Command Line Interface

Command Line Interface#

cryosparc-tools includes a simple command line interface (CLI) for managing your CryoSPARC instance.

After installation, run commands from your terminal in this format:

python -m cryosparc.tools <command> [options]

Currently, this only supports the login command.

Run with the --help flag to see available commands and options:

python -m cryosparc.tools --help

Commands#

login#

Log in to a CryoSPARC instance.

python -m cryosparc.tools login --url <URL>

Replace <URL> with the URL you use to access CryoSPARC from your web browser, e.g., http://localhost:39000. Enter your CryoSPARC email and password when prompted.

This saves a login token to a local file, used to authenticate scripts that use the CryoSPARC function without needing to include your credentials in the script:

from cryosparc.tools import CryoSPARC

cs = CryoSPARC("http://localhost:39000")
project = cs.find_project("P1")

The token expires after 2 weeks by default. To renew it, run the login command again. Specify flag --expires <DATE>, with <DATE> in YYYY-MM-DD format, to set a longer expiration date. For example:

python -m cryosparc.tools login --url http://localhost:39000 --expires 2025-12-31

This sets the token to expire on December 31, 2025. Note that the expiration date cannot be more than 1 year in the future.

You may also specify one or both of --email and --password flags to provide your credentials directly.

python -m cryosparc.tools login --url http://localhost:39000 \
  --email "ali@example.com" \
  --password "mysecretpassword" \
  --expires 2025-12-31

Advanced Usage#

You may log in to multiple CryoSPARC instances or with different user accounts by running the command multiple times with different URLs and email addresses. For example:

python -m cryosparc.tools login --url http://localhost:39000 --email ali@example.com
python -m cryosparc.tools login --url http://localhost:39000 --email saara@example.com
python -m cryosparc.tools login --url https://cryosparc.example.com --email suhail@example.com

In your Python script, specify an email argument to use a specific login when multiple logins are active:

from cryosparc.tools import CryoSPARC

local_cs = CryoSPARC("http://localhost:39000", email="saara@example.com")
remote_cs = CryoSPARC("https://cryosparc.example.com", email="suhail@example.com")

If no email is specified, the first login created for the given URL will be used.

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