cmdy 0.4.0

Shell language to run command in python

cmdy

"Shell language" to run command in python

Installation

pip install cmdy

Usage

See Demo

Basic usage

from cmdy import ls
print(ls())

for line in ls().iter():
    print('Got:', line, end='')

With non-keyword arguments

from cmdy import tar
print(tar("cvf", "/tmp/test.tar", "./cmdy"))

With keyword arguments

from cmdy import curl
curl("http://duckduckgo.com/", o="/tmp/page.html", silent=True)
# curl http://duckduckgo.com/ -o /tmp/page.html --silent

Order keyword arguments

curl("http://duckduckgo.com/", "-o", "/tmp/page.html", "--silent")
# or

from diot import OrderedDiot
kwargs = OrderedDiot()
kwargs.silent = True
kwargs.o = '/tmp/page.html'
curl("http://duckduckgo.com/", kwargs)
# You can also use collections.OrderedDict

Prefix and separator for keyword arguments

from cmdy import bedtools, bcftools
bedtools.intersect(wa=True, wb=True,
                   a='query.bed', b=['d1.bed', 'd2.bed', 'd3.bed'],
                   names=['d1', 'd2', 'd3'], sorted=True,
                   _prefix='-').h().strcmd
# 'bedtools intersect -wa -wb -a query.bed \
# -b d1.bed d2.bed d3.bed -names d1 d2 d3 -sorted'

# default prefix is auto
bcftools.query(_=['a.vcf', 'b.vcf'], H=True,
               format='%CHROM\t%POS\t%REF\t%ALT\n').h().strcmd

# "bcftools query -H --format '%CHROM\t%POS\t%REF\t%ALT\n' a.vcf b.vcf"

ls(l=True, block_size='KB', _sep='auto').h().cmd
['ls', '-l', '--block-size=KB']

Mixed combinations of prefices and separators in one command

from cmdy import java
# Note this is just an example for old verion picard.
# Picard is changing it's style

picard = java(jar='picard.jar', _prefix='', _sep='=', _sub=True)
c = picard.SortSam(I='input.bam', O='sorted.bam',
               SORTED_ORDER='coordinate',
               _prefix='', _sep='=', _deform=None).h
print(c.cmd)

# same as the above
java({'jar': 'picard.jar', '_prefix': '-', '_sep': ' '},
     'SortSam', I='input.bam', O='sorted.bam',
     SORTED_ORDER='coordinate', _prefix='', _sep='=', _deform=None).h().cmd

# _deform prevents SORTED_ORDER to be deformed to SORTED-ORDER

# ['java', 'jar=picard.jar',
#  'SortSam', 'I=input.bam', 'O=sorted.bam', 'SORTED_ORDER=coordinate']

Subcommands

from cmdy import git
git.branch(v=True).fg
# <CmdyResult: ['git', 'branch', '-v']>

# What if I have separate arguments for main and sub-command?
git(git_dir='.', _sub=True).branch(v=True).h
# <CmdyHolding: ['git', '--git-dir', '.', 'branch', '-v']>

Duplicated keys for list arguments:

from cmdy import sort
print(sort(k=['1,1', '2,2'], t='_', _='./.editorconfig', _dupkey=True))
# sort -k 1,1 -k 2,2 ./.editorconfig

Return code and exception

from cmdy import x
x()

Traceback (most recent call last):
  File "<ipython-input-16-092cc5b72e61>", line 2, in <module>
    x()
/path/.../to/cmdy/__init__.py", line 146, in __call__
    ready_cfgargs, ready_popenargs, _will())
/path/.../to/cmdy/__init__.py", line 201, in __new__
    result = holding.run()
/path/.../to/cmdy/__init__.py", line 854, in run
    return orig_run(self, wait)
/path/.../to/cmdy/__init__.py", line 717, in run
    return orig_run(self, wait)
/path/.../to/cmdy/__init__.py", line 327, in run
    ret = CmdyResult(self._run(), self)
/path/.../to/cmdy/__init__.py", line 271, in _run
    raise CmdyExecNotFoundError(str(fnfe)) from None
cmdy.cmdy_util.CmdyExecNotFoundError: [Errno 2] No such file or directory: 'x': 'x'

from cmdy import ls
ls('non-existing-file')

Traceback (most recent call last):
  File "<ipython-input-17-132683fc2227>", line 2, in <module>
    ls('non-existing-file')
/path/.../to/cmdy/__init__.py", line 146, in __call__
    ready_cfgargs, ready_popenargs, _will())
/path/.../to/cmdy/__init__.py", line 204, in __new__
    return result.wait()
/path/.../to/cmdy/__init__.py", line 407, in wait
    raise CmdyReturnCodeError(self)
cmdy.cmdy_util.CmdyReturnCodeError: Unexpected RETURN CODE 2, expecting: [0]

  [   PID] 167164

  [   CMD] ['ls non-existing-file']

  [STDOUT]

  [STDERR] ls: cannot access non-existing-file: No such file or directory

Don't raise exception but store the return code

from cmdy import ls
result = ls('non-existing-file', _raise=False)
result.rc # 2

Tolerance on return code

from cmdy import ls
# or _okcode=[0,2]
ls('non-existing-file', _okcode='0,2').rc # 2

Timeouts

from cmdy import sleep
sleep(3, _timeout=1)

Traceback (most recent call last):
  File "<ipython-input-20-47b0ec7af55f>", line 2, in <module>
    sleep(3, _timeout=1)
/path/.../to/cmdy/__init__.py", line 146, in __call__
    ready_cfgargs, ready_popenargs, _will())
/path/.../to/cmdy/__init__.py", line 204, in __new__
    return result.wait()
/path/.../to/cmdy/__init__.py", line 404, in wait
    ) from None
cmdy.cmdy_util.CmdyTimeoutError: Timeout after 1 seconds.

Redirections

from cmdy import cat
cat('./pytest.ini').redirect > '/tmp/pytest.ini'
print(cat('/tmp/pytest.ini'))

Appending

# r short for redirect
cat('./pytest.ini').r >> '/tmp/pytest.ini'
print(cat('/tmp/pytest.ini')) # content doubled

Redirecting to a file handler

with open('/tmp/pytest.ini', 'w') as f
    cat('./pytest.ini').r > f

print(cat('/tmp/pytest.ini'))

STDIN, STDOUT and/or STDERR redirections

from cmdy import STDIN, STDOUT, STDERR, DEVNULL

c = cat().r(STDIN) < '/tmp/pytest.ini'
print(c)

# Mixed
c = cat().r(STDIN, STDOUT) ^ '/tmp/pytest.ini' > DEVNULL
# we can't fetch result from a redirected pipe
print(c.stdout)

# Why not '<' for STDIN?
# Because the priority of the operator is not in sequential order.
# We can use < for STDIN, but we need to ensure it runs first
c = (cat().r(STDIN, STDOUT) < '/tmp/pytest.ini') > DEVNULL
print(c.stdout)

# A simple rule for multiple redirections to always use ">" in the last place

# Redirect stderr to stdout
from cmdy import bash
c = bash(c="cat 1>&2").r(STDIN, STDERR) ^ '/tmp/pytest.ini' > STDOUT
print(c.stdout)

# Redirect the world
c = bash(c="cat 1>&2").r(STDIN, STDOUT, STDERR) ^ '/tmp/pytest.ini' ^ DEVNULL > STDOUT
print(c.stdout) # None
print(c.stderr) # None

Pipings

from cmdy import grep
c = ls().p | grep('README')
print(c)
# README.md
# README.rst

# p short for pipe
c = ls().p | grep('README').p | grep('md')
print(c) # README.md
print(c.piped_strcmds) # ['ls', 'grep README', 'grep md']

from cmdy import _CMDY_EVENT
# !!! Pipings should be consumed immediately!
# !!! DO NOT do this
ls().p
ls() # <- Will not run as expected
# All commands will be locked as holding until pipings are consumed
_CMDY_EVENT.clear()
print(ls()) # runs

# See Advanced/Holdings if you want to hold a piping command for a while

Running command in foreground

ls().fg

from cmdy import tail
tail('/tmp/pytest.ini', f=True, _timeout=3).fg
# This mimics the `tail -f` program
# You will see the content comes out one after another
# and then program hangs for 3s

You can also write an echo-like program easily. See 'echo.py'

Iterating on output

for line in ls().iter():
    print(line, end='')

Iterating on stderr

for line in bash(c="cat /tmp/pytest.ini 1>&2").iter(STDERR):
    print(line, end='')

Getting live output

# Like we did for `tail -f` program
# This time, we can do something with each output line

# Let's use a thread to write content to a file
# And we try to get the live contents using cmdy
import time
from threading import Thread
def live_write(file, n):

    with open(file, 'w', buffering=1) as f:
        # Let's write something every half second
        for i in range(n):
            f.write(str(i) + '\n')
            time.sleep(.5)

test_file = '/tmp/tail-f.txt'
Thread(target=live_write, args=(test_file, 10)).start()

from cmdy import tail

tail_iter = tail(f=True, _=test_file).iter()

for line in tail_iter:
    # Do whatever you want with the line
    print('We got:', line, end='')
    if line.strip() == '8':
        break

# make sure thread ends
time.sleep(2)

# What about timeout?

# Of course you can use a timer to check inside the loop
# You can also set a timeout for each fetch

# Terminate after 10 queries

Thread(target=live_write, args=(test_file, 10)).start()

from cmdy import tail

tail_iter = tail(f=True, _=test_file).iter()

for i in range(10):
    print('We got:', tail_iter.next(timeout=1), end='')

Advanced

Baking the cmdy object

Sometimes, you may want to run the same program a couple of times, with the same set of arguments or configurations, and you don't want to type those arguments every time, then you can bake the Cmdy object with that same arguments or configurations.

For example, if you want to run ls as ls -l all the time:

from cmdy import ls
ll = ls.bake(l=True)
print(ll().h.cmd) # ['ls', '-l']
print(ll(a=True).h.cmd) # ['ls', '-l', '-a']
# I don't want the l flag for some commands occasionally
print(ll(l=False).h.cmd) # ['ls']

# Bake a baked command
lla = ll.bake(a=True)
print(lla().h.cmd) # ['ls', '-l', '-a']

# I know git is always gonna run with subcommand
git = git.bake(_sub=True)
# don't bother to pass _sub=True every time
print(git(git_dir='.').branch(v=True).h)
# <CmdyHolding: ['git', '--git-dir', '.', 'branch', '-v']>
print(git().status().h)
# <CmdyHolding: ['git', 'status']>

# What if I have a subcommand call 'bake'?
from cmdy import git, CmdyActionError

print(git.branch().h.cmd) # ['git', 'branch']
print(type(git.bake())) # <class 'cmdy.Cmdy'>

# run the git with _sub
print(git(_sub=True).bake().h.cmd) # ['git', 'bake']

Baking the whole module

import cmdy
# run version of the whole world
sh = cmdy(version=True)
# anything under sh directly will be supposed to have subcommand
from sh import git, gcc
print(git().h)
# <CmdyHolding: ['git', '--version']>
print(gcc().h)
# <CmdyHolding: ['gcc', '--version']>

Note that module baking is deep copying, except the exception classes and some utils. This means, you would expect following behavior:

import cmdy
from cmdy import CmdyHolding, CmdyExecNotFoundError

sh = cmdy()

c = sh.echo().h
print(type(c)) # <class 'cmdy.CmdyHolding'>
print(isinstance(c, CmdyHolding)) # False
print(isinstance(c, sh.CmdyHolding)) # True

try:
    sh.notexisting()
except CmdyExecNotFoundError:
    # we can catch it, as CmdyExecNotFoundError is sh.CmdyExecNotFoundError
    print('Catched!')

Holding objects

You may have noticed that we have a couple of examples above with a final call .h or .h(), which is holding the command from running.

You can do that, too, if you have multiple operations

print(ls().h) # <CmdyHolding: ['ls']>

# however, you cannot hold after some actions
ls().r.h
# CmdyActionError: Should be called in the first place: .h() or .hold()

Once a command is on hold (by .h, .hold, .h() or .hold())

You have to explictly call run() to set the command running

from time import time
tic = time()
c = sleep(2).h
print(f'Time elapsed: {time() - tic:.3f} s')
# Time elapsed: 0.022 s

# not running even with fg
c.fg
print(f'Time elapsed: {time() - tic:.3f} s')
# Time elapsed: 0.034 s
c.run()
print(f'Time elapsed: {time() - tic:.3f} s')
# Time elapsed: 2.043 s

Reuse of command

# After you set a command running,
# you can retrieve the holding object,
# and reuse it
from cmdy import ls
c = ls().fg
# nothing will be produced
c.holding.reset().r > DEVNULL

Async mode

import curio
from cmdy import ls
a = ls().a # async command is never blocking!

async def main():
    async for line in a:
        print(line, end='')

curio.run(main())

Extending cmdy

All those actions for holding/result objects were implemented internally as plugins. You can right your own plugins, too.

A plugin has to be defined as a class and then instantiated.

There are 6 APIs for developing a plugin for cmdy

• cmdy_plugin: A decorator for the plugin class
• cmdy_plugin_hold_then: A decorator to decorate methods in the plugin class, which define actions after a holding object. Arguments:
  • alias: The alias of this action (e.g. r/redir for redirect)
  • final: Whether this is a final action, meaning no other actions should be followed
  • prop: Whether this action can be called as a property
  • hold_right: Should I put right following action on hold? This is useful when we have connectors which then can set the command running. (e.g > for redirect and | for pipe)
• cmdy_plugin_run_then: A decorator to decorate methods in the plugin class, which define actions after a sync result object. Arguments are similar as cmdy_plugin_hold_then except that prop and hold_right are not avaialbe.
• cmdy_plugin_async_run_then: Async verion of cmdy_plugin_run_then
• cmdy_plugin_add_method: A decorator to decorate methods in the plugin class, which add methods to the CmdyHolding, CmdyResult or CmdyAsyncResult class. cls is the only argument that specifies which class we are hacking.
• cmdy_plugin_add_property: Property version of cmdy_plugin_add_method

Notes on name conflicts:

If we need to add the methods to multiple classes in the plugin with the same name, you can define a different name with extra underscore suffix(es).

Notes on module baking:

• As we mentioned before, cmdy module baking are deep copying. So when we can pass the class name instead of the class itself (which you may be not sure which one to use, the orginal one or the one from the baking module) to the add_method and add_property hooks.

• Plugin enable and disable only take effect within the same module. For example:

  import cmdy
  from cmdy import CMDY_PLUGIN_FG
  sh = cmdy()
  # only affects cmdy not sh
  CMDY_PLUGIN_FG.disable()
  # to disable this plugin for sh as well:
  sh.CMDY_PLUGIN_FG.disable()
  

# An example to define a plugin
from cmdy import (cmdy_plugin,
                  cmdy_plugin_hold_then,
                  cmdy_plugin_add_method,
                  ls,
                  CmdyActionError)

@cmdy_plugin
class MyPlugin:
    @cmdy_plugin_add_method("CmdyHolding")
    def say_hello(self):
        return 'Hello world!'

    @cmdy_plugin_hold_then('hello')
    def helloworld(self):
        print(self.say_hello())
        # keep chaining
        return self

myplugin = MyPlugin()

# command will never run,
# because we didn't do self.run() in helloworld(self)
ls().helloworld() # prints Hello world!
# property calls enabled by default
ls().helloworld # prints Hello world!
# we have alias
ls().hello # prints Hello world!