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chore(medcat-trainer): CU-869a4br6j Create a copy of the v1 medcat-trainer in the v1 folder (#97)
* build(medcat-trainer): CU-869a4br6j Create Github actions for medcat-trainer v1
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‎.github/workflows/medcat-trainer-v1_ci.yml‎

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name: medcat-trainer-v1 ci-build
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on:
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pull_request:
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paths:
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- 'v1/medcat-trainer/**'
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- '.github/workflows/medcat-trainer-v1**'
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defaults:
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run:
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working-directory: ./v1/medcat-trainer
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jobs:
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# Test and build client library
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test-client:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout main
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uses: actions/checkout@v4
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with:
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ref: ${{ github.ref }}
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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 requests pytest build
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- name: Install client package in development mode
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run: |
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cd client
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pip install -e .
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- name: Run client tests
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run: |
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cd client
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python -m pytest tests/ -v
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- name: Build client package
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run: |
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cd client
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python -m build
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# Build and test webapp container
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build-and-push:
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runs-on: ubuntu-latest
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needs: test-client
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steps:
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- name: Checkout main
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uses: actions/checkout@v4
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with:
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ref: ${{ github.ref }}
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- name: Build
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env:
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IMAGE_TAG: ${{ env.RELEASE_VERSION }}
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run: |
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docker build -t cogstacksystems/medcat-trainer:dev-latest webapp/.
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- name: Run Django Tests
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env:
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IMAGE_TAG: ${{ env.RELEASE_VERSION }}
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run: |
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# run tests
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docker run --rm cogstacksystems/medcat-trainer:dev-latest python manage.py test

‎.github/workflows/medcat-trainer-v1_qa.yml‎

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name: medcat-trainer-v1 qa-build
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on:
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push:
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branches: [ main ]
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defaults:
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run:
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working-directory: ./v1/medcat-trainer
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jobs:
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# Test and build client library
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test-client:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout main
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uses: actions/checkout@v4
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with:
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ref: 'main'
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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 requests pytest build
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- name: Install client package in development mode
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run: |
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cd client
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pip install -e .
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- name: Run client tests
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run: |
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cd client
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python -m pytest tests/ -v
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- name: Build client package
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run: |
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cd client
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python -m build
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# - name: Publish dev distribution to Test PyPI
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# uses: pypa/[email protected]
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# with:
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# password: ${{ secrets.MEDCAT_TRAINER_TEST_PYPI_API_TOKEN }}
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# repository_url: https://test.pypi.org/legacy/
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# packages_dir: v1/medcat-trainer/client/dist
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# Build and test webapp container
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build-and-push:
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runs-on: ubuntu-latest
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needs: test-client
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steps:
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- name: Checkout main
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uses: actions/checkout@v4
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with:
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ref: 'main'
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- name: Build
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run: |
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docker build -t cogstacksystems/medcat-trainer:v1-latest webapp/.
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- name: Run Django Tests
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env:
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IMAGE_TAG: latest
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run: |
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# run tests
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docker run --rm cogstacksystems/medcat-trainer:v1-latest python manage.py test
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- name: Login to DockerHub
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uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
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- name: Push to DockerHub
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run: |
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docker push cogstacksystems/medcat-trainer:v1-latest

‎.github/workflows/medcat-trainer-v1_release.yml‎

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name: medcat-trainer-v1 release-build
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on:
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push:
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tags:
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- 'medcat-trainer/v1.*.*'
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defaults:
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run:
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working-directory: ./v1/medcat-trainer
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jobs:
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# Test, build and publish client library
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test-and-publish-client:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout main
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uses: actions/checkout@v4
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with:
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ref: "main"
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- name: Release Tag
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# If GITHUB_REF=refs/tags/medcat-trainer/v0.1.2, this returns v0.1.2. Note it's including the "v" though it probably shouldnt
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run: echo "RELEASE_VERSION=${GITHUB_REF##refs/*/}" >> $GITHUB_ENV
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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 requests pytest build twine
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- name: Install client package in development mode
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run: |
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cd client
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pip install -e .
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- name: Run client tests
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run: |
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cd client
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python -m pytest tests/ -v
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- name: Build client package
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run: |
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cd client
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python -m build
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- name: Publish production distribution to PyPI
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if: startsWith(github.ref, 'refs/tags') && ! github.event.release.prerelease
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uses: pypa/[email protected]
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with:
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# TODO CU-869a25n7e Use Trusted Platform Publisher based PyPI release
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password: ${{ secrets.PYPI_API_TOKEN }}
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packages_dir: v1/medcat-trainer/client/dist
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# Build and test webapp container
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build-and-push:
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runs-on: ubuntu-latest
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needs: test-and-publish-client
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steps:
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- name: Checkout main
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uses: actions/checkout@v4
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with:
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ref: "main"
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- name: Release Tag
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# If GITHUB_REF=refs/tags/medcat-trainer/v0.1.2, this returns v0.1.2. Note it's including the "v" though it probably shouldnt
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run: echo "RELEASE_VERSION=${GITHUB_REF##refs/*/}" >> $GITHUB_ENV
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- name: Build
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env:
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IMAGE_TAG: ${{ env.RELEASE_VERSION }}
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run: |
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docker build -t cogstacksystems/medcat-trainer:$IMAGE_TAG webapp/.
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- name: Run Django Tests
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env:
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IMAGE_TAG: ${{ env.RELEASE_VERSION }}
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run: |
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# run tests
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docker run --rm cogstacksystems/medcat-trainer:$IMAGE_TAG python manage.py test
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- name: Login to DockerHub
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uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
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- name: Push to DockerHub
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env:
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IMAGE_TAG: ${{ env.RELEASE_VERSION }}
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run: |
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docker push cogstacksystems/medcat-trainer:$IMAGE_TAG
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‎v1/medcat-trainer/.env-example‎

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# MedCAT
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SPACY_MODELS="en_core_web_sm en_core_web_md en_core_web_lg"
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# Ports
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MCTRAINER_PORT=8001
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SOLR_PORT=8983

‎v1/medcat-trainer/.gitignore‎

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#Directories to be ignored fully
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/books/
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/articles/
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/other/
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/output/
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/graphics/
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/webapp/models/*
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data/
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tmp/
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*_tmp/
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.idea
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/webapp/frontend/dist/*
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/webapp/api/media/*
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/webapp/api/static/*
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# Configuration
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.env
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# Keep folders with this
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!.keep
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#tmp and similar files
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.nfs*
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*.pyc
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*.out
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*.swp
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*.swn
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tmp_*
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t_*
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tmp_*
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*_tmp
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*.swo
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*.lyx.emergency
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*.lyx#
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*~
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*.log
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*hidden*
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db.sqlite3
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nohup.out
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tmp.py
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# docs outputs
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docs/_build
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# macOS system files
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.DS_Store
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*/.DS_Store
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# Jupyter Notebook checkpoints
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*/.ipynb_checkpoints/*

‎v1/medcat-trainer/.readthedocs.yaml‎

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# .readthedocs.yaml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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version: 2
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build:
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os: ubuntu-20.04
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tools:
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python: "3.9"
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sphinx:
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configuration: medcat-trainer/docs/conf.py
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python:
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install:
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- requirements: medcat-trainer/docs/requirements.txt

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