Module bussilab.cli_documentation
Documentation for command line tools
This module only contains the documentation of the subcommands used in the
command line interface.
For all the subcommands, a short help identical to that generated by the
-h option is shown. In addition, if present, the docstring of the
function is also shown here.
list
usage: bussilab list [-h]
List available python modules.
options:
-h, --help show this help message and exit
check
usage: bussilab check [-h] [--import]
Check installed features
options:
-h, --help show this help message and exit
--import check if all the submodules can be imported
wham
usage: bussilab wham [-h] -b BIAS [-o OUT] [--use-frame-weight]
[--traj-weight [TRAJ_WEIGHT ...]] [-T T] [-m MAXITER]
[-t THRESHOLD] [-v]
Perform binless WHAM
options:
-h, --help show this help message and exit
-b BIAS, --bias BIAS File containing bias potential (default: None)
-o OUT, --out OUT Output file with weights (default: None)
--use-frame-weight
--traj-weight [TRAJ_WEIGHT ...]
-T T, --temperature T
system temperature in energy units (default: 1.0)
-m MAXITER, --maxiter MAXITER
maximum number of iterations (default: 1000)
-t THRESHOLD, --threshold THRESHOLD
threshold for convergence (default: 1e-40)
-v, --verbose
jrun
usage: bussilab jrun [-h] [-d] [--lab] [--port PORT] [--screen-cmd SCREEN_CMD]
[--screen-log SCREEN_LOG] [--python-exec PYTHON_EXEC]
[-S SOCKNAME] [--no-screen] [--keep-ld-library-path]
[--detach]
Run jupyter server
options:
-h, --help show this help message and exit
-d, --dry-run show command instead of executing it (default: False)
--lab use jupyterlab (default: False)
--port PORT set port (default: 0)
--screen-cmd SCREEN_CMD
screen command (default: screen)
--screen-log SCREEN_LOG
screen logfile (no logfile by default) (default: )
--python-exec PYTHON_EXEC
python executable (default: )
-S SOCKNAME, --sockname SOCKNAME
screen sockname (default: (path):(port):jupyter)
--no-screen do not run screen (default: False)
--keep-ld-library-path
(ignored, this is the default now) (default: False)
--detach detach screen (default: False)
This is a tool to run a jupyter server within a screen command. The typical usage would be
cd /path/to/your/notebook/dir
bussilab jrun
A free port is identified first (can be overridden with the --port
option) and a jupyter server is then run
inside a screen instance.
You will thus have to type CTRL+aCTRL+d in order to detach the screen
letting it run in the background.
Alternatively, you can immediately detach the screen with
cd /path/to/your/notebook/dir
bussilab jrun --detach
Notice that, since the server is run inside a screen instance, in order
to visualize python outputs that has been sent directly to the terminal you
should connect to the screen instance later. By default, a socket name
containing the path where the server is running is used, with / replaced
by :. It should thus be easy to use screen -ls to find the proper screen
instance.
jremote
usage: bussilab jremote [-h] [-d] [-l] [--port PORT] [-i INDEX]
[--python-exec PYTHON_EXEC] [--server-url SERVER_URL]
[--open-cmd OPEN_CMD]
server
Run jupyter client
positional arguments:
server server URL (e.g. giorgione.phys.sissa.it)
options:
-h, --help show this help message and exit
-d, --dry-run show command instead of executing it (default: False)
-l, --list-only only report a list or servers (default: False)
--port PORT set port (default: 0)
-i INDEX, --index INDEX
choose server, by default interactive choice (default:
0)
--python-exec PYTHON_EXEC
remote python executable (e.g. module load python3
python-home; python) (default: python)
--server-url SERVER_URL
URL on server (default: choose interactively)
(default: )
--open-cmd OPEN_CMD open command (detected automatically by default)
(default: )
This is a tool to connect to a remote running jupyter server. The typical usage would be
bussilab jremote server.url
A list of jupyter servers running on the selected machines will be shown, and one of them can be picked typing its progressive number. In case there is a single server running, it will be opened by default.
Notice that if the name of the python executable on the server is
different from plain python you can override it with
--python-exec. You can also run other scripts before, for instance
loading relevant modules:
bussilab jremote giorgione.phys.sissa.it --python-exec --python-exec "module load python3 python-home; python3"
If you recurrently connect to the same workstation, it is convenient
to write a small script like this one, call it jremote and put it in
your path:
export PYTHONPATH=/path/to/bussilab/source
python -m bussilab jremote giorgione.phys.sissa.it --python-exec "module load python3 python-home ; python3"
Here replace python with the name of your python interpreter (might be
python3.7).
pip_upgrade_all
usage: bussilab pip_upgrade_all [-h] [--user]
Upgrade all packages with pip
options:
-h, --help show this help message and exit
--user install/upgrade in user location (default: False)
This is a tool to upgrade all your packages with pip. It is a convenient way to upgrade all the packages without the need to list them explicitly.
Warning: this uses pip, so it might not work as expected if you are working in conda.
The typical usage would be
bussilab pip_upgrade_all
If you installed packages in your home you should use
bussilab pip_upgrade_all --user
notify
usage: bussilab notify [-h] [-m MESSAGE]
[-c CHANNEL | -u UPDATE | -d DELETE | -r REPLY | -R REPLY_BROADCAST | -X REACT]
[-f FILE] [-t TITLE] [--no-footer]
[--screenlog SCREENLOG]
[--screenlog-maxlines SCREENLOG_MAXLINES] [--type TYPE]
[--token TOKEN] [-q]
Send a notification to Slack
options:
-h, --help show this help message and exit
-m MESSAGE, --message MESSAGE
message (default: None)
-c CHANNEL, --channel CHANNEL
channel (check ~/.bussilabrc by default) (default:
None)
-u UPDATE, --update UPDATE
url of the message to be updated (default: None)
-d DELETE, --delete DELETE
url of the message to be deleted (default: None)
-r REPLY, --reply REPLY
url of the message to be replied (default: None)
-R REPLY_BROADCAST, --reply-broadcast REPLY_BROADCAST
url of the message to be broadcast-replied (default:
None)
-X REACT, --react REACT
react to a message (default: None)
-f FILE, --file FILE path to a file to be uploaded (incompatible with -u
and -d) (default: None)
-t TITLE, --title TITLE
title of the message (default: None)
--no-footer ignore footer (default: False)
--screenlog SCREENLOG
screenlog file (default: None)
--screenlog-maxlines SCREENLOG_MAXLINES
maximum number of lines in screenlog (0 means all)
(default: 0)
--type TYPE 'plain_text' or 'mrkdwn' (default: mrkdwn)
--token TOKEN token (check ~/.bussilabrc by default (default: None)
-q, --quiet quiet (do not write output) (default: False)
This is a tool to send a notification to Slack.
See the documentation of bussilab.notify.
cron
usage: bussilab cron [-h] [--quick-start]
[--quick-start-skip-steps QUICK_START_SKIP_STEPS]
[--quick-start-event QUICK_START_EVENT]
[--cron-file CRON_FILE] [--screen-cmd SCREEN_CMD]
[--screen-log SCREEN_LOG] [--no-screen]
[--keep-ld-library-path] [-S SOCKNAME]
[--python-exec PYTHON_EXEC] [--detach] [--unique]
[--window] [--period PERIOD] [--max-times MAX_TIMES]
Run cron
options:
-h, --help show this help message and exit
--quick-start run immediately (default: False)
--quick-start-skip-steps QUICK_START_SKIP_STEPS
skip steps on quick start (default: None)
--quick-start-event QUICK_START_EVENT
event number for quick start (default: None)
--cron-file CRON_FILE
path to cron file (default: None)
--screen-cmd SCREEN_CMD
screen command (default: screen)
--screen-log SCREEN_LOG
screen logfile (no logfile by default) (default: )
--no-screen do not run screen (default: False)
--keep-ld-library-path
(ignored, this is the default now) (default: False)
-S SOCKNAME, --sockname SOCKNAME
screen sockname (default: (path):cron)
--python-exec PYTHON_EXEC
python executable (default: )
--detach detach screen (default: False)
--unique allow only one screen with this socket (default:
False)
--window run a new window within the same screen (default:
False)
--period PERIOD period (seconds) default read from cron file or set to
3600 (default: None)
--max-times MAX_TIMES
maximum number of calls (default: None)
required
usage: bussilab required [-h] [--macports | --conda] [--pyver PYVER]
print requirements
options:
-h, --help show this help message and exit
--macports conda syntax (default: False)
--conda macports syntax (default: False)
--pyver PYVER pyversion (e.g. 38), for macports only (default: )