cellpy.cli

Module Contents

Functions

cli()	cellpy - command line interface.
dump_env_file(env_filename)	saves (writes) the env to file
echo_missing_modules()	prints out the missing modules
edit(name, default_editor, debug, silent)	Edit your cellpy config or database files.
get_default_config_file_path([init_filename])	gets the path to the default config-file
get_dst_file(user_dir, init_filename)	gets the destination path for the config-file
get_package_prm_dir()	gets the folder where the cellpy package lives
info(version, configloc, params, check)	This will give you some valuable information about your cellpy.
new(template, directory, project, experiment, ...)	Set up a batch experiment (might need git installed).
pull(tests, examples, clone, directory, password)	Download examples or tests from the big internet (needs git).
run(journal, key, folder, cellpy_project, debug, ...)	Run a cellpy process (for example a batch-job).
save_prm_file(prm_filename)	saves (writes) the prms to file
serve(lab, directory, executable)	Start a Jupyter server.
setup(interactive, not_relative, dry_run, reset, ...)	This will help you to set up cellpy.

Attributes

DEFAULT_EDITOR
DIFFICULT_MISSING_MODULES
EDITORS
GITHUB_PWD_VAR_NAME
REPO
USER
VERSION

cli()

cellpy - command line interface.

dump_env_file(env_filename)

saves (writes) the env to file

echo_missing_modules()

prints out the missing modules

edit(name, default_editor, debug, silent)

Edit your cellpy config or database files.

You can use this to edit the configuration file, the database file, or the environment file. If you do not specify which file to edit, the configuration file will be opened.

Examples

edit your cellpy configuration file

cellpy edit config

or just

cellpy edit

edit your cellpy database file

cellpy edit db

edit your cellpy environment file using notepad.exe (on Windows)

cellpy edit env -e notepad.exe

get_default_config_file_path(init_filename=None)

gets the path to the default config-file

get_dst_file(user_dir, init_filename)

gets the destination path for the config-file

get_package_prm_dir()

gets the folder where the cellpy package lives

info(version, configloc, params, check)

This will give you some valuable information about your cellpy.

new(template, directory, project, experiment, local_user_template, serve_, run_, lab, jupyter_executable, list_)

Set up a batch experiment (might need git installed).

pull(tests, examples, clone, directory, password)

Download examples or tests from the big internet (needs git).

run(journal, key, folder, cellpy_project, debug, silent, raw, cellpyfile, minimal, nom_cap, batch_col, project, list_, name)

Run a cellpy process (for example a batch-job).

You can use this to launch specific applications.

Examples

run a batch job described in a journal file

cellpy run -j my_experiment.json

save_prm_file(prm_filename)

saves (writes) the prms to file

serve(lab, directory, executable)

Start a Jupyter server.

setup(interactive, not_relative, dry_run, reset, root_dir, folder_name, test_user, silent, no_deps)

This will help you to set up cellpy.

DEFAULT_EDITOR = 'vim'

DIFFICULT_MISSING_MODULES

EDITORS

GITHUB_PWD_VAR_NAME = 'GD_PWD'

REPO = 'jepegit/cellpy'

USER = 'jepegit'

VERSION