helical 0.0.1a0__tar.gz

helical-0.0.1a0/.github/workflows/get_embeddings.yml

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+name: Get Embeddings
+
+on:
+  workflow_dispatch:
+
+jobs:
+  build:
+  
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: setup python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11.8
+          cache: 'pip' # caching pip dependencies
+
+      - name: Install dependencies
+        run: |
+            pip install .
+            
+      # First download before tests as they make use of the downloaded files 
+      - name: Download all files
+        run: |
+          python ci/download_all.py
+
+      - name: Execute script to get embeddings
+        run: |
+          python ci/probing_tutorial_helpers/get_all_data_embeddings.py
+      
+      - name: Upload numpy embeddings data
+        uses: actions/upload-artifact@v2
+        with:
+          name: upload-data
+          path: data/
+
+      

helical-0.0.1a0/.github/workflows/main.yml

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+name: CI Pipeline
+
+on:
+  pull_request:
+    branches:
+      - main
+      - release
+
+jobs:
+  build:
+  
+    runs-on: ubuntu-latest
+    timeout-minutes: 60 
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: setup python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11.8
+          cache: 'pip' # caching pip dependencies
+
+      - name: Install dependencies
+        run: |
+            pip install -r requirements-dev.txt
+            pip install .
+            
+      # First download before tests as they make use of the downloaded files 
+      - name: Download all files
+        run: |
+          python ci/download_all.py
+
+      - name: Execute unittests
+        run: |
+          pytest --cov-report=html:html_cov --cov-branch --cov-report term --cov=helical ci/
+      
+      - name: Upload coverage report
+        uses: actions/upload-artifact@v2
+        with:
+          name: coverage-report
+          path: html_cov/
+
+      # Does not seem to work but would be nice to have
+      # - name: Pytest coverage comment
+      #   uses: MishaKav/pytest-coverage-comment@main
+      #   with:
+      #     pytest-coverage-path: ./pytest-coverage.txt
+      #     junitxml-path: ./pytest.xml
+
+      - name: Execute Geneformer
+        run: |
+          python examples/run_models/run_geneformer.py
+
+      - name: Execute scGPT
+        run: |
+          python examples/run_models/run_scgpt.py
+
+      - name: Execute UCE
+        run: |
+          python examples/run_models/run_uce.py
+
+      - name: Execute Hyena
+        run: |
+          python examples/run_models/run_hyena_dna.py

helical-0.0.1a0/.gitignore

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+*.egg-info
+__pycache__
+.vscode
+dist/*
+
+# Data/Models
+data/*
+examples/data/*
+singularity/*
+*.sqlite3
+*.h5ad
+*.h5
+*.torch
+*.keras
+*.pt
+*.npz
+*.arrow
+*zip
+*.npy
+
+*.pickle
+*.pkl
+*.bin
+*.dataset
+*.ipynb_checkpoints
+results*
+
+# Log
+debug.log
+
+# Mac Files
+*.DS_Store
+
+/docs/conf.py
+/docs/_build
+/docs/_autosummary
+_build
+/docs/source
+
+# From unit tests
+ci/tests/test_output
+
+# Keep unit tests data
+!ci/tests/data/valid_nn_head/*
+!ci/tests/data/*
+
+# Hydra
+outputs

helical-0.0.1a0/.readthedocs.yaml

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+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+  jobs:
+    pre_build:
+      # Generate on-the-fly Sphinx configuration from Jupyter Book's _config.yml
+      - "SPHINX_APIDOC_OPTIONS=members,show-inheritance sphinx-apidoc -f -d 0 -o docs/source ./"
+      - "jupyter-book config sphinx ./"
+
+sphinx:
+  builder: html
+  configuration: ./conf.py
+  fail_on_warning: false
+
+python:
+   install:
+   - requirements: docs/requirements.txt
+   - requirements: requirements.txt
+   - method: pip
+     path: .
+
+formats:
+  - epub

helical-0.0.1a0/CITATION.bib

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+@software{helical,
+  author = {Maxime Allard, Benoit Putzeys, Rick Schneider, Mathieu Klop},
+  title = {Helical Python Package},
+  year = {2024},
+  publisher = {GitHub},
+  journal = {GitHub Repository},
+  howpublished = {\url{https://github.com/helicalAI/helical}},
+}

helical-0.0.1a0/Dockerfile

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+FROM python:3.11
+
+RUN apt-get update -y \
+    && apt-get upgrade -y \
+    && apt-get -y install build-essential \
+        wget \
+        git \
+        curl \
+        gcc \
+        gfortran \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+   
+
+RUN pip install --upgrade --force-reinstall git+https://github.com/helicalAI/helical.git
+
+# Define the entry point for the container
+ENTRYPOINT ["/bin/bash"]