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Use sane defaults for paths #42

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kdpenner opened this issue Nov 21, 2020 · 0 comments
Open

Use sane defaults for paths #42

kdpenner opened this issue Nov 21, 2020 · 0 comments

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@kdpenner
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kdpenner commented Nov 21, 2020

A few issues.

  1. I installed the package in a conda environment. For every line in patients.py with
os.path.join(os.path.dirname(__file__), "../data/"+string)

the path has the prefix /Users/kpenner/miniconda3/envs/rtlive/lib/python3.9/site-packages/covid/../data/

Some place like ~/.local/share/covid/data/ is logical.

  1. The tutorial should mention that you need to use download_patient_data() before you do anything.

  2. I have to untar latestdata.tar.gz. If I don't and pass the .tar.gz here:

    patients = pd.read_csv(
    file_path,
    parse_dates=False,
    usecols=["country", "date_onset_symptoms", "date_confirmation"],
    low_memory=False,
    )

    pandas throws ValueError: Passed header names mismatches usecols. If I drop usecols, the output of patients.columns is Index(['././@PaxHeader'], dtype='object').

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