diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..7da1f96 --- /dev/null +++ b/.flake8 @@ -0,0 +1,2 @@ +[flake8] +max-line-length = 100 diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml new file mode 100644 index 0000000..9ded3e0 --- /dev/null +++ b/.github/workflows/docs.yaml @@ -0,0 +1,37 @@ +name: Deploy docs + +on: + push: + branches: + - main + +jobs: + docs: + name: Deploy docs + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.10.x" + + - name: Upgrade pip + run: | + pip install -U pip poetry + + - name: Install package and doc dependencies + run: | + poetry install + + - name: Generate docs + run: | + poetry run docs + + - name: Deploy docs + uses: JamesIves/github-pages-deploy-action@v4.2.3 + with: + branch: gh-pages + folder: docs/fhir_utils diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml new file mode 100644 index 0000000..0e7ee46 --- /dev/null +++ b/.github/workflows/lint.yaml @@ -0,0 +1,35 @@ +name: CI - Lint + +on: + push: + +jobs: + lint: + name: ${{ matrix.os }}${{ matrix.arch }} - Python ${{ matrix.python-version }} - lint + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest] + arch: [x64] + python-version: ["3.10.x"] + steps: + - name: Checkout + uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + architecture: ${{ matrix.arch }} + + - name: Set up Poetry and upgrade pip + run: | + pip install -U pip poetry + + - name: Install this package + run: | + poetry install + + - name: Run tests + run: | + poetry run lint diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml new file mode 100644 index 0000000..978fa3a --- /dev/null +++ b/.github/workflows/tests.yaml @@ -0,0 +1,35 @@ +name: CI - Tests + +on: + push: + +jobs: + tests: + name: ${{ matrix.os }}${{ matrix.arch }} - Python ${{ matrix.python-version }} - tests + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest] + arch: [x64] + python-version: ["3.10.x"] + steps: + - name: Checkout + uses: actions/checkout@v2 + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + architecture: ${{ matrix.arch }} + + - name: Set up Poetry and upgrade pip + run: | + pip install -U pip poetry + + - name: Install this package + run: | + poetry install + + - name: Run tests + run: | + poetry run test diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..f7c807f --- /dev/null +++ b/.gitignore @@ -0,0 +1,132 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# 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/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# VS Code +.vscode/ \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..8cdc530 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,20 @@ +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.2.0 + hooks: + - id: check-added-large-files # prevents adding large files + - id: detect-private-key # detects private keys + - id: fix-byte-order-marker # fixes BOM + - id: fix-encoding-pragma # fixes encoding pragma + - id: no-commit-to-branch # prevents committing to protected branches + - id: trailing-whitespace # prevents trailing whitespace +- repo: https://github.com/psf/black + rev: 22.3.0 + hooks: + - id: black + language_version: python3.10 + exclude: 'pipelines\/\{\{cookiecutter\.project_name\}\}.*' +- repo: https://github.com/PyCQA/flake8 + rev: 4.0.1 + hooks: + - id: flake8 diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md new file mode 100644 index 0000000..537e86d --- /dev/null +++ b/README.md @@ -0,0 +1,17 @@ +# FHIR utilities + +This repository contains a set of utilities for working with FHIR resources. + +## Installation + +```bash +pip install fhir-utils +``` + +## Development + +```bash +git clone https://github.com/prefeitura-rio/fhir-utils +cd fhir-utils +poetry install +``` diff --git a/fhir_utils/__init__.py b/fhir_utils/__init__.py new file mode 100644 index 0000000..45ba86e --- /dev/null +++ b/fhir_utils/__init__.py @@ -0,0 +1,3 @@ +# -*- coding: utf-8 -*- +from .conf import settings # noqa +from .version import __version__ # noqa diff --git a/fhir_utils/conf.py b/fhir_utils/conf.py new file mode 100644 index 0000000..b59b552 --- /dev/null +++ b/fhir_utils/conf.py @@ -0,0 +1,64 @@ +# -*- coding: utf-8 -*- +from os import getenv +from typing import Callable, Union + +from loguru import logger + + +def getenv_or_action( + key: str, action: Union[Callable[[str], str], str], default: str = None +) -> str: + """ + Get an environment variable or execute an action. + + Args: + key (str): The name of the environment variable. + action (Union[Callable[[str], str], str]): The action to execute if the + environment variable is not set. Can be a callable or a string. If a + callable is provided, it will be called with the key as the only + argument. If a string is provided, it will check if this callback + is implemented here and call it. If not, it will raise an exception. + default (str, optional): The default value to return if the environment + variable is not set and no action is provided. Defaults to None. + + Returns: + str: The value of the environment variable or the result of the action. + """ + + def _raise(key: str) -> str: + raise Exception( + f"Environment variable {key} is not set and no action is provided." + ) + + def _warn(key: str) -> str: + logger.warning(f"Environment variable {key} is not set. Using default value.") + return default + + def _pass(key: str) -> str: + return default + + _val = getenv(key) + if _val is None: + if action in [None, "pass"]: + return _pass(key) + elif callable(action): + return action(key) + elif isinstance(action, str): + if action == "raise": + return _raise(key) + elif action == "warn": + return _warn(key) + else: + raise ValueError( + f'Action "{action}" is not implemented in getenv_or_action.' + ) + else: + return default + return _val + + +class Settings: + __slots__ = () + + +settings = Settings() diff --git a/fhir_utils/version.py b/fhir_utils/version.py new file mode 100644 index 0000000..2ad579c --- /dev/null +++ b/fhir_utils/version.py @@ -0,0 +1,4 @@ +# -*- coding: utf-8 -*- +import importlib.metadata + +__version__ = importlib.metadata.version("fhir_utils") diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..a0a3598 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,539 @@ +# This file is automatically @generated by 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"scripts.test:main" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/pytest.ini b/pytest.ini new file mode 100644 index 0000000..77409e9 --- /dev/null +++ b/pytest.ini @@ -0,0 +1,9 @@ +[pytest] +testpaths = + tests +norecursedirs=dist build .tox scripts +addopts = + --doctest-modules + --cov=fhir_utils + -r a + -v diff --git a/scripts/__init__.py b/scripts/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/scripts/docs.py b/scripts/docs.py new file mode 100644 index 0000000..ce36515 --- /dev/null +++ b/scripts/docs.py @@ -0,0 +1,10 @@ +# -*- coding: utf-8 -*- +import subprocess + + +def main(): + """ + Lint all python files in the project. + """ + command = "pdoc3 --html --html-dir docs fhir_utils" + subprocess.run(command, shell=True) diff --git a/scripts/lint.py b/scripts/lint.py new file mode 100644 index 0000000..c3bf29f --- /dev/null +++ b/scripts/lint.py @@ -0,0 +1,11 @@ +# -*- coding: utf-8 -*- +from glob import glob +import subprocess + + +def main(): + """ + Lint all python files in the project. + """ + files = glob("**/*.py", recursive=True) + subprocess.run(["flake8", *files]) diff --git a/scripts/test.py b/scripts/test.py new file mode 100644 index 0000000..b2203d0 --- /dev/null +++ b/scripts/test.py @@ -0,0 +1,6 @@ +# -*- coding: utf-8 -*- +import pytest + + +def main(): + pytest.main([]) diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_sanity.py b/tests/test_sanity.py new file mode 100644 index 0000000..7fcfa18 --- /dev/null +++ b/tests/test_sanity.py @@ -0,0 +1,3 @@ +# -*- coding: utf-8 -*- +def test_sanity(): + assert True