fairmat-readers-transmission

A package developed by FAIRmat and collaborators that contains file readers for various transmission spectrophotometry file formats.

Install and use

To use the readers, install the package using pip and import the read_file function. It will check the file extension and, using an appropriate file reader, return a Python dictionary containing the data.

pip install fairmat-readers-transmission

from fairmat_readers_transmission import read_file

file_path = "<filepath>.asc"
data_dict =  read_file(file_path)

You can also import individual file readers.

from fairmat_readers_transmission import read_perkin_elmers_asc

file_path = "<filepath>.asc"
data_dict =  read_perkin_elmers_asc(file_path)

Currently, the following file extensions are supported:

Development

The package is still under development. To contribute, start with simply raising an issue on the repo.

Contributing code

In case you want to contribute a piece of code, or a whole new reader, clone the repo in your local and start a virtual Python environment inside the directory.

git clone git@github.com:FAIRmat-NFDI/readers-transmission.git
cd readers-transmission
python3 -m venv .pyenv
source .pyenv/bin/activate

Then install the package in editable mode (-e flag), with dev dependencies. You can also run the pytest to confirm all went well. As a recommended practice, you can also install the pre-commit hook for linting (more on this here).

python -m pip install --upgrade pip
pip install -e .[dev]
pytest
pre-commit install

Now you can start tinkering around on a new branch (or a fork). If you want to contribute the code back to the upstream, simply create a Pull Request (PR), and we will get back to you. As a good practice, add tests for new readers and make sure existing tests (pytest) are passing before creating PR.

Ruff

We have placed GitHub actions for checking the linting. This can lead to your PR failing the CI tests in case your code is not correctly linted or formatted. Best way to avoid this is to use Ruff for automatic linting and formatting. This is already part of the dev environment and you can run Ruff before committing:

ruff check --fix
ruff format

Ruff pre-commit hook

Additionally, we also provide pre-commit hook for Ruff. This will run Ruff every time you try to commit and raise errors (and provide fixes) in case your code needs linting or formatting. You simply have to add these fixes and commit again.

To use this pre-commit hook, make sure to run the following in the terminal after you clone the repo:

pre-commit install