Add CodeSpell to Actions, and fix some spellings

.codespellrc

@@ -0,0 +1,25 @@
+[codespell]
+
+skip = *.git,
+       ./.vscode,
+       *.pyc,
+       __pycache__,
+       ./build,
+       ./dist,
+       ./docs/_build,
+       ./htmlcov,
+       ./src/openflexure_microscope_server/static,
+       .venv,
+       *.egg-info,
+       report.xml,
+       dev-requirements.txt,
+       coverage.yml,
+       coverage.lcov,
+       coverage.xml,
+       LICENSE,
+
+# The regex allows it to also check snake case strings. This stops codespell doing
+# autocorrection. If a lot of changes are needed this can be commented out.
+# Having this does mean that contractions in variable names will be marked as spelt
+# incorrectly.
+regex = [a-zA-Z0-9\-'’]+

.github/workflows/test.yml

@@ -54,6 +54,9 @@ jobs:
       - name: Format with Ruff
         run: ruff format --check .
 
+      - name: Check spelling
+        run: codespell .
+
       - name: Lint with Flake8 (for docstrings)
         if: ${{ contains('3.12,3.13', matrix.python) }}
         # Flake8 crashes on Python < 3.12, so we exclude those versions.

dev-requirements.txt

@@ -32,12 +32,8 @@ click==8.2.1
     #   rich-toolkit
     #   typer
     #   uvicorn
-colorama==0.4.6
-    # via
-    #   click
-    #   pytest
-    #   sphinx
-    #   uvicorn
+codespell==2.4.1
+    # via labthings-fastapi (pyproject.toml)
 coverage==7.9.2
     # via pytest-cov
 dnspython==2.7.0
@@ -53,10 +49,6 @@ email-validator==2.2.0
     # via
     #   fastapi
     #   pydantic
-exceptiongroup==1.3.0
-    # via
-    #   anyio
-    #   pytest
 fastapi==0.116.1
     # via labthings-fastapi (pyproject.toml)
 fastapi-cli==0.0.8
@@ -247,14 +239,6 @@ sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
 starlette==0.47.1
     # via fastapi
-tomli==2.2.1
-    # via
-    #   coverage
-    #   flake8-pyproject
-    #   mypy
-    #   pydoclint
-    #   pytest
-    #   sphinx
 typer==0.16.0
     # via
     #   fastapi-cli
@@ -265,20 +249,16 @@ typing-extensions==4.14.1
     # via
     #   labthings-fastapi (pyproject.toml)
     #   anyio
-    #   astroid
-    #   exceptiongroup
     #   fastapi
     #   mypy
     #   pydantic
     #   pydantic-core
     #   pydantic-extra-types
     #   referencing
-    #   rich
     #   rich-toolkit
     #   starlette
     #   typer
     #   typing-inspection
-    #   uvicorn
 typing-inspection==0.4.1
     # via pydantic-settings
 ujson==5.10.0
@@ -292,6 +272,8 @@ uvicorn==0.35.0
     #   fastapi
     #   fastapi-cli
     #   fastapi-cloud-cli
+uvloop==0.21.0
+    # via uvicorn
 watchfiles==1.1.0
     # via uvicorn
 websockets==15.0.1

docs/source/quickstart/quickstart.rst

@@ -36,7 +36,7 @@ You can also interact with it from another Python instance, for example by runni
 .. literalinclude:: counter_client.py
     :language: python
 
-It's best to write ``Thing`` subclasses in Python packages that can be imported. This makes them easier to re-use and distribute, and also allows us to run a LabThings server from the command line, configured by a configuration file. An example config file is below:
+It's best to write ``Thing`` subclasses in Python packages that can be imported. This makes them easier to reuse and distribute, and also allows us to run a LabThings server from the command line, configured by a configuration file. An example config file is below:
 
 .. literalinclude:: example_config.json
     :language: JSON

docs/source/quickstart/quickstart_example.sh

@@ -1,4 +1,4 @@
-echo "Setting up environemnt"
+echo "Setting up environment"
 # BEGIN venv
 python -m venv .venv --prompt labthings
 source .venv/bin/activate  # or .venv/Scripts/activate on Windows

docs/source/wot_core_concepts.rst

@@ -39,7 +39,7 @@ Events
 
 An event "describes an event source that pushes data asynchronously from the Thing to the Consumer. Here not state, but state transitions (i.e., events) are communicated. Events MAY be triggered through conditions that are not exposed as Properties."
 
-Common examples are notifying clients when a Property is changed, or when an Action starts or finishes. However, Thing developers can introduce new Events such as warnings, status messages, and logs. For example, a device may emit an events when the internal temperature gets too high, or when an interlock is tripped. This Event can then be pushed to both users AND other Things, allowing automtic response to external conditions.
+Common examples are notifying clients when a Property is changed, or when an Action starts or finishes. However, Thing developers can introduce new Events such as warnings, status messages, and logs. For example, a device may emit an events when the internal temperature gets too high, or when an interlock is tripped. This Event can then be pushed to both users AND other Things, allowing automatic response to external conditions.
 
 A good example of this might be having Things automatically pause data-acquisition Actions upon detection of an overheat or interlock Event from another Thing. Events are not currently implemented in `labthings-fastapi`, but are planned for future releases.
 

pyproject.toml

@@ -40,6 +40,7 @@ dev = [
   "sphinx-rtd-theme",
   "sphinx>=7.2",
   "sphinx-autoapi",
+  "codespell",
 ]
 
 [project.urls]

src/labthings_fastapi/client/in_server.py

@@ -117,9 +117,9 @@
         obj: Optional[DirectThingClient] = None,
         _objtype: Optional[type[DirectThingClient]] = None,
     ):
         if obj is None:
             return self
         return getattr(obj._wrapped_thing, self.name)
 
     def __set__(self, obj: DirectThingClient, value: Any):
         setattr(obj._wrapped_thing, self.name, value)
@@ -143,7 +143,7 @@
     dictionary. This makes the assumption that, if a name is reused, it is
     reused for the same dependency.
 
-    When names are re-used, we check if the values match. If not, this
+    When names are reused, we check if the values match. If not, this
     exception is raised.
     """
 
@@ -293,7 +293,7 @@
         else:
             for affordance in ["property", "action", "event"]:
                 if hasattr(item, f"{affordance}_affordance"):
                     logging.warning(
                         f"DirectThingClient doesn't support custom affordances, "
                         f"ignoring {name}"
                     )

src/labthings_fastapi/decorators/__init__.py

@@ -106,7 +106,7 @@ def thing_action(
     :param \**kwargs: Keyword arguments are passed to the constructor
         of `.ActionDescriptor`.
 
-    :return: Whether used with or without argumnts, the result is that
+    :return: Whether used with or without arguments, the result is that
         the method is wrapped in an `.ActionDescriptor`, so it can be
         called as usual, but will also be exposed over HTTP.
     """

src/labthings_fastapi/dependencies/__init__.py

@@ -4,7 +4,7 @@
 example invoking actions or accessing properties on other `.Thing`\ s or
 calling methods provided by the server.
 
-:ref:`dependencies` are a `FastAPI concept`_ that is re-used in LabThings to allow
+:ref:`dependencies` are a `FastAPI concept`_ that is reused in LabThings to allow
 :ref:`actions` to request resources in a way that plays nicely with type hints
 and is easy to intercept for testing.
 

src/labthings_fastapi/dependencies/blocking_portal.py

@@ -39,16 +39,16 @@
     :param request: The `fastapi.Request` object, supplied by the :ref:`dependencies`
         mechanism.
 
-    :return: the `anyio.from_thread.BlockingPortal` allowing access to te
+    :return: the `anyio.from_thread.BlockingPortal` allowing access to the
         `.ThingServer`\ 's event loop.
     """
     portal = find_thing_server(request.app).blocking_portal
     assert portal is not None, RuntimeError(
         "Could not get the blocking portal from the server."
         # This should never happen, as the blocking portal is added
         # and removed in `.ThingServer.lifecycle`.
     )
     return portal
 
 
 BlockingPortal = Annotated[

src/labthings_fastapi/descriptors/action.py

@@ -123,11 +123,11 @@
 
     @overload
     def __get__(self, obj: Literal[None], type=None) -> ActionDescriptor:  # noqa: D105
         ...
 
     @overload
     def __get__(self, obj: Thing, type=None) -> Callable:  # noqa: D105
         ...
 
     def __get__(
         self, obj: Optional[Thing], type: Optional[type[Thing]] = None
@@ -207,20 +207,20 @@
         try:
             runner = get_blocking_portal(obj)
             if not runner:
                 thing_name = obj.__class__.__name__
                 msg = (
                     f"Cannot emit action changed event. Is {thing_name} connected to "
                     "a running server?"
                 )
                 raise NotConnectedToServerError(msg)
             runner.start_task_soon(
                 self.emit_changed_event_async,
                 obj,
                 status,
             )
         except Exception:
             # TODO: in the unit test, the get_blocking_portal throws exception
             ...
 
     async def emit_changed_event_async(self, obj: Thing, value: Any) -> None:
         """Notify subscribers that the action status has changed.
@@ -249,7 +249,7 @@
 
         This function creates two functions to handle ``GET`` and ``POST``
         requests to the action's endpoint, and adds them to the `fastapi.FastAPI`
-        aplication.
+        application.
 
         :param app: The `fastapi.FastAPI` app to add the endpoint to.
         :param thing: The `.Thing` to which the action is attached. Bear in

src/labthings_fastapi/descriptors/property.py

@@ -208,7 +208,7 @@ def _observers_set(self, obj: Thing):
     def emit_changed_event(self, obj: Thing, value: Any) -> None:
         """Notify subscribers that the property has changed.
 
-        This function is run when properties are upadated. It must be run from
+        This function is run when properties are updated. It must be run from
         within a thread. This could be the `Invocation` thread of a running action, or
         the property should be updated over via a client/http. It must be run from a
         thread as it is communicating with the event loop via an `asyncio` blocking

src/labthings_fastapi/example_things/__init__.py

@@ -119,7 +119,7 @@ def action_with_only_kwargs(self, **kwargs: dict) -> None:
 
 
 class ThingWithBrokenAffordances(Thing):
-    """A Thing that raises exceptions in actions/properites."""
+    """A Thing that raises exceptions in actions/properties."""
 
     @thing_action
     def broken_action(self):

src/labthings_fastapi/outputs/blob.py

@@ -304,7 +304,7 @@ class Blob(BaseModel):
     separate HTTP request.
 
     `.Blob` objects created by a `.ThingClient` contain a URL pointing to the
-    data, which will be downloaded when it is requred.
+    data, which will be downloaded when it is required.
 
     `.Blob` objects that store their data in a file or in memory will have the
     ``href`` attribute set to the special value `blob://local`.
@@ -457,7 +457,7 @@ def content(self) -> bytes:
         this property to download the output.
 
         This property is read-only. You should also only read it once, as no
-        guarantees are given about cacheing - reading it many times risks
+        guarantees are given about caching - reading it many times risks
         reading the file from disk many times, or re-downloading an artifact.
 
         :return: a `bytes` object containing the data.
@@ -714,7 +714,7 @@ async def blob_serialisation_context_manager(
 
     In order to serialise a `.Blob` to a JSON-serialisable dictionary, we must
     add it to the `.BlobDataManager` and use that to generate a URL. This
-    requres that the serialisation code (which may be nested deep within a
+    requires that the serialisation code (which may be nested deep within a
     `pydantic.BaseModel`) has access to the `.BlobDataManager` and also the
     `fastapi.Request.url_for` method. At time of writing, there was not an
     obvious way to pass these functions in to the serialisation code.

src/labthings_fastapi/outputs/mjpeg_stream.py

@@ -209,7 +209,7 @@ async def buffer_for_reading(self, i: int) -> AsyncIterator[bytes]:
         after any ``with`` statement has finished).
 
         Using a context manager is intended to allow future versions of this
-        code to manage access to the ringbuffer (e.g. allowing buffer re-use).
+        code to manage access to the ringbuffer (e.g. allowing buffer reuse).
         Currently, buffers are always created as fresh `bytes` objects, so
         this context manager does not provide additional functionality
         over `.MJPEGStream.ringbuffer_entry`.

src/labthings_fastapi/server/fallback.py

@@ -50,7 +50,7 @@ def __init__(self, *args: Any, **kwargs: Any) -> None:
     </style>
 </head>
 <body>
-    <h1>LabThings Could't Load</h1>
+    <h1>LabThings Couldn't Load</h1>
     <p>Something went wrong when setting up your LabThings server.</p>
     <p>Please check your configuration and try again.</p>
     <p>More details may be shown below:</p>

src/labthings_fastapi/thing.py

@@ -258,7 +258,7 @@ def thing_state(self) -> Mapping:
         it requires calls e.g. to a serial instrument, bear in mind it may be called
         quite often and shouldn't take too long.
 
-        Some measure of cacheing here is a nice aim for the future, but not yet
+        Some measure of caching here is a nice aim for the future, but not yet
         implemented.
         """
         if self._labthings_thing_state is None:

src/labthings_fastapi/thing_description/__init__.py

@@ -42,7 +42,7 @@ def is_a_reference(d: JSONSchema) -> bool:
 def look_up_reference(reference: str, d: JSONSchema) -> JSONSchema:
     """Look up a reference in a JSONSchema.
 
-    JSONSchema allows references, where chunks of JSON may be re-used.
+    JSONSchema allows references, where chunks of JSON may be reused.
     Thing Description does not allow references, so we need to resolve
     them and paste them in-line.
 
@@ -93,7 +93,7 @@ def is_an_object(d: JSONSchema) -> bool:
 def convert_object(d: JSONSchema) -> JSONSchema:
     """Convert an object from JSONSchema to Thing Description.
 
-    Convert JSONSchema objets to Thing Description datatypes.
+    Convert JSONSchema objects to Thing Description datatypes.
 
     Currently, this deletes the ``additionalProperties`` keyword, which is
     not supported by Thing Description.

tests/test_example_thing.py

@@ -48,12 +48,12 @@ def test_thing_with_broken_affordances():
         thing.broken_property()
 
 
-def test_thing_that_cant_instantiate():
+def test_thing_that_cannot_instantiate():
     with pytest.raises(Exception):
         ThingThatCantInstantiate()
 
 
-def test_thing_that_cant_start():
+def test_thing_that_cannot_start():
     thing = ThingThatCantStart()
     assert isinstance(thing, ThingThatCantStart)
     with pytest.raises(Exception):

tests/test_fallback.py

@@ -54,11 +54,11 @@ def test_fallback_with_server():
 
 
 def test_fallback_with_log():
-    app.log_history = "Fake log conetent"
+    app.log_history = "Fake log content"
     with TestClient(app) as client:
         response = client.get("/")
         html = response.text
         assert "Something went wrong" in html
         assert "No logging info available" not in html
         assert "<p>Logging info</p>" in html
-        assert "Fake log conetent" in html
+        assert "Fake log content" in html

tests/test_server_cli.py

@@ -136,7 +136,7 @@ def test_invalid_thing():
 def test_fallback():
     """test the fallback option
 
-    startd a dummy server with an error page -
+    started a dummy server with an error page -
     it terminates once the server starts.
     """
     config_json = json.dumps(
@@ -155,7 +155,7 @@ def test_invalid_config():
         check_serve_from_cli(["-c", "non_existent_file.json"])
 
 
-def test_thing_that_cant_start():
+def test_thing_that_cannot_start():
     """Check it fails for a thing that can't start"""
     config_json = json.dumps(
         {