Command line overview for solidipes

solidipes is a command line tool that allows you to initialize a study directory, upload it to Zenodo, and generate reports.

command line options for solidipes

argument command	Attributes
init : Initialize a study directory	positional arguments: directory: Path to the directory to initialize. Defaults to the current directory. Cannot be your home directory. optional arguments: -h: help message --force: Force the creation of solidipes configuration files in the current directory. WARNING: This could erase an existing .solidipes directory! usage: solidipes init [-h] [--force] [directory]
view: Opens a new browser window with the data (e.g. table, image)	positional arguments: path: Path to file to be viewed optional arguments: -h: show this help message and exit usage: solidipes view [-h] path
upload: Upload dataset to an online repository	positional arguments: {zenodo}: Target hosting platform zenodo: upload study to Zenodo optional arguments: -h: show this help message and exit usage: solidipes upload [-h] {zenodo} ...
upload zenodo: Upload study to Zenodo	positional arguments: directory: Path to the directory containing the study to upload. Default directory: root of the current Solidipes study. optional arguments: -h: show this help message and exit --sandbox: use Zenodo sandbox test platform --access_token ACCESS_TOKEN: Provide the Zenodo token --new-deposition: create a new deposition instead of updating a previously created one --existing-deposition [EXISTING_IDENTIFIER]: URL or DOI of the unpublished study to update usage: solidipes upload zenodo [-h] [--sandbox] [--access_token ACCESS_TOKEN] [--new-deposition] [--existing-deposition [EXISTING_IDENTIFIER]] [directory]
report: Generate a .py report	positional arguments: {curation,jtcam,web_report}: The report to generate curation: controls sanity of the data jtcam: opens a web report for the JTCAM Journal web_report: generates web_report (it also runs curation) dir_path: Path to directory containing data files additional_arguments: Arguments to forward to the report optional arguments: -h: show this help message and exit usage: solidipes report [-h] {curation,jtcam,web_report} dir_path ...
download: Download content from Zenodo	positional arguments: identifier: URL or DOI of the study to download destination: Path to the destination folder optional arguments: -h: show this help message and exit --only-metadata: Only download metadata (overrides destination directory’s metadata!) usage: solidipes download [-h] [--only-metadata] identifier [destination]