Fix typos found by codespell (#676)

.github/workflows/pr-linter.yml

@@ -37,9 +37,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 black
+        pip install flake8 black codespell
     - name: Check code formatting
       run: black . --check
+    - name: Check spelling
+      run: codespell -L halp,ot,pres -d pynetdicom
     - name: Check for syntax errors
       run: python -m flake8 --select=E901,E999,F821,F822,F823 ${{ steps.pydiff.outputs.pyfiles }} --ignore F821
     - name: Check for style warnings

build_tools/circle/push_doc.sh

@@ -3,7 +3,7 @@
 # This script is meant to be called in the "deploy" step defined
 # in .circleci/config.yml. See https://circleci.com/docs/2.0 for more details.
 
-# We have three possibily workflows:
+# We have three possible workflows:
 #   If the git branch is 'master' then we want to commit and merge the dev/
 #       docs on gh-pages
 #   If the git branch is [0-9].[0.9].X (i.e. 0.9.X, 1.0.X, 1.2.X, 41.21.X) then

docs/apps/echoscu.rst

@@ -20,7 +20,7 @@ The source code for the application can be found `here
 Usage
 =====
 
-The following example shows what happens when it's succesfully run on
+The following example shows what happens when it is successfully run on
 an SCP at IP ``127.0.0.1`` and listen port ``11112`` that supports the
 Verification service:
 

docs/apps/findscu.rst

@@ -23,7 +23,7 @@ The source code for the application can be found `here
 Usage
 =====
 
-The following example shows what happens when it is succesfully run on
+The following example shows what happens when it is successfully run on
 an SCP at IP ``127.0.0.1`` and listen port ``11112`` that supports the
 Query/Retrieve (Find) service:
 

docs/apps/getscu.rst

@@ -23,7 +23,7 @@ The source code for the application can be found `here
 Usage
 =====
 
-The following example shows what happens when it is succesfully run on
+The following example shows what happens when it is successfully run on
 an SCP at IP ``127.0.0.1`` and listen port ``11112`` that supports the
 Query/Retrieve (Get) service:
 

docs/apps/movescu.rst

@@ -25,7 +25,7 @@ The source code for the application can be found `here
 Usage
 =====
 
-The following example shows what happens when it is succesfully run on
+The following example shows what happens when it is successfully run on
 an SCP at IP ``127.0.0.1`` and listen port ``11112`` that supports the
 Query/Retrieve service with the default *Move Destination* AE title
 ``STORESCP``:

docs/apps/storescu.rst

@@ -19,7 +19,7 @@ The source code for the application can be found `here
 Usage
 =====
 
-The following example shows what happens when it is succesfully run on
+The following example shows what happens when it is successfully run on
 an SCP at IP ``127.0.0.1`` and listen port ``11112`` that supports the *Storage
 Service*:
 

docs/examples/mpps.rst

@@ -125,7 +125,7 @@ MPPS - Set SCU
 Once the MPPS SOP Instance has successfully been created, the modality can send
 one or more N-SET requests to the MPPS SCP in order to update the attributes
 of the SOP Instance. When the procedure has been completed a final N-SET
-request is sent containing a *Modification List* with an (0040,0252) *Peformed
+request is sent containing a *Modification List* with an (0040,0252) *Performed
 Procedure Step Status* of ``"COMPLETED"``.
 
 .. code-block:: python

docs/examples/print.rst

@@ -38,7 +38,7 @@ Which utilise the following SOP Classes:
   of the printer.
 
 There are also the following SOP Classes that are not included under
-the Meta Print Mangement SOP Classes and which may optionally be supported:
+the Meta Print Management SOP Classes and which may optionally be supported:
 
 * *Basic Annotation Box SOP Class* used with N-SET to describe the presentation
   of an annotation on a film.

docs/examples/qr_find.rst

@@ -121,7 +121,7 @@ to see the requirements for the ``evt.EVT_C_FIND`` handler.
                         inst for inst in instances if inst.PatientName == ds.PatientName
                     ]
 
-                # Skip the other possibile values...
+                # Skip the other possible values...
 
             # Skip the other possible attributes...
 

docs/examples/qr_get.rst

@@ -39,7 +39,7 @@ the SERIES level.
 
 One extra step needed with the Query/Retrieve (Get) Service is
 that during association we need to include a :class:`SCP/SCU Role Selection
-Negotation <pynetdicom.pdu_items.SCP_SCU_RoleSelectionSubItem>`
+Negotiation <pynetdicom.pdu_items.SCP_SCU_RoleSelectionSubItem>`
 item for each of the supported presentation contexts that may be used with
 the C-STORE requests.
 

docs/service_classes/rt_machine.rst

@@ -6,7 +6,7 @@ The :dcm:`RT Machine Verification Service Class<part04/chapter_DD.html>`
 defines a service that uses the DIMSE N-CREATE, N-SET, N-DELETE, N-ACTION,
 N-EVENT-REPORT and N-GET services to
 facilitate the independent verification of geometric and dosimetric settings
-on a radiation delivery system priot to delivery of treatment.
+on a radiation delivery system prior to delivery of treatment.
 
 .. _rt_machine_sops:
 

pynetdicom/acse.py

@@ -162,7 +162,7 @@ def _check_sop_class_extended(self) -> List[SOPClassExtendedNegotiation]:
 
         if not isinstance(user_response, (type(None), dict)):
             LOGGER.error(
-                "Invalid type returned by handler bount to " "'evt.EVT_SOP_EXTENDED'"
+                "Invalid type returned by handler bound to " "'evt.EVT_SOP_EXTENDED'"
             )
             user_response = {}
 
@@ -428,7 +428,7 @@ def _negotiate_as_acceptor(self) -> None:
         # Callbacks/Logging
         evt.trigger(self.assoc, evt.EVT_ACCEPTED, {})
 
-        # Assocation established OK
+        # Association established OK
         self.assoc.is_established = True
         evt.trigger(self.assoc, evt.EVT_ESTABLISHED, {})
 

pynetdicom/association.py

@@ -780,8 +780,8 @@ def unbind(self, event: evt.EventType, handler: Callable) -> None:
     def _c_store_scp(self, req: C_STORE) -> None:
         """A C-STORE SCP implementation.
 
-        Handles C-STORE requests from the peer over the same assocation as the
-        local AE sent a C-MOVE or C-GET request.
+        Handles C-STORE requests from the peer over the same association as
+        the local AE sent a C-MOVE or C-GET request.
 
         Must always send a C-STORE response back to the peer.
 
@@ -1422,7 +1422,7 @@ def send_c_get(
             req.Identifier = BytesIO(bytestream)
         else:
             LOGGER.error("Failed to encode the supplied Identifier dataset")
-            raise ValueError("Failed to encode the supplied Identifer dataset")
+            raise ValueError("Failed to encode the supplied Identifier dataset")
 
         LOGGER.info(f"Sending Get Request: MsgID {msg_id}")
         LOGGER.info("")
@@ -1526,7 +1526,7 @@ def send_c_move(
 
             *Query/Retrieve Service, Hanging Protocol Query/Retrieve Service,
             Defined Procedure Protocol Query/Retrieve Service, Color Palette
-            Query/Retrieve Service* , *Implant Template Query/Retreive
+            Query/Retrieve Service* , *Implant Template Query/Retrieve
             Service* and *Protocol Approval Query/Retrieve Service*
             specific (DICOM Standard, Part 4, Annexes C, U, Y, X, BB and HH):
 
@@ -1993,7 +1993,7 @@ def _wrap_find_responses(
                 yield status, identifier
                 continue
 
-            # Only reach this point if status is Sucess, Warning, Failure
+            # Only reach this point if status is Success, Warning, Failure
             #   or Cancel
             self._reactor_checkpoint.set()
             yield status, identifier
@@ -2133,7 +2133,7 @@ def _wrap_get_move_responses(
                         LOGGER.exception(exc)
                         identifier = None
 
-            # Only reach this point if status is Sucess, Warning, Failure
+            # Only reach this point if status is Success, Warning, Failure
             #   or Cancel
             self._reactor_checkpoint.set()
             yield status, identifier

pynetdicom/dimse_messages.py

@@ -772,7 +772,7 @@ def primitive_to_message(self, primitive: DimsePrimitiveType) -> None:
                 else:
                     del self.command_set[elem.tag]
 
-        # Theres a one-to-one relationship in the _MESSAGE_TYPES dict, so
+        # There's a one-to-one relationship in the _MESSAGE_TYPES dict, so
         #   invert it for convenience
         rev_type = {vv[0]: kk for kk, vv in _MESSAGE_TYPES.items()}
         self.command_set.CommandField = rev_type[cls_type_name]

pynetdicom/dul.py

@@ -184,7 +184,7 @@ def _is_transport_event(self) -> bool:
             return True
 
         # By this point the connection should be established
-        #   If theres incoming data on the connection then check the PDU
+        #   If there's incoming data on the connection then check the PDU
         #   type
         # Fix for #28 - caused by peer disconnecting before run loop is
         #   stopped by assoc.release()

pynetdicom/events.py

@@ -997,7 +997,7 @@ def _sop_extended_handler(event: Event) -> Dict[UID, bytes]:
 
 
 def _user_identity_handler(event: Event) -> Tuple[bool, Optional[bytes]]:
-    """Default hander for when a user identity negotiation item is included
+    """Default handler for when a user identity negotiation item is included
     with the association request.
 
     See _handlers.doc_handler_userid for detailed documentation.

pynetdicom/fsm.py

@@ -1005,9 +1005,10 @@ def AA_8(dul: "DULServiceProvider") -> str:
 
 
 # Finite State Machine
-# Machine State Defintions, PS3.8 Tables 9-1, 9-2, 9-3, 9-4, 9-5
+# Machine State Definitions, PS3.8 Tables 9-1, 9-2, 9-3, 9-4, 9-5
 # pylint: disable=line-too-long
 STATES = {
+    # No association
     "Sta1": "Idle",
     # Association establishment
     "Sta2": "Transport connection open (Awaiting A-ASSOCIATE-RQ PDU)",
@@ -1023,11 +1024,13 @@ def AA_8(dul: "DULServiceProvider") -> str:
     "Sta10": "Release collision acceptor side; awaiting A-RELEASE-RP PDU",
     "Sta11": "Release collision requestor side; awaiting A-RELEASE-RP PDU",
     "Sta12": "Release collision acceptor side; awaiting A-RELEASE response primitive (from local user)",
+    # Waiting for transport connection close
     "Sta13": "Awaiting Transport Connection Close Indication (Association no longer exists)",
 }
 
 # State Machine Action Definitions, PS3.8 Tables 9-6, 9-7, 9-8, 9-9
 ACTIONS = {
+    # Association establishment related actions
     "AE-1": (
         "Issue TRANSPORT CONNECT request primitive to local transport service",
         AE_1,
@@ -1058,7 +1061,7 @@ def AA_8(dul: "DULServiceProvider") -> str:
     # Data transfer related actions
     "DT-1": ("Send P-DATA-TF PDU", DT_1, "Sta6"),
     "DT-2": ("Send P-DATA indication primitive", DT_2, "Sta6"),
-    # Assocation Release related actions
+    # Association Release related actions
     "AR-1": ("Send A-RELEASE-RQ PDU", AR_1, "Sta7"),
     "AR-2": ("Issue A-RELEASE indication primitive", AR_2, "Sta8"),
     "AR-3": (
@@ -1114,7 +1117,7 @@ def AA_8(dul: "DULServiceProvider") -> str:
     "Evt3": "A-ASSOCIATE-AC PDU (received on transport connection)",
     "Evt4": "A-ASSOCIATE-RJ PDU (received on transport connection)",
     "Evt5": "Transport connection indication (local transport service)",
-    "Evt6": "A-ASSOCIATE-RQ PDU (on tranport connection)",
+    "Evt6": "A-ASSOCIATE-RQ PDU (on transport connection)",
     "Evt7": "A-ASSOCIATE response primitive (accept)",
     "Evt8": "A-ASSOCIATE response primitive (reject)",
     "Evt9": "P-DATA request primitive",

pynetdicom/pdu_items.py

@@ -2364,7 +2364,7 @@ def uid_length(self) -> int:
 class SOPClassExtendedNegotiationSubItem(PDUItem):
     """A SOP Class Extended Negotiation Sub-item.
 
-    A SOP Class Extended Negotation Sub-item allows peer Application Entities
+    A SOP Class Extended Negotiation Sub-item allows peer Application Entities
     to exchange application information defined by specific Service Class
     specifications.
 
@@ -2565,7 +2565,7 @@ def uid(self) -> Optional[UID]:
         return self.sop_class_uid
 
 
-# Overriden _generate_items, _wrap_generate_items
+# Overridden _generate_items, _wrap_generate_items
 class SOPClassCommonExtendedNegotiationSubItem(PDUItem):
     """A SOP Class Common Extended Negotiation Sub-item.
 
@@ -3356,7 +3356,7 @@ def __str__(self) -> str:
 
 
 # P-DATA-TF Item
-# Overriden item_type
+# Overridden item_type
 class PresentationDataValueItem(PDUItem):
     """A Presentation Data Value Item.
 

pynetdicom/pdu_primitives.py

@@ -1,5 +1,5 @@
 """
-Implementaion of the service parameter primitives.
+Implementation of the service parameter primitives.
 """
 import logging
 from typing import Optional, List, Any, Union, Tuple, cast, Type

pynetdicom/service_class.py

@@ -296,7 +296,7 @@ def _c_find_scp(self, req: C_FIND, context: "PresentationContext") -> None:
             else:
                 (rsp_status, dataset) = cast(UserReturnType, result)
 
-            # Event hander has aborted or released
+            # Event handler has aborted or released
             if not self.assoc.is_established:
                 return
 
@@ -362,7 +362,7 @@ def _c_find_scp(self, req: C_FIND, context: "PresentationContext") -> None:
 
                 self.dimse.send_msg(rsp, cx_id)
 
-        # Event hander has aborted or released
+        # Event handler has aborted or released
         if not self.assoc.is_established:
             return
 
@@ -1422,7 +1422,7 @@ def SCP(self, req: C_ECHO, context: "PresentationContext") -> None:
                 evt.EVT_C_ECHO,
                 {"request": req, "context": context.as_tuple},
             )
-            # Event hander has aborted or released
+            # Event handler has aborted or released
             if not self.assoc.is_established:
                 return
 
@@ -1714,7 +1714,7 @@ def _add_failed_instance(ds: Dataset) -> None:
             else:
                 (rsp_status, dataset) = cast(UserReturnType, result)
 
-            # Event hander has aborted or released - after any yields
+            # Event handler has aborted or released - after any yields
             if not self.assoc.is_established:
                 return
 
@@ -1927,7 +1927,7 @@ def _add_failed_instance(ds: Dataset) -> None:
                 rsp.NumberOfCompletedSuboperations = store_results[3]
                 self.dimse.send_msg(rsp, cx_id)
 
-        # Event hander has aborted or released - prevent final message
+        # Event handler has aborted or released - prevent final message
         if not self.assoc.is_established:
             return
 
@@ -2138,7 +2138,7 @@ def _add_failed_instance(ds: Dataset) -> None:
             else:
                 (rsp_status, dataset) = cast(UserReturnType, result)
 
-            # Event hander has aborted or released - during any status yields
+            # Event handler has aborted or released - during any status yields
             if not self.assoc.is_established:
                 store_assoc.release()
                 return
@@ -2335,7 +2335,7 @@ def _add_failed_instance(ds: Dataset) -> None:
 
         store_assoc.release()
 
-        # Event hander has aborted or released - after any yields
+        # Event handler has aborted or released - after any yields
         if not self.assoc.is_established:
             return
 
@@ -2495,7 +2495,7 @@ def SCP(self, req: C_FIND, context: "PresentationContext") -> None:
             responses = cast(Iterator[UserReturnType], responses)
             (rsp_status, rsp_identifier) = next(responses)
         except (StopIteration, TypeError):
-            # Event hander has aborted or released - before any yields
+            # Event handler has aborted or released - before any yields
             if not self.assoc.is_established:
                 return
 
@@ -2512,7 +2512,7 @@ def SCP(self, req: C_FIND, context: "PresentationContext") -> None:
             self.dimse.send_msg(rsp, cx_id)
             return
 
-        # Event hander has aborted or released
+        # Event handler has aborted or released
         if not self.assoc.is_established:
             return