abidoc.py

This script provides a command line interface to the Abinit documentation. For example, the documentation for the ecut input variable can be obtained with:

abidoc.py man ecut

For the full list of commands use:

$ abidoc.py --help
usage: abidoc.py [-h] [-V]
                 {man,graphviz,browse,apropos,find,withdim,list,manager,scheduler,abibuild}
                 ...

optional arguments:
  -h, --help            show this help message and exit
  -V, --version         show program's version number and exit

subcommands:
  Valid subcommands

  {man,graphviz,browse,apropos,find,withdim,list,manager,scheduler,abibuild}
                        sub-command help
    man                 Show documentation for varname.
    graphviz            Draw variable dependencies with graphviz package.See
                        https://graphviz.readthedocs.io/.
    browse              Open documentation in browser.
    apropos             Find variables related to varname.
    find                Find all variables whose name contains varname.
    withdim             Find all arrays depending on the given dimension.
    list                List all variables.
    manager             Document the TaskManager options.
    scheduler           Document the options available in scheduler.yml.
    abibuild            Show ABINIT build information and exit.

Usage example:

    abidoc.py man ecut        --> Show documentation for ecut input variable.
    abidoc.py graphviz acell  --> Draw parents and children of variable with graphviz package.
    abidoc.py browse acell    --> Open url in external browser.
    abidoc.py apropos ecut    --> To search in the database for the variables related to ecut.
    abidoc.py find paw        --> To search in the database for the variables whose name contains paw.
    abidoc.py list            --> Print full list of variables.
    abidoc.py withdim natom   --> Print arrays depending on natom.
    abidoc.py scheduler       --> Document scheduler options.
    abidoc.py manager         --> Document manager options.

Use `abidoc.py --help` for help and `abidoc.py COMMAND --help` to get the documentation for `COMMAND`.
Use `-v` to increase verbosity level (can be supplied multiple times e.g -vv).

Complete command line reference

usage: abidoc.py [-h] [-V]
                 {man,graphviz,browse,apropos,find,withdim,list,manager,scheduler,abibuild}
                 ...

Named Arguments

-V, --version

show program’s version number and exit

subcommands

Valid subcommands

command

Possible choices: man, graphviz, browse, apropos, find, withdim, list, manager, scheduler, abibuild

sub-command help

Sub-commands:

man

Show documentation for varname.

abidoc.py man [-h] [-v] [--loglevel LOGLEVEL] [-c CODENAME] varname

Positional Arguments

varname

ABINIT variable

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: “ERROR”

-c, --codename

Code name e.g. anaddb, optic… Default: abinit

Default: “abinit”

graphviz

Draw variable dependencies with graphviz package.See https://graphviz.readthedocs.io/.

abidoc.py graphviz [-h] [-v] [--loglevel LOGLEVEL] [-c CODENAME] [-e ENGINE]
                   varname

Positional Arguments

varname

ABINIT variable

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: “ERROR”

-c, --codename

Code name e.g. anaddb, optic… Default: abinit

Default: “abinit”

-e, --engine

graphviz engine: [‘dot’, ‘neato’, ‘twopi’, ‘circo’, ‘fdp’, ‘sfdp’, ‘patchwork’, ‘osage’]. Default: automatic i.e. the engine is automatically selected. See http://www.graphviz.org/pdf/dot.1.pdf Use conda install python-graphviz or pip install graphviz to install the python package

Default: “automatic”

browse

Open documentation in browser.

abidoc.py browse [-h] [-v] [--loglevel LOGLEVEL] [-c CODENAME] varname

Positional Arguments

varname

ABINIT variable

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: “ERROR”

-c, --codename

Code name e.g. anaddb, optic… Default: abinit

Default: “abinit”

apropos

Find variables related to varname.

abidoc.py apropos [-h] [-v] [--loglevel LOGLEVEL] [-c CODENAME] varname

Positional Arguments

varname

ABINIT variable

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: “ERROR”

-c, --codename

Code name e.g. anaddb, optic… Default: abinit

Default: “abinit”

find

Find all variables whose name contains varname.

abidoc.py find [-h] [-v] [--loglevel LOGLEVEL] [-c CODENAME] varname

Positional Arguments

varname

ABINIT variable

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: “ERROR”

-c, --codename

Code name e.g. anaddb, optic… Default: abinit

Default: “abinit”

withdim

Find all arrays depending on the given dimension.

abidoc.py withdim [-h] [-v] [--loglevel LOGLEVEL] [-c CODENAME] dimname

Positional Arguments

dimname

Dimension name

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: “ERROR”

-c, --codename

Code name e.g. anaddb, optic… Default: abinit

Default: “abinit”

list

List all variables.

abidoc.py list [-h] [-v] [--loglevel LOGLEVEL] [-c CODENAME] [--mode MODE]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: “ERROR”

-c, --codename

Code name e.g. anaddb, optic… Default: abinit

Default: “abinit”

--mode

Sort mode, a for alphabethical, s for varset, c for characteristics.

Default: “a”

manager

Document the TaskManager options.

abidoc.py manager [-h] [-v] [--loglevel LOGLEVEL] [-c CODENAME] [qtype]

Positional Arguments

qtype

Write job script to terminal if qtype=’script’ else document the qparams for the given QueueAdapter qtype e.g. slurm.

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: “ERROR”

-c, --codename

Code name e.g. anaddb, optic… Default: abinit

Default: “abinit”

scheduler

Document the options available in scheduler.yml.

abidoc.py scheduler [-h] [-v] [--loglevel LOGLEVEL] [-c CODENAME]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: “ERROR”

-c, --codename

Code name e.g. anaddb, optic… Default: abinit

Default: “abinit”

abibuild

Show ABINIT build information and exit.

abidoc.py abibuild [-h] [-v] [--loglevel LOGLEVEL] [-c CODENAME]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: “ERROR”

-c, --codename

Code name e.g. anaddb, optic… Default: abinit

Default: “abinit”