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Merge pull request #131 from maxsch3/update_versions
Update versions and resolve vulnerabilities
2 parents 2d36fad + 7c36ebb commit 911d5c5

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+255
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‎.github/workflows/master-pipeline.yml‎

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name: Python package
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on:
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push:
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branches:
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- 'master'
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jobs:
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test-code:
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name: "Test code"
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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- name: Test with pytest
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run: |
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pip install pytest pytest-cov pytest-dependency
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PYTHONPATH="$PYTHONPATH:./keras-batchflow" pytest tests --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
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page_build:
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name: "Build and deploy documentation to staging"
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needs: test-code
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runs-on: ubuntu-latest
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environment: github-pages-staging
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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pip install -r build_requirements.txt
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pip install -e .
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- name: Build docs
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run: |
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mkdocs build --verbose --clean --strict
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- name: Deploy
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uses: JamesIves/github-pages-deploy-action@v4
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with:
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branch: gh-pages # The branch the action should deploy to.
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folder: site
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repository-name: maxsch3/keras-batchflow-test
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ssh-key: ${{ secrets.GH_DEPLOY_SECRET }}

‎.github/workflows/release-pipeline.yml‎

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name: Python package
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on:
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release:
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types: ['published']
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jobs:
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page_build:
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name: "Build documentation"
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade build
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pip install -r requirements.txt
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pip install -r build_requirements.txt
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pip install -e .
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- name: Setup Pages
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uses: actions/configure-pages@v4
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- name: Build docs
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run: |
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mkdocs build --verbose --clean --strict
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- name: Upload page artifact
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uses: actions/upload-pages-artifact@v3
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with:
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path: ./site
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pypi_build:
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name: Build pypi package
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install --upgrade build
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pip install -r requirements.txt
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pip install -r build_requirements.txt
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pip install -e .
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- name: Build pypi package
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run: |
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python -m build
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- name: Upload build package as artifact
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uses: actions/upload-artifact@v3
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with:
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name: python-package-distributions
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path: dist/
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deploy_page:
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name: 'Deploy release documentation'
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needs: [page_build, pypi_build]
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# Grant GITHUB_TOKEN the permissions required to make a Pages deployment
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permissions:
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pages: write # to deploy to Pages
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id-token: write # to verify the deployment originates from an appropriate source
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actions: read # to download an artifact uploaded by `actions/upload-pages-artifact@v3`
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# Deploy to the github-pages environment
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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# Specify runner + deployment step
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runs-on: ubuntu-latest
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4
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deploy_pypi:
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name: Publish to pypi
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needs: [page_build, pypi_build]
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/keras-batchflow
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permissions:
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id-token: write
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v3
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with:
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name: python-package-distributions
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path: dist/
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- name: Publish distribution 📦 to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_TOKEN }}

‎.github/workflows/test-pipeline.yml‎

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name: Python package
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on:
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push:
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branches:
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- '*'
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- '!master'
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jobs:
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test-code:
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name: "Test code"
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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- name: Test with pytest
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run: |
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pip install pytest pytest-cov pytest-dependency
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PYTHONPATH="$PYTHONPATH:./keras-batchflow" pytest tests --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
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test-doc-build:
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name: "Test documentation build"
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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pip install -r build_requirements.txt
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pip install -e .
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- name: Test doc build
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run: |
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mkdocs build --verbose --clean --strict

‎.travis.yml‎

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language: python
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python:
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# - "2.7"
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# - "3.4"
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# - "3.5"
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- "3.6"
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- "3.7"
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- "3.8"
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- "3.9"
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- "3.10"
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env:
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- framework=TF1
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# - framework=TF1
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- framework=TF2
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script:
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include:
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- stage: deploy-test
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if: branch = master
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python: "3.6"
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python: "3.10"
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script: skip
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install:
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- pip install -r requirements_tf1.txt
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branch: master
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- stage: deploy-prod
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if: tag IS present
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python: "3.6"
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python: "3.10"
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script: skip
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install:
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- pip install -r requirements_tf1.txt

‎build_requirements.txt‎

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setuptools-scm==3.5.0
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mkdocs==1.1.2
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mkdocs-jupyter==0.13.0
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notebook==6.1.5
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pymdown-extensions==6.3
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nbconvert==5.6.1
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setuptools-scm
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mkdocs
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mkdocs-jupyter
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notebook
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pymdown-extensions
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nbconvert
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git+https://github.com/tomchristie/mkautodoc.git#egg=mkautodoc

‎requirements.txt‎

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pandas>=2.0.0
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scikit-learn
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tensorflow-cpu

‎requirements_tf1.txt‎

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This file was deleted.

‎requirements_tf2.txt‎

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‎setup.py‎

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download_url='https://github.com/maxsch3/batchflow',
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license='MIT',
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setup_requires=['setuptools_scm'],
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install_requires=['numpy>=1.9.1',
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'scipy>=0.14',
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install_requires=['numpy>=1.20.0',
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'scikit-learn',
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'pandas'],
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'pandas>=2.0.0'],
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extras_require={
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'visualize': ['pydot>=1.2.4'],
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'tests': ['pytest',
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'Intended Audience :: Science/Research',
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'License :: OSI Approved :: MIT License',
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'Programming Language :: Python :: 3',
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'Programming Language :: Python :: 3.6',
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'Programming Language :: Python :: 3.10',
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'Topic :: Software Development :: Libraries',
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'Topic :: Software Development :: Libraries :: Python Modules'
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],

‎test/test_base_random_cell_transform.py‎ renamed to ‎tests/test_base_random_cell_transform.py‎

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def test_transform_many_cols(self):
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ct = LocalVersionTransform([.0, 1.], cols=['var1', 'var2'])
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batch = ct.transform(self.df.copy())
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# make a bigger batch to make sure augmenatation will always be used on the batch
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# when batch is small there is a small chance the batch will sieve through without augmentation due to its
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# random nature
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seed_df = self.df.sample(100, replace=True)
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batch = ct.transform(seed_df.copy())
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assert isinstance(batch, pd.DataFrame)
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assert batch.shape == self.df.shape
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assert not batch.equals(self.df)
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batch = self.df.copy()
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assert batch.shape == seed_df.shape
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assert not batch.equals(seed_df)
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batch = seed_df.copy()
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batch1 = ct.transform(batch)
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# test if transform does in-place transform
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assert batch1.equals(batch)

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