Merge branch 'ak-link' into ak-zarr-fix

.github/workflows/docs.yml

@@ -3,7 +3,7 @@ name: Build Docs
 on:
   push:
     branches:
-      - master
+      - ak-link
   pull_request:
 
 jobs:
@@ -13,10 +13,10 @@ jobs:
       fail-fast: false
       matrix:
         python:
-          - 3.8
-          #- 3.9
-          #- 3.10
-          #- 3.11
+          - '3.8'
+          - '3.9'
+          - '3.10'
+          - '3.11'
     steps:
     - name: Check out repository
       uses: actions/checkout@v4

docs/source/cmdline/dandi.rst

@@ -1,12 +1,12 @@
 :program:`lincbrain`
-================
+====================
 
 ::
 
     lincbrain [<global options>] <subcommand> [<arguments>]
 
-A command-line client for interacting with the `DANDI Archive
-<http://dandiarchive.org>`_.
+A command-line client for interacting with the `LINC Data Platform
+<http://lincbrain.org>`_.
 
 Global Options
 --------------

docs/source/cmdline/delete.rst

@@ -1,5 +1,5 @@
 :program:`lincbrain delete`
-=======================
+===========================
 
 ::
 
@@ -10,7 +10,7 @@ Delete datasets and assets from the server.
 Each argument must be either a file path pointing to an asset file or directory
 in a local datasets (in which case the corresponding assets are deleted on the
 remote server) or a :ref:`resource identifier <resource_ids>` pointing to a
-remote asset, directory, or entire Dandiset.
+remote asset, directory, or entire dataset.
 
 Options
 -------

docs/source/cmdline/digest.rst

@@ -1,5 +1,5 @@
 :program:`lincbrain digest`
-=======================
+===========================
 
 ::
 

docs/source/cmdline/download.rst

@@ -1,11 +1,11 @@
 :program:`lincbrain download`
-=========================
+=============================
 
 ::
 
     lincbrain [<global options>] download [<options>] <url> ...
 
-Download one or more Dandisets, assets, or folders of assets from DANDI.
+Download one or more datasets, assets, or folders of assets from LINC.
 
 See :ref:`resource_ids` for allowed URL formats.
 

docs/source/cmdline/instances.rst

@@ -1,11 +1,11 @@
 :program:`lincbrain instances`
-==========================
+==============================
 
 ::
 
     lincbrain [<global options>] instances
 
-List known Dandi Archive instances that can be passed to the
+List known LINC Archive instances that can be passed to the
 ``-i``/``--dandi-instance`` option of other subcommands for the CLI to
 interact with.  Output is in YAML.
 
@@ -14,11 +14,11 @@ Example output:
 .. code:: yaml
 
     dandi:
-      api: https://api.dandiarchive.org/api
-      gui: https://gui.dandiarchive.org
+      api: https://api.lincbrain.org/api
+      gui: https://lincbrain.org
     dandi-api-local-docker-tests:
       api: http://localhost:8000/api
       gui: http://localhost:8085
     dandi-staging:
-      api: https://api-staging.dandiarchive.org/api
-      gui: https://gui-staging.dandiarchive.org
+      api: https://staging-api.lincbrain.org/api
+      gui: https://staging.lincbrain.org

docs/source/cmdline/ls.rst

@@ -1,11 +1,11 @@
 :program:`lincbrain ls`
-===================
+=======================
 
 ::
 
     lincbrain [<global options>] ls [<options>] [<path|url> ...]
 
-List :file:`*.nwb` files' and Dandisets' metadata.
+List :file:`*.nwb` files' and datasets' metadata.
 
 The arguments may be either :ref:`resource identifiers <resource_ids>` or paths
 to local files/directories.
@@ -42,7 +42,7 @@ Options
 
 .. option:: -r, --recursive
 
-    Recurse into Dandisets/directories.  Only :file:`*.nwb` files will be
+    Recurse into datasets/directories.  Only :file:`*.nwb` files will be
     considered.
 
 .. option:: --schema <version>

docs/source/cmdline/move.rst

@@ -1,5 +1,5 @@
 :program:`lincbrain move`
-=====================
+=========================
 
 ::
 
@@ -24,10 +24,10 @@ single source path is renamed to the given destination path.
 
 Alternatively, if the ``--regex`` option is given, then there must be exactly
 two arguments on the command line: a `Python regular expression`_ and a
-replacement string, possibly containing regex backreferences.  :program:`dandi
+replacement string, possibly containing regex backreferences.  :program:`lincbrain
 move` will then apply the regular expression to the path of every asset in the
 current directory recursively (using paths relative to the current directory,
-if in a subdirectory of a Dandiset); if a path matches, the matching portion is
+if in a subdirectory of a dataset); if a path matches, the matching portion is
 replaced with the replacement string, after expanding any backreferences.
 
 .. _Python regular expression: https://docs.python.org/3/library/re.html
@@ -76,7 +76,7 @@ Options
 
     Whether to operate on the local dataset in the current directory, a remote
     dataset (either one specified by the ``--dandiset`` option or else the one
-    corresponding to the local Dandiset), or both at once.  If ``auto`` (the
+    corresponding to the local dataset), or both at once.  If ``auto`` (the
     default) is given, it is treated the same as ``remote`` if a ``--dandiset``
     option is given and as ``both`` otherwise.
 
@@ -106,7 +106,7 @@ Examples
   To rename the file only in the local or remote instance, insert ``--work-on
   local`` or ``--work-on remote`` after ``move``.
 
-- When not working in a local clone of a Dandiset, a file can be renamed in a
+- When not working in a local clone of a dataset, a file can be renamed in a
   remote dataset on a server by providing a resource identifier for the
   dataset to the ``--dandiset`` option.  For example, in order to operate on
   dataset 123456 on the main ``lincbrain`` instance, use::

docs/source/cmdline/organize.rst

@@ -1,7 +1,7 @@
-.. _dandi_organize:
+.. _lincbrain_organize:
 
 :program:`lincbrain organize`
-=========================
+=============================
 
 ::
 
@@ -35,17 +35,17 @@ In addition, an "obj" key with a value corresponding to the crc32 checksum of
 "object_id" is added if the aforementioned keys and the list of modalities are
 not sufficient to disambiguate different files.
 
-You can visit https://dandiarchive.org for a growing collection of
-(re)organized dandisets.
+You can visit https://lincbrain.org for a growing collection of
+(re)organized datasets.
 
 Options
 -------
 
 .. option:: -d, --dandiset-path <dir>
 
-    The root directory of the Dandiset to organize files under.  If not
-    specified, the Dandiset under the current directory is assumed.  For
-    'simulate' mode, the target Dandiset/directory must not exist.
+    The root directory of the dataset to organize files under.  If not
+    specified, the dataset under the current directory is assumed.  For
+    'simulate' mode, the target dataset/directory must not exist.
 
 .. option:: -f, --files-mode [dry|simulate|copy|move|hardlink|symlink|auto]
 

docs/source/cmdline/service-scripts.rst

@@ -1,5 +1,5 @@
 :program:`lincbrain service-scripts`
-================================
+====================================
 
 ::
 
@@ -17,8 +17,8 @@ utility operations.
 
 Recompute & update the metadata for NWB assets on a remote server.
 
-``<url>`` must point to a draft Dandiset or one or more assets inside a draft
-Dandiset.  See :ref:`resource_ids` for allowed URL formats.
+``<url>`` must point to a draft dataset or one or more assets inside a draft
+dataset.  See :ref:`resource_ids` for allowed URL formats.
 
 Running this command requires the fsspec_ library to be installed with the
 ``http`` extra (e.g., ``pip install "fsspec[http]"``).
@@ -38,7 +38,7 @@ Options
 
     - ``newer-schema-version`` (default) — when the ``schemaVersion`` in the
       asset's current metadata is missing or older than the schema version
-      currently in use by DANDI
+      currently in use by LINC
 
     - ``always`` — always
 
@@ -58,12 +58,12 @@ Options
 
 .. option:: -d, --dandiset <DANDISET ID>
 
-    Specify the ID of the Dandiset to operate on.  This option is required.
+    Specify the ID of the dataset to operate on.  This option is required.
 
 .. option:: -i, --dandi-instance <instance>
 
-    DANDI instance (either a base URL or a known instance name) where the
-    Dandiset is located [default: ``dandi``]
+    LINC Data Platform instance (either a base URL or a known instance name) where the
+    dataset is located [default: ``lincbrain``]
 
 .. option:: -e, --existing [ask|overwrite|skip]
 

docs/source/cmdline/shell-completion.rst

@@ -1,9 +1,9 @@
 :program:`lincbrain shell-completion`
-=================================
+=====================================
 
 ::
 
-    dandi [<global options>] shell-completion [<options>]
+    lincbrain [<global options>] shell-completion [<options>]
 
 Emit a shell script for enabling command completion.
 
@@ -12,8 +12,8 @@ completion.
 
 Example::
 
-    $ source <(dandi shell-completion)
-    $ dandi --<PRESS TAB to display available option>
+    $ source <(lincbrain shell-completion)
+    $ lincbrain --<PRESS TAB to display available option>
 
 Options
 -------

docs/source/cmdline/upload.rst

@@ -1,5 +1,5 @@
 :program:`lincbrain upload`
-=======================
+===========================
 
 ::
 
@@ -13,7 +13,7 @@ paths (or the current directory, if no paths are specified) or a parent
 directory thereof.
 
 Local datasets should pass validation.  For that, the assets should first be
-organized using the :ref:`dandi_organize` command.
+organized using the :ref:`lincbrain_organize` command.
 
 By default, all :file:`*.nwb`, :file:`*.zarr`, and :file:`*.ngff` assets in the
 dataset (ignoring directories starting with a period) will be considered for
@@ -78,4 +78,4 @@ set to a nonempty value.
 
 .. option:: --upload-dandiset-metadata
 
-    Update Dandiset metadata based on the local :file:`dandiset.yaml` file
+    Update dataset metadata based on the local :file:`dandiset.yaml` file

docs/source/cmdline/validate.rst

@@ -1,5 +1,5 @@
-:program:`dandi validate`
-=========================
+:program:`lincbrain validate`
+=============================
 
 ::
 

docs/source/conf.py

@@ -20,8 +20,8 @@
 import lincbrain
 
 project = "lincbrain"
-copyright = "2021-2023, DANDI Team"
-author = "DANDI Team"
+copyright = "2023-2024, LINC Team"
+author = "LINC Team"
 
 # The full version, including alpha/beta/rc tags
 version = lincbrain.__version__

docs/source/index.rst

@@ -1,9 +1,13 @@
-Welcome to the dandi documentation
-==================================
+Welcome to the lincbrain documentation
+======================================
 
-The `dandi <https://github.com/dandi/dandi-cli>`_ library provides both a
-command line interface (CLI) and a Python API for interacting with `DANDI
-Archive <https://dandiarchive.org>`_.
+The `lincbrain <https://github.com/lincbrain/linc-cli>`_ library provides both a
+command line interface (CLI) and a Python API for interacting with `LINC Data
+Platform <https://lincbrain.org>`_.
+
+The `lincbrain` CLI tool is a fork of the `dandi` CLI tool -- https://github.com/dandi/dandi-cli thus, there are a
+handful of references to `dandi` and `Dandisets` throughout these docs. Nevertheless, these docs (and the subsequent
+instructions alongside), should be reflected as accurate.
 
 .. toctree::
    :maxdepth: 2

docs/source/modref/consts.rst

@@ -1,7 +1,7 @@
-``dandi.consts``
-================
+``lincbrain.consts``
+====================
 
-.. automodule:: dandi.consts
+.. automodule:: lincbrain.consts
 
     .. NOTE: Due to <https://github.com/sphinx-doc/sphinx/issues/1063>, only
        data values with doc comments are included by automodule::, even with

docs/source/modref/dandiapi.rst

@@ -1,15 +1,15 @@
-.. module:: dandi.dandiapi
+.. module:: lincbrain.dandiapi
 
-``dandi.dandiapi``
-==================
+``lincbrain.dandiapi``
+======================
 
-This module provides functionality for interacting with a Dandi Archive server
+This module provides functionality for interacting with a LINC Data Platform server
 via the REST API.  Interaction begins with the creation of a `DandiAPIClient`
 instance, which can be used to retrieve `RemoteDandiset` objects (representing
-Dandisets on the server) and `BaseRemoteAsset` objects (representing assets
+datasets on the server) and `BaseRemoteAsset` objects (representing assets
 without any data associating them with their Dandisets).  `RemoteDandiset`
 objects can, in turn, be used to retrieve `RemoteAsset` objects (representing
-assets associated with Dandisets).  Aside from `DandiAPIClient`, none of these
+assets associated with datasets).  Aside from `DandiAPIClient`, none of these
 classes should be instantiated directly by the user.
 
 All operations that merely fetch data from the server can be done without
@@ -21,7 +21,7 @@ method.
 
 Example code for printing the metadata of all assets with "two-photon" in their
 ``metadata.measurementTechnique[].name`` for the latest published version of
-every Dandiset:
+every dataset:
 
 .. literalinclude:: /examples/dandiapi-example.py
     :language: python
@@ -33,7 +33,7 @@ be passed to functions of pynwb etc.
 .. literalinclude:: /examples/dandiapi-as_readable.py
     :language: python
 
-You can see more usages of DANDI API to assist with data streaming at
+You can see more usages of LINC API to assist with data streaming at
 `PyNWB: Streaming NWB files <https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/streaming.html>`_.
 
 Client
@@ -44,8 +44,8 @@ Client
 .. autoclass:: DandiAPIClient
     :show-inheritance:
 
-Dandisets
----------
+Datasets
+--------
 
 .. autoclass:: RemoteDandiset()
 

docs/source/modref/dandiarchive.rst

@@ -1,6 +1,6 @@
-``dandi.dandiarchive``
-======================
+``lincbrain.dandiarchive``
+==========================
 
-.. automodule:: dandi.dandiarchive
+.. automodule:: lincbrain.dandiarchive
     :member-order: bysource
     :show-inheritance: