Prediction

In the unitcov/forecast_pipeline folder, run notebook in exactly the following order

1. Run pipeline_data_gathering.ipynb
2. Run pipeline_GLM.ipynb
3. Run pipeline_forecast_case.ipynb and pipeline_forecast_death.ipynb

Do varification

For local validation, follow the instruction here. I suggest that we do varification after adding the submission (and/or modifying meta file) in the covid-forecast-hub repo, by running python3 code/validation/test-formatting.py. It will run validation for both forecasting data and meta file. (But don't use add . in the push step below, only add your file(s), since validation also produces some log files that may cause conflict.)

Resource on creating a pull reqeust:

https://opensource.com/article/19/7/create-pull-request-github

Submission Steps:

1. Fork the the reichlab/covid19-forecast-hub repo (only for the first time);

   How: on the repo webpage, click on the Fork button in the top-right corner. This creates a new copy of repo under your GitHub user account with a URL like: https://github.com/<YourUserName>/covid19-forecast-hub.

2. Clone it to your local system (only for the first time) ;

   How: Open a terminal, move to a location where you want to keep your local version of the repo, run bash comment git clone https://github.com/<YourUserName>/covid-forecast-hub

3. Make a new branch (only for the first time);

   How: Inside you local repo, run bash comment git checkout -b [new_branch]. [new_branch] is a name you should pick up (carefully), such as zed_submission_branch. Don't just use new_branch literally.

4. Make your changes:

   How: we do the prediction in the unitcov repo. After we get the submission file in the submission folder, we add the file to the data-processed/UChicagoCHATTOPADHYAY-UnIT folder in the covid-forecast-hub repo. (We may want to make due modifications to the meta file that is already in the folder). Don't forget to run validation! (discussed above)

5. Push it back to your repo;

   How:

   • git add [forecast_datafile] [meta file];
   • git commit -m "UChicagoCHATTOPADHYAY-UnIT forecast on [date]"
   • git push

6. Click the Compare & pull request button (only for the first time), then just follow the instruction on the webpage;

   How for the second time on:

   • in reichlab/covid19-forecast-hub, click the Pull request button;
   • click the green New pull request button;
   • choose your fork;
   • choose your branch;
   • Then just following the instruction on the webpage.