diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index da77570..c417682 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,16 +1,16 @@ # Please contribute to pyMBE! ## Bug reporting -If you discover any strange feature or unexpected behaviour of the library, please report it by opening an issue in this Gitlab repository or contacting Dr. Pablo M. Blanco (pablb@ntnu.no) or any other member of the pyMBE development team. -Once a ticket is open in Gitlab, we will work to fix the issue as soon as possible. +If you discover any strange feature or unexpected behaviour of the library, please report it by opening an issue in this GitHub repository or contacting Dr. Pablo M. Blanco (pablb@ntnu.no) or any other member of the pyMBE development team. +Once a ticket is open in GitHub, we will work to fix the issue as soon as possible. ## New contributors New developers are welcomed to contribute to extend the functionalities of the pyMBE library. -To contribute to the pyMBE library, first one needs to be added as a member of this Gitlab repository. +To contribute to the pyMBE library, first one needs to be added as a member of this GitHub repository. If you want to contribute to the development of the pyMBE library, please contact Dr. Pablo M. Blanco (pablb@ntnu.no) ## Rules to contribute to pyMBE -All new features of pyMBE must be developed in a branch of this Gitlab repository and must be reported to a member of the pyMBE development team. Any new version of the code must reproduce all the data stored in `reference_data/`. The scripts provided in `tests/` can be used to quickly set-up simulations with pyMBE to reproduce such data sets. All new code will be reviewed by at least one member of the pyMBE development team before being merged into the stable version of the library to ensure that a functional version of the code is always available. +Class methods are sorted in alphabetical order. diff --git a/README.md b/README.md index 33444fd..459b631 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,7 @@ pyMBE provides tools to facilitate building up molecules with complex architectu - [Pandas](https://pandas.pydata.org/) v1.5.3 - [Pint-Pandas](https://pypi.org/project/Pint-Pandas/) v0.5 - [Numpy](https://numpy.org/) +- [SciPy](https://scipy.org/) - [pdoc](https://pdoc.dev/) (for building the docs) ## Branches @@ -75,3 +76,16 @@ make tutorial provided that you have modified the `$ESPResSo_build_path` variable in `Makefile` to match the path where you have built ESPResSo. +### Run the testsuite + +To make sure your code is valid, please run the testsuite before submitting your contribution: + +```sh +PYTHONPATH=$(realpath .) make testsuite +``` + +When contributing new features, consider adding a unit test in the `testsuite/` +folder and a corresponding line in the `testsuite` target of the Makefile. + +Every contribution is automatically tested in CI using EESSI (https://www.eessi.io) +and the [EESSI GitHub Action](https://github.com/marketplace/actions/eessi). diff --git a/requirements.txt b/requirements.txt index 0b86f9f..03666d4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -3,5 +3,6 @@ pandas>=1.5.3 pint>=0.20.01 pint-pandas==0.5 biopandas==0.5.1.dev0 +scipy matplotlib tqdm