diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 7fa52ce..bc90375 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -1,16 +1,20 @@ name: ๐Ÿงช Integration Tests -on: [push, pull_request] +on: [push, pull_request, workflow_dispatch] jobs: tests: name: โš—๏ธ Application Tests - uses: ./.github/workflows/pytest.yml + uses: WGBH-MLA/.github/.github/workflows/pytest.yml@main + secrets: inherit + with: + pdm_args: -G test + pytest_args: -v lint: name: ๐Ÿ‘• Lint - uses: ./.github/workflows/lint.yml + uses: WGBH-MLA/.github/.github/workflows/lint.yml@main black: name: ๐Ÿ–ค Black - uses: ./.github/workflows/black.yml + uses: WGBH-MLA/.github/.github/workflows/black.yml@main diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml deleted file mode 100644 index 70bb597..0000000 --- a/.github/workflows/lint.yml +++ /dev/null @@ -1,30 +0,0 @@ -name: ๐Ÿ‘– Lint - -on: - workflow_call: - inputs: - python_version: - description: The version of python to setup - default: 3.11 - type: string - -jobs: - lint: - name: ๐Ÿ‘• Linter - runs-on: ubuntu-latest - - steps: - - name: ๐Ÿ“ฐ Checkout - uses: actions/checkout@v3 - - - name: ๐Ÿ Setup Python - uses: actions/setup-python@v4 - id: setup-python - with: - python-version: ${{ inputs.python_version }} - - - name: ๐ŸŒจ๏ธ Install flake8 - run: pip install flake8 - - - name: ๐Ÿ‘” Run Linter - run: flake8 -v diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml deleted file mode 100644 index 814e705..0000000 --- a/.github/workflows/pytest.yml +++ /dev/null @@ -1,61 +0,0 @@ -name: ๐Ÿ pytest - -on: - workflow_call: - inputs: - python_version: - description: The version of python to setup - default: 3.11 - type: string - - poetry_args: - description: Additional args to pass to poetry. - type: string - default: --with test - - pytest_args: - description: Additional args to pass to pytest. - type: string - -jobs: - run_pytest: - name: ๐Ÿ pytest - runs-on: ubuntu-latest - environment: Codecov - - steps: - - name: ๐Ÿ“ฐ Checkout - uses: actions/checkout@v3 - - - name: ๐Ÿ Setup Python - uses: actions/setup-python@v4 - id: setup-python - with: - python-version: ${{ inputs.python_version }} - - - name: ๐Ÿ““ Setup poetry - run: pipx install poetry - - - name: ๐Ÿ’ธ Load cached venv - id: cached-poetry-dependencies - uses: actions/cache@v3 - with: - path: .venv - key: venv-test-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} - - - name: ๐Ÿ‹ Download dependencies - if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' - run: poetry install --no-interaction --no-root ${{ inputs.poetry_args }} - - - name: ๐Ÿ—๏ธ Install dependencies - run: poetry install --no-interaction ${{ inputs.poetry_args }} - - - name: ๐Ÿงช Run pytest suite - run: poetry run pytest -v --cov --cov-report lcov ${{ inputs.pytest_args }} - - - name: ๐Ÿ“ˆ Uploade coverage report - # run this step, even if the tests fail - if: success() || failure() - uses: codecov/codecov-action@v3 - with: - token: ${{ secrets.CODECOV_TOKEN }} diff --git a/Dockerfile b/Dockerfile index 49bb0cf..96c6e8b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,7 +3,7 @@ RUN pip install -U pip uvicorn WORKDIR /app -COPY pyproject.toml poetry.lock README.md ./ +COPY pyproject.toml pdm.lock README.md ./ COPY fastclam fastclam RUN pip install . diff --git a/fastclam/__init__.py b/fastclam/__init__.py index 119595c..aba8f1d 100644 --- a/fastclam/__init__.py +++ b/fastclam/__init__.py @@ -10,3 +10,6 @@ [localhost:8000/docs](http://localhost:8000/docs) """ +from ._version import __version__ + +__all__ = ['__version__'] diff --git a/fastclam/_version.py b/fastclam/_version.py new file mode 100644 index 0000000..7fd229a --- /dev/null +++ b/fastclam/_version.py @@ -0,0 +1 @@ +__version__ = '0.2.0' diff --git a/fastclam/app.py b/fastclam/app.py index 7037f01..2635028 100644 --- a/fastclam/app.py +++ b/fastclam/app.py @@ -4,21 +4,21 @@ from xml.etree.ElementTree import ParseError import requests -from clams.source import generate_source_mmif +from clams.source import generate_source_mmif_from_file from fastapi import FastAPI, HTTPException from fastapi.responses import PlainTextResponse from starlette.exceptions import HTTPException as StarletteHTTPException +from ._version import __version__ from .log import log from .models import Inputs, Pipeline -from .version import __VERSION__ class MMIFException(HTTPException): pass -app = FastAPI(title='FastCLAM') +app = FastAPI(title='FastCLAM', version=__version__) @app.exception_handler(StarletteHTTPException) @@ -29,14 +29,14 @@ async def http_exception_handler(request, exc): @app.get('/') def home() -> dict: """Return version info""" - return {'FastCLAM': __VERSION__} + return {'FastCLAM': __version__} @app.post('/source') def generate_source(files: Inputs) -> dict: """Generate a new source MMIF from multiple input files""" log.info(f'sourcing media {files.files}') - mmif = generate_source_mmif(files.files) + mmif = generate_source_mmif_from_file(files.files) json_value = loads(str(mmif)) log.debug(f'sourced: {json_value}') return json_value @@ -76,7 +76,7 @@ def run_pipeline(pipeline: Pipeline) -> list | dict | str: log.debug(response.content) raise HTTPException( status_code=response.status_code, - detail=f'Unsuccessful response from {app}: {response.status_code} - {response.content}', + detail=f'Unsuccessful response from {app}: {response.status_code} - {response.content}', # noqa E501 ) content_type = response.headers.get('Content-Type') if 'application/json' in content_type: @@ -95,7 +95,7 @@ def run_pipeline(pipeline: Pipeline) -> list | dict | str: log.debug(response.content) raise MMIFException( status_code=499, - detail=f'Failed to parse XML from {app}: {response.status_code} - {response.content}', + detail=f'Failed to parse XML from {app}: {response.status_code} - {response.content}', # noqa E501 ) log.info(f'Ran {len(pipeline.files)} files through {len(pipeline.apps)} apps') diff --git a/fastclam/log.py b/fastclam/log.py index 752ce9a..b94eebb 100644 --- a/fastclam/log.py +++ b/fastclam/log.py @@ -5,7 +5,7 @@ handlers=[ { "sink": RichHandler(), - "format": "{time:YYYY-MM-DD HH:mm:ss.SSS} | {level: <8} | {name}:{function}:{line} - {message}", + "format": "{time:YYYY-MM-DD HH:mm:ss.SSS} | {level: <8} | {name}:{function}:{line} - {message}", # noqa E501 } ] ) diff --git a/fastclam/version.py b/fastclam/version.py deleted file mode 100644 index 61beabf..0000000 --- a/fastclam/version.py +++ /dev/null @@ -1 +0,0 @@ -__VERSION__ = 'v0.1.0' diff --git a/pdm.lock b/pdm.lock new file mode 100644 index 0000000..6e5dbfe --- /dev/null +++ b/pdm.lock @@ -0,0 +1,930 @@ +# This file is @generated by PDM. +# It is not intended for manual editing. + +[metadata] +groups = ["default", "dev", "test"] +cross_platform = true +static_urls = false +lock_version = "4.3" +content_hash = "sha256:f2e616705b95c064cb6f65beb6ba67ebbf57acb1958812fbf41bf944374c1c61" + +[[package]] +name = "aniso8601" +version = "9.0.1" +summary = "A library for parsing ISO 8601 strings." +files = [ + {file = "aniso8601-9.0.1-py2.py3-none-any.whl", hash = "sha256:1d2b7ef82963909e93c4f24ce48d4de9e66009a21bf1c1e1c85bdd0812fe412f"}, + {file = "aniso8601-9.0.1.tar.gz", hash = "sha256:72e3117667eedf66951bb2d93f4296a56b94b078a8a95905a052611fb3f1b973"}, +] + +[[package]] +name = "anyio" +version = "3.7.1" +requires_python = ">=3.7" +summary = "High level compatibility layer for multiple asynchronous event loop implementations" +dependencies = [ + "idna>=2.8", + "sniffio>=1.1", +] +files = [ + {file = "anyio-3.7.1-py3-none-any.whl", hash = "sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5"}, + {file = "anyio-3.7.1.tar.gz", hash = "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780"}, +] + +[[package]] +name = "attrs" +version = "23.1.0" +requires_python = ">=3.7" +summary = "Classes Without Boilerplate" +files = [ + {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"}, + {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"}, +] + +[[package]] +name = "black" +version = "23.7.0" +requires_python = ">=3.8" +summary = "The uncompromising code formatter." +dependencies = [ + "click>=8.0.0", + "mypy-extensions>=0.4.3", + "packaging>=22.0", + "pathspec>=0.9.0", + "platformdirs>=2", +] +files = [ + {file = "black-23.7.0-cp311-cp311-macosx_10_16_arm64.whl", hash = "sha256:b5b0ee6d96b345a8b420100b7d71ebfdd19fab5e8301aff48ec270042cd40ac2"}, + {file = "black-23.7.0-cp311-cp311-macosx_10_16_universal2.whl", hash = "sha256:893695a76b140881531062d48476ebe4a48f5d1e9388177e175d76234ca247cd"}, + {file = "black-23.7.0-cp311-cp311-macosx_10_16_x86_64.whl", hash = "sha256:c333286dc3ddca6fdff74670b911cccedacb4ef0a60b34e491b8a67c833b343a"}, + {file = "black-23.7.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:831d8f54c3a8c8cf55f64d0422ee875eecac26f5f649fb6c1df65316b67c8926"}, + {file = "black-23.7.0-cp311-cp311-win_amd64.whl", hash = "sha256:7f3bf2dec7d541b4619b8ce526bda74a6b0bffc480a163fed32eb8b3c9aed8ad"}, + {file = "black-23.7.0-py3-none-any.whl", hash = "sha256:9fd59d418c60c0348505f2ddf9609c1e1de8e7493eab96198fc89d9f865e7a96"}, + {file = "black-23.7.0.tar.gz", hash = "sha256:022a582720b0d9480ed82576c920a8c1dde97cc38ff11d8d8859b3bd6ca9eedb"}, +] + +[[package]] +name = "blinker" +version = "1.6.2" +requires_python = ">=3.7" +summary = "Fast, simple object-to-object and broadcast signaling" +files = [ + {file = "blinker-1.6.2-py3-none-any.whl", hash = "sha256:c3d739772abb7bc2860abf5f2ec284223d9ad5c76da018234f6f50d6f31ab1f0"}, + {file = "blinker-1.6.2.tar.gz", hash = "sha256:4afd3de66ef3a9f8067559fb7a1cbe555c17dcbe15971b05d1b625c3e7abe213"}, +] + +[[package]] +name = "certifi" +version = "2023.7.22" +requires_python = ">=3.6" +summary = "Python package for providing Mozilla's CA Bundle." +files = [ + {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"}, + {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.2.0" +requires_python = ">=3.7.0" +summary = "The Real First Universal Charset Detector. 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