Update docs: bring the command-line reference in sync with the CLI

docs/source/cmdline/download.rst

@@ -65,3 +65,23 @@ Options
 .. option:: --sync
 
     Delete local assets that do not exist on the server after downloading
+
+.. option:: --zarr FILTER
+
+    Only download the entries of Zarr assets that match the given filter.  The
+    filter is either the predefined name ``metadata``, which selects the Zarr
+    metadata files (``.zarray``, ``.zattrs``, ``.zgroup``, ``.zmetadata``, and
+    ``zarr.json``), or ``TYPE:PATTERN``, where ``TYPE`` is one of:
+
+    - ``glob`` — ``PATTERN`` is a glob matched against the entry's path within
+      the Zarr, with ``**`` matching across directories (e.g.,
+      ``glob:0/**/*``)
+
+    - ``path`` — ``PATTERN`` is a path within the Zarr; the entry at that path
+      and all entries under it are downloaded
+
+    - ``regex`` — ``PATTERN`` is a regular expression searched for in the
+      entry's path within the Zarr
+
+    Can be specified multiple times, in which case an entry is downloaded if it
+    matches any of the filters.

docs/source/cmdline/organize.rst

@@ -65,6 +65,11 @@ Options
     What to do if files without sufficient metadata are encountered  [default:
     ``fail``]
 
+.. option:: -J, --jobs N
+
+    Number of parallel jobs to use while organizing, e.g., for extracting the
+    metadata from the files  [default: one per CPU core]
+
 .. option:: --media-files-mode [copy|move|symlink|hardlink]
 
     How to relocate video files referenced by NWB files [default: ``symlink``]

docs/source/cmdline/upload.rst

@@ -60,6 +60,15 @@ Options
     Data should pass validation before uploading.  Use of this option is highly
     discouraged.
 
+.. option:: --zarr-mode [full|patch]
+
+    How to synchronize Zarr assets with the server:
+
+    - ``full`` [default] — make the Zarr on the server identical to the local
+      one, deleting entries on the server that do not exist locally
+    - ``patch`` — upload new and changed entries only, without deleting
+      anything on the server
+
 
 Development Options
 -------------------

docs/source/cmdline/validate-bids.rst

@@ -0,0 +1,34 @@
+:program:`dandi validate-bids`
+==============================
+
+::
+
+    dandi [<global options>] validate-bids [<options>] [<path> ...]
+
+Validate BIDS paths.
+
+.. note::
+
+    This command is deprecated: :ref:`dandi validate <dandi_validate>`
+    validates BIDS datasets along with everything else and should be used
+    instead.  ``dandi validate-bids`` now merely invokes it with the given
+    paths and :option:`--grouping` (after emitting a deprecation warning).
+
+Options
+-------
+
+.. option:: -g, --grouping [none|path]
+
+    How to group the reported results  [default: ``none``]
+
+.. option:: --report-path <path>
+
+    Accepted for backwards compatibility but ignored
+
+.. option:: -r, --report
+
+    Accepted for backwards compatibility but ignored
+
+.. option:: --schema VERSION
+
+    Accepted for backwards compatibility but ignored

docs/source/cmdline/validate.rst

@@ -1,30 +1,87 @@
+.. _dandi_validate:
+
 :program:`dandi validate`
 =========================
 
 ::
 
-    dandi [<global options>] validate [<path> ...]
+    dandi [<global options>] validate [<options>] [<path> ...]
 
 Validate files for data standards compliance.
 
 Exits with non-zero exit code if any file is not compliant.
 
+The validation results are automatically saved as a JSON Lines companion file
+next to the dandi-cli log file (unless :option:`--output` is used or
+:option:`--load` is active).  Use :option:`--load` to re-render saved results
+later with different grouping, filtering, or format options.
+
 Options
 -------
 
-.. option:: -g, --grouping [none|path]
+.. option:: -g, --grouping [none|path|severity|id|validator|standard|dandiset]
 
-    Set how to group reported errors & warnings: by path or not at all
-    (default)
+    How to group the reported results.  Repeat the option for hierarchical
+    nesting, e.g., ``-g severity -g id``.  [default: ``none``]
 
 .. option:: --ignore REGEX
 
-    Ignore any validation errors & warnings whose ID matches the given regular
+    Ignore any validation results whose ID matches the given regular
     expression
 
-.. option:: --min-severity [HINT|WARNING|ERROR]
+.. option:: --min-severity [INFO|HINT|WARNING|ERROR|CRITICAL]
+
+    Only display results with severities at or above this level  [default:
+    ``HINT``]
+
+.. option:: -f, --format [text|json|json_pp|json_lines|yaml]
+
+    Output format  [default: ``text``]
+
+.. option:: -o, --output <file>
+
+    Write the output to the given file instead of standard output.  This
+    requires a structured :option:`--format`; if none is given, the format is
+    inferred from the file's extension (``.json``, ``.jsonl``, ``.yaml``, or
+    ``.yml``).  :option:`--grouping` cannot be combined with the ``json_lines``
+    format.
+
+.. option:: --summary, --no-summary
+
+    Whether to show summary statistics (counts of results by severity,
+    validator, and standard) after the results  [default: ``--no-summary``]
+
+.. option:: --max-per-group N
+
+    Limit the number of results shown per group (or in total when not
+    grouping); the excess is replaced by a count of omitted results
+
+.. option:: --missing-file-content [error|only-non-data|skip]
+
+    How to handle files whose content is unavailable, such as the broken
+    symbolic links of a DataLad_ dataset (a git-annex_ repository) whose
+    content has not been fetched:
+
+    ``error``
+        Emit a concise ``DANDI.FILE_CONTENT_MISSING`` error for each such file
+        (default)
+
+    ``skip``
+        Skip each such file, emitting a warning
+
+    ``only-non-data``
+        Skip content-dependent validators (pynwb, nwbinspector, ...) for each
+        such file but still validate its path layout
+
+.. option:: --load <file>
+
+    Instead of running validation, load previously saved results from the
+    given JSON Lines file (e.g., an automatically saved companion file) and
+    render them.  Can be specified multiple times; cannot be combined with
+    paths.
 
-    Only display issues with severities above this level (HINT by default)
+.. _DataLad: https://www.datalad.org
+.. _git-annex: https://git-annex.branchable.com
 
 
 Development Options