[DATALAD RUNCMD] run codespell throughout

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

Author: yarikoptic

CHANGELOG.md

@@ -31,7 +31,7 @@
 - Fixed - Fix queries with backslashes ([#999](https://github.com/datajoint/datajoint-python/issues/999)) PR [#1052](https://github.com/datajoint/datajoint-python/pull/1052)
 
 ### 0.13.7 -- Jul 13, 2022
-- Fixed - Fix networkx incompatable change by version pinning to 2.6.3 (#1035) PR #1036
+- Fixed - Fix networkx incompatible change by version pinning to 2.6.3 (#1035) PR #1036
 - Added - Support for serializing numpy datetime64 types (#1022) PR #1036
 - Changed - Add traceback to default logging PR #1036
 

datajoint/__init__.py

@@ -1,5 +1,5 @@
 """
-DataJoint for Python is a framework for building data piplines using MySQL databases
+DataJoint for Python is a framework for building data pipelines using MySQL databases
 to represent pipeline structure and bulk storage systems for large objects.
 DataJoint is built on the foundation of the relational data model and prescribes a
 consistent method for organizing, populating, and querying data.

datajoint/autopopulate.py

@@ -118,7 +118,7 @@ def _job_key(self, key):
 
     def _jobs_to_do(self, restrictions):
         """
-        :return: the query yeilding the keys to be computed (derived from self.key_source)
+        :return: the query yielding the keys to be computed (derived from self.key_source)
         """
         if self.restriction:
             raise DataJointError(

datajoint/blob.py

@@ -449,7 +449,7 @@ def pack_dict(self, d):
         )
 
     def read_struct(self):
-        """deserialize matlab stuct"""
+        """deserialize matlab struct"""
         n_dims = self.read_value()
         shape = self.read_value(count=n_dims)
         n_elem = np.prod(shape, dtype=int)

datajoint/connection.py

@@ -113,7 +113,7 @@ def conn(
     :param init_fun: initialization function
     :param reset: whether the connection should be reset or not
     :param use_tls: TLS encryption option. Valid options are: True (required), False
-        (required no TLS), None (TLS prefered, default), dict (Manually specify values per
+        (required no TLS), None (TLS preferred, default), dict (Manually specify values per
         https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options).
     """
     if not hasattr(conn, "connection") or reset:

datajoint/schemas.py

@@ -21,7 +21,7 @@
 
 def ordered_dir(class_):
     """
-    List (most) attributes of the class including inherited ones, similar to `dir` build-in function,
+    List (most) attributes of the class including inherited ones, similar to `dir` built-in function,
     but respects order of attribute declaration as much as possible.
 
     :param class_: class to list members for

datajoint/table.py

@@ -230,7 +230,7 @@ def ancestors(self, as_objects=False):
 
     def parts(self, as_objects=False):
         """
-        return part tables either as entries in a dict with foreign key informaiton or a list of objects
+        return part tables either as entries in a dict with foreign key information or a list of objects
 
         :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects.
         """

docs/src/develop.md

@@ -83,7 +83,7 @@ black tests --check -v
 
 Jupyter notebooks are supported in this environment. This means that when you `import datajoint`, it will use the current state of the source.
 
-Be sure to see the reference documenation if you are new to [running Jupyter notebooks w/ VSCode](https://code.visualstudio.com/docs/datascience/jupyter-notebooks#_create-or-open-a-jupyter-notebook).
+Be sure to see the reference documentation if you are new to [running Jupyter notebooks w/ VSCode](https://code.visualstudio.com/docs/datascience/jupyter-notebooks#_create-or-open-a-jupyter-notebook).
 
 ### Debugger
 

docs/src/existing-pipelines.md

@@ -58,7 +58,7 @@ schema.spawn_missing_classes()
 
 While `spawn_missing_classes` creates the new classes in the local namespace, it is
 often more convenient to import a schema with its Python module, equivalent to the
-Python command. We can mimmick this import without having access to the schema using
+Python command. We can mimic this import without having access to the schema using
 the `VirtualModule` class object:
 
 ```python

docs/src/faq.md

@@ -23,7 +23,7 @@ languages must comply to the same data model and computation approach as defined
 ## Can I use DataJoint with my current database?
 
 Researchers use many different tools to keep records, from simple formalized file
-heirarchies to complete software packages for colony management and standard file types
+hierarchies to complete software packages for colony management and standard file types
 like NWB. Existing projects have built interfaces with many such tools, such as
 [PyRAT](https://github.com/SFB1089/adamacs/blob/main/notebooks/03_pyrat_insert.ipynb).
 The only requirement for interface is that tool has an open API. Contact