🛂 Migrates poetry to pdm (#12)

* Migrates poetry to pdm

* Migrates to shared .github/workflows

* Fixes pytest args, lint errors

* Fixes docker build steps

.github/workflows/CI.yml

@@ -1,16 +1,20 @@
 name: 🧪 Integration Tests
 
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
 
 jobs:
   tests:
     name: ⚗️ 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: 👕 Lint
-    uses: ./.github/workflows/lint.yml
+    uses: WGBH-MLA/.github/.github/workflows/lint.yml@main
 
   black:
     name: 🖤 Black
-    uses: ./.github/workflows/black.yml
+    uses: WGBH-MLA/.github/.github/workflows/black.yml@main

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 .

fastclam/__init__.py

@@ -10,3 +10,6 @@
         [localhost:8000/docs](http://localhost:8000/docs)
 
 """
+from ._version import __version__
+
+__all__ = ['__version__']

fastclam/_version.py

@@ -0,0 +1 @@
+__version__ = '0.2.0'

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')

fastclam/log.py

@@ -5,7 +5,7 @@
     handlers=[
         {
             "sink": RichHandler(),
-            "format": "<green>{time:YYYY-MM-DD HH:mm:ss.SSS}</green> | <level>{level: <8}</level> | <cyan>{name}</cyan>:<cyan>{function}</cyan>:<cyan>{line}</cyan> - <level>{message}</level>",
+            "format": "<green>{time:YYYY-MM-DD HH:mm:ss.SSS}</green> | <level>{level: <8}</level> | <cyan>{name}</cyan>:<cyan>{function}</cyan>:<cyan>{line}</cyan> - <level>{message}</level>",  # noqa E501
         }
     ]
 )