Merge branch 'master' into semver

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 5.16.0
+current_version = 5.18.0
 commit = True
 tag = True
 

.github/workflows/format.yml

@@ -0,0 +1,22 @@
+name: Lint and Format
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: master
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+  # Allows other workflows to trigger this workflow
+  workflow_call:
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with: # the --extend-select flag adds import sorting
+          args: check . --extend-select I
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: format . --check

README.md

@@ -1,10 +1,15 @@
 # CAVEclient
 
+![PyPI - Version](https://img.shields.io/pypi/v/CAVEclient)
+[![build status](https://github.com/CAVEconnectome/CAVEclient/actions/workflows/daily.yml/badge.svg)](https://github.com/CAVEconnectome/CAVEclient/actions/workflows/daily.yml) [![Downloads](https://static.pepy.tech/badge/caveclient)](https://pepy.tech/project/caveclient)
+
 CAVE is short for Connectome Annotation Versioning Engine. CAVE is a set of microservices
 that provide a framework for storing and versioning connectomics data and large sets of
 dynamic annotations, metadata, and segmentations. This repository supplies client-side
 code to easily interact with the microservices in CAVE.
 
+A full description of the Connectome Annotation Versioning Engine can be found [in this paper](https://www.biorxiv.org/content/10.1101/2023.07.26.550598v1).
+
 ## Installation
 
 `CAVEclient` can be installed from PyPI:
@@ -15,4 +20,4 @@ pip install caveclient
 
 ## Documentation
 
-You can find full documentation at [caveclient.readthedocs.io](https://caveclient.readthedocs.io/).
+You can find full documentation at [caveconnectome.github.io/CAVEclient](https://caveconnectome.github.io/CAVEclient).

caveclient/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "5.16.0"
+__version__ = "5.18.0"
 
 from .frameworkclient import CAVEclient
 

caveclient/base.py

@@ -1,20 +1,21 @@
-import urllib
-import requests
+import datetime
 import json
 import logging
-
-logger = logging.getLogger(__name__)
+import urllib
 import webbrowser
 
-from .session_config import patch_session
 import numpy as np
-import datetime
 import pandas as pd
+import requests
+
+from .session_config import patch_session
+
+logger = logging.getLogger(__name__)
 
 
 class BaseEncoder(json.JSONEncoder):
     def default(self, obj):
-        if isinstance(obj, np.ndarray) or isinstance(obj, pd.Series):
+        if isinstance(obj, (np.ndarray, pd.Series, pd.Index)):
             return obj.tolist()
         if isinstance(obj, set):
             return list(obj)
@@ -105,7 +106,7 @@ def _check_authorization_redirect(response):
 {first_url}
 with the current auth configuration.\n
 Read the documentation at 
-https://seung-lab.github.io/CAVEclient/tutorials/authentication/
+https://caveconnectome.github.io/CAVEclient/tutorials/authentication/
 or follow instructions under 
 client.auth.get_new_token() for how to set a valid API token.
 after initializing a global client with
@@ -149,7 +150,7 @@ def _api_endpoints(
                 verify=verify,
             )
             avail_vs_server = set(avail_vs_server)
-        except:
+        except:  # noqa: E722
             avail_vs_server = None
 
         avail_vs_client = set(endpoint_versions.keys())

caveclient/chunkedgraph.py

@@ -1,4 +1,5 @@
 """PyChunkedgraph service python interface"""
+
 import datetime
 import json
 import logging
@@ -852,6 +853,8 @@ def level2_chunk_graph(self, root_id, bounds=None) -> list:
         url = self._endpoints["lvl2_graph"].format_map(endpoint_mapping)
         response = self.session.get(url, params=query_d)
 
+        r = handle_response(response)
+
         used_bounds = response.headers.get("Used-Bounds")
         used_bounds = used_bounds == "true" or used_bounds == "True"
         if bounds is not None and not used_bounds:
@@ -863,8 +866,6 @@ def level2_chunk_graph(self, root_id, bounds=None) -> list:
             )
             raise ValueError(warning)
 
-        r = handle_response(response)
-
         return r["edge_graph"]
 
     def remesh_level2_chunks(self, chunk_ids) -> None:

caveclient/datastack_lookup.py

@@ -1,7 +1,8 @@
-import os
 import json
-from . import auth
 import logging
+import os
+
+from . import auth
 
 logger = logging.getLogger(__name__)
 
@@ -16,7 +17,7 @@ def read_map(filename=None):
         with open(os.path.expanduser(filename), "r") as f:
             data = json.load(f)
         return data
-    except:
+    except:  # noqa E722
         return {}
 
 

caveclient/emannotationschemas.py

@@ -1,6 +1,14 @@
+from __future__ import annotations
+
+import logging
+
+from requests import HTTPError
+
+from .auth import AuthClient
 from .base import ClientBase, _api_endpoints, handle_response
 from .endpoints import schema_api_versions, schema_endpoints_common
-from .auth import AuthClient
+
+logger = logging.getLogger(__name__)
 
 server_key = "emas_server_address"
 
@@ -65,7 +73,7 @@ def __init__(
             over_client=over_client,
         )
 
-    def get_schemas(self):
+    def get_schemas(self) -> list[str]:
         """Get the available schema types
 
         Returns
@@ -78,7 +86,7 @@ def get_schemas(self):
         response = self.session.get(url)
         return handle_response(response)
 
-    def schema_definition(self, schema_type):
+    def schema_definition(self, schema_type: str) -> dict[str]:
         """Get the definition of a specified schema_type
 
         Parameters
@@ -97,6 +105,50 @@ def schema_definition(self, schema_type):
         response = self.session.get(url)
         return handle_response(response)
 
+    def schema_definition_multi(self, schema_types: list[str]) -> dict:
+        """Get the definition of multiple schema_types
+
+        Parameters
+        ----------
+        schema_types : list
+            List of schema names
+
+        Returns
+        -------
+        dict
+            Dictionary of schema definitions. Keys are schema names, values are definitions.
+        """
+        endpoint_mapping = self.default_url_mapping
+        url = self._endpoints["schema_definition_multi"].format_map(endpoint_mapping)
+        data = {"schema_names": ",".join(schema_types)}
+        response = self.session.post(url, params=data)
+        try:
+            return handle_response(response)
+        except HTTPError:
+            logger.warning(
+                'Client requested an schema service endpoint (see "schema_definition_multi") not yet available on your deployment. Please talk to your admin about updating your deployment'
+            )
+            return None
+
+    def schema_definition_all(self) -> dict[str]:
+        """Get the definition of all schema_types
+
+        Returns
+        -------
+        dict
+            Dictionary of schema definitions. Keys are schema names, values are definitions.
+        """
+        endpoint_mapping = self.default_url_mapping
+        url = self._endpoints["schema_definition_all"].format_map(endpoint_mapping)
+        response = self.session.get(url)
+        try:
+            return handle_response(response)
+        except HTTPError:
+            logger.warning(
+                'Client requested an schema service endpoint (see "schema_definition_all") not yet available on your deployment. Please talk to your admin about updating your deployment'
+            )
+            return None
+
 
 client_mapping = {
     1: SchemaClientLegacy,

caveclient/endpoints.py

@@ -201,6 +201,8 @@
 schema_endpoints_v2 = {
     "schema": schema_v2 + "/type",
     "schema_definition": schema_v2 + "/type/{schema_type}",
+    "schema_definition_multi": schema_v2 + "/types",
+    "schema_definition_all": schema_v2 + "/types_all",
 }
 
 schema_api_versions = {1: schema_endpoints_v1, 2: schema_endpoints_v2}