move standard deps to project.toml

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

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"]