From 0b09ad718832504fb58973a358d0c5d6c4322f10 Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Mon, 17 Jun 2024 16:42:39 +0200 Subject: [PATCH] move standard deps to project.toml --- env/deeprank2.yml | 18 ------------------ pyproject.toml | 20 ++++++++++++++++++++ 2 files changed, 20 insertions(+), 18 deletions(-) diff --git a/env/deeprank2.yml b/env/deeprank2.yml index a60925bf..be4a6cf1 100644 --- a/env/deeprank2.yml +++ b/env/deeprank2.yml @@ -9,9 +9,7 @@ channels: dependencies: - python==3.10 - pip>=23.3 - - notebook>=7.0.6 - sbl::libcifpp>=5.1.0 - - markov_clustering>=0.0.6 - pytorch=2.1.1 - torchvision>=0.16.1 - torchaudio>=2.1.1 @@ -21,21 +19,5 @@ dependencies: - pytorch-sparse>=0.6.18 - pytorch-cluster>=1.6.3 - pytorch-spline-conv>=1.2.2 - - tables>=3.8.0 - - numpy>=1.21.5 - - scipy>=1.13.1 - - h5py>=3.6.0 - - networkx>=2.6.3 - - matplotlib>=3.5.1 - - scikit-learn>=1.0.2 - - chart-studio>=1.1.0 - biopython>=1.81 - - pdb2sql>=0.5.1 - - python-louvain>=0.16 - - tqdm>=4.63.0 - freesasa>=2.1.0 - - tensorboard>=0.9.0 - - protobuf>=3.20.1 - - ruff>=0.3.0 - - dill>=0.3.8 - - pyarrow>=15.0.0 diff --git a/pyproject.toml b/pyproject.toml index 6b79b106..a796ec9c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,6 +34,25 @@ classifiers = [ "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10", ] +dependencies = [ + "notebook >= 7.0.6", + "markov_clustering >= 0.0.6", + "tensorboard>=0.9.0", + "protobuf >= 3.20.1", + "dill >= 0.3.8", + "pyarrow >= 15.0.0", + "tables >= 3.8.0", + "numpy >= 1.21.5", + "scipy >= 1.13.1", + "h5py >= 3.6.0", + "networkx >= 2.6.3", + "matplotlib >= 3.5.1", + "scikit-learn >= 1.0.2", + "chart-studio >= 1.1.0", + "pdb2sql >= 0.5.1", + "python-louvain >= 0.16", + "tqdm >= 4.63.0" + ] [project.optional-dependencies] # development dependency groups @@ -45,6 +64,7 @@ test = [ "pytest-cov", "pytest-runner", "coveralls", + "ruff>=0.3.0" ] publishing = ["build", "twine", "wheel"] notebooks = ["nbmake"]