fix some linking

CAVEconnectome · Feb 16, 2024 · 3c1a144 · 3c1a144
1 parent 0736cd2
commit 3c1a144
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Showing 10 changed files with 44 additions and 48 deletions.
diff --git a/caveclient/__init__.py b/caveclient/__init__.py
@@ -1,3 +1,5 @@
 __version__ = "5.15.2"
 
 from .frameworkclient import CAVEclient
+
+__all__ = ["CAVEclient"]
diff --git a/caveclient/annotationengine.py b/caveclient/annotationengine.py
@@ -1,5 +1,5 @@
 import json
-from typing import Iterable, List, Mapping
+from typing import Iterable, List, Mapping, Union
 
 import numpy as np
 import pandas as pd
@@ -30,7 +30,7 @@ def AnnotationClient(
     ----------
     server_address : str
         server_address to use to connect to (i.e. https://minniev1.microns-daf.com)
-    datastack_name : str
+    dataset_name : str
         Name of the datastack.
     auth_client : AuthClient or None, optional
         Authentication client to use to connect to server. If None, do not use authentication.
@@ -48,6 +48,7 @@ def AnnotationClient(
         Sets the max number of threads in the pool, by default None. If None, defaults to requests package default.
     over_client:
         client to overwrite configuration with
+        
     Returns
     -------
     ClientBaseWithDatastack
@@ -272,7 +273,7 @@ def create_table(
             Name of the new table. Cannot be the same as an existing table
         schema_name: str
             Name of the schema for the new table.
-        descrption: str
+        description: str
             Human readable description for what is in the table.
             Should include information about who generated the table
             What data it covers, and how it should be interpreted.
@@ -316,6 +317,7 @@ def create_table(
             Text the user will see when querying this table. Can be used to warn users of flaws,
             and uncertainty in the data, or to advertise citations that should be used with this table.
             Defaults to None, no text. If you want to remove text, send empty string.
+
         Returns
         -------
         json
@@ -713,7 +715,7 @@ def update_annotation_df(
     def delete_annotation(
         self,
         table_name: str,
-        annotation_ids: (dict or List),
+        annotation_ids: Union[dict, List],
         aligned_volume_name: str = None,
     ):
         """Delete one or more annotations in a table. Annotations that are
@@ -723,7 +725,7 @@ def delete_annotation(
         ----------
         table_name : str
             Name of the table where annotations will be added
-        data : dict or list,
+        annotation_ids : dict or list,
             A list of (or a single) dict of schematized annotation data matching the target table.
             each dict must contain an "id" field which is the ID of the annotation to update
         aligned_volume_name : str or None, optional

diff --git a/caveclient/auth.py b/caveclient/auth.py
@@ -272,7 +272,7 @@ def get_user_information(self, user_ids):
 
         Parameters
         ----------
-        user_id : list of int
+        user_ids : list of int
             user_ids to look up
         """
         endpoint_mapping = self._default_endpoint_mapping

diff --git a/caveclient/datastack_lookup.py b/caveclient/datastack_lookup.py
@@ -66,7 +66,7 @@ def reset_server_address_cache(datastack, filename=None):
 
     Parameters
     ----------
-    datastacks : str or list of str, optional
+    datastack : str or list of str, optional
         Datastack names to remove from the cache, by default None
     filename : str, optional
         Name of the cache file, by default None

diff --git a/caveclient/frameworkclient.py b/caveclient/frameworkclient.py
@@ -43,14 +43,14 @@ def __new__(
 
         Then:
 
-        - `client.annotation` is an `AnnotationClient` (see [client.annotation](../../client_api/annotation/))
-        - `client.auth` is an `AuthClient` (see [client.auth](../../client_api/auth/))
-        - `client.chunkedgraph` is a `ChunkedGraphClient` (see [client.chunkedgraph](../../client_api/chunkedgraph/))
-        - `client.info` is an `InfoServiceClient` (see [client.info](../../client_api/info/))
-        - `client.l2cache` is an `L2CacheClient` (see [client.l2cache](../../client_api/l2cache/))
-        - `client.materialize` is a `MaterializationClient` (see [client.materialize](../../client_api/materialize/))
-        - `client.schema` is a `SchemaClient` (see [client.schema](../../client_api/schema/))
-        - `client.state` is a neuroglancer `JSONService` (see [client.state](../../client_api/state/))
+        - `client.annotation` is an `AnnotationClient` (see [client.annotation](../client_api/annotation.md))
+        - `client.auth` is an `AuthClient` (see [client.auth](../client_api/auth.md))
+        - `client.chunkedgraph` is a `ChunkedGraphClient` (see [client.chunkedgraph](../client_api/chunkedgraph.md))
+        - `client.info` is an `InfoServiceClient` (see [client.info](../client_api/info.md))
+        - `client.l2cache` is an `L2CacheClient` (see [client.l2cache](../client_api/l2cache.md))
+        - `client.materialize` is a `MaterializationClient` (see [client.materialize](../client_api/materialize.md))
+        - `client.schema` is a `SchemaClient` (see [client.schema](../client_api/schema.md))
+        - `client.state` is a neuroglancer `JSONService` (see [client.state](../client_api/state.md))
 
 
         All subclients are loaded lazily and share the same datastack name, server address, and auth tokens where used.
@@ -139,10 +139,10 @@ def __init__(
 
         Then:
 
-        - `client.auth` is an `AuthClient` (see [client.auth](../../client_api/auth/))
-        - `client.info` is an `InfoServiceClient` (see [client.info](../../client_api/info/))
-        - `client.schema` is a `SchemaClient` (see [client.schema](../../client_api/schema/))
-        - `client.state` is a neuroglancer `JSONService` (see [client.state](../../client_api/state/))
+        - `client.auth` is an `AuthClient` (see [client.auth](../client_api/auth.md))
+        - `client.info` is an `InfoServiceClient` (see [client.info](../client_api/info.md))
+        - `client.schema` is a `SchemaClient` (see [client.schema](../client_api/schema.md))
+        - `client.state` is a neuroglancer `JSONService` (see [client.state](../client_api/state.md))
 
         All subclients are loaded lazily and share the same datastack name, server address, and auth tokens (where used).
 
@@ -223,7 +223,7 @@ def server_address(self):
     @property
     def auth(self):
         """
-        A client for the auth service. See [client.auth](../../client_api/auth/) for more information.
+        A client for the auth service. See [client.auth](../client_api/auth.md) for more information.
         """
         if self._auth is None:
             self._auth = AuthClient(**self._auth_config)
@@ -232,7 +232,7 @@ def auth(self):
     @property
     def info(self) -> InfoServiceClient:
         """
-        A client for the info service. See [client.info](../../client_api/info/) for more information.
+        A client for the info service. See [client.info](../client_api/info.md) for more information.
         """
         if self._info is None:
             self._info = InfoServiceClient(
@@ -250,7 +250,7 @@ def info(self) -> InfoServiceClient:
     @property
     def state(self):
         """
-        A client for the neuroglancer state service. See [client.state](../../client_api/state/)
+        A client for the neuroglancer state service. See [client.state](../client_api/state.md)
         for more information.
         """
         if self._state is None:
@@ -267,7 +267,7 @@ def state(self):
     @property
     def schema(self):
         """
-        A client for the EM Annotation Schemas service. See [client.schema](../../client_api/schema/)
+        A client for the EM Annotation Schemas service. See [client.schema](../client_api/schema.md)
         for more information.
         """
         if self._schema is None:
@@ -324,14 +324,14 @@ def __init__(
 
         Then
 
-        - `client.annotation` is an `AnnotationClient` (see [client.annotation](../../client_api/annotation/))
-        - `client.auth` is an `AuthClient` (see [client.auth](../../client_api/auth/))
-        - `client.chunkedgraph` is a `ChunkedGraphClient` (see [client.chunkedgraph](../../client_api/chunkedgraph/))
-        - `client.info` is an `InfoServiceClient` (see [client.info](../../client_api/info/))
-        - `client.l2cache` is an `L2CacheClient` (see [client.l2cache](../../client_api/l2cache/))
-        - `client.materialize` is a `MaterializationClient` (see [client.materialize](../../client_api/materialize/))
-        - `client.schema` is a `SchemaClient` (see [client.schema](../../client_api/schema/))
-        - `client.state` is a neuroglancer `JSONService` (see [client.state](../../client_api/state/))
+        - `client.annotation` is an `AnnotationClient` (see [client.annotation](../client_api/annotation.md))
+        - `client.auth` is an `AuthClient` (see [client.auth](../client_api/auth.md))
+        - `client.chunkedgraph` is a `ChunkedGraphClient` (see [client.chunkedgraph](../client_api/chunkedgraph.md))
+        - `client.info` is an `InfoServiceClient` (see [client.info](../client_api/info.md))
+        - `client.l2cache` is an `L2CacheClient` (see [client.l2cache](../client_api/l2cache.md))
+        - `client.materialize` is a `MaterializationClient` (see [client.materialize](../client_api/materialize.md))
+        - `client.schema` is a `SchemaClient` (see [client.schema](../client_api/schema.md))
+        - `client.state` is a neuroglancer `JSONService` (see [client.state](../client_api/state.md))
 
         All subclients are loaded lazily and share the same datastack name, server address, and auth tokens where used.
 
@@ -403,7 +403,7 @@ def datastack_name(self) -> str:
     @property
     def chunkedgraph(self):
         """
-        A client for the chunkedgraph service. See [client.chunkedgraph](../../client_api/chunkedgraph/)
+        A client for the chunkedgraph service. See [client.chunkedgraph](../client_api/chunkedgraph.md)
         for more information.
         """
         if self._chunkedgraph is None:
@@ -424,7 +424,7 @@ def chunkedgraph(self):
     @property
     def annotation(self):
         """
-        A client for the annotation service. See [client.annotation](../../client_api/annotation/)
+        A client for the annotation service. See [client.annotation](../client_api/annotation.md)
         for more information.
         """
         if self._annotation is None:
@@ -442,7 +442,7 @@ def annotation(self):
     @property
     def materialize(self):
         """
-        A client for the materialization service. See [client.materialize](../../client_api/materialize/)
+        A client for the materialization service. See [client.materialize](../client_api/materialize.md)
         for more information.
         """
         if self._materialize is None:
@@ -462,7 +462,7 @@ def materialize(self):
     @property
     def state(self):
         """
-        A client for the neuroglancer state service. See [client.state](../../client_api/state/)
+        A client for the neuroglancer state service. See [client.state](../client_api/state.md)
         for more information.
         """
         if self._state is None:
@@ -480,7 +480,7 @@ def state(self):
     @property
     def l2cache(self):
         """
-        A client for the L2 cache service. See [client.l2cache](../../client_api/l2cache/)
+        A client for the L2 cache service. See [client.l2cache](../client_api/l2cache.md)
         for more information.
         """
         if self._l2cache is None:

diff --git a/caveclient/l2cache.py b/caveclient/l2cache.py
@@ -126,9 +126,6 @@ def get_l2data(self, l2_ids, attributes=None):
     def cache_metadata(self):
         """Retrieves the meta data for the cache
 
-        Parameters
-        ----------
-
         Returns
         -------
         dict
@@ -147,8 +144,6 @@ def attributes(self):
 
     def table_mapping(self):
         """Retrieves table mappings for l2 cache.
-        Parameters
-        ----------
 
         Returns
         -------

diff --git a/caveclient/materializationengine.py b/caveclient/materializationengine.py
@@ -1246,9 +1246,6 @@ def live_live_query(
         filter_spatial_dict: dict of dicts, optional
             A dictionary with tables as keys, values are dicts with column keys and values
             of 2x3 list of bounds.
-        filter_regex_dict: dict of dicts, optional
-            A dictionary with tables as keys, values are dicts with column keys and values
-            of regex strings.
         select_columns: dict of lists of str, optional
             A dictionary with tables as keys, values are lists of columns to select.
         offset:

diff --git a/docs/client_api/annotation.md b/docs/client_api/annotation.md
@@ -8,7 +8,7 @@ title: client.annotation
     type(client.annotation)
     ```
     Extended documentation for all versions of the annotation client can be found
-    [here](../extended_api/annotation.md).
+    [here](../extended_api/annotationengine.md).
 
 ::: caveclient.annotationengine.AnnotationClientV2
     options:

diff --git a/docs/extended_api/materialization.md → docs/extended_api/materializationengine.md b/docs/extended_api/materialization.md → docs/extended_api/materializationengine.md
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -17,7 +17,7 @@ nav:
     - tutorials/schemas.md
     - tutorials/state.md
     - tutorials/materialization.md
-  - Client API: 
+  - Client API: # these match the client property names
     - client_api/index.md
     - client_api/client.md
     - client_api/annotation.md
@@ -28,7 +28,7 @@ nav:
     - client_api/materialize.md
     - client_api/schema.md
     - client_api/state.md
-  - Extended API:
+  - Extended API: # these match the python file names
     - extended_api/index.md
     - extended_api/annotationengine.md
     - extended_api/auth.md
@@ -40,7 +40,7 @@ nav:
     - extended_api/infoservice.md
     - extended_api/jsonservice.md
     - extended_api/l2cache.md
-    - extended_api/materialization.md
+    - extended_api/materializationengine.md
     - extended_api/session_config.md
   - Glossary: glossary.md
   - Contributing: contributing.md