update dependencies

app.py

@@ -5,7 +5,6 @@ import tempfile
 
 import biotite.structure as bs
 import gradio as gr
-import huggingface_hub
 import matplotlib.colors as mcolors
 import matplotlib.patches as mpatches
 import matplotlib.pyplot as plt

pyproject.toml

@@ -3,41 +3,24 @@ name = "rocketshp-space"
 version = "0.1.0"
 description = "Add your description here"
 readme = "README.md"
-requires-python = ">=3.11"
+requires-python = ">=3.11,<3.13"
 dependencies = [
-    "biopython>=1.79",
-    "biotite==0.41.2",
-    "datasets>=4.3.0",
-    "esm==3.1.3",
+    "biotite",
+    "esm",
     "gradio[oauth]>=5.49.1",
     "gradio-molecule3d>=0.0.7",
-    "h5py>=3.15.1",
     "huggingface-hub>=0.36.0",
-    "lightning>=2.4.0",
-    "loguru>=0.7.3",
-    "matplotlib>=3.10.7",
-    "mdanalysis>=2.9.0",
-    "mdanalysisdata>=0.9.0",
-    "neptune>=1.13.0",
-    "nglview>=4.0",
-    "numpy>=1.23.5",
-    "numpy-indexed>=0.3.7",
-    "omegaconf>=2.3.0",
-    "openpyxl>=3.1.5",
-    "pandas>=2.3.3",
-    "python-dateutil>=2.9.0.post0",
-    "python-dotenv>=1.1.1",
-    "rocketshp",
-    "scikit-learn>=1.7.2",
-    "scipy>=1.16.2",
-    "seaborn>=0.13.2",
-    "statsmodels>=0.14.5",
-    "tokenizers>=0.20.3",
-    "torchmetrics>=1.8.2",
-    "tqdm>=4.67.1",
-    "transformers>=4.46.3",
-    "typer>=0.20.0",
+    "loguru",
+    "matplotlib",
+    "numpy>=1.23.5<2",
+    "omegaconf",
+    "torch",
+    "pandas",
+    "transformers",
+    "scipy",
+    "tqdm",
+    "rocketshp @ git+https://github.com/FlatironInstitute/RocketSHP.git"
 ]
 
 [tool.uv.sources]
-rocketshp = { git = "https://github.com/FlatironInstitute/RocketSHP" }
+esm = { git = "https://github.com/samsledje/esm"}

requirements.txt

@@ -1,32 +1,16 @@
-biopython>=1.79,
-biotite==0.41.2,
-datasets>=4.3.0,
-esm==3.1.3,
-gradio[oauth]>=5.49.1,
-gradio-molecule3d>=0.0.7,
-h5py>=3.15.1,
-huggingface-hub>=0.36.0,
-lightning>=2.4.0,
-loguru>=0.7.3,
-matplotlib>=3.10.7,
-mdanalysis>=2.9.0,
-mdanalysisdata>=0.9.0,
-neptune>=1.13.0,
-nglview>=4.0,
-numpy>=1.23.5,
-numpy-indexed>=0.3.7,
-omegaconf>=2.3.0,
-openpyxl>=3.1.5,
-pandas>=2.3.3,
-python-dateutil>=2.9.0.post0,
-python-dotenv>=1.1.1,
-scikit-learn>=1.7.2,
-scipy>=1.16.2,
-seaborn>=0.13.2,
-statsmodels>=0.14.5,
-tokenizers>=0.20.3,
-torchmetrics>=1.8.2,
-tqdm>=4.67.1,
-transformers>=4.46.3,
-typer>=0.20.0,
-git+https://github.com/FlatironInstitute/RocketSHP.git
+"biotite",
+"esm",
+"gradio[oauth]>=5.49.1",
+"gradio-molecule3d>=0.0.7",
+"huggingface-hub>=0.36.0",
+"loguru",
+"matplotlib",
+"numpy>=1.23.5<2",
+"omegaconf",
+"torch",
+"pandas",
+"transformers",
+"scipy",
+"tqdm",
+git+https://github.com/samsledje/esm.git,
+git+https://github.com/FlatironInstitute/RocketSHP.git,