Explicitly specify encoding

The update to pylint means we were failing because open()
doesn't specify the encoding everywhere.  I have now specified utf-8
everywhere.  This was patchy before, and is default behaviour on the
Pi.  There's a slim chance it will cause some issues on Windows, but
that shouldn't affect anyone outside the developers.

I've also ignored a couple of new spurious warnings, and explicitly
ignored some unused variables.

openflexure_microscope/api/app.py

@@ -261,10 +261,10 @@ def generate_openapi():
     if fname.endswith(".json"):
         import json
 
-        with open(fname, "w") as fd:
+        with open(fname, "w", encoding="utf-8") as fd:
             json.dump(labthing.spec.to_dict(), fd)
     else:
-        with open(fname, "w") as fd:
+        with open(fname, "w", encoding="utf-8") as fd:
             fd.write(labthing.spec.to_yaml())
 
 

openflexure_microscope/api/default_extensions/autofocus.py

@@ -245,7 +245,7 @@ def extension_action(args=None):
                 # Run the action
                 return func(self.extension, **arguments)
 
-            def get(self, *args, **kwargs):  # pylint: disable=useless-super-delegation
+            def get(self, *args, **kwargs):  # pylint: disable=useless-super-delegation,arguments-differ
                 # Explicitly wrap the `get` method to allow us to add a docstring
                 return super().get(*args, **kwargs)
 

openflexure_microscope/api/default_extensions/camera_stage_mapping.py

@@ -200,7 +200,7 @@ class CSMExtension(BaseExtension):
             "linear_calibration_y": cal_y,
         }
 
-        with open(CSM_DATAFILE_PATH, "w") as f:
+        with open(CSM_DATAFILE_PATH, "w", encoding="utf-8") as f:
             json.dump(data, f, cls=JSONEncoder)
 
         return data

openflexure_microscope/api/utilities/__init__.py

@@ -81,7 +81,7 @@ def init_default_extensions(extension_dir: str):
         create_file(default_ext_path)
 
         logging.info("Populating %s...", (default_ext_path))
-        with open(default_ext_path, "w") as outfile:
+        with open(default_ext_path, "w", encoding="utf-8") as outfile:
             outfile.write(_DEFAULT_EXTENSION_INIT)
 
 

openflexure_microscope/camera/base.py

@@ -54,7 +54,7 @@ class FrameStream(io.BytesIO):
         t: Optional[Type[BaseException]],
         value: Optional[BaseException],
         traceback: Optional[TracebackType],
-    ) -> Optional[bool]:
+    ) -> None:
         self.stop_tracking()
         return super().__exit__(t, value, traceback)
 

openflexure_microscope/captures/capture.py

@@ -120,7 +120,8 @@ class CaptureObject(object):
         logging.debug("Finished writing to disk %s", self.file)
 
     def open(self, mode):
-        return open(self.file, mode)
+        # We don't specify an encoding because this will be a binary file.
+        return open(self.file, mode) # pylint: disable=unspecified-encoding
 
     def split_file_path(self, filepath: str):
         """

openflexure_microscope/config.py

@@ -88,7 +88,7 @@ def load_json_file(config_path) -> dict:
 
     logging.info("Loading %s...", config_path)
 
-    with open(config_path) as config_file:
+    with open(config_path, encoding="utf-8") as config_file:
         try:
             config_data = json.load(config_file)
         except json.decoder.JSONDecodeError as e:
@@ -112,7 +112,7 @@ def save_json_file(config_path: str, config_dict: dict):
     logging.info("Saving %s...", config_path)
     logging.debug(config_dict)
 
-    with open(config_path, "w") as outfile:
+    with open(config_path, "w", encoding="utf-8") as outfile:
         json.dump(config_dict, outfile, cls=JSONEncoder, indent=2, sort_keys=True)
 
 
@@ -150,7 +150,7 @@ def initialise_file(config_path, populate: str = "{}\n"):
         create_file(config_path)
 
         logging.info("Populating %s...", (config_path))
-        with open(config_path, "w") as outfile:
+        with open(config_path, "w", encoding="utf-8") as outfile:
             outfile.write(populate)
 
 

openflexure_microscope/rescue/check_picamera.py

@@ -26,7 +26,7 @@ def main():
 
     try:
         import picamerax
-    except Exception as e:  # pylint: disable=W0703
+    except Exception as _:  # pylint: disable=W0703
         error_sources.append(PICAMERA_IMPORT_ERROR)
     else:
         try:

openflexure_microscope/rescue/check_sangaboard.py

@@ -20,7 +20,7 @@ def main():
             # Try connecting on the specified port
             try:
                 stage = Sangaboard(stage_port)
-            except FileNotFoundError as e:
+            except FileNotFoundError as _:
                 if stage_port:
                     error_sources.append(
                         ErrorSource(

scripts/zenodo/upload_to_zenodo.py

@@ -31,7 +31,7 @@ def script_directory(path):
 
 
 def get_meta():
-    with open(script_directory("metadata.yaml")) as f:
+    with open(script_directory("metadata.yaml"), encoding="utf-8") as f:
         metadata = f.read()
 
     return yaml.safe_load(metadata)
@@ -51,7 +51,7 @@ def main():
         zenodo.upload_file(deposit["id"], path)
 
     link = deposit["links"]["latest_draft_html"]
-    with open("zenodo-link.html", "w") as f:
+    with open("zenodo-link.html", "w", encoding="utf-8") as f:
         f.write(f'<a href="{link}">{link}</a>')
 
 

tests/test_app.py

@@ -28,7 +28,7 @@ def test_thing_description_valid():
     # TODO: it would be nice to put this into LabThings
     # First load the schema from file and check it validates
     schema_fname = os.path.join(os.path.dirname(__file__), "w3c_td_schema.json")
-    schema = json.load(open(schema_fname, "r"))
+    schema = json.load(open(schema_fname, "r"), encoding="utf-8")
     jsonschema.Draft7Validator.check_schema(schema)
 
     # Build a TD dictionary