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Commit 896d8a6

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BioGeekBioGeek
committedJul 8, 2024
Update notebooks, add pinned requirements
1 parent edaffd0 commit 896d8a6

8 files changed

+375
-49
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‎.codespell-ignores.txt

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te
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fo
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ot
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wya
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sohw
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bu

‎.gitignore

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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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data/
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*_submission.csv

‎.pre-commit-config.yaml

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rev: 0.7.1
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hooks:
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- id: nbstripout
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- repo: https://github.com/codespell-project/codespell
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rev: v2.3.0
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hooks:
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- id: codespell
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name: codespell
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description: Checks for common misspellings in text files.
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entry: codespell --skip="*.js,*.html,*.css, *.svg" --ignore-words=.codespell-ignores.txt
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language: python
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types: [text]
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- repo: https://github.com/PyCQA/flake8
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rev: 7.1.0
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hooks:
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- id: flake8
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args:
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- --max-line-length=100
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- --max-cognitive-complexity=15
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- --ignore=E203,E266,E501,W503,F722
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additional_dependencies:
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- pep8-naming==0.13.3
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- flake8-absolute-import==1.0.0.1
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- flake8-bugbear==22.12.6
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- flake8-builtins==2.0.1
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- flake8-class-attributes-order==0.1.3
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- flake8-cognitive-complexity==0.1.0
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- flake8-comprehensions==3.10.1
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- flake8-pytest-style==1.6.0
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.6.0
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hooks:
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- id: debug-statements # Check for debugger imports
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- id: requirements-txt-fixer # Order requirements alphabetically
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- id: check-ast # Simply check whether the files parse as valid python
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- id: check-case-conflict # Check for files that would conflict in case-insensitive filesystems
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- id: check-builtin-literals # Require literal syntax when initializing empty or zero Python builtin types
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- id: check-docstring-first # Check a common error of defining a docstring after code
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- id: check-merge-conflict # Check for files that contain merge conflict strings
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- id: check-yaml # Check yaml files
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args: ["--unsafe"]
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- id: end-of-file-fixer # Ensure that a file is either empty, or ends with one newline
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- id: mixed-line-ending # Replace or checks mixed line ending
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- id: trailing-whitespace # This hook trims trailing whitespace
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- repo: https://github.com/kynan/nbstripout
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rev: 0.7.1
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hooks:
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- id: nbstripout
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.5.1
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hooks:
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# Run the linter.
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- id: ruff
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args: [--fix, --ignore, F722]
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# Run the formatter.
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- id: ruff-format

‎README.md

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# hackathon_indabaX_2024
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# hackathon_indabaX_2024

‎hackathon_advanced_notebook.ipynb

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"id": "SfuI1iQ6KI9J"
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},
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"source": [
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"All notebook submition should be made on Zindi, which will rank submissions based on accuracy, F1-score, and other metrics."
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"All notebook submissions should be made on Zindi, which will rank submissions based on accuracy, F1-score, and other metrics."
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]
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},
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{
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},
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"outputs": [],
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"source": [
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"%%capture\n",
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"!pip install -r requirements.txt"
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"!pip install -r rasterio xarray numpy pandas torch torchvision Pillow Absl-py"
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]
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},
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{

‎hackathon_beginner_notebook.ipynb

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‎requirements.in

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pandas
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numpy
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scikit-learn
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torch
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torcheval
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gsutil
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pre-commit
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rasterio
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xarray
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numpy
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torchvision
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Pillow
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Absl-py

‎requirements.txt

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# This file was autogenerated by uv via the following command:
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# uv pip compile requirements.in -o requirements.txt
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absl-py==2.1.0
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# via -r requirements.in
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affine==2.4.0
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# via rasterio
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aiohttp==3.9.5
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# via google-auth
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aiosignal==1.3.1
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# via aiohttp
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argcomplete==3.4.0
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# via gsutil
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async-timeout==4.0.3
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# via aiohttp
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attrs==23.2.0
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# via
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# aiohttp
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# rasterio
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boto==2.49.0
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# via gcs-oauth2-boto-plugin
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cachetools==5.3.3
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# via google-auth
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certifi==2024.7.4
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# via
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# rasterio
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# requests
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cffi==1.16.0
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# via cryptography
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cfgv==3.4.0
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# via pre-commit
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charset-normalizer==3.3.2
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# via requests
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click==8.1.7
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# via
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# click-plugins
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# cligj
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# rasterio
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click-plugins==1.1.1
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# via rasterio
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cligj==0.7.2
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# via rasterio
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crcmod==1.7
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# via gsutil
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cryptography==42.0.8
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# via pyopenssl
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distlib==0.3.8
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# via virtualenv
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fasteners==0.19
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# via
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# google-apitools
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# gsutil
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filelock==3.15.4
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# via
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# torch
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# triton
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# virtualenv
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frozenlist==1.4.1
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# via
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# aiohttp
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# aiosignal
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fsspec==2024.6.1
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# via torch
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gcs-oauth2-boto-plugin==3.2
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# via gsutil
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google-apitools==0.5.32
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# via gsutil
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google-auth==2.17.0
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# via
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# gcs-oauth2-boto-plugin
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# google-auth-httplib2
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# gsutil
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google-auth-httplib2==0.2.0
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# via
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# gcs-oauth2-boto-plugin
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# gsutil
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google-reauth==0.1.1
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# via
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# gcs-oauth2-boto-plugin
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# gsutil
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gsutil==5.30
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# via -r requirements.in
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httplib2==0.20.4
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# via
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# gcs-oauth2-boto-plugin
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# google-apitools
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# google-auth-httplib2
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# gsutil
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# oauth2client
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identify==2.6.0
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# via pre-commit
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idna==3.7
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# via
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# requests
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# yarl
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jinja2==3.1.4
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# via torch
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joblib==1.4.2
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# via scikit-learn
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markupsafe==2.1.5
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# via jinja2
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monotonic==1.6
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# via gsutil
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mpmath==1.3.0
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# via sympy
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multidict==6.0.5
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# via
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# aiohttp
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# yarl
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networkx==3.3
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# via torch
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nodeenv==1.9.1
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# via pre-commit
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numpy==2.0.0
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# via
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# -r requirements.in
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# pandas
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# rasterio
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# scikit-learn
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# scipy
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# snuggs
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# torchvision
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# xarray
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nvidia-cublas-cu12==12.1.3.1
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# via
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# nvidia-cudnn-cu12
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# nvidia-cusolver-cu12
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# torch
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nvidia-cuda-cupti-cu12==12.1.105
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# via torch
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nvidia-cuda-nvrtc-cu12==12.1.105
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# via torch
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nvidia-cuda-runtime-cu12==12.1.105
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# via torch
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nvidia-cudnn-cu12==8.9.2.26
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# via torch
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nvidia-cufft-cu12==11.0.2.54
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# via torch
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nvidia-curand-cu12==10.3.2.106
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# via torch
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nvidia-cusolver-cu12==11.4.5.107
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# via torch
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nvidia-cusparse-cu12==12.1.0.106
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# via
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# nvidia-cusolver-cu12
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# torch
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nvidia-nccl-cu12==2.20.5
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# via torch
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nvidia-nvjitlink-cu12==12.5.82
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# via
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# nvidia-cusolver-cu12
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# nvidia-cusparse-cu12
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nvidia-nvtx-cu12==12.1.105
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# via torch
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oauth2client==4.1.3
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# via
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# gcs-oauth2-boto-plugin
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# google-apitools
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packaging==24.1
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# via xarray
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pandas==2.2.2
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# via
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# -r requirements.in
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# xarray
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pillow==10.4.0
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# via
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# -r requirements.in
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# torchvision
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platformdirs==4.2.2
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# via virtualenv
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pre-commit==3.7.1
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# via -r requirements.in
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pyasn1==0.6.0
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# via
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# oauth2client
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# pyasn1-modules
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# rsa
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pyasn1-modules==0.4.0
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# via
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# google-auth
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# oauth2client
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pycparser==2.22
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# via cffi
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pyopenssl==24.1.0
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# via
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# gcs-oauth2-boto-plugin
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# gsutil
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pyparsing==3.1.2
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# via
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# httplib2
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# snuggs
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python-dateutil==2.9.0.post0
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# via pandas
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pytz==2024.1
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# via pandas
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pyu2f==0.1.5
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# via google-reauth
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pyyaml==6.0.1
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# via pre-commit
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rasterio==1.3.10
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# via -r requirements.in
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requests==2.32.3
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# via google-auth
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retry-decorator==1.1.1
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# via
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# gcs-oauth2-boto-plugin
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# gsutil
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rsa==4.7.2
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# via
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# gcs-oauth2-boto-plugin
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# google-auth
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# oauth2client
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scikit-learn==1.5.1
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# via -r requirements.in
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scipy==1.14.0
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# via scikit-learn
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setuptools==70.2.0
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# via rasterio
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six==1.16.0
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# via
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# gcs-oauth2-boto-plugin
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# google-apitools
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# google-auth
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# gsutil
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# oauth2client
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# python-dateutil
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# pyu2f
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snuggs==1.4.7
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# via rasterio
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sympy==1.12.1
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# via torch
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threadpoolctl==3.5.0
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# via scikit-learn
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torch==2.3.1
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# via
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# -r requirements.in
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# torchvision
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torcheval==0.0.7
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# via -r requirements.in
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torchvision==0.18.1
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# via -r requirements.in
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triton==2.3.1
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# via torch
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typing-extensions==4.12.2
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# via
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# torch
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# torcheval
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tzdata==2024.1
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# via pandas
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urllib3==2.2.2
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# via requests
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virtualenv==20.26.3
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# via pre-commit
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xarray==2024.6.0
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# via -r requirements.in
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yarl==1.9.4
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# via aiohttp

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