`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
/usr/share/miniconda/envs/abipy/bin/abidoc.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').require('abipy==0.9.8')
usage: abidoc.py [-h] [-V]
                 {man,graphviz,browse,apropos,find,withdim,list,manager,scheduler,abibuild,urls}
                 ...

options:
  -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,urls}
                        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.
    urls                Produce Yaml file with varname --> ulrs.

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,urls}
                 ...

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, urls

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'

urls¶

Produce Yaml file with varname –> ulrs.

abidoc.py urls [-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'

abidoc.py¶

Named Arguments¶

subcommands¶

Sub-commands¶

man¶

Positional Arguments¶

Named Arguments¶

graphviz¶

Positional Arguments¶

Named Arguments¶

browse¶

Positional Arguments¶

Named Arguments¶

apropos¶

Positional Arguments¶

Named Arguments¶

find¶

Positional Arguments¶

Named Arguments¶

withdim¶

Positional Arguments¶

Named Arguments¶

list¶

Named Arguments¶

manager¶

Positional Arguments¶

Named Arguments¶

scheduler¶

Named Arguments¶

abibuild¶

Named Arguments¶

urls¶

Named Arguments¶

`abidoc.py`¶