dhti-elixir-base 0.1.0__tar.gz

dhti_elixir_base-0.1.0/.devcontainer/Dockerfile

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+# [Choice] Python version: 3, 3.9, 3.8, 3.7, 3.6
+ARG VARIANT="3.11"
+FROM mcr.microsoft.com/vscode/devcontainers/python:${VARIANT}
+
+# [Option] Install Node.js
+ARG INSTALL_NODE="true"
+ARG NODE_VERSION="lts/*"
+RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# [Optional] If your pip requirements rarely change, uncomment this section to add them to the image.
+# COPY requirements.txt /tmp/pip-tmp/
+# RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/requirements.txt \
+#    && rm -rf /tmp/pip-tmp
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+# [Optional] Uncomment this line to install global node packages.
+# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1

dhti_elixir_base-0.1.0/.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+    "name": "dhti-elixir-base",
+    // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+    "image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye",
+    "runArgs": [
+        // avoid UID/GID remapping under rootless Podman
+        "--userns=keep-id"
+      ],
+    "features": {},
+
+    // Use 'postCreateCommand' to run commands after the container is created.
+    "postCreateCommand": "./.devcontainer/postCreateCommand.sh",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        "vscode": {
+            "extensions": ["ms-python.python", "editorconfig.editorconfig"],
+            "settings": {
+                "python.testing.pytestArgs": ["tests"],
+                "python.testing.unittestEnabled": false,
+                "python.testing.pytestEnabled": true,
+                "python.defaultInterpreterPath": "/workspaces/dhti-elixir-base/.venv/bin/python",
+                "python.testing.pytestPath": "/workspaces/dhti-elixir-base/.venv/bin/pytest"
+            }
+        }
+    }
+}

dhti_elixir_base-0.1.0/.devcontainer/postCreateCommand.sh

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+#! /usr/bin/env bash
+
+# Install uv
+curl -LsSf https://astral.sh/uv/install.sh | sh
+
+# Install Dependencies
+uv sync
+
+# Install pre-commit hooks
+uv run pre-commit install --install-hooks

dhti_elixir_base-0.1.0/.github/actions/setup-python-env/action.yml

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+name: "Setup Python Environment"
+description: "Set up Python environment for the given Python version"
+
+inputs:
+  python-version:
+    description: "Python version to use"
+    required: true
+    default: "3.11"
+  uv-version:
+    description: "uv version to use"
+    required: true
+    default: "0.8.8"
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        version: ${{ inputs.uv-version }}
+        enable-cache: 'true'
+        cache-suffix: ${{ matrix.python-version }}
+
+    - name: Install Python dependencies
+      run: uv sync --frozen
+      shell: bash

dhti_elixir_base-0.1.0/.github/config.yml

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+# Configurations for todo: https://probot.github.io/apps/todo/
+# Automatically add issues from @todo with @body
+# /**
+#  * @todo What needs to be done
+#  * @body How to do it.
+# */
+
+# https://github.com/behaviorbot/welcome
+newIssueWelcomeComment: >
+  Thank you for raising this issue. We will try and get back to you as soon as possible.
+
+  Be sure to star ✨ the repository for a priority response!
+
+  Please make sure you have given us as much context as possible.
+
+
+newPRWelcomeComment: >
+  Thank you for submitting a pull request.
+
+  Please make sure you have followed our contributing guidelines in CONTRIBUTING.md. We will review it as soon as possible.
+
+  Be sure to star ✨ the repository.
+
+firstPRMergeComment: >
+  Congrats on merging your first pull request! 🎉🎉🎉

dhti_elixir_base-0.1.0/.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    # open-pull-requests-limit: 10
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

dhti_elixir_base-0.1.0/.github/workflows/bump.yml

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+name: Generate changelog
+
+on:
+  push:
+    branches:
+      - "release/**"
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+
+    steps:
+    - name: Checkout Latest Commit
+      uses: actions/checkout@v4
+
+    - name: "✏️ Generate release changelog"
+      uses: janheinrichmerker/action-github-changelog-generator@v2.4
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        user: dermatologist
+        maxIssues: 15
+        httpCache: true
+
+    - name: Commit changes
+      uses: EndBug/add-and-commit@v9
+      with:
+        default_author: github_actions
+        add: '*.md'

dhti_elixir_base-0.1.0/.github/workflows/docs.yml

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+name: Generate and publish gh-pages
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+# https://packaging.python.org/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy-docs:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Deploy documentation
+        run: uv run mkdocs gh-deploy --force

dhti_elixir_base-0.1.0/.github/workflows/publish.yml

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+name: Upload Python Package to PyPi
+# https://docs.github.com/en/actions/guides/building-and-testing-python
+# https://packaging.python.org/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up the environment
+      uses: ./.github/actions/setup-python-env
+
+    - name: Build and publish
+      run: |
+        uv build
+    - name: Publish distribution 📦 to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

dhti_elixir_base-0.1.0/.github/workflows/pytest.yml

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+name: Python Test
+
+on:
+  schedule:
+    - cron: '1 1 2,16 * *'  # every 2nd and 16th at 01:01. To flag any dependency issues.
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - master
+      - develop
+      - main
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ['3.11']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up the environment
+      uses: ./.github/actions/setup-python-env
+
+    - name: Run tests
+      run: uv run python -m pytest tests --cov --cov-config=pyproject.toml --cov-report=xml
+
+  check-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out
+        uses: actions/checkout@v4
+
+      - name: Set up the environment
+        uses: ./.github/actions/setup-python-env
+
+      - name: Check if documentation can be built
+        run: uv run mkdocs build -s

dhti_elixir_base-0.1.0/.github/workflows/tox.yml

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+name: Tox Test
+
+on:
+  push:
+    branches:
+      - master
+      - main
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ['3.11']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up the environment
+      uses: ./.github/actions/setup-python-env
+
+    - name: Test with tox
+      run: |
+        uv run tox

dhti_elixir_base-0.1.0/.github/workflows/upgrade.yml

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+name: Dependencies upgrade
+
+on: workflow_dispatch
+
+jobs:
+  flake-update:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: astral-sh/setup-uv@v6
+
+    # https://docs.astral.sh/uv/concepts/projects/#upgrading-locked-package-versions
+    - run: uv lock --upgrade
+
+    - name: Create Pull Request
+      uses: peter-evans/create-pull-request@v7
+      with:
+        title: "[Automated] Dependencies upgrade"
+        commit-message: "[Automated] Dependencies upgrade"
+        branch: "auto/uv-sync-upgrade"
+        add-paths: uv.lock
+        delete-branch: true
+        labels: |
+            automated pr
+        body-path: result
+        draft: true

dhti_elixir_base-0.1.0/.gitignore

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+notebooks/fhirdata
+# Temporary and binary files
+*~
+*.py[cod]
+*.so
+*.cfg
+!.isort.cfg
+!setup.cfg
+*.orig
+*.log
+*.pot
+__pycache__/*
+.cache/*
+.*.swp
+*/.ipynb_checkpoints/*
+.DS_Store
+
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
+.vscode
+tags
+
+# Package files
+*.egg
+*.eggs/
+.installed.cfg
+*.egg-info
+
+# Unittest and coverage
+htmlcov/*
+.coverage
+.coverage.*
+.tox
+junit*.xml
+coverage.xml
+.pytest_cache/
+
+# Build and docs folder/files
+build/*
+dist/*
+sdist/*
+docs/api/*
+docs/_rst/*
+docs/_build/*
+cover/*
+MANIFEST
+site/*
+# Per-project virtualenvs
+.venv*/
+.conda*/

dhti_elixir_base-0.1.0/AUTHORS.md

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+# Contributors
+
+* dermatologist [github@gulfdoctor.net](mailto:github@gulfdoctor.net)

dhti_elixir_base-0.1.0/CHANGELOG.md

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+# Changelog
+
+## [Unreleased](https://github.com/dermatologist/dhti-elixir-base/tree/HEAD)
+
+[Full Changelog](https://github.com/dermatologist/dhti-elixir-base/compare/d517931ed8f51462438dab94a86806f10268fd05...HEAD)
+
+**Merged pull requests:**
+
+- Feature/uv build 1 [\#40](https://github.com/dermatologist/dhti-elixir-base/pull/40) ([dermatologist](https://github.com/dermatologist))
+- Feature/mcp 1 [\#39](https://github.com/dermatologist/dhti-elixir-base/pull/39) ([dermatologist](https://github.com/dermatologist))
+
+
+
+\* *This Changelog was automatically generated by [github_changelog_generator](https://github.com/github-changelog-generator/github-changelog-generator)*

dhti_elixir_base-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,70 @@
+# # Contributing to `dhti-elixir-base`
+
+## Please note:
+
+* (Optional) We adopt [Git Flow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow). Most feature branches are pushed to the repository and deleted when merged to *develop* branch.
+* (**Important**): Submit pull requests to the *develop* branch or *feature/* branches
+* Use *GitHub Issues* for feature requests and bug reports. Include as much information as possible while reporting bugs.
+
+
+## Contributing (Step-by-step)
+
+1. [Fork the repo](http://help.github.com/fork-a-repo) and clone it to your local computer, and set up the upstream remote:
+
+        git clone https://github.com/YourGitHubHandle/dhti-elixir-base.git
+        cd dhti-elixir-base
+        git remote add upstream https://github.com/dermatologist/dhti-elixir-base.git
+
+2. Checkout out a new local branch based on your master and update it to the latest (BRANCH-123 is the branch name, You can name it whatever you want. Try to give it a meaningful name. If you are fixing an issue, please include the issue #).
+
+        git checkout -b BRANCH-123 develop
+        git clean -df
+        git pull --rebase upstream develop
+
+ > Please keep your code clean. If you find another bug, you want to fix while being in a new branch, please fix it in a separated branch instead.
+
+3. Push the branch to your fork. Treat it as a backup.
+
+        git push origin BRANCH-123
+
+4. Code
+
+  * Adhere to common conventions you see in the existing code.
+  * Include tests as much as possible, and ensure they pass.
+
+5. Commit to your branch
+
+         git commit -m "BRANCH-123: Put change summary here (can be a ticket title)"
+
+  **NEVER leave the commit message blank!** Provide a detailed, clear, and complete description of your commit!
+
+6. Update your branch to the latest code.
+
+        git pull --rebase upstream develop
+
+7. **Important** If you have made many commits, please squash them into atomic units of work. (Most Git GUIs such as sourcetree and smartgit offer a squash option)
+
+
+        git checkout develop
+        git pull --rebase upstream develop
+        git merge --squash BRANCH-123
+        git commit -m "fix: 123"
+
+  Push changes to your fork:
+
+        git push
+
+8. Issue a Pull Request
+
+  In order to make a pull request:
+  * Click "Pull Request".
+  * Choose the develop branch
+  * Click 'Create pull request'
+  * Fill in some details about your potential patch including a meaningful title.
+  * Click "Create pull request".
+
+  Thanks for that -- we'll get to your pull request ASAP. We love pull requests!
+
+## Feedback
+
+   If you need to contact me, see my contact details on my profile page.

dhti_elixir_base-0.1.0/Dockerfile

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+# Install uv
+FROM python:3.12-slim
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
+
+# Change the working directory to the `app` directory
+WORKDIR /app
+
+# Copy the lockfile and `pyproject.toml` into the image
+COPY uv.lock /app/uv.lock
+COPY pyproject.toml /app/pyproject.toml
+
+# Install dependencies
+RUN uv sync --frozen --no-install-project
+
+# Copy the project into the image
+COPY . /app
+
+# Sync the project
+RUN uv sync --frozen
+
+CMD [ "python", "src/dhti_elixir_base/foo.py" ]