "end_time": "2020-03-30T15:47:01.762893",
"exception": false,
- "start_time": "2020-03-30T15:01:08.253552",
+ "start_time": "2020-03-30T15:47:01.717259",
"status": "completed"
},
"tags": []
@@ -126,13 +152,13 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.037513,
- "end_time": "2020-03-30T15:01:08.336655",
+ "duration": 0.039386,
+ "end_time": "2020-03-30T15:47:01.817068",
"exception": false,
- "start_time": "2020-03-30T15:01:08.299142",
+ "start_time": "2020-03-30T15:47:01.777682",
"status": "completed"
},
"tags": []
@@ -148,10 +174,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007906,
- "end_time": "2020-03-30T15:01:08.353544",
+ "duration": 0.010648,
+ "end_time": "2020-03-30T15:47:01.842058",
"exception": false,
- "start_time": "2020-03-30T15:01:08.345638",
+ "start_time": "2020-03-30T15:47:01.831410",
"status": "completed"
},
"tags": []
@@ -162,13 +188,13 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.064453,
- "end_time": "2020-03-30T15:01:08.426377",
+ "duration": 0.094679,
+ "end_time": "2020-03-30T15:47:01.946901",
"exception": false,
- "start_time": "2020-03-30T15:01:08.361924",
+ "start_time": "2020-03-30T15:47:01.852222",
"status": "completed"
},
"tags": []
@@ -178,10 +204,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-99e5f6cb77784a22802456bb0a1c20b3\"></div>\n",
+ "<div id=\"altair-viz-218b5174c39541b7aface1108ea9c035\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-99e5f6cb77784a22802456bb0a1c20b3\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-218b5174c39541b7aface1108ea9c035\");\n",
" const paths = {\n",
" \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
" \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
@@ -229,9 +255,26 @@
"alt.HConcatChart(...)"
]
},
- "execution_count": 7,
"metadata": {},
- "output_type": "execute_result"
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</a>\n",
+ "<br>\n",
+ "Analysis and Visualization:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
+ "</p>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
}
],
"source": [
@@ -241,22 +284,24 @@
"total = base.mark_point(color='orange', filled=True, size=100, opacity=1).encode(alt.Y('total_cases', title=\"Cases (orange)\"))\n",
"tests = base.encode(alt.Y('tests', title=\"Tests (blue)\"))\n",
"totals = alt.layer(tests, total)\n",
- "alt.hconcat(totals, daily, \n",
+ "chart = alt.hconcat(totals, daily, \n",
" title='Total and daily tests and cases nationwide'\n",
").configure_title(\n",
" anchor='middle'\n",
- ")"
+ ")\n",
+ "display(chart)\n",
+ "display(html_credits)"
]
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.050324,
- "end_time": "2020-03-30T15:01:08.485994",
+ "duration": 0.066053,
+ "end_time": "2020-03-30T15:47:02.028176",
"exception": false,
- "start_time": "2020-03-30T15:01:08.435670",
+ "start_time": "2020-03-30T15:47:01.962123",
"status": "completed"
},
"tags": []
@@ -284,13 +329,13 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.355166,
- "end_time": "2020-03-30T15:01:08.850692",
+ "duration": 0.61369,
+ "end_time": "2020-03-30T15:47:02.660735",
"exception": false,
- "start_time": "2020-03-30T15:01:08.495526",
+ "start_time": "2020-03-30T15:47:02.047045",
"status": "completed"
},
"tags": []
@@ -309,13 +354,13 @@
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.039941,
- "end_time": "2020-03-30T15:01:08.900658",
+ "duration": 0.054045,
+ "end_time": "2020-03-30T15:47:02.733032",
"exception": false,
- "start_time": "2020-03-30T15:01:08.860717",
+ "start_time": "2020-03-30T15:47:02.678987",
"status": "completed"
},
"tags": []
@@ -331,10 +376,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008303,
- "end_time": "2020-03-30T15:01:08.917821",
+ "duration": 0.012923,
+ "end_time": "2020-03-30T15:47:02.761696",
"exception": false,
- "start_time": "2020-03-30T15:01:08.909518",
+ "start_time": "2020-03-30T15:47:02.748773",
"status": "completed"
},
"tags": []
@@ -345,13 +390,13 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 12,
"metadata": {
"papermill": {
- "duration": 0.104273,
- "end_time": "2020-03-30T15:01:09.031061",
+ "duration": 0.166371,
+ "end_time": "2020-03-30T15:47:02.940836",
"exception": false,
- "start_time": "2020-03-30T15:01:08.926788",
+ "start_time": "2020-03-30T15:47:02.774465",
"status": "completed"
},
"tags": []
@@ -361,10 +406,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-4d8b655768c74270a1f4685519d07a3c\"></div>\n",
+ "<div id=\"altair-viz-90ec7a0498ed43cbaf44277379a07bad\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-4d8b655768c74270a1f4685519d07a3c\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-90ec7a0498ed43cbaf44277379a07bad\");\n",
" const paths = {\n",
" \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
" \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
@@ -412,9 +457,26 @@
"alt.FacetChart(...)"
]
},
- "execution_count": 11,
"metadata": {},
- "output_type": "execute_result"
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</a>\n",
+ "<br>\n",
+ "Analysis and Visualization:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
+ "</p>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
}
],
"source": [
@@ -426,24 +488,26 @@
" width=200,\n",
" height=200)\n",
"totals = alt.layer(total, death)\n",
- "totals.facet(facet='region', \n",
+ "chart = totals.facet(facet='region', \n",
" columns=5, \n",
" align='each', \n",
" title='Total cases (orange) and deaths (black) by region'\n",
").configure_title(\n",
" anchor='middle'\n",
- ")"
+ ")\n",
+ "display(chart)\n",
+ "display(html_credits)"
]
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 13,
"metadata": {
"papermill": {
- "duration": 0.105389,
- "end_time": "2020-03-30T15:01:09.149647",
+ "duration": 0.155288,
+ "end_time": "2020-03-30T15:47:03.118439",
"exception": false,
- "start_time": "2020-03-30T15:01:09.044258",
+ "start_time": "2020-03-30T15:47:02.963151",
"status": "completed"
},
"tags": []
@@ -453,10 +517,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-12b38561ee274de39a98b8477bffbccb\"></div>\n",
+ "<div id=\"altair-viz-83b23d0ce38f495c8c89111b787f2cb1\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-12b38561ee274de39a98b8477bffbccb\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-83b23d0ce38f495c8c89111b787f2cb1\");\n",
" const paths = {\n",
" \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
" \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
@@ -504,9 +568,26 @@
"alt.FacetChart(...)"
]
},
- "execution_count": 12,
"metadata": {},
- "output_type": "execute_result"
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</a>\n",
+ "<br>\n",
+ "Analysis and Visualization:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
+ "</p>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
}
],
"source": [
@@ -518,24 +599,26 @@
" width=200,\n",
" height=200)\n",
"totals = alt.layer(total, death)\n",
- "totals.facet(facet='region', \n",
+ "chart = totals.facet(facet='region', \n",
" columns=5, \n",
" align='each', \n",
" title='Total cases (orange) and deaths (black) by region per 100k population'\n",
").configure_title(\n",
" anchor='middle'\n",
- ")"
+ ")\n",
+ "display(chart)\n",
+ "display(html_credits)"
]
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 14,
"metadata": {
"papermill": {
- "duration": 0.06734,
- "end_time": "2020-03-30T15:01:09.235215",
+ "duration": 0.112092,
+ "end_time": "2020-03-30T15:47:03.263790",
"exception": false,
- "start_time": "2020-03-30T15:01:09.167875",
+ "start_time": "2020-03-30T15:47:03.151698",
"status": "completed"
},
"tags": []
@@ -550,13 +633,13 @@
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": 15,
"metadata": {
"papermill": {
- "duration": 0.120633,
- "end_time": "2020-03-30T15:01:09.373534",
+ "duration": 0.169858,
+ "end_time": "2020-03-30T15:47:03.469457",
"exception": false,
- "start_time": "2020-03-30T15:01:09.252901",
+ "start_time": "2020-03-30T15:47:03.299599",
"status": "completed"
},
"tags": []
@@ -566,10 +649,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-7e4038f6a90040628bd21b68f5c43724\"></div>\n",
+ "<div id=\"altair-viz-5e5f4ac644f74bf0a985b1aa082570bc\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-7e4038f6a90040628bd21b68f5c43724\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-5e5f4ac644f74bf0a985b1aa082570bc\");\n",
" const paths = {\n",
" \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
" \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
@@ -617,9 +700,26 @@
"alt.FacetChart(...)"
]
},
- "execution_count": 14,
"metadata": {},
- "output_type": "execute_result"
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</a>\n",
+ "<br>\n",
+ "Analysis and Visualization:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
+ "</p>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
}
],
"source": [
@@ -630,39 +730,25 @@
")\n",
"daily_new = base.mark_bar(color='orange').encode(alt.Y('total_cases_diff', title='N'))\n",
"daily_dead = base.mark_line(color='black').encode(alt.Y('dead_diff'))\n",
- "(daily_new + daily_dead).facet(\n",
+ "chart = (daily_new + daily_dead).facet(\n",
" facet='region', \n",
" columns=5, \n",
" align='each', \n",
" title='Daily new cases (orange) and deaths (black) by region',\n",
").configure_title(\n",
" anchor='middle'\n",
- ")"
+ ")\n",
+ "display(chart)\n",
+ "display(html_credits)"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "papermill": {
- "duration": 0.021361,
- "end_time": "2020-03-30T15:01:09.418072",
- "exception": false,
- "start_time": "2020-03-30T15:01:09.396711",
- "status": "completed"
- },
- "tags": []
- },
- "outputs": [],
- "source": []
}
],
"metadata": {
"hide_input": true,
"kernelspec": {
- "display_name": "Python 3.7.7 64-bit ('.venv': venv)",
+ "display_name": "Python 3",
"language": "python",
- "name": "python37764bitvenvvenvdef91c48e9bd43a4b394e5189f093471"
+ "name": "python3"
},
"language_info": {
"codemirror_mode": {
@@ -674,11 +760,11 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.7.7"
+ "version": "3.7.3"
},
"papermill": {
- "duration": 3.022458,
- "end_time": "2020-03-30T15:01:09.755307",
+ "duration": 3.777963,
+ "end_time": "2020-03-30T15:47:03.822983",
"environment_variables": {},
"exception": null,
"input_path": "notebooks/examples/italy-covid-19.ipynb",
@@ -686,7 +772,7 @@
"parameters": {
"data_folder": "./data/covid-19-italy/"
},
- "start_time": "2020-03-30T15:01:06.732849",
+ "start_time": "2020-03-30T15:47:00.045020",
"version": "1.1.0"
}
},
--
GitLab