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MEmilio Plot Package

Content

  • Introduction
  • Installation
  • Dependencies
  • Running the scripts
  • Testing and Coverage
  • Pylint
  • Additional tools
  • Notes for developers (!)
  • Troubleshooting

Introduction

This package provides modules and scripts to plot epidemiological or simulation data as returned by other packages of the MEmilio software.

Installation

Use the provided setup.py script to install the package and its dependencies.

To install the package, use (from the directory that contains setup.py)

.. code:: sh

pip install .

This copies everything required to your site-packages.

For developement of code use the command

.. code:: sh

pip install -e .[dev]

This command allows you to work on the code without having to reinstall the package after a change. It also installs all additional dependencies required for development and maintenance.

Dependencies

Required python packages:

  • pandas>=1.2.2
  • matplotlib
  • numpy>=1.22,<1.25
  • openpyxl
  • xlrd
  • requests
  • pyxlsb
  • wget
  • folium
  • matplotlib
  • mapclassify
  • geopandas
  • h5py
  • imageio
  • datetime

Testing and Coverage

The following packages are used by the tests:

  • pyfakefs (creates fake directory to test that expected folders are created and data is written)
  • coverage

See Installation on how to install all these dependencies automatically.

To run the tests make

.. code:: sh

python -m unittest

To get the coverage report do

.. code:: sh

python -m coverage run -m unittest
python -m coverage report
python -m coverage xml -o coverage_python.xml
python -m coverage html -d coverage_python

Coverage report for actual master:

:Coverage Report: https://scicompmod.github.io/memilio/coverage/python/

Inspection via pylint

The following packages have to be installed to run pylint:

  • pylint
  • pylint-json2html

See Installation on how to install all these dependencies automatically.

Run pylint with the commands

.. code:: sh

python setup.py pylint
pylint-json2html -f jsonextended -o build_pylint/pylint.html < build_pylint/pylint_extended.json

Pylint report for actual master:

:Pylint Report: https://dlr-sc.github.io/memilio/pylint/

Notes for developers

If a new functionality shall be added please stick to the following instructions:

When you start creating a new script:

  • use doxygen like comments in code as
    • add description in the beginning of the file

      • Header

      • @brief name descr

      • longer description

    • add description in the beginning of every function directly after the definition
      • start and end with """
      • add a short description to first line
      • afterwards add a longer description

      • @param name of parameter

      • @return type description

General

  • Always add unittests
  • Check test coverage report, if every new feature is covered.
  • Check the pylint report just comments with "refactor" are allowed.