Start testing and linting

.github/workflows/ci.yml

@@ -0,0 +1,28 @@
+name: Python testing
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox tox-gh-actions
+
+    - name: Test with tox
+      run: tox

ai4papi/__init__.py

@@ -14,6 +14,8 @@
 # License for the specific language governing permissions and limitations
 # under the License.
 
+"""AI4EOSC Platform API."""
+
 from . import version
 
 __version__ = version.release_string

ai4papi/auth.py

@@ -1,25 +1,24 @@
-"""
-Authentication for private methods of the API (mainly managing deployments)
-
-Implementation notes:
-====================
-Authentication is implemented using `get_user_infos_from_access_token` instead
-of `get_user_infos_from_request` (as done in the FastAPI example in the flaat docs).
-There are two advantages of this:
-* the main one is that it would enable us enable to take advantage of Swagger's builtin
-  Authentication and Authorization [1] in the Swagger interface (generated by FastAPI).
-  This is not possible using the `Request` object, as data from `Request` cannot be validated and
-  documented by OpenAPI [2].
-
-  [1] https://swagger.io/docs/specification/authentication/
-  [2] https://fastapi.tiangolo.com/advanced/using-request-directly/?h=request#details-about-the-request-object
-
-* the decorator `flaat.is_authenticated()` around each function is no longer needed, 
-  as authentication is checked automatically by `authorization=Depends(security)` without needing extra code.
-
-The curl calls still remain the same, but now in the http://localhost/docs you will see an authorize
- button where you can copy paste your token. So you will be able to access authenticated methods from the interface.
-"""
+"""Authentication for private methods of the API (mainly managing deployments)."""
+
+# Implementation notes:
+# Authentication is implemented using `get_user_infos_from_access_token` instead
+# of `get_user_infos_from_request` (as done in the FastAPI example in the flaat docs).
+# There are two advantages of this:
+# * the main one is that it would enable us enable to take advantage of Swagger's
+#   builtin Authentication and Authorization [1] in the Swagger interface (generated by
+#   FastAPI).  This is not possible using the `Request` object, as data from `Request`
+#   cannot be validated and documented by OpenAPI [2].
+#
+#   [1] https://swagger.io/docs/specification/authentication/
+#   [2] https://fastapi.tiangolo.com/advanced/using-request-directly
+#
+# * the decorator `flaat.is_authenticated()` around each function is no longer needed,
+#   as authentication is checked automatically by `authorization=Depends(security)`
+#   without needing extra code.
+#
+# The curl calls still remain the same, but now in the http://localhost/docs you will
+# see an authorize button where you can copy paste your token. So you will be able to
+# access authenticated methods from the interface.
 
 import re
 
@@ -35,56 +34,53 @@
 
 
 def get_user_info(token):
-
+    """Return user information from a token."""
     try:
         user_infos = flaat.get_user_infos_from_access_token(token)
     except Exception as e:
         raise HTTPException(
             status_code=403,
             detail=str(e),
-            )
+        )
 
     # Check output
     if user_infos is None:
         raise HTTPException(
             status_code=403,
             detail="Invalid token",
-            )
-    
+        )
+
     # Check scopes
-    if user_infos.get('eduperson_entitlement') is None:
+    if user_infos.get("eduperson_entitlement") is None:
         raise HTTPException(
             status_code=403,
-            detail="Check you enabled the `eduperson_entitlement` scope for your token.",
-            )
+            detail="Check you enabled the `eduperson_entitlement` scope for the token.",
+        )
 
     # Parse Virtual Organizations manually from URNs
     # If more complexity is need in the future, check https://github.com/oarepo/urnparse
     vos = []
-    for i in user_infos.get('eduperson_entitlement'):
-        vos.append(
-            re.search(r"group:(.+?):", i).group(1)
-        )
+    for i in user_infos.get("eduperson_entitlement"):
+        vos.append(re.search(r"group:(.+?):", i).group(1))
 
     # Filter VOs to keep only the ones relevant to us
-    vos = set(vos).intersection(
-        set(MAIN_CONF['auth']['VO'])
-    )
+    vos = set(vos).intersection(set(MAIN_CONF["auth"]["VO"]))
     vos = sorted(vos)
 
     # Check if VOs is empty after filtering
     if not vos:
         raise HTTPException(
             status_code=403,
-            detail=f"You should belong to at least one of the Virtual Organizations supported by the project: {vos}.",
-            )
+            detail="You should belong to at least one of the Virtual Organizations "
+            f"supported by the project: {vos}.",
+        )
 
     # Generate user info dict
     out = {
-        'id': user_infos.get('sub'),  # subject, user-ID
-        'issuer': user_infos.get('iss'),  # URL of the access token issuer
-        'name': user_infos.get('name'),
-        'vo': vos, 
+        "id": user_infos.get("sub"),  # subject, user-ID
+        "issuer": user_infos.get("iss"),  # URL of the access token issuer
+        "name": user_infos.get("name"),
+        "vo": vos,
     }
 
     return out

ai4papi/cli.py

@@ -1,19 +1,17 @@
-"""
-Command Line Interface to the API
+"""Command Line Interface to the API."""
 
-Implementation notes:
-====================
-Typer is not implement directly as a decorator around the run() function in main.py
-because it gave errors while trying to run `uvicorn main:app --reload`.
-Just have it in a separate file, clean and easy.
-"""
+# Implementation notes:
+# Typer is not implement directly as a decorator around the run() function in main.py
+# because it gave errors while trying to run `uvicorn main:app --reload`.  Just have it
+# in a separate file, clean and easy.
 
 import typer
 
 from ai4papi import main
 
 
 def run():
+    """Run the API."""
     typer.run(main.run)
 
 

ai4papi/conf.py

@@ -1,6 +1,4 @@
-"""
-Manage configurations of the API.
-"""
+"""Manage configurations of the API."""
 
 from pathlib import Path
 
@@ -10,27 +8,28 @@
 
 Nomad = nomad.Nomad()
 
-CONF_DIR = Path(__file__).parents[1].absolute() / 'etc'
+CONF_DIR = Path(__file__).parents[1].absolute() / "etc"
 
 # Load main API configuration
-with open(CONF_DIR / 'main_conf.yaml', 'r') as f:
+with open(CONF_DIR / "main_conf.yaml", "r") as f:
     MAIN_CONF = yaml.safe_load(f)
 
 # Load default Nomad job configuration
-with open(CONF_DIR / 'job.nomad', 'r') as f:
+with open(CONF_DIR / "job.nomad", "r") as f:
     job_raw_nomad = f.read()
     NOMAD_JOB_CONF = Nomad.jobs.parse(job_raw_nomad)
 
 # Load user customizable parameters
-with open(CONF_DIR / 'userconf.yaml', 'r') as f:
+with open(CONF_DIR / "userconf.yaml", "r") as f:
     USER_CONF = yaml.safe_load(f)
 
 USER_CONF_VALUES = {}
 for group_name, params in USER_CONF.items():
     USER_CONF_VALUES[group_name] = {}
     for k, v in params.items():
-        assert 'name' in v.keys(), f"Parameter {k} needs to have a name."
-        assert 'value' in v.keys(), f"Parameter {k} needs to have a value."
-
-        USER_CONF_VALUES[group_name][k] = v['value']
+        if "name" not in v.keys():
+            raise KeyError(f"Parameter {k} needs to have a name in `userconf.yaml`.")
+        if "value" not in v.keys():
+            raise KeyError(f"Parameter {k} needs to have a value in `userconf.yaml`.")
 
+        USER_CONF_VALUES[group_name][k] = v["value"]

ai4papi/main.py

@@ -1,9 +1,11 @@
-"""
-Create an app with FastAPI
-"""
+"""AI4EOSC Plaform API (AI4PAPI) with FastAPI."""
+
+import ipaddress
+import typing
 
 import fastapi
 from fastapi.security import HTTPBearer
+import typer
 import uvicorn
 
 from ai4papi.routers import v1
@@ -38,6 +40,7 @@
 def root(
     request: fastapi.Request,
 ):
+    """Get version and documentation endpoints."""
     root = str(request.url_for("root"))
     versions = [v1.get_version(request)]
 
@@ -65,11 +68,12 @@ def root(
 
 
 def run(
-        host:str = "0.0.0.0",
-        port:int = 8080,
-        ssl_keyfile:str = None,
-        ssl_certfile:str = None,
-    ):
+    host: ipaddress.IPv4Address = ipaddress.IPv4Address("127.0.0.1"),  # noqa(B008)
+    port: int = 8080,
+    ssl_keyfile: typing.Optional[pathlib.Path] = typer.Option(None),  # noqa(B008)
+    ssl_certfile: typing.Optional[pathlib.Path] = typer.Option(None),  # noqa(B008)
+):
+    """Run the API in uvicorn."""
     uvicorn.run(
         app,
         host=host,

ai4papi/routers/__init__.py

@@ -0,0 +1 @@
+"""Route definition and management."""

ai4papi/routers/v1/__init__.py

@@ -1,3 +1,4 @@
+"""V1 routes."""
 
 import fastapi
 
@@ -16,6 +17,7 @@
     tags=["API", "version"],
 )
 def get_version(request: fastapi.Request):
+    """Get V1 version information."""
     root = str(request.url_for("get_version"))
     # root = "/"
     version = {