Contributing to CARS

CARS is an open source software : don’t hesitate to hack it and contribute !

Please go to the GitHub repository for source code.

Contact: cars AT cnes.fr

Developer Install

We recommend to use a virtualenv environment, so that CARS do not interfere with other packages installed on your system.

Clone CARS repository from GitHub :

git clone https://github.com/CNES/cars.git
cd cars

Install CARS in a virtualenv in developer mode

make install-dev # CARS installed in ``venv`` virtualenv

Run CARS in virtualenv

source venv/bin/activate
source venv/bin/env_cars.sh
cars -h

The detailed development install method is described in Makefile

Particularly, it uses the following pip editable install:

pip install -e .[dev]

With this pip install mode, source code modifications directly impacts cars command line.

Setting up a development environment with docker

To setup a development environment with docker, run the following command:

docker build -t cars-dev -f Dockerfile .
docker run -it  -v "$(pwd)":/app/cars  --entrypoint=/bin/bash cars-dev

You’re ready to use CARS, all files in the current directory are mounted in the container.

Coding guide

Here are some rules to apply when developing a new functionality:

Comments: Include a comments ratio high enough and use explicit variables names. A comment by code block of several lines is necessary to explain a new functionality.
Test: Each new functionality shall have a corresponding test in its module’s test file. This test shall, if possible, check the function’s outputs and the corresponding degraded cases.
Documentation: All functions shall be documented (object, parameters, return values).
Use type hints: Use the type hints provided by the typing python module.
Use doctype: Follow sphinx default doctype for automatic API.
Quality code: Correct project quality code errors with pre-commit automatic workflow (see below).
Factorization: Factorize the code as much as possible. The command line tools shall only include the main workflow and rely on the cars python modules.
Be careful with user interface upgrade: If major modifications of the user interface or of the tool’s behaviour are done, update the user documentation (and the notebooks if necessary).
Logging and no print: The usage of the print() function is forbidden: use the logging python standard module instead.
Limit classes: If possible, limit the use of classes at one or 2 levels and opt for a functional approach when possible. The classes are reserved for data modelling if it is impossible to do so using xarray and for the good level of modularity.
Limit new dependencies: Do not add new dependencies unless it is absolutely necessary, and only if it has a permissive license.

Pre-commit validation

A pre-commit validation is installed with code quality tools (see below). It is installed automatically by make install-dev command.

Here is the way to install it manually:

pre-commit install -t pre-commit # for commit rules
pre-commit install -t pre-push   # for push rules

This installs the pre-commit hook in .git/hooks/pre-commit and .git/hooks/pre-push from .pre-commit-config.yaml file configuration.

It is possible to test pre-commit before committing:

pre-commit run --all-files                # Run all hooks on all files
pre-commit run --files cars/__init__.py   # Run all hooks on one file
pre-commit run pylint                     # Run only pylint hook

Documentation

CARS contains its Sphinx Documentation in the code in docs directory.

To generate documentation, use:

make docs

The documentation is then build in docs/build directory and can be consulted with a web browser.

Documentation can be edited in docs/source/ RST files.

Jupyter notebooks

CARS contains notebooks in tutorials directory.

To generate a Jupyter kernel with CARS installation, use:

make notebook

Follow indications to run a jupyter notebook.

Kernel is created with following command (with cars-version updated):

python -m ipykernel install --sys-prefix --name=cars-version --display-name=cars-version

To run the jupyter notebook, use:

jupyter notebook

Code quality

CARS uses Isort, Black, Flake8 and Pylint quality code checking.

Use the following command in CARS virtualenv to check the code with these tools:

make lint

Use the following command to format the code with isort and black:

make format

Isort

Isort is a Python utility / library to sort imports alphabetically, and automatically separated into sections and by type.

CARS isort configuration is done in pyproject.toml

Isort manual usage examples:

cd CARS_HOME
isort --check cars tests  # Check code with isort, does nothing
isort --diff cars tests   # Show isort diff modifications
isort cars tests          # Apply modifications

Isort messages can be avoided when really needed with “# isort:skip” on the incriminated line.

Black

Black is a quick and deterministic code formatter to help focus on the content.

CARS black configuration is done in pyproject.toml

If necessary, Black doesn’t reformat blocks that start with “# fmt: off” and end with # fmt: on, or lines that ends with “# fmt: skip”. “# fmt: on/off” have to be on the same level of indentation.

Black manual usage examples:

cd CARS_HOME
black --check cars tests  # Check code with black with no modifications
black --diff cars tests   # Show black diff modifications
black cars tests          # Apply modifications

Flake8

Flake8 is a command-line utility for enforcing style consistency across Python projects. By default it includes lint checks provided by the PyFlakes project , PEP-0008 inspired style checks provided by the PyCodeStyle project , and McCabe complexity checking provided by the McCabe project. It will also run third-party extensions if they are found and installed.

CARS flake8 configuration is done in setup.cfg

Flake8 messages can be avoided (in particular cases !) adding “# noqa” in the file or line for all messages. It is better to choose filter message with “# noqa: E731” (with E371 example being the error number). Look at examples in source code.

Flake8 manual usage examples:

cd CARS_HOME
flake8 cars tests           # Run all flake8 tests

Pylint

Pylint is a global linting tool which helps to have many information on source code.

CARS pylint configuration is done in dedicated .pylintrc file.

Pylint messages can be avoided (in particular cases !) adding “# pylint: disable=error-message-name” in the file or line. Look at examples in source code.

Pylint manual usage examples:

cd CARS_HOME
pylint tests cars       # Run all pylint tests
pylint --list-msgs          # Get pylint detailed errors information

Tests

CARS includes a set of tests executed with pytest tool.

To launch tests:

make test

It launches only the unit_tests and pbs_cluster_tests test targets

Before the tests execution, the CARS_TEST_TEMPORARY_DIR can be defined to indicate where to write the temporary data bound to the test procedure (if the variable is not set, cars will use default temporary directory).

Several kinds of tests are identified by specific pytest markers:

the unit tests defined by the unit_tests marker: make test-unit
the PBS cluster tests defined by the pbs_cluster_tests marker: make test-pbs-cluster
the SLURM cluster tests defined by the slurm_cluster_tests marker: make test-slurm-cluster
the Jupyter notebooks test defined by the notebook_tests marker: make test-notebook

Advanced testing

To execute the tests manually, use pytest at the CARS projects’s root (after initializing the environment):

python -m pytest

To run only the unit tests:

cd cars/
pytest -m unit_tests

To run only the PBS cluster tests:

cd cars/
pytest -m pbs_cluster_tests

To run only the Jupyter notebooks tests:

cd cars/
pytest -m notebook_tests

It is possible to obtain the code coverage level of the tests by installing the pytest-cov module and use the --cov option.

cd cars/
python -m pytest --cov=cars

It is also possible to execute only a specific part of the test, either by indicating the test file to run:

cd cars/
python -m pytest tests/test_tiling.py

Or by using the -k option which will execute the tests which names contain the option’s value:

cd cars/
python -m pytest -k end2end

By default, pytest does not display the traces generated by the tests but only the tests’ status (passed or failed). To get all traces, the following options have to be added to the command line (which can be combined with the previous options):

cd cars/
python -m pytest -s -o log_cli=true -o log_cli_level=INFO