diff --git a/README.md b/README.md index b119b5a..9a7fa7d 100644 --- a/README.md +++ b/README.md @@ -40,7 +40,15 @@ Or if you are a developer working in a local cloned version, you can install: Alternatively to the [PyPI version](https://pypi.org/project/DIMet/), our tool is also available as a [conda package](https://bioconda.github.io/recipes/dimet/README.html). Moreover, it can be used via Docker (`docker pull quay.io/biocontainers/dimet:0.1.4`) or singularity (`depot.galaxyproject.org/singularity/dimet:0.1.4--pyhdfd78af_0`) containers. +## Developer Setup +To start contributing to DIMet you require a python environment with python >= 3.9 and [poetry]() installed. +Poetry is a python build system and package manager and is used to build and develop DIMet. + +After creating the environment, the project can be installed with +```bash +poetry install +``` ## Code organization @@ -56,6 +64,7 @@ Alternatively to the [PyPI version](https://pypi.org/project/DIMet/), our tool i * With pytest, by running `pytest` from `DIMet` * Alternatively, place yourself in `DIMet/tests` and execute `python -m unittest` +* If the project was installed with `poetry install`, tests can also be run using `poetry run pytest` or from VSCode's GUI ----------------------------------------------------------------------------------------------- @@ -93,8 +102,8 @@ For any information or help running DIMet, you can get in touch with: (2) CBiB - University of Bordeaux, 146, rue Leo Saignat, Bordeaux, France - (3) Spectrometric Data Processing and Analysis, - Masaryk University, Brno, Czech Republic + (3) RECETOX + Faculty of Science, Masaryk University, Kotlářksá 2, 611 37 Brno, Czech Republic (4) University of Freiburg, Freiburg, Germany diff --git a/pyproject.toml b/pyproject.toml index fa751e1..1113bd3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,20 +20,19 @@ repository = "https://github.com/cbib/DIMet.git" [tool.poetry.dependencies] python = "^3.9" -click = "*" -coverage = "*" -matplotlib = "~=3.7.1" -numpy = "~=1.23.1" -pandas = "~=1.5.3" -pydantic = "^1.10.8" -python-dotenv = "^1" -pyyaml = "~=6.0" -scikit-learn = "~=1.1.1" -scipy = "~=1.9.1" -seaborn = "~=0.11.2" -statsmodels="~=0.13.5" -hydra-core="~=1.3.2" -hydra-colorlog="~=1.2.0" +click = "^8.1.7" +numpy = "^1.26.4" +scipy = "^1.12.0" +statsmodels = "^0.14.1" +pandas = "^2.2.0" +pydantic = "^2.6.1" +python-dotenv = "^1.0.1" +pyyaml = "^6.0.1" +scikit-learn = "^1.4.0" +seaborn = "^0.13.2" +hydra-core = "^1.3.2" +hydra-colorlog = "^1.2.0" + [tool.poetry.group.test.dependencies] pytest="*" diff --git a/src/dimet/processing/fit_statistical_distribution.py b/src/dimet/processing/fit_statistical_distribution.py index 9d269d8..0e57868 100644 --- a/src/dimet/processing/fit_statistical_distribution.py +++ b/src/dimet/processing/fit_statistical_distribution.py @@ -109,7 +109,7 @@ def best_fit_distribution(data, bins=200): stats.gamma, stats.gengamma, stats.genhalflogistic, - stats.gilbrat, + stats.gibrat, stats.gompertz, stats.gumbel_r, stats.gumbel_l,