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Dec 12, 2022
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dandi-cli readme edit #1170

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dandi-cli readme edit
melster1010 Dec 1, 2022
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fix spelling
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Update dandi and ls --help output
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57 changes: 32 additions & 25 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,29 +6,32 @@
[![PyPI version fury.io](https://badge.fury.io/py/dandi.svg)](https://pypi.python.org/pypi/dandi/)
[![Documentation Status](https://readthedocs.org/projects/dandi/badge/?version=latest)](https://dandi.readthedocs.io/en/latest/?badge=latest)

This project is under heavy development. Beware of [hidden](I-wish-we-knew) and
[disclosed](https://github.com/dandi/dandi-cli/issues) issues, or
The [DANDI Python client](https://pypi.org/project/dandi/) allows you to:

* Download `Dandisets` and individual subject folders or files
* Organize your data locally before upload
* Upload `Dandisets`

**Note**: This project is under heavy development. See [the issues log](https://github.com/dandi/dandi-cli/issues) or
[Work-in-Progress (WiP)](https://github.com/dandi/dandi-cli/pulls).

## Installation

At the moment DANDI client releases are [available from PyPI](https://pypi.org/project/dandi)
and [conda-forge](https://anaconda.org/conda-forge/dandi). You could
install them in your Python (native, virtualenv, or conda) environment via
DANDI Client releases are [available from PyPI](https://pypi.org/project/dandi)
and [conda-forge](https://anaconda.org/conda-forge/dandi). Install them in your Python (native, virtualenv, or
conda) environment via

pip install dandi

or

conda install -c conda-forge dandi

if you are in a conda environment.

## dandi tool
## CLI Tool

This package provides a `dandi` command line utility with a basic interface
which should assist you in preparing and uploading your data to and/or obtaining
data from the http://dandiarchive.org:
This package provides a command line utility with a basic interface
to help you prepare and upload your data to, or obtain data from, the [DANDI archive](http://dandiarchive.org):

```bash
$> dandi
Expand All @@ -46,21 +49,21 @@ Usage: dandi [OPTIONS] COMMAND [ARGS]...
Options:
--version
-l, --log-level [DEBUG|INFO|WARNING|ERROR|CRITICAL]
Log level name [default: INFO]
--pdb Fall into pdb if errors out
Log level name [default: INFO].
--pdb Fall into pdb if errors out.
--help Show this message and exit.

Commands:
download Download a file or entire folder from DANDI
download Download a file or entire folder from DANDI.
ls List .nwb files and dandisets metadata.
organize (Re)organize files according to the metadata.
register Register a new dandiset in the DANDI archive
register Register a new dandiset in the DANDI archive.
upload Upload dandiset (files) to DANDI archive.
validate Validate files for NWB (and DANDI) compliance.
```

Each of the commands has a set of options to alter their behavior. Please run
`dandi COMMAND --help` to get more information, e.g.
Each of the commands has a set of options to alter its behavior. Run
`dandi COMMAND --help` to get more information:

```
$> dandi ls --help
Expand All @@ -71,7 +74,7 @@ Usage: dandi ls [OPTIONS] [PATHS]...
Options:
-F, --fields TEXT Comma-separated list of fields to display.
An empty value to trigger a list of
available fields to be printed out
available fields to be printed out.
-f, --format [auto|pyout|json|json_pp|yaml]
Choose the format/frontend for output. If
'auto', 'pyout' will be used in case of
Expand All @@ -80,16 +83,20 @@ Options:
--help Show this message and exit.
```

See [DANDI Handbook](https://www.dandiarchive.org/handbook/10_using_dandi/)
for examples on how to use this client in various use cases.

## Development/contributing
## Third-party Components

Please see [DEVELOPMENT.md](./DEVELOPMENT.md) file.
**dandi/tests/skip.py** -- from https://github.com/ReproNim/reproman, as of v0.2.1-40-gf4f026d
Copyright (c) 2016-2020 ReproMan Team
Comment on lines -86 to +124
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@waxlamp waxlamp Dec 12, 2022

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Also out of scope for this PR, but I think this section can be struck. I don't think it adds any useful information about DANDI CLI.

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@melster1010 melster1010 Dec 13, 2022

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Added to my Phase 2 docs backlog for 2023.


## 3rd party components included
## Resources

### dandi/tests/skip.py
* To learn how to interact with the DANDI archive and for examples on how to use the DANDI Client in various use cases,
see [the handbook](https://www.dandiarchive.org/handbook/).
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@waxlamp waxlamp Dec 12, 2022

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I think it might be useful to highlight sections of the handbook specifically related to the CLI:

Suggested change
see [the handbook](https://www.dandiarchive.org/handbook/).
see [the handbook](https://www.dandiarchive.org/handbook/),
specifically the sections on using the CLI to
[download](https://www.dandiarchive.org/handbook/12_download/) and
[upload](https://www.dandiarchive.org/handbook/13_upload/) `Dandisets`.

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@melster1010 melster1010 Dec 13, 2022

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I agree that specific guidance would be useful. Added to my Phase 2 docs backlog for 2023.


From https://github.com/ReproNim/reproman, as of v0.2.1-40-gf4f026d
Copyright (c) 2016-2020 ReproMan Team
* To get help:
- ask a question: https://github.com/dandi/helpdesk/discussions
- file a feature request or bug report: https://github.com/dandi/helpdesk/issues/new/choose
- contact the DANDI team: [email protected]

* To understand how to contribute to the dandi-cli repository, see the [DEVELOPMENT.md](./DEVELOPMENT.md) file.