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Fixed affiliation and updated poetry #24

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Feb 14, 2024
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13 changes: 11 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -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

-----------------------------------------------------------------------------------------------

Expand Down Expand Up @@ -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
Expand Down
27 changes: 13 additions & 14 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -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="*"
Expand Down
2 changes: 1 addition & 1 deletion src/dimet/processing/fit_statistical_distribution.py
Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down
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