Add suggestions for pyright changes from review

Based on suggestions from @victorlin in review of
#530

1. Assert value instead of type to be consistent with other assertions
in the repo.
2. Use type narrowing instead of coercion
3. nextstrain_dot_org/download: Always write raw bytes
`iter_content` can potentially return bytes if the `response.encoding`
is None,¹ so just always write raw bytes.

¹ <https://github.com/psf/requests/blob/6404f345e562d962abe6700a1c357ec1e7e18232/src/requests/utils.py#L599-L600>

Author: joverlee521

nextstrain/cli/pathogens.py

@@ -454,10 +454,11 @@ def setup(self, dry_run: bool = False, force: bool = False) -> SetupStatus:
                 """) from err
 
         except requests.exceptions.HTTPError as err:
-            assert type(err.response) is requests.Response
+            assert err.response is not None
             if 400 <= err.response.status_code <= 499:
+                auth = err.response.request.headers["Authorization"]
                 if (err.response.status_code in {401, 403}
-                and (auth := str(err.response.request.headers["Authorization"]))
+                and isinstance(auth, str)
                 and auth.startswith("Basic ")):
                     user = b64decode(auth.split(" ", 1)[1]).decode("utf-8").split(":", 1)[0]
 

nextstrain/cli/remote/nextstrain_dot_org.py

@@ -390,9 +390,8 @@ def download(url: URL, local_path: Path, recursively: bool = False, dry_run: boo
                         continue
 
                     # Stream response data to local file
-                    with destination.open("w") as local_file:
-                        for chunk in response.iter_content(chunk_size = None, decode_unicode = True):
-                            assert type(chunk) is str
+                    with destination.open("wb") as local_file:
+                        for chunk in response.iter_content(chunk_size = None):
                             local_file.write(chunk)
 
 
@@ -825,7 +824,7 @@ def raise_for_status(origin: Origin, response: requests.Response) -> None:
         response.raise_for_status()
 
     except requests.exceptions.HTTPError as err:
-        assert type(err.response) is requests.Response
+        assert err.response is not None
         status = err.response.status_code
 
         if status == 400: