all: update publish

update:
    jupyter nbconvert --to=html --no-input --ExecutePreprocessor.enabled=True TM-status-report.ipynb

publish:
    git add *.html
    git commit -m "update covid-19 reports `date --iso=s`"
    git push origin master

Updating hourly

To complete the process automation, we add a cron job to run everything once an hour.

Open your cron configuration file with using the command:

crontab -e

Add a time definition like 15 * * * * for our make all command for reporting. Here we need to also use the --directory option to set the working directory for make, since the crontab is not in the root of our repository by default.

# update reports every hour at 15 minutes past to github-pages
15 * * * * make --directory /home/user/your/repo/ all

Here are some examples of other cron time definitions:

* * * * * - run every minute (nice for debugging)
10 12 * * * - run every day ten minutes past noon
0 0,6,12,18 * * * - run every six hours

For the final automation part, you’ll need to create a new set of ssh keys for github and then configure them as deploy keys in the setting of you github repository. Make sure to mark the keys as having write access. The ssh keys must be generated as passwordless, by entering an empty passphrase in the ssh-keygen command, otherwise cron will not be able to push run git push correctly.

In short, run:

ssh-keygen -t rsa -b 4096 -C "your_email@example.com"

using :

use your own your email address
an appropriate file name, /home/you/.ssh/id_rsa_cron_deploy_key
an empty passphrase

all: update publish

update:
	jupyter nbconvert --to=html --no-input --ExecutePreprocessor.enabled=True --ExecutePreprocessor.timeout=-1 TM-status-report.ipynb

publish:
	git add *.html *.csv
	git commit -m "update covid-19 reports `date --iso=s`"
	GIT_SSH_COMMAND='ssh -i ~/.ssh/id_rsa_cron_deploy_key' git push origin master