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mbarber
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cleanup
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6 files changed

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‎.github/workflows/release_conda.yaml‎

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name: Release Conda Workflow
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on:
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push:
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tags:
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- 'disabled'
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Check out code
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uses: actions/checkout@v2
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- name: Install Poetry
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run: |
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curl -sSL https://install.python-poetry.org | python -
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.x'
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- name: Install Dependencies
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run: |
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poetry install
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- name: Install testing
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run: |
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python -m pip install --upgrade pip
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pip install pytest pandas coverage coverage-badge
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- name: Run tests
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run: |
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coverage run -m pytest ./tests/api/
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- name: Build Package
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run: |
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conda build ./recipe
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@master
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}

‎.github/workflows/release_pypi.yaml‎

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name: Release Workflow
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on:
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push:
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tags:
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- 'disabled'
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Check out code
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uses: actions/checkout@v2
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- name: Install Poetry
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run: |
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curl -sSL https://install.python-poetry.org | python -
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.x'
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- name: Install Dependencies
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run: |
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poetry install
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- name: Install testing
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run: |
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python -m pip install --upgrade pip
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pip install pytest pandas coverage coverage-badge
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- name: Run tests
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run: |
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coverage run -m pytest ./tests/api/
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- name: Build Package
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run: |
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poetry build
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@master
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}

‎.github/workflows/s3.yaml‎

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name: Sphinx Build and Sync to S3
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on:
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push:
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branches:
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- develop
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- prod
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- test
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jobs:
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build_and_sync:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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- name: Install Poetry
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run: |
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curl -sSL https://install.python-poetry.org | python -
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- name: Install Pandoc
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run: |
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sudo apt-get update
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sudo apt-get install -y pandoc
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.x'
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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 pytest sphinx recommonmark sphinx_markdown_tables sphinx_markdown_builder nbsphinx sphinx-rtd-theme pandas requests tqdm pydantic coverage coverage-badge
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- name: Run tests and generate coverage badge
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run: |
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coverage run -m pytest ./tests/api/
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coverage html
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mv htmlcov apidocs/source/
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rm ./apidocs/source/coverage.svg
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coverage-badge -o apidocs/source/coverage.svg
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- name: Build HTML with Sphinx
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run: |
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cd apidocs
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make html
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- name: Get bucket name
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shell: bash
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run: |
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branch=$(echo ${GITHUB_REF#refs/heads/}); \
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if [ $branch == 'develop' ]; \
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then bucket=openprotein-docs-dev; \
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elif [ $branch == 'prod' ]; \
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then bucket=openprotein-docs-prod; \
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elif [ $branch == 'test' ]; \
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then bucket=openprotein-docs-dev; \
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else exit 1; fi; \
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echo $bucket; \
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echo "bucket=$bucket" >> $GITHUB_OUTPUT
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id: bucket_name
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- name: Get distribution ID
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shell: bash
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run: |
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branch=$(echo ${GITHUB_REF#refs/heads/}); \
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if [ $branch == 'develop' ]; \
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then dist=E3SMW2DYY71HHW; \
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elif [ $branch == 'prod' ]; \
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then dist=E1CUT1CP31D5NK; \
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elif [ $branch == 'test' ]; \
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then dist=E3SMW2DYY71HHW; \
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else exit 1; fi; \
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echo $dist; \
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echo "dist=$dist" >> $GITHUB_OUTPUT
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id: dist_id
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- name: Configure AWS credentials
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uses: aws-actions/configure-aws-credentials@v1
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with:
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aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
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aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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aws-region: us-east-1
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- name: Sync apidocs to S3
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env:
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AWS_S3_BUCKET: ${{ steps.bucket_name.outputs.bucket }}
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shell: bash
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run: |
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aws s3 sync apidocs/build/html s3://${AWS_S3_BUCKET}/apidocs/
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- name: Invalidate CloudFront cache
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env:
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DISTRIBUTION_ID: ${{ steps.dist_id.outputs.dist }}
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run: |
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aws cloudfront create-invalidation --distribution-id ${DISTRIBUTION_ID} --paths "/apidocs/*"

‎.gitignore‎

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# SECRETS FILE
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secrets.config
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poetry.lock
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/.github/*
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/.github/s3.yaml
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/htmlcov
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/apidocs/build
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# VS code

recipe/meta.yaml renamed to anaconda_build/meta.yaml

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build:
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noarch: python
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number: 1
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number: 2
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script: "{{ PYTHON }} -m pip install . --no-deps -vv"
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requirements:

‎pyproject.toml‎

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[tool.poetry]
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name = "openprotein_python"
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packages = [{include = "openprotein"}]
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version = "0.2.1"
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version = "0.2.1.post1"
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description = "OpenProtein Python interface."
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license = "MIT"
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readme = "README.md"

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