init repo git repository

.gitignore

@@ -0,0 +1,3 @@
+output
+data
+.svn

README.md

@@ -0,0 +1,18 @@
+# README
+
+A simple covid plotter. Data are provided by : https://github.com/owid/covid-19-data/tree/master/public/data
+
+## Installation
+
+```bash
+pip install -r requirements.txt
+```
+
+## Launch
+
+```bash
+python main.py <country_trigram> <var_1> <var_2> <var..n>
+# Ex : python main.py FRA new_cases_smoothed new_deaths_smoothed people_fully_vaccinated hosp_patients
+```
+
+**NOTE** : `-r` option is used to fetch update data

main.py

@@ -0,0 +1,159 @@
+import argparse
+import json
+import logging
+import matplotlib.pyplot as plt
+import numpy as np
+import os
+from numpy.core.fromnumeric import var
+import requests
+
+from cycler import cycler
+from datetime import datetime as dt
+from typing import List, Optional, Tuple
+
+FORMAT = "%(asctime)s - %(levelname)s - %(message)s"
+logging.basicConfig(format=FORMAT, level=logging.INFO)
+
+DATA_URL = "https://covid.ourworldindata.org/data/owid-covid-data.{extension}"
+DATA_REPOSITORY = "data"
+OUTPUT_REPOSITORY = "output"
+
+
+class DataProvider:
+    """
+    src data : https://github.com/owid/covid-19-data/tree/master/public/data
+    """
+
+    def __init__(self, country_key: Optional[str] = "FRA", refresh=False):
+        self._dic_data = None
+        if len(country_key) != 3:
+            raise ValueError(
+                "country key provided : '{}' is invalid. It must be a trigram like : 'FRA'".format(
+                    country_key
+                )
+            )
+        self._country_key = country_key.upper()
+        self._get_data(refresh=refresh)
+
+    def _get_var_by_date(
+        self,
+        var_name: str,
+    ) -> Tuple[List[dt], np.array]:
+        if self._country_key not in self._dic_data.keys():
+            logging.info("country keys : {}".format(self._dic_data.keys()))
+            raise IndexError(
+                "'{}' country trigram key does not exist in the data".format(
+                    self._country_key
+                )
+            )
+        data = self._dic_data[self._country_key]["data"]
+        lst_date, lst_var = [], []
+        for dic in data:
+            date = dt.strptime(dic["date"], "%Y-%m-%d")
+            lst_date.append(date)
+            if var_name not in dic:
+                lst_var.append(None)
+                continue
+            lst_var.append(dic[var_name])
+        if not any(lst_var):
+            logging.warning("no data for variable : '{}'".format(var_name))
+        return lst_date, np.asarray(lst_var, np.float64)
+
+    def _get_data(
+        self,
+        file_path: Optional[str] = None,
+        extension: Optional[str] = "json",
+        refresh=False,
+    ) -> None:
+        os.makedirs(DATA_REPOSITORY, exist_ok=True)
+        data_url = DATA_URL.format(extension=extension)
+        if data_url.endswith("/"):
+            data_url = data_url[:-1]
+        file_path = (
+            os.path.join(DATA_REPOSITORY, data_url.split("/")[-1])
+            if file_path is None
+            else file_path
+        )
+        if not os.path.isfile(file_path) or refresh:
+            r = requests.get(data_url)
+            if not r.content:
+                raise ValueError("no data provided froim the url : {}".format(data_url))
+            with open(file_path, "wb") as f:
+                f.write(r.content)
+                self._dic_data = json.loads(r.content)
+                return
+        self._dic_data = json.load(open(file_path, "rb"))
+
+    def plot(self, lst_var_name: List[str], output_path: Optional[str] = None) -> None:
+        if not lst_var_name:
+            logging.error("no var name list provided to fetch data")
+            return
+        os.makedirs(OUTPUT_REPOSITORY, exist_ok=True)
+        if output_path is None:
+            output_path = os.path.join(
+                OUTPUT_REPOSITORY,
+                "{}-{}.png".format(
+                    self._country_key.lower(), dt.strftime(dt.now(), "%Y%m%d")
+                ),
+            )
+        fig, ax = plt.subplots(
+            figsize=(10 if len(lst_var_name) < 3 else 10 + 1.2 * (len(lst_var_name)), 7)
+        )
+        fig.subplots_adjust(right=0.7)
+        colors = plt.rcParams["axes.prop_cycle"]()
+        for idx, var_name in enumerate(lst_var_name):
+            lst_date, np_var = self._get_var_by_date(var_name)
+            color = next(colors)["color"]
+            if not idx:
+                ax.plot(
+                    lst_date,
+                    np_var,
+                    ".-",
+                    label="{}".format(var_name),
+                    color=color,
+                    markersize=4,
+                )
+                ax.yaxis.label.set_color(color)
+                ax.tick_params(axis="y", colors=color)
+                ax.set_ylabel(var_name)
+                continue
+            sub_ax = ax.twinx()
+            if idx > 1:
+                shift = 1.15 + (0.15 * (idx - 2))
+                sub_ax.spines.right.set_position(("axes", shift))
+            sub_ax.plot(
+                lst_date,
+                np_var,
+                ".-",
+                label="{}".format(var_name),
+                color=color,
+                markersize=4,
+            )
+            sub_ax.yaxis.label.set_color(color)
+            sub_ax.tick_params(axis="y", colors=color)
+            sub_ax.set_ylabel(var_name)
+        ax.tick_params(axis="x")
+        ax.set_xlabel("date")
+        ax.grid(True)
+        fig.autofmt_xdate()
+        plt.title(self._country_key)
+        plt.savefig(output_path)
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("country", type=str, help="country's trigram")
+    parser.add_argument("variables", nargs="+", help="variable list to fetch data")
+    parser.add_argument(
+        "-r",
+        "--refresh",
+        action="store_true",
+        default=False,
+        help="redownload data for updates",
+    )
+
+    args = parser.parse_args()
+
+    data_provider = DataProvider(args.country, refresh=args.refresh)
+    data_provider.plot(args.variables)

requirements.txt

@@ -0,0 +1,20 @@
+appdirs==1.4.4
+black==21.5b1
+certifi==2020.12.5
+chardet==4.0.0
+click==8.0.1
+cycler==0.10.0
+idna==2.10
+kiwisolver==1.3.1
+matplotlib==3.4.2
+mypy-extensions==0.4.3
+numpy==1.20.3
+pathspec==0.8.1
+Pillow==8.2.0
+pyparsing==2.4.7
+python-dateutil==2.8.1
+regex==2021.4.4
+requests==2.25.1
+six==1.16.0
+toml==0.10.2
+urllib3==1.26.4