Please work

clean_requirements.py

@@ -0,0 +1,57 @@
+"""
+Clean pip freeze output for HuggingFace Spaces deployment
+Usage: python clean_requirements.py < raw_freeze.txt > requirements.txt
+"""
+
+import sys
+import re
+
+def clean_requirements(lines):
+    """Clean pip freeze output for deployment."""
+    cleaned = []
+    
+    for line in lines:
+        line = line.strip()
+        
+        # Skip empty lines and comments
+        if not line or line.startswith('#'):
+            continue
+        
+        # Skip editable installs (local packages)
+        if line.startswith('-e') or line.startswith('file://'):
+            print(f"# Skipped local package: {line}", file=sys.stderr)
+            continue
+        
+        # Skip packages installed from git
+        if 'git+' in line or '@' in line and 'git' in line:
+            print(f"# Skipped git package: {line}", file=sys.stderr)
+            continue
+        
+        # Remove local version identifiers (+cpu, +cu118, etc)
+        # torch==2.0.1+cpu -> torch==2.0.1
+        line = re.sub(r'\+[a-z0-9]+', '', line)
+        
+        # Remove platform-specific wheel info
+        # some-package @ file:///... -> some-package==version
+        if ' @ ' in line:
+            # Extract just package name and try to find version
+            pkg_name = line.split(' @ ')[0].strip()
+            print(f"# Simplified: {line} -> {pkg_name}", file=sys.stderr)
+            # Try to keep just the package name without version
+            # HF Spaces will resolve the version
+            cleaned.append(pkg_name)
+            continue
+        
+        cleaned.append(line)
+    
+    return cleaned
+
+if __name__ == '__main__':
+    lines = sys.stdin.readlines()
+    cleaned = clean_requirements(lines)
+    
+    print("# Requirements generated from pip freeze")
+    print("# Cleaned for HuggingFace Spaces deployment\n")
+    
+    for line in sorted(set(cleaned)):  # Remove duplicates and sort
+        print(line)

raw_freeze.txt

@@ -0,0 +1,251 @@
+aiobotocore==2.24.1
+aiofiles==24.1.0
+aiohappyeyeballs==2.6.1
+aiohttp==3.12.15
+aioitertools==0.12.0
+aiosignal==1.4.0
+anndata==0.12.2
+annotated-types==0.7.0
+anthropic==0.64.0
+anyio==4.10.0
+appdirs==1.4.4
+array-api-compat==1.12.0
+asciitree==0.3.3
+asttokens==3.0.0
+attrs==25.3.0
+beautifulsoup4==4.13.5
+biolearn==0.8.1
+botocore==1.39.11
+Brotli==1.1.0
+cachetools==5.5.2
+certifi==2025.8.3
+cffi==2.0.0
+charset-normalizer==3.4.3
+clarabel==0.11.1
+click==8.2.1
+cloudpickle==3.1.1
+colorcet==3.1.0
+comm==0.2.3
+contourpy==1.3.2
+cvxpy==1.6.0
+cycler==0.12.1
+cyclopts==3.23.0
+dask==2024.11.2
+dask-expr==1.1.19
+dask-image==2024.5.3
+datashader==0.18.2
+debugpy==1.8.17
+decorator==5.2.1
+Deprecated==1.2.18
+distro==1.9.0
+docstring_parser==0.17.0
+docutils==0.22
+dotenv==0.9.9
+ecos==2.0.14
+einops==0.8.0
+environs==11.0.0
+et_xmlfile==2.0.0
+executing==2.2.1
+fastapi==0.116.1
+fasteners==0.20
+ffmpy==0.6.1
+filelock==3.19.1
+fonttools==4.59.1
+frozenlist==1.7.0
+fsspec==2025.7.0
+geopandas==1.1.1
+google==3.0.0
+google-auth==2.40.3
+google-genai==1.38.0
+gradio==5.44.0
+gradio_client==1.12.1
+greenlet==3.2.4
+groovy==0.1.2
+h11==0.16.0
+h5py==3.14.0
+hf-xet==1.1.8
+histolab==0.7.0
+httpcore==1.0.9
+httpx==0.28.1
+huggingface-hub==0.34.4
+idna==3.10
+imagecodecs==2025.8.2
+imageio==2.37.0
+importlib_metadata==8.7.0
+ipykernel==7.0.1
+ipython==9.6.0
+ipython_pygments_lexers==1.1.1
+jedi==0.19.2
+Jinja2==3.1.6
+jiter==0.10.0
+jmespath==1.0.1
+joblib==1.5.1
+jsonpatch==1.33
+jsonpointer==3.0.0
+jupyter_client==8.6.3
+jupyter_core==5.9.1
+kiwisolver==1.4.9
+langchain==0.3.27
+langchain-anthropic==0.3.19
+langchain-core==0.3.75
+langchain-huggingface==0.3.1
+langchain-ollama==0.3.7
+langchain-openai==0.3.32
+langchain-text-splitters==0.3.9
+langgraph==0.6.6
+langgraph-checkpoint==2.1.1
+langgraph-prebuilt==0.6.4
+langgraph-sdk==0.2.3
+langsmith==0.4.18
+lazy_loader==0.4
+lazyslide==0.8.1
+legacy-api-wrap==1.4.1
+legendkit==0.3.6
+llvmlite==0.44.0
+locket==1.0.0
+markdown-it-py==4.0.0
+MarkupSafe==3.0.2
+marshmallow==4.0.1
+matplotlib==3.10.5
+matplotlib-inline==0.1.7
+matplotlib-scalebar==0.9.0
+mdurl==0.1.2
+mpmath==1.3.0
+multidict==6.6.4
+multipledispatch==1.0.0
+multiscale_spatial_image==2.0.3
+natsort==8.4.0
+nest-asyncio==1.6.0
+networkx==3.5
+nltk==3.9.1
+numba==0.61.2
+numcodecs==0.15.1
+numpy==1.24.4
+nvidia-cublas-cu12==12.6.4.1
+nvidia-cuda-cupti-cu12==12.6.80
+nvidia-cuda-nvrtc-cu12==12.6.77
+nvidia-cuda-runtime-cu12==12.6.77
+nvidia-cudnn-cu12==9.5.1.17
+nvidia-cufft-cu12==11.3.0.4
+nvidia-cufile-cu12==1.11.1.6
+nvidia-curand-cu12==10.3.7.77
+nvidia-cusolver-cu12==11.7.1.2
+nvidia-cusparse-cu12==12.5.4.2
+nvidia-cusparselt-cu12==0.6.3
+nvidia-nccl-cu12==2.26.2
+nvidia-nvjitlink-cu12==12.6.85
+nvidia-nvtx-cu12==12.6.77
+ollama==0.5.3
+ome-zarr==0.11.1
+openai==1.102.0
+opencv-python-headless==4.11.0.86
+openpyxl==3.1.5
+openslide-bin==4.0.0.8
+openslide-python==1.4.2
+orjson==3.11.3
+ormsgpack==1.10.0
+osqp==1.0.5
+packaging==25.0
+pandas==2.3.2
+param==2.2.1
+parso==0.8.5
+partd==1.4.2
+pexpect==4.9.0
+pillow==10.4.0
+PIMS==0.7
+platformdirs==4.4.0
+pooch==1.8.2
+prompt_toolkit==3.0.52
+propcache==0.3.2
+protobuf==6.32.1
+psutil==7.0.0
+ptyprocess==0.7.0
+PubChemPy==1.0.5
+pure_eval==0.2.3
+pyaging==0.1.27
+pyarrow==21.0.0
+pyasn1==0.6.1
+pyasn1_modules==0.4.2
+pycparser==2.23
+pyct==0.5.0
+pydantic==2.11.7
+pydantic_core==2.33.2
+pydub==0.25.1
+Pygments==2.19.2
+pyogrio==0.11.1
+pyparsing==3.2.3
+pyproj==3.7.2
+python-dateutil==2.9.0
+python-dotenv==1.1.1
+python-multipart==0.0.20
+pytz==2025.2
+PyWavelets==1.8.0
+PyYAML==6.0.2
+pyzmq==27.1.0
+rdkit==2025.9.1
+regex==2025.7.34
+requests==2.32.5
+requests-toolbelt==1.0.0
+rich==14.1.0
+rich-rst==1.3.1
+rsa==4.9.1
+ruff==0.12.10
+s3fs==2025.7.0
+sacremoses==0.1.1
+safehttpx==0.1.6
+safetensors==0.6.2
+scikit-image==0.19.3
+scikit-learn==1.7.1
+scipy==1.16.1
+scs==3.2.9
+seaborn==0.13.2
+semantic-version==2.10.0
+shapely==2.1.1
+shellingham==1.5.4
+six==1.17.0
+slicerator==1.1.0
+sniffio==1.3.1
+soupsieve==2.8
+spatial_image==1.2.3
+spatialdata==0.5.0
+SQLAlchemy==2.0.43
+stack-data==0.6.3
+starlette==0.47.3
+sympy==1.14.0
+tenacity==9.1.2
+threadpoolctl==3.6.0
+tifffile==2025.5.10
+tiffslide==2.5.1
+tiktoken==0.11.0
+timm==1.0.19
+tokenizers==0.21.4
+tomlkit==0.13.3
+toolz==1.0.0
+torch==2.7.1
+torchvision==0.23.0
+tornado==6.5.2
+tqdm==4.67.1
+traitlets==5.14.3
+transformers==4.53.3
+triton==3.3.1
+typer==0.16.1
+typing-inspection==0.4.1
+typing_extensions==4.15.0
+tzdata==2025.2
+urllib3==2.5.0
+uvicorn==0.35.0
+wcwidth==0.2.14
+websockets==15.0.1
+wrapt==1.17.3
+wsidata==0.7.1
+xarray==2025.8.0
+xarray-dataclass==3.0.0
+xarray-schema==0.0.3
+xarray-spatial==0.4.0
+xformers==0.0.31
+xlrd==2.0.2
+xxhash==3.5.0
+yarl==1.20.1
+zarr==2.18.7
+zipp==3.23.0
+zstandard==0.24.0

requirements.txt

@@ -1,3 +1,16 @@
+# Requirements generated from pip freeze
+# Cleaned for HuggingFace Spaces deployment
+
+Brotli==1.1.0
+Deprecated==1.2.18
+Jinja2==3.1.6
+MarkupSafe==3.0.2
+PIMS==0.7
+PubChemPy==1.0.5
+PyWavelets==1.8.0
+PyYAML==6.0.2
+Pygments==2.19.2
+SQLAlchemy==2.0.43
 aiobotocore==2.24.1
 aiofiles==24.1.0
 aiohappyeyeballs==2.6.1
@@ -16,7 +29,6 @@ attrs==25.3.0
 beautifulsoup4==4.13.5
 biolearn==0.8.1
 botocore==1.39.11
-Brotli==1.1.0
 cachetools==5.5.2
 certifi==2025.8.3
 cffi==2.0.0
@@ -30,13 +42,12 @@ contourpy==1.3.2
 cvxpy==1.6.0
 cycler==0.12.1
 cyclopts==3.23.0
-dask==2024.11.2
 dask-expr==1.1.19
 dask-image==2024.5.3
+dask==2024.11.2
 datashader==0.18.2
 debugpy==1.8.17
 decorator==5.2.1
-Deprecated==1.2.18
 distro==1.9.0
 docstring_parser==0.17.0
 docutils==0.22
@@ -54,9 +65,9 @@ fonttools==4.59.1
 frozenlist==1.7.0
 fsspec==2025.7.0
 geopandas==1.1.1
-google==3.0.0
 google-auth==2.40.3
 google-genai==1.38.0
+google==3.0.0
 gradio==5.44.0
 gradio_client==1.12.1
 greenlet==3.2.4
@@ -76,7 +87,6 @@ ipykernel==7.0.1
 ipython==9.6.0
 ipython_pygments_lexers==1.1.1
 jedi==0.19.2
-Jinja2==3.1.6
 jiter==0.10.0
 jmespath==1.0.1
 joblib==1.5.1
@@ -85,17 +95,17 @@ jsonpointer==3.0.0
 jupyter_client==8.6.3
 jupyter_core==5.9.1
 kiwisolver==1.4.9
-langchain==0.3.27
 langchain-anthropic==0.3.19
 langchain-core==0.3.75
 langchain-huggingface==0.3.1
 langchain-ollama==0.3.7
 langchain-openai==0.3.32
 langchain-text-splitters==0.3.9
-langgraph==0.6.6
+langchain==0.3.27
 langgraph-checkpoint==2.1.1
 langgraph-prebuilt==0.6.4
 langgraph-sdk==0.2.3
+langgraph==0.6.6
 langsmith==0.4.18
 lazy_loader==0.4
 lazyslide==0.8.1
@@ -104,11 +114,10 @@ legendkit==0.3.6
 llvmlite==0.44.0
 locket==1.0.0
 markdown-it-py==4.0.0
-MarkupSafe==3.0.2
 marshmallow==4.0.1
-matplotlib==3.10.5
 matplotlib-inline==0.1.7
 matplotlib-scalebar==0.9.0
+matplotlib==3.10.5
 mdurl==0.1.2
 mpmath==1.3.0
 multidict==6.6.4
@@ -152,7 +161,6 @@ parso==0.8.5
 partd==1.4.2
 pexpect==4.9.0
 pillow==10.4.0
-PIMS==0.7
 platformdirs==4.4.0
 pooch==1.8.2
 prompt_toolkit==3.0.52
@@ -160,7 +168,6 @@ propcache==0.3.2
 protobuf==6.32.1
 psutil==7.0.0
 ptyprocess==0.7.0
-PubChemPy==1.0.5
 pure_eval==0.2.3
 pyaging==0.1.27
 pyarrow==21.0.0
@@ -171,7 +178,6 @@ pyct==0.5.0
 pydantic==2.11.7
 pydantic_core==2.33.2
 pydub==0.25.1
-Pygments==2.19.2
 pyogrio==0.11.1
 pyparsing==3.2.3
 pyproj==3.7.2
@@ -179,15 +185,13 @@ python-dateutil==2.9.0
 python-dotenv==1.1.1
 python-multipart==0.0.20
 pytz==2025.2
-PyWavelets==1.8.0
-PyYAML==6.0.2
 pyzmq==27.1.0
 rdkit==2025.9.1
 regex==2025.7.34
-requests==2.32.5
 requests-toolbelt==1.0.0
-rich==14.1.0
+requests==2.32.5
 rich-rst==1.3.1
+rich==14.1.0
 rsa==4.9.1
 ruff==0.12.10
 s3fs==2025.7.0
@@ -208,7 +212,6 @@ sniffio==1.3.1
 soupsieve==2.8
 spatial_image==1.2.3
 spatialdata==0.5.0
-SQLAlchemy==2.0.43
 stack-data==0.6.3
 starlette==0.47.3
 sympy==1.14.0
@@ -238,10 +241,10 @@ wcwidth==0.2.14
 websockets==15.0.1
 wrapt==1.17.3
 wsidata==0.7.1
-xarray==2025.8.0
 xarray-dataclass==3.0.0
 xarray-schema==0.0.3
 xarray-spatial==0.4.0
+xarray==2025.8.0
 xformers==0.0.31
 xlrd==2.0.2
 xxhash==3.5.0