Updates

.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

.github/workflows/build-and-publish.yaml

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+name: Build and publish to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          lfs: 'true'
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build setuptools oldest-supported-numpy flake8
+      - name: Check for syntax errors
+        run: |
+          flake8 ./favapy --count --select=E9,F63,F7,F82 --show-source --statistics
+      - name: Build sdist and wheels
+        run: python -m build
+      - uses: actions/upload-artifact@v2
+        with:
+          name: dist
+          path: dist/*
+
+
+  build-streamlit-image:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+    - uses: actions/checkout@v2
+    - id: latest_release
+      uses: pozetroninc/github-action-get-latest-release@master
+      with:
+        owner: mikelkou
+        repo: VAE_Functional_associations
+    - name: Login to GitHub Container Registry
+      uses: docker/login-action@v1
+      with:
+        registry: ghcr.io
+        username: ${{ github.repository_owner }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    - name: Build and push to ghcr.io
+      uses: docker/build-push-action@v2
+      with:
+        context: .
+        push: true
+        tags: |
+          ghcr.io/mikelkou/favapy:${{ steps.latest_release.outputs.release }}
+          ghcr.io/mikelkou/favapy:latest
+
+  publish-to-pypi:
+    needs: [build]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: dist
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}

.github/workflows/codecov.yml

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+comment:
+  layout: "reach, diff, flags, footer"
+  behavior: default
+  require_changes: true
+  branches:
+    only:
+      - test

.github/workflows/test.yaml

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+name: Test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.8"
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+      DATA_DIR: ${{ github.workspace }}/data
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+      - name: Install dependencies
+        run: |
+          pip install ${{ matrix.pip-flags }} ".[dev,test]"
+
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          pytest -v --cov --color=yes

.gitignore

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+Results/
+
+.pytest_cache/
+.DS_Store
+
+
+# Custom MS2PIP stuff
+#data/
+*_pyx.c
+*_pyx_*.c
+ms2pip/models_xgboost/*.xgboost
+
+# Pytest
+.pytest_cache/
+
+# Remote Sync for Atom
+.remote-sync.json
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+pip-wheel-metadata/
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+.venv/
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+# vscode
+.vscode/
+.vs/
+
+# vim
+/tags
+*.swp
+.DS_Store
+.DS_Store
+Supplementary Material/FAVA_logo/QR_code/ALL_ABOUT_FAVA_cream.png
+Supplementary Material/FAVA_logo/QR_code/qrcode_1656596837809_.png
+Supplementary Material/FAVA_logo/QR_code/qrcode_24866566_f4a1ed76ec8a9cbc2e44710b95f19ea3 (1).png
+Supplementary Material/FAVA_logo/QR_code/qrcode_24866566_f4a1ed76ec8a9cbc2e44710b95f19ea3 (2).png
+Supplementary Material/FAVA_logo/QR_code/qrcode_24866566_f4a1ed76ec8a9cbc2e44710b95f19ea3 (3).png
+Supplementary Material/FAVA_logo/QR_code/qrcode_24866566_f4a1ed76ec8a9cbc2e44710b95f19ea3 (4).png
+Supplementary Material/FAVA_logo/QR_code/qrcode_24866566_f4a1ed76ec8a9cbc2e44710b95f19ea3 (5).png
+Supplementary Material/FAVA_logo/QR_code/qrcode_24866566_f4a1ed76ec8a9cbc2e44710b95f19ea3.png
+%userprofile%.condapkgs/urls
+*.q
+*.json
+%userprofile%.condapkgs/cache/.227b7582.q.icloud
+%userprofile%.condapkgs/cache/.53d7ef51.q.icloud
+cache/data-filtered_gene_bc_matrices-hg19-matrix.h5ad
+data/cache/data-filtered_gene_bc_matrices-hg19-matrix.h5ad

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.7.0
+    hooks:
+    - id: nbqa-pyupgrade
+      args: [--py38-plus]
+    - id: nbqa-black
+    - id: nbqa-isort

.readthedocs.yaml

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+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

Dockerfile

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+FROM python:3
+
+COPY favapy/ pyproject.toml setup.cfg ./
+
+RUN pip install tensorflow keras numpy pandas
+
+CMD [ "python", "-m", "favapy" ]