rebranding

CAVEconnectome · Jun 22, 2021 · 1a2a9ac · 1a2a9ac
1 parent 0c7d825
commit 1a2a9ac
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -3,4 +3,4 @@ current_version = 3.1.0
 commit = True
 tag = True
 
-[bumpversion:file:annotationframeworkclient/__init__.py]
+[bumpversion:file:caveclient/__init__.py]
diff --git a/FlyWireSynapseTutorial.ipynb b/FlyWireSynapseTutorial.ipynb
@@ -7,18 +7,18 @@
     "# The FrameworkClient\n",
     "\n",
     "The FrameworkClient is a client side library to allow easy interaction with the services within CAVE (connectome annotation versioning engine, also known as Dynamic Annotation Framework), eg. the annotations, stateserver. The github repository is public:\n",
-    "https://github.com/seung-lab/AnnotationFrameworkClient\n",
+    "https://github.com/seung-lab/CAVEclient\n",
     "\n",
     "The library can be installed directly from the github repository or from the prebuilt versions using pip:\n",
     "```\n",
-    "pip install annotationframeworkclient\n",
+    "pip install caveclient\n",
     "```\n",
     "\n",
     "\n",
     "## Tutorials\n",
     "\n",
     "This tutorial mainly covers the interactions with the materialized annotation tables. More information and better explanations of the other functionalities of the client can be found in the following tutorial. Please be advised that depending on your permission level you may not be able to execute all queries in this tutorial with the preset parameters as it was written with defaults for iarpa's microns project:\n",
-    "https://github.com/seung-lab/AnnotationFrameworkClient/blob/master/FrameworkClientExamples.ipynb\n",
+    "https://github.com/seung-lab/CAVEclient/blob/master/FrameworkClientExamples.ipynb\n",
     "\n",
     "\n",
     "## Authentication & Authorization\n",
@@ -49,7 +49,7 @@
    "source": [
     "import numpy as np\n",
     "import datetime\n",
-    "from annotationframeworkclient import FrameworkClient"
+    "from caveclient import FrameworkClient"
    ]
   },
   {
@@ -1056,11 +1056,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Before using live materializations, please make sure that your installation of the annotationframeworkclient is `>= 3.1.0`. You can upgrade your installed version with \n",
+    "Before using live materializations, please make sure that your installation of the caveclient is `>= 3.1.0`. You can upgrade your installed version with \n",
     "\n",
     "\n",
     "```\n",
-    "pip install annotationframeworkclient --upgrade\n",
+    "pip install caveclient --upgrade\n",
     "```\n",
     "\n",
     "To make sure the latest version of the library is used in this notebook after an upgrade it is best to reload the notebook kernel. Your current version is:"
@@ -1083,8 +1083,8 @@
     }
    ],
    "source": [
-    "import annotationframeworkclient\n",
-    "annotationframeworkclient.__version__"
+    "import caveclient\n",
+    "caveclient.__version__"
    ]
   },
   {
@@ -1479,8 +1479,8 @@
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
       "\u001b[0;32m<timed exec>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n",
-      "\u001b[0;32m~/AnnotationFrameworkClient/annotationframeworkclient/materializationengine.py\u001b[0m in \u001b[0;36mlive_query\u001b[0;34m(self, table, timestamp, filter_in_dict, filter_out_dict, filter_equal_dict, filter_spatial, join_args, select_columns, offset, limit, datastack_name, split_positions, post_filter)\u001b[0m\n\u001b[1;32m    867\u001b[0m         \u001b[0;31m# most recent materialization\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    868\u001b[0m         \u001b[0;32mwith\u001b[0m \u001b[0mTimeIt\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"map_filters\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 869\u001b[0;31m             past_filters, future_map = self.map_filters(\n\u001b[0m\u001b[1;32m    870\u001b[0m                 \u001b[0;34m[\u001b[0m\u001b[0mfilter_in_dict\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfilter_out_dict\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfilter_equal_dict\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    871\u001b[0m                 \u001b[0mtimestamp\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/AnnotationFrameworkClient/annotationframeworkclient/materializationengine.py\u001b[0m in \u001b[0;36mmap_filters\u001b[0;34m(self, filters, timestamp, timestamp_past)\u001b[0m\n\u001b[1;32m    685\u001b[0m                 \u001b[0mtoo_recent_str\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    686\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 687\u001b[0;31m             raise ValueError(\n\u001b[0m\u001b[1;32m    688\u001b[0m                 \u001b[0;34mf\"Timestamp incompatible with IDs: {too_old_str}{too_recent_str}use chunkedgraph client to find valid ID(s)\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    689\u001b[0m             )\n",
+      "\u001b[0;32m~/CAVEclient/caveclient/materializationengine.py\u001b[0m in \u001b[0;36mlive_query\u001b[0;34m(self, table, timestamp, filter_in_dict, filter_out_dict, filter_equal_dict, filter_spatial, join_args, select_columns, offset, limit, datastack_name, split_positions, post_filter)\u001b[0m\n\u001b[1;32m    867\u001b[0m         \u001b[0;31m# most recent materialization\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    868\u001b[0m         \u001b[0;32mwith\u001b[0m \u001b[0mTimeIt\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"map_filters\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 869\u001b[0;31m             past_filters, future_map = self.map_filters(\n\u001b[0m\u001b[1;32m    870\u001b[0m                 \u001b[0;34m[\u001b[0m\u001b[0mfilter_in_dict\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfilter_out_dict\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfilter_equal_dict\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    871\u001b[0m                 \u001b[0mtimestamp\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/CAVEclient/caveclient/materializationengine.py\u001b[0m in \u001b[0;36mmap_filters\u001b[0;34m(self, filters, timestamp, timestamp_past)\u001b[0m\n\u001b[1;32m    685\u001b[0m                 \u001b[0mtoo_recent_str\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    686\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 687\u001b[0;31m             raise ValueError(\n\u001b[0m\u001b[1;32m    688\u001b[0m                 \u001b[0;34mf\"Timestamp incompatible with IDs: {too_old_str}{too_recent_str}use chunkedgraph client to find valid ID(s)\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    689\u001b[0m             )\n",
       "\u001b[0;31mValueError\u001b[0m: Timestamp incompatible with IDs: [720575940627185911] are expired, use chunkedgraph client to find valid ID(s)"
      ]
     }
@@ -1603,7 +1603,7 @@
    "source": [
     "### Programmatically - Spatial lookup\n",
     "\n",
-    "The client interface allows users to query a root id for a given supervoxel id (see Section 5 in [the related tutorial](https://github.com/seung-lab/AnnotationFrameworkClient/blob/master/FrameworkClientExamples.ipynb). Supervoxel ids can be retrieved from the segmentation using [cloudvolume](https://github.com/seung-lab/cloud-volume/)."
+    "The client interface allows users to query a root id for a given supervoxel id (see Section 5 in [the related tutorial](https://github.com/seung-lab/CAVEclient/blob/master/FrameworkClientExamples.ipynb). Supervoxel ids can be retrieved from the segmentation using [cloudvolume](https://github.com/seung-lab/cloud-volume/)."
    ]
   },
   {
@@ -1659,7 +1659,7 @@
     "\n",
     "We are building infrastructure into neuroglancer to display this information there while browsing neurons. Until this is ready, the most convenient way to visualize this information in neuroglancer is to programmatically create neuroglancer state and to upload them to the state server. The links can then be distributed. \n",
     "\n",
-    "[NeuroglancerAnnotationUI (nglui)](https://github.com/seung-lab/NeuroglancerAnnotationUI)  makes programmatic creation of neuroglancer states convenient. The [statebuilder examples](https://github.com/seung-lab/NeuroglancerAnnotationUI/blob/master/examples/statebuilder_examples.ipynb) shows how one can directly from dataframes as the one above to neuroglancer states. The [related tutorial on this client](https://github.com/seung-lab/AnnotationFrameworkClient/blob/master/FrameworkClientExamples.ipynb) shows under \"4. JSON Service\" how this client can be used to upload states to the server and to create neuroglancer links.\n"
+    "[NeuroglancerAnnotationUI (nglui)](https://github.com/seung-lab/NeuroglancerAnnotationUI)  makes programmatic creation of neuroglancer states convenient. The [statebuilder examples](https://github.com/seung-lab/NeuroglancerAnnotationUI/blob/master/examples/statebuilder_examples.ipynb) shows how one can directly from dataframes as the one above to neuroglancer states. The [related tutorial on this client](https://github.com/seung-lab/CAVEclient/blob/master/FrameworkClientExamples.ipynb) shows under \"4. JSON Service\" how this client can be used to upload states to the server and to create neuroglancer links.\n"
    ]
   },
   {

diff --git a/FrameworkClientExamples.ipynb b/FrameworkClientExamples.ipynb
@@ -6,7 +6,7 @@
    "source": [
     "### 1. One client to rule them all\n",
     "\n",
-    "The Dynamic Annotation Framework consists of a number of different services, each with a specific set of tasks that it can perform through REST endpoints. This module is designed to ease programmatic interaction with all of the various endpoints. Going forward, we also will be increasingly using authentication tokens for programmatic access to most if not all of the services. In order to collect a given server, datastack name, and user token together into a coherent package that can be used on multiple endpoints, we will use a FrameworkClient that can build appropriately configured clients for each of the specific services.\n",
+    "The Connectome Annotation Versioning Engine framework consists of a number of different services, each with a specific set of tasks that it can perform through REST endpoints. This module is designed to ease programmatic interaction with all of the various endpoints. Going forward, we also will be increasingly using authentication tokens for programmatic access to most if not all of the services. In order to collect a given server, datastack name, and user token together into a coherent package that can be used on multiple endpoints, we will use a FrameworkClient that can build appropriately configured clients for each of the specific services.\n",
     "\n",
     "The following examples cover each of the client subtypes that are associated with a single service. The ImageryClient, which is a more complex collection of tools, will be covered elsewhere."
    ]
@@ -30,7 +30,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from annotationframeworkclient import FrameworkClient\n",
+    "from caveclient import FrameworkClient\n",
     "\n",
     "client = FrameworkClient()\n",
     "client.auth.get_new_token()"
@@ -58,7 +58,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from annotationframeworkclient import FrameworkClient\n",
+    "from caveclient import FrameworkClient\n",
     "\n",
     "datastack_name = 'minnie65_phase3_v0'\n",
     "client = FrameworkClient(datastack_name)"
@@ -310,7 +310,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from annotationframeworkclient import FrameworkClient\n",
+    "from caveclient import FrameworkClient\n",
     "\n",
     "datastack_name = 'minnie65_phase3_v0'\n",
     "client = FrameworkClient(datastack_name)"
@@ -542,4 +542,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/README.rst b/README.rst
@@ -1,11 +1,11 @@
-.. image:: https://readthedocs.org/projects/annotationframeworkclient/badge/?version=latest
-    :target: https://annotationframeworkclient.readthedocs.io/en/latest/?badge=latest
+.. image:: https://readthedocs.org/projects/caveclient/badge/?version=latest
+    :target: https://caveclient.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
-.. image:: https://github.com/seung-lab/AnnotationFrameworkClient/workflows/Annotation%20Framework%20Client/badge.svg
-    :target: https://github.com/seung-lab/AnnotationFrameworkClient/actions
+.. image:: https://github.com/seung-lab/CAVEclient/workflows/Annotation%20Framework%20Client/badge.svg
+    :target: https://github.com/seung-lab/CAVEclient/actions
     :alt: Actions Status
 
-AnnotationFrameworkClient
+CAVEclient
 ###########################
 This repository supplies client side code to interact with microservices 
 in the Connectome Annotation Versioning Engine (CAVE).
diff --git a/annotationframeworkclient/auth.py b/annotationframeworkclient/auth.py
@@ -40,7 +40,7 @@ def __init__(
         server_address=default_global_server_address,
     ):
         if token_file is None:
-            server=urllib.parse.urlparse(server_address).netloc
+            server = urllib.parse.urlparse(server_address).netloc
             server_file = server + "-cave-secret.json"
             server_file_path = os.path.join(default_token_location, server_file)
             server_file_path = os.path.expanduser(server_file_path)
@@ -63,7 +63,7 @@ def __init__(
 
     @property
     def token(self):
-        """Secret token used to authenticate yourself to the Dynamic Annotation Framework services."""
+        """Secret token used to authenticate yourself to the Connectome Annotation Versioning Engine services."""
         return self._token
 
     @token.setter

diff --git a/annotationframeworkclient/materializationengine.py b/annotationframeworkclient/materializationengine.py
@@ -3,7 +3,7 @@
 from typing import ValuesView
 
 from numpy.lib.function_base import iterable
-import annotationframeworkclient
+import caveclient
 from .base import (
     ClientBaseWithDataset,
     ClientBaseWithDatastack,

diff --git a/docs/api/annotationframeworkclient.rst b/docs/api/annotationframeworkclient.rst
@@ -1,93 +1,93 @@
-annotationframeworkclient package
+caveclient package
 =================================
 
 Submodules
 ----------
 
-annotationframeworkclient.annotationengine module
+caveclient.annotationengine module
 -------------------------------------------------
 
-.. automodule:: annotationframeworkclient.annotationengine
+.. automodule:: caveclient.annotationengine
    :members:
    :undoc-members:
    :show-inheritance:
 
-annotationframeworkclient.auth module
+caveclient.auth module
 -------------------------------------
 
-.. automodule:: annotationframeworkclient.auth
+.. automodule:: caveclient.auth
    :members:
    :undoc-members:
    :show-inheritance:
 
-annotationframeworkclient.base module
+caveclient.base module
 -------------------------------------
 
-.. automodule:: annotationframeworkclient.base
+.. automodule:: caveclient.base
    :members:
    :undoc-members:
    :show-inheritance:
 
-annotationframeworkclient.chunkedgraph module
+caveclient.chunkedgraph module
 ---------------------------------------------
 
-.. automodule:: annotationframeworkclient.chunkedgraph
+.. automodule:: caveclient.chunkedgraph
    :members:
    :undoc-members:
    :show-inheritance:
 
-annotationframeworkclient.emannotationschemas module
+caveclient.emannotationschemas module
 ----------------------------------------------------
 
-.. automodule:: annotationframeworkclient.emannotationschemas
+.. automodule:: caveclient.emannotationschemas
    :members:
    :undoc-members:
    :show-inheritance:
 
-annotationframeworkclient.endpoints module
+caveclient.endpoints module
 ------------------------------------------
 
-.. automodule:: annotationframeworkclient.endpoints
+.. automodule:: caveclient.endpoints
    :members:
    :undoc-members:
    :show-inheritance:
 
-annotationframeworkclient.format\_utils module
+caveclient.format\_utils module
 ----------------------------------------------
 
-.. automodule:: annotationframeworkclient.format_utils
+.. automodule:: caveclient.format_utils
    :members:
    :undoc-members:
    :show-inheritance:
 
-annotationframeworkclient.frameworkclient module
+caveclient.frameworkclient module
 ------------------------------------------------
 
-.. automodule:: annotationframeworkclient.frameworkclient
+.. automodule:: caveclient.frameworkclient
    :members:
    :undoc-members:
    :show-inheritance:
 
-annotationframeworkclient.infoservice module
+caveclient.infoservice module
 --------------------------------------------
 
-.. automodule:: annotationframeworkclient.infoservice
+.. automodule:: caveclient.infoservice
    :members:
    :undoc-members:
    :show-inheritance:
 
-annotationframeworkclient.jsonservice module
+caveclient.jsonservice module
 --------------------------------------------
 
-.. automodule:: annotationframeworkclient.jsonservice
+.. automodule:: caveclient.jsonservice
    :members:
    :undoc-members:
    :show-inheritance:
 
-annotationframeworkclient.materializationengine module
+caveclient.materializationengine module
 ------------------------------------------------------
 
-.. automodule:: annotationframeworkclient.materializationengine
+.. automodule:: caveclient.materializationengine
    :members:
    :undoc-members:
    :show-inheritance:
@@ -96,7 +96,7 @@ annotationframeworkclient.materializationengine module
 Module contents
 ---------------
 
-.. automodule:: annotationframeworkclient
+.. automodule:: caveclient
    :members:
    :undoc-members:
    :show-inheritance:
diff --git a/docs/api/modules.rst b/docs/api/modules.rst
@@ -1,7 +1,7 @@
-annotationframeworkclient
+caveclient
 =========================
 
 .. toctree::
    :maxdepth: 4
 
-   annotationframeworkclient
+   caveclient
diff --git a/docs/conf.py b/docs/conf.py
@@ -13,44 +13,50 @@
 import sphinx_rtd_theme
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
+
+sys.path.insert(0, os.path.abspath(".."))
 
 # -- Project information -----------------------------------------------------
 
-project = 'AnnotationFrameworkClient'
-copyright = '2020, Casey Schneider-Mizell, Forrest Collman, Sven Dorkenwald'
-author = 'Casey Schneider-Mizell, Forrest Collman, Sven Dorkenwald'
+project = "CAVEclient"
+copyright = "2020, Casey Schneider-Mizell, Forrest Collman, Sven Dorkenwald"
+author = "Casey Schneider-Mizell, Forrest Collman, Sven Dorkenwald"
 
 # The full version, including alpha/beta/rc tags
-release = '1.0'
+release = "1.0"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.coverage',
-              'sphinx.ext.napoleon', 'sphinx.ext.viewcode', 'sphinx_rtd_theme']
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_rtd_theme",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
-master_doc = 'index'
+master_doc = "index"
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]