Command line interface#

MiniAn installs a single minian command with two command groups:

minian notebooks lists and copies the notebooks bundled with the package.
minian data lists, downloads, and locates the demo datasets (hosted on Zenodo, fetched on demand, cached, and checksum-verified).

The full set of commands and options is below.

MiniAn command line tools: fetch demo data and copy out notebooks.

usage: minian [-h] {data,notebooks} ...

subcommands#

group: Possible choices: data, notebooks

Sub-commands#

data#

Fetch demo datasets from Zenodo. Downloads are cached under the OS cache dir; set the MINIAN_CACHE_DIR environment variable to override the location (point it at a prepopulated cache to run offline).

minian data [-h] {list,download,path} ...

subcommands#

data_command: Possible choices: list, download, path

Sub-commands#

list#

list datasets and sizes

minian data list [-h]

download#

download and cache a dataset

minian data download [-h] [--all] [name]

Positional Arguments#

name: dataset name (see list)

Named Arguments#

--all

select every dataset

Default: False

path#

print a dataset’s local path (fetching if needed)

minian data path [-h] name

Positional Arguments#

name: dataset name

notebooks#

copy bundled notebooks out of the package

minian notebooks [-h] {list,copy} ...

subcommands#

notebooks_command: Possible choices: list, copy

Sub-commands#

list#

list available notebooks

minian notebooks list [-h]

copy#

copy a notebook into a directory

minian notebooks copy [-h] [--all] [-o OUTPUT] [name]

Positional Arguments#

name: notebook name (see list)

Named Arguments#

--all

select every notebook

Default: False

-o, --output

destination directory (default: ./minian-notebooks)