edited dockerfiles

data/create_pfam_data.ipynb

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:f3a501ca1d972d4e54cc335e10da2bbf637f5be700553a06d35754ae76c23f85
-size 60030
+oid sha256:a8d332d401cafe959a623a6449ec05ebe1e6e38a1782deee72bfff94eefb21f0
+size 56885

dockerfile

@@ -31,6 +31,7 @@ RUN conda tos accept \
 
 # Create the env and clean up
 RUN conda env create -f environment.yml && \
+    conda run -n protein-conformal pip install --force-reinstall gradio>=4.0.0 && \
     conda clean -afy
 
 # 7. Copy the rest of your code
@@ -39,8 +40,9 @@ COPY . /workspace/
 # 8. Activate env by default
 SHELL ["conda", "run", "-n", "protein-conformal", "/bin/bash", "-c"]
 
-# 9. Expose Gradio port
+# # 9. Expose Gradio port
 EXPOSE 7860
 
-# 10. Default command: start your Gradio app
-CMD ["python", "-m", "protein_conformal.gradio_app"]
+# # 10. Default command: start your Gradio app 
+# SHELL ["conda", "run", "-n", "protein-conformal", "/bin/bash", "-c"]
+# # CMD python -m protein_conformal.gradio_app --share --host 0.0.0.0

environment.yml

@@ -16,7 +16,7 @@ dependencies:
   - scikit-learn>=1.0.0
 
   # Machine Learning & Deep Learning
-  - pytorch>=2.0.0
+  - pytorch>=2.1.0
   - cpuonly  # CPU-only PyTorch for Windows compatibility
   - transformers>=4.30.0
 
@@ -26,8 +26,7 @@ dependencies:
   # Bioinformatics
   - biopython>=1.81
 
-  # Web frameworks and APIs
-  - gradio>=3.50.0
+  # Web frameworks and APIs  
   - fastapi>=0.90.0
   - uvicorn>=0.18.0
   - jinja2>=3.1.0
@@ -53,6 +52,7 @@ dependencies:
   # Pip dependencies (packages not available via conda)
   - pip
   - pip:
+    - gradio>=4.0.0  # Install from PyPI with prebuilt frontend assets
     - py3Dmol>=1.8.0  # 3D molecular visualization for Gradio
 
 # Installation instructions:

pfam/analyze_protein_vec_results.ipynb

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:b8d2f7b45d20e8454f32382094c420d90d143b272f0593e6f5e5cfb2e5a0a4f4
-size 1033684
+oid sha256:fdd1428a36407709111721d753b86c4416e27c7b135397aabc643a3f32fbd598
+size 718299