Useful commands

Git setup

Type the following line so git remembers your credential and you don't have to enter your token 6 times per day:

git config --global credential.helper store
git config --global user.name "{NAME SURNAME}"
git config --global user.email [e-mail]
git config --global pull.rebase false # so you use merge as the default reconciliation method

Get a notification on your phone/mail when a run is done

We use ntfy.sh for notification. Install ntfy on your Iphone or Android device. Then subscribe to the channel ntfy.sh/flepimop_alerts where you'll receive notifications when runs are done.

• End of job notifications goes as urgent priority.

Install slack integration

Within included example postprocessing scripts, we include a helper script that sends a slack message with some output snapshots of our model output. So our 🤖-friend can send us some notifications once a run is done.

cd /scratch4/struelo1/flepimop-code/
nano slack_credentials.sh
# and fill the file:
export SLACK_WEBHOOK="{THE SLACK WEBHOOK FOR CSP_PRODUCTION}"
export SLACK_TOKEN="{THE SLACK TOKEN}"

Delphi Epidata API

If you are using the Delph Epidata API, first register for a key. Once you have a key, add that below where you see [YOUR API KEY]. Alternatively, you can put that key in your config file in the inference section as gt_api_key: "YOUR API KEY".

export DELPHI_API_KEY="[YOUR API KEY]"

🚀 Run inference using slurm (do everytime)

TODO: add how to run test, and everything

Don't paste them if you don't know what they do

Filepaths structure

in configs with a setup name: USA

model_output/{FileType}/{Prefix}{Index}.{run_id}.{FileType}.{Extension}
                           ^ 
                          setup name(USA)/scenario(inference/med)/run_id/{Inference stuff}
                                                                           ^ global/{final, intermediate}/slot#.

where, eg:

• the index is 1

• the run_id is 2021.12.14.23:56:12.CET

• the prefix is USA/inference/med/2021.12.14.23:56:12.CET/global/intermediate/000000001.

Steps to first local run

export COVID_PATH=$(pwd)/COVIDScenarioPipeline
export DATA_PATH=$(pwd)/COVID19_USA
conda activate covidSP
cd $COVID_PATH
Rscript local_install.R
pip install --no-deps -e gempyor_pkg # before: python setup.py develop --no-deps
git lfs install
git lfs pull
export CENSUS_API_KEY=YOUR_KEY
cd $DATA_PATH
git restore data/
export CONFIG_PATH=config_smh_r11_optsev_highie_base_deathscases_blk1.yml
Rscript $COVID_PATH/R/scripts/build_US_setup.R
Rscript $COVID_PATH/R/scripts/create_seeding.R
Rscript $COVID_PATH/R/scripts/full_filter.R -j 1 -n 1 -k 1

where:

• $n$ is slots

• $j$ is core

• $k$ is iteration per slot

Launch the docker locally

docker pull hopkinsidd/covidscenariopipeline:latest-dev
docker run -it -v "$(pwd)":/home/app/covidsp hopkinsidd/covidscenariopipeline:latest-dev

Pipeline git-fu (dealing with the commute_data)

because a big file get changed and added automatically. Since Git 2.13 (Q2 2017), you can stash individual files, with git stash push. One of these should work.

git restore --staged sample_data/united-states-commutes/commute_data.csv
git stash push sample_data/united-states-commutes/commute_data.csv
git reset sample_data/united-states-commutes/commute_data.csv