custom env

requirements.txt

@@ -1,130 +1,251 @@
-# # Core dependencies
-# requests
-# pandas
-# numpy
-# pydantic
-
-# # Gradio - CRITICAL FIX: was 4.4.1 (typo), should be 4.44.1
-# gradio
-
-# # LangChain ecosystem
-# langchain-core
-# langchain-openai
-# langchain-anthropic
-# langgraph
-
-# # LLM API SDKs
-# openai
-# anthropic
-# python-dotenv
-
-# # Pin problematic dependencies BEFORE lazyslide to avoid backtracking
-# # xarray==2024.10.0
-# # shapely==2.0.6
-# # scipy==1.11.4
-# # numba==0.60.0
-# # dask==2024.11.2
-# scipy
-# shapely
-
-# # ML/Vision dependencies
-# torch
-# torchvision
-# timm
-# transformers
-# huggingface-hub
-# Pillow
-
-# # LazySlide - now should install quickly with pinned deps above
-# lazyslide
-
-# # PRISM dependencies
-# python-environ
-# protobuf
-# sacremoses
-
-# # Whole slide image support
-# # openslide-python
-
-# # Additional tools (optional - comment out if build still times out)
-# scikit-image
-# opencv-python-headless
-# matplotlib
-# EXACT VERSION PINS - Builds in <5 minutes on HF Spaces
-# These versions are known to work together
-
-# ============================================
-# CORE (Required)
-# ============================================
-gradio==5.7.0
-python-dotenv==1.0.0
-requests==2.32.3
-
-# ============================================
-# DATA (Minimal)
-# ============================================
-numpy==1.26.4
-pandas==2.2.2
-Pillow==11.0.0
-
-# ============================================
-# LLM APIs
-# ============================================
-anthropic==0.71.0
-pydantic==2.9.2
-
-# ============================================
-# LANGCHAIN (Core only)
-# ============================================
-langchain-core==0.3.28
-langchain-anthropic==0.3.6
-
-# ============================================
-# LAZYSLIDE DEPENDENCY STACK - ALL PRE-PINNED
-# This section ensures pip doesn't backtrack
-# ============================================
-
-# First layer - base numerical libs
-llvmlite==0.43.0
-numba==0.60.0
-scipy==1.13.1
-
-# Second layer - spatial/geo
-shapely==2.0.6
-pyproj==3.6.1
-
-# Third layer - data processing
-toolz==0.12.1
-cloudpickle==3.0.0
-partd==1.4.1
-dask==2024.5.0
-fsspec==2024.3.1
-
-# Fourth layer - array/dataframe
-xarray==2024.3.0
-
-# Fifth layer - geospatial
-geopandas==0.14.4
-
-# Sixth layer - imaging
-tifffile==2024.8.30
-zarr==2.18.3
-
-# Finally - lazyslide (should install quickly now)
-lazyslide==0.9.2
-
-# ============================================
-# OPTIONAL - Comment out if not needed
-# ============================================
-# transformers==4.46.0
-# huggingface-hub==0.26.3
-
-# ============================================
-# DO NOT ADD - These cause resolution issues:
-# ============================================
-# torch  # Too heavy for free tier, causes OOM
-# torchvision
-# timm
-# opencv-python-headless
-# scikit-image
-# matplotlib
+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

t.txt

@@ -0,0 +1,130 @@
+# # Core dependencies
+# requests
+# pandas
+# numpy
+# pydantic
+
+# # Gradio - CRITICAL FIX: was 4.4.1 (typo), should be 4.44.1
+# gradio
+
+# # LangChain ecosystem
+# langchain-core
+# langchain-openai
+# langchain-anthropic
+# langgraph
+
+# # LLM API SDKs
+# openai
+# anthropic
+# python-dotenv
+
+# # Pin problematic dependencies BEFORE lazyslide to avoid backtracking
+# # xarray==2024.10.0
+# # shapely==2.0.6
+# # scipy==1.11.4
+# # numba==0.60.0
+# # dask==2024.11.2
+# scipy
+# shapely
+
+# # ML/Vision dependencies
+# torch
+# torchvision
+# timm
+# transformers
+# huggingface-hub
+# Pillow
+
+# # LazySlide - now should install quickly with pinned deps above
+# lazyslide
+
+# # PRISM dependencies
+# python-environ
+# protobuf
+# sacremoses
+
+# # Whole slide image support
+# # openslide-python
+
+# # Additional tools (optional - comment out if build still times out)
+# scikit-image
+# opencv-python-headless
+# matplotlib
+# EXACT VERSION PINS - Builds in <5 minutes on HF Spaces
+# These versions are known to work together
+
+# ============================================
+# CORE (Required)
+# ============================================
+gradio==5.7.0
+python-dotenv==1.0.0
+requests==2.32.3
+
+# ============================================
+# DATA (Minimal)
+# ============================================
+numpy==1.26.4
+pandas==2.2.2
+Pillow==11.0.0
+
+# ============================================
+# LLM APIs
+# ============================================
+anthropic==0.71.0
+pydantic==2.9.2
+
+# ============================================
+# LANGCHAIN (Core only)
+# ============================================
+langchain-core==0.3.28
+langchain-anthropic==0.3.6
+
+# ============================================
+# LAZYSLIDE DEPENDENCY STACK - ALL PRE-PINNED
+# This section ensures pip doesn't backtrack
+# ============================================
+
+# First layer - base numerical libs
+llvmlite==0.43.0
+numba==0.60.0
+scipy==1.13.1
+
+# Second layer - spatial/geo
+shapely==2.0.6
+pyproj==3.6.1
+
+# Third layer - data processing
+toolz==0.12.1
+cloudpickle==3.0.0
+partd==1.4.1
+dask==2024.5.0
+fsspec==2024.3.1
+
+# Fourth layer - array/dataframe
+xarray==2024.3.0
+
+# Fifth layer - geospatial
+geopandas==0.14.4
+
+# Sixth layer - imaging
+tifffile==2024.8.30
+zarr==2.18.3
+
+# Finally - lazyslide (should install quickly now)
+lazyslide==0.9.2
+
+# ============================================
+# OPTIONAL - Comment out if not needed
+# ============================================
+# transformers==4.46.0
+# huggingface-hub==0.26.3
+
+# ============================================
+# DO NOT ADD - These cause resolution issues:
+# ============================================
+# torch  # Too heavy for free tier, causes OOM
+# torchvision
+# timm
+# opencv-python-headless
+# scikit-image
+# matplotlib