Update dev doc rebase2

.github/workflows/ci.yml

@@ -67,9 +67,10 @@ jobs:
 
         -   name: Upload to Codecov
             if: matrix.python-version == 3.8
-            uses: codecov/codecov-action@v1
+            uses: codecov/codecov-action@v4
             with:
                 name: pytests
                 flags: pytests
                 file: ./coverage.xml
+                token: ${{ secrets.CODECOV_TOKEN }}
                 fail_ci_if_error: true

.pre-commit-config.yaml

@@ -20,11 +20,13 @@ repos:
     - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.812
+    rev: v1.10.0
     hooks:
     - id: mypy
       additional_dependencies:
-      - pydantic~=1.8.2
+      - pydantic~=1.10.0
+      - types-python-dateutil
+      - types-docutils
       exclude: >
         (?x)^(
             docs/.*|
@@ -34,14 +36,14 @@ repos:
         )$
 
   - repo: https://github.com/PyCQA/pylint
-    rev: v2.8.3
+    rev: v3.2.2
     hooks:
     - id: pylint
       additional_dependencies:
       - aiida-core~=2.0
       - fastapi~=0.65.1
       - uvicorn[standard]~=0.19.0
-      - pydantic~=1.8.2
+      - pydantic~=1.10.0
       - graphene<3
       - lark
       - python-dateutil~=2.0

README.md

@@ -43,9 +43,36 @@ See the [examples](https://github.com/aiidateam/aiida-restapi/tree/master/exampl
 ```shell
 git clone https://github.com/aiidateam/aiida-restapi .
 cd aiida-restapi
-pip install -e .[pre-commit,testing]  # install extra dependencies
-pre-commit install  # install pre-commit hooks
-pytest -v  # discover and run all tests
+```
+
+### Setting up pre-commit
+
+We use pre-commit to take care for the formatting, type checking and linting.
+```shell
+pip install -e .[pre-commit]  # install extra dependencies
+pre-commit run # running pre-commit on changes
+pre-commit run --all-files # running pre-commit on every file
+pre-commit run pylint --all-files # run only the linter on every file
+```
+One can also set up pre-commit to be run on every commit
+```shell
+pre-commit install
+# pre-commit uninstall # to disable it again
+```
+
+### Running tests
+
+With tox the tests can be run
+```shell
+pip install tox
+tox -e py311 # run all tests for Python 3.11
+tox -av # see all supported environments
+```
+tox will creat a custom environment to run the tests in. If you want to run the
+tests inside your current environment
+```shell
+pip install -e .[testing]  # install extra dependencies
+pytest -v
 ```
 
 See the [developer guide](http://aiida-restapi.readthedocs.io/en/latest/developer_guide/index.html) for more information.

aiida_restapi/models.py

@@ -94,9 +94,7 @@ def get_entities(
                 order_by
             ), f"order_by not subset of projectable properties: {project!r}"
             query.order_by({"fields": order_by})
-        return [
-            cls(**result["fields"]) for result in query.dict()  # type: ignore[call-arg]
-        ]
+        return [cls(**result["fields"]) for result in query.dict()]
 
 
 class Comment(AiidaModel):

aiida_restapi/routers/computers.py

@@ -45,9 +45,9 @@ async def read_computer(comp_id: int) -> Optional[Computer]:
 @with_dbenv()
 async def create_computer(
     computer: Computer,
-    current_user: User = Depends(
+    current_user: User = Depends(  # pylint: disable=unused-argument
         get_current_active_user
-    ),  # pylint: disable=unused-argument
+    ),
 ) -> Computer:
     """Create new AiiDA computer."""
     orm_computer = orm.Computer(**computer.dict(exclude_unset=True)).store()

aiida_restapi/routers/daemon.py

@@ -41,9 +41,9 @@ async def get_daemon_status() -> DaemonStatusModel:
 @router.post("/daemon/start", response_model=DaemonStatusModel)
 @with_dbenv()
 async def get_daemon_start(
-    current_user: User = Depends(
+    current_user: User = Depends(  # pylint: disable=unused-argument
         get_current_active_user
-    ),  # pylint: disable=unused-argument
+    ),
 ) -> DaemonStatusModel:
     """Start the daemon."""
     client = get_daemon_client()
@@ -64,9 +64,9 @@ async def get_daemon_start(
 @router.post("/daemon/stop", response_model=DaemonStatusModel)
 @with_dbenv()
 async def get_daemon_stop(
-    current_user: User = Depends(
+    current_user: User = Depends(  # pylint: disable=unused-argument
         get_current_active_user
-    ),  # pylint: disable=unused-argument
+    ),
 ) -> DaemonStatusModel:
     """Stop the daemon."""
     client = get_daemon_client()

aiida_restapi/routers/groups.py

@@ -44,9 +44,9 @@ async def read_group(group_id: int) -> Optional[Group]:
 @with_dbenv()
 async def create_group(
     group: Group_Post,
-    current_user: User = Depends(
+    current_user: User = Depends(  # pylint: disable=unused-argument
         get_current_active_user
-    ),  # pylint: disable=unused-argument
+    ),
 ) -> Group:
     """Create new AiiDA group."""
     orm_group = orm.Group(**group.dict(exclude_unset=True)).store()

aiida_restapi/routers/nodes.py

@@ -42,9 +42,9 @@ async def read_node(nodes_id: int) -> Optional[models.Node]:
 @with_dbenv()
 async def create_node(
     node: models.Node_Post,
-    current_user: models.User = Depends(
+    current_user: models.User = Depends(  # pylint: disable=unused-argument
         get_current_active_user
-    ),  # pylint: disable=unused-argument
+    ),
 ) -> models.Node:
     """Create new AiiDA node."""
     node_dict = node.dict(exclude_unset=True)
@@ -68,9 +68,9 @@ async def create_node(
 async def create_upload_file(
     upload_file: bytes = File(...),
     params: models.Node_Post = Depends(models.Node_Post.as_form),  # type: ignore # pylint: disable=maybe-no-member
-    current_user: models.User = Depends(
+    current_user: models.User = Depends(  # pylint: disable=unused-argument
         get_current_active_user
-    ),  # pylint: disable=unused-argument
+    ),
 ) -> models.Node:
     """Endpoint for uploading file data"""
     node_dict = params.dict(exclude_unset=True, exclude_none=True)

aiida_restapi/routers/process.py

@@ -79,9 +79,9 @@ async def read_process(proc_id: int) -> Optional[Process]:
 @with_dbenv()
 async def post_process(
     process: Process_Post,
-    current_user: User = Depends(
+    current_user: User = Depends(  # pylint: disable=unused-argument
         get_current_active_user
-    ),  # pylint: disable=unused-argument
+    ),
 ) -> Optional[Process]:
     """Create new process."""
     process_dict = process.dict(exclude_unset=True, exclude_none=True)
@@ -93,7 +93,7 @@ async def post_process(
     except ValueError as exc:
         raise HTTPException(
             status_code=404,
-            detail="Entry point '{}' not recognized.".format(entry_point),
+            detail=f"Entry point '{entry_point}' not recognized.",
         ) from exc
 
     process_node = submit(entry_point_process, **inputs)

aiida_restapi/routers/users.py

@@ -42,9 +42,9 @@ async def read_user(user_id: int) -> Optional[User]:
 @with_dbenv()
 async def create_user(
     user: User,
-    current_user: User = Depends(
+    current_user: User = Depends(  # pylint: disable=unused-argument
         get_current_active_user
-    ),  # pylint: disable=unused-argument
+    ),
 ) -> User:
     """Create new AiiDA user."""
     orm_user = orm.User(**user.dict(exclude_unset=True)).store()

examples/daemon_management/script.py

@@ -44,8 +44,12 @@ def request(
     else:
         headers = {}
 
-    response = requests.request(
-        method, f"{BASE_URL}/{url}", json=json, data=data, headers=headers
+    response = requests.request(  # pylint: disable=missing-timeout
+        method,
+        f"{BASE_URL}/{url}",
+        json=json,
+        data=data,
+        headers=headers,
     )
 
     try:
@@ -62,8 +66,7 @@ def request(
             click.echo(error["message"])
 
         return None
-    else:
-        return response.json()
+    return response.json()
 
 
 def authenticate(

examples/process_management/script.py

@@ -45,7 +45,7 @@ def request(
     else:
         headers = {}
 
-    response = requests.request(
+    response = requests.request(  # pylint: disable=missing-timeout
         method, f"{BASE_URL}/{url}", json=json, data=data, headers=headers
     )
 
@@ -63,8 +63,7 @@ def request(
             click.echo(error["message"])
 
         return None
-    else:
-        return response.json()
+    return response.json()
 
 
 def authenticate(

examples/submit_quantumespresso_pw/script.py

@@ -44,7 +44,7 @@ def request(
     else:
         headers = {}
 
-    response = requests.request(
+    response = requests.request(  # pylint: disable=missing-timeout
         method, f"{BASE_URL}/{url}", json=json, data=data, headers=headers
     )
 
@@ -62,8 +62,7 @@ def request(
             click.echo(error["message"])
 
         return None
-    else:
-        return response.json()
+    return response.json()
 
 
 def authenticate(

pyproject.toml

@@ -55,6 +55,7 @@ pre-commit = [
     'pre-commit~=2.12'
 ]
 testing = [
+    'aiida-restapi[auth]',
     'pgtest~=1.3.1',
     'wheel~=0.31',
     'coverage',
@@ -130,12 +131,19 @@ warn_untyped_fields = false
 [tool.tox]
 legacy_tox_ini = """
 [tox]
-envlist = py38
+envlist =
+    py38
+    py311
 
 [testenv]
 usedevelop = true
 
-[testenv:py{38,39,310}]
+[testenv:py{38,39,310,311}]
+description =
+    py38: Installs test dependencies and runs tests using python 3.8
+    py39: Installs test dependencies and runs tests using python 3.9
+    py310: Installs test dependencies and runs tests using python 3.10
+    py311: Installs test dependencies and runs tests using python 3.11
 extras =
     auth
     testing
@@ -149,18 +157,25 @@ commands = pytest {posargs}
 # now you can run `tox -e verdi quicksetup`, then `tox -e serve`
 
 [testenv:verdi]
+description =
+    Runs a verdi command within a tox environment that sets the AIIDA_PATH
 setenv =
     AIIDA_PATH = {toxinidir}/.tox/.aiida
 commands = verdi {posargs}
 
 [testenv:serve]
+description =
+    Start the web API server within a tox environment that sets the AIIDA_PATH
 extras =
     auth
 setenv =
     AIIDA_PATH = {toxinidir}/.tox/.aiida
 commands = uvicorn aiida_restapi:app {posargs:--reload}
 
 [testenv:docs-{update,clean}]
+description =
+    docs-clean: Build the documentation (remove any existing build)
+    docs-update: Build the documentation (modify any existing build)
 extras =
     auth
     docs

tests/test_computers.py

@@ -33,7 +33,7 @@ def test_get_single_computers(
     """Test retrieving a single computer."""
 
     for comp_id in default_computers:
-        response = client.get("/computers/{}".format(comp_id))
+        response = client.get(f"/computers/{comp_id}")
         assert response.status_code == 200
 
 

tests/test_groups.py

@@ -30,7 +30,7 @@ def test_get_single_group(default_groups, client):  # pylint: disable=unused-arg
     """Test retrieving a single group."""
 
     for group_id in default_groups:
-        response = client.get("/groups/{}".format(group_id))
+        response = client.get(f"/groups/{group_id}")
         assert response.status_code == 200
 
 

tests/test_nodes.py

@@ -31,7 +31,7 @@ def test_get_single_nodes(default_nodes, client):  # pylint: disable=unused-argu
     """Test retrieving a single nodes."""
 
     for nodes_id in default_nodes:
-        response = client.get("/nodes/{}".format(nodes_id))
+        response = client.get(f"/nodes/{nodes_id}")
         assert response.status_code == 200
 
 
@@ -299,7 +299,7 @@ def test_create_bool_with_extra(
         },
     )
 
-    check_response = client.get("/nodes/{}".format(response.json()["id"]))
+    check_response = client.get(f"/nodes/{response.json()['id']}")
 
     assert check_response.status_code == 200, response.content
     assert check_response.json()["extras"]["extra_one"] == "value_1"

tests/test_processes.py

@@ -40,7 +40,7 @@ def test_get_single_processes(
 ):  # pylint: disable=unused-argument
     """Test retrieving a single processes."""
     for proc_id in example_processes:
-        response = client.get("/processes/{}".format(proc_id))
+        response = client.get(f"/processes/{proc_id}")
         assert response.status_code == 200
 
 

tests/test_users.py

@@ -5,7 +5,7 @@
 def test_get_single_user(default_users, client):  # pylint: disable=unused-argument
     """Test retrieving a single user."""
     for user_id in default_users:
-        response = client.get("/users/{}".format(user_id))
+        response = client.get(f"/users/{user_id}")
         assert response.status_code == 200