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        "author": "pwwang",
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            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
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        "description": "# cmdy\nA handy package to run command from python\n\n## Installation\n```shell\n# latest version\npip install git+https://github.com/pwwang/cmdy\n# released version\npip install cmdy\n```\n\n## Why another one beyond `sh`?\n- `oncotator` not running with `sh`, no matter what I tried.\n- Unable to replace arguments with baked command, see example below:\n  ```python\n  from sh import ls\n  ls = ls.bake(l = True)\n  print(ls()) # ls -l\n  # but now I somehow want to run `ls` (without `-l`) command with `ls()`\n  ls(l = False) # not work\n  ```\n- Unable to save configurations for commands, since commands have their solid preferences. \n- Unable to specify full path of an executable.\n- No pipe/redirection notations.\n\n## Basic usage\n```python\nfrom cmdy import ls\nprint(ls())\n```\n### With arguments\nLike `sh`, `cmdy` can have non-keyword arguments, but keyword arguments preferred.\n```python\nfrom cmdy import tar\ntar(\"cvf\", \"/tmp/test.tar\", \"/my/home/directory/\")\n```\n\n### With keyword arguments\n```python\ncurl(\"http://duckduckgo.com/\", o=\"page.html\", silent=True)\n# curl http://duckduckgo.com/ -o page.html --silent\n```\n__Order keyword arguments:__  \n```python\ncurl(\"http://duckduckgo.com/\", \"-o\", \"page.html\", \"--silent\")\n# or \nfrom collections import OrderedDict\ncurl(\"http://duckduckgo.com/\", OrderedDict([('o', 'page.html'), ('silent', True)]))\n```\n\n__Prefix and separator for keyword arguments:__  \n```python\nfrom cmdy import bedtools, bcftools, ls\nbedtools.intersect(wa = True, wb = True, a = 'query.bed', b = ['d1.bed', 'd2.bed', 'd3.bed'], names = ['d1', 'd2', 'd3'], sorted = True, _prefix = '-')\n#bedtools intersect -wa -wb -a query.bed -b d1.bed d2.bed d3.bed -names d1 d2 d3 -sorted\n\nbcftools.query(_ = ['a.vcf', 'b.vcf'], H = True, format = '%CHROM\\t%POS\\t%REF\\t%ALT\\n')\n# bcftools query --format '%CHROM\\t%POS\\t%REF\\t%ALT\\n' -H a.vcf b.vcf\n# _prefix defaults to 'auto' ('-' for short options, '--' for long)\n# You may also define arbitrary prefix:\n# command(a = 1, bc = 2, _prefix = '---')\n# command ---a 1 ---bc 2\n\nls(l = True, block_size = 'KB', _sep = 'auto')\n# ls -l --block-size=KB\n# _sep defaults to ' '. 'auto' means ' ' for short options, '=' for long\n```\n\n__Different combinations of prefices and separators in one command:__\n```python\nfrom cmdy import java\n# Note this is just an example for old verion picard. Picard is changing it's style\njava({'jar': 'picard.jar', '_prefix': '-', '_sep': ' '}, 'SortSam', I = 'input.bam', O = 'sorted.bam', SORTED_ORDER = 'coordinate', _raw = True, _prefix = '', _sep = '=')\n# java -jar picard.jar SortSam I=input.bam O=sorted.bam SORT_ORDER=coordinate\n# The first dictionary usees _prefix and _sep in itself if specified, otherwise uses the ones specified with kwargs.\n# _raw = True keeps SORTED_ORDER as it is, otherwise, it'll be transformed into SORTED-ORDER\n# This is useful when some command has option like '--block-size', but you can still use 'block_size' as keyword argument.\n```\n\n__Duplicated keys for list arguments:__\n```python\nfrom cmdy import sort\nsort(k = ['1,1', '2,2n'], _ = 'a.bed', _dupkey = True)\n# sort -k 1,1 -k 2,2n a.bed\n```\n\n## Return codes and exceptions\n```python\nfrom cmdy import x\nx()\n```\n\n```shell\n    ... ...\n    raise CmdyReturnCodeException(self)\n          \u2502                       \u2514\n          \u2514 <class 'cmdy.CmdyReturnCodeException'>\ncmdy.CmdyReturnCodeException: Unexpected RETURN CODE 127, expecting: [0]\n\n  [PID]    38254\n\n  [CMD]    x\n\n  [STDERR] /bin/sh: x: command not found\n\n```\nYou can use try/catch to catch it:  \n```python\nfrom cmdy import x, CmdyReturnCodeException\ntry:\n  x()\nexcept CmdyReturnCodeException as ex\n  print('Command returned %s' % ex.cmdy.rc)\n```\n\nYou can allow multiple return codes by: `x(_okcode = [0, 127])` or `x(_okcode = '0,127')`\n\n## Redirection\n```python\nfrom cmdy import ifconfig\nifconfig(_out=\"/tmp/interfaces\")\n# or you can use shell redirection notation\nifconfig(_out = \">\") > \"/tmp/interfaces\"\n# or \n# ifconfig(_out = \"/tmp/interfaces\")\n\n## append\nifconfig(_out = \">\") >> \"/tmp/interfaces\"\n# or\n# ifconfig(_out_ = \"/tmp/interfaces\")\n\n# redirect stderr\nifconfig(_err = \">\") > \"/tmp/ifconfig.errors\"\n# or ifconfig(_err = \"/tmp/ifconfig.errors\")\n```\n\n## Iteration on output\n```python \nfrom cmdy import tail\nfor line in tail(_ = 'test.txt', _iter = True):\n  print(line)\n```\n\n## Background processes\nFor command you want to run it in non-block mode, you probably would like to use `_bg` keyword:  \n```python\nfor line in tail(_ = 'test.txt', _bg = True, _iter = True):\n  print(line)\n```\n\n```python\n# blocks\nsleep(3)\nprint(\"...3 seconds later\")\n\n# doesn't block\np = sleep(3, _bg=True)\nprint(\"prints immediately!\")\np.wait()\nprint(\"...and 3 seconds later\")\n```\n\nCallbacks for background processes:  \n```python\nimport time\nfrom cmdy import sleep\ndef callback(cmdy):\n  print(cmdy.rc)\np = sleep(3, _bg = callback)\np.wait()\n# prints 0\n```\n\n## Baking\n```python\nfrom cmdy import java\npicard = java.bake(dict(jar = 'picard.jar', _sep = ' ', _prefix = '-'))\n#picard.SortSam(...)\n```\n\nUnlike `sh`, `cmdy` holds the keyword arguments, and updates them while baked into a new command. This enables it to replace some arguments with the new baked command.  \n```python\nfrom cmdy import ls\n\nls = ls.bake(l = True)\n# or ls = ls(l = True, _bake = True)\nls() # ls -l\n\n# I don't want -l anymore\nls(l = False)\n```\n\nNote that non-keyword arguments is not updatable.  \n```python\nls = ls.bake('-l')\nls() # ls -l\n\n# Not work, still ls -l\nls(l = False)\n```\n\nBake the whole module:  \n```python\nimport cmdy\ncmdy = cmdy(_fg = True)\n# all commands under new module is running at foreground (stdout = sys.stdout, stderr = stderr)\nfrom cmdy import ls\nls()\n```\n\n## Piping\n```python\n# get the permission column\nls(l = True, _pipe = True) | cut(f = 1, _fg = True)\n```\n\n## Sub-commands\n```python\nfrom cmdy import git\nprint(git.branch(v = True))\n```\n\n## Aliasing/Specifying full path of executables for commands\n```python\nfrom cmdy import fc_cache, python\nfc_cache(_exe = 'fc-cache', vf = '~/.fonts/', _prefix = '-')\n# fc-cache -vf ~/.fonts/\n\npython(_exe = '/home/user/miniconda3/bin/python3', version = True)\n# /home/user/miniconda3/bin/python3 --version\n```\nAlways alias `fc_cache` to `fc-cache` and point `python` to `/home/user/miniconda3/bin/python3`, add the following to your `~/.cmdy.ini`  \n```ini\n[fc_cache]\n_exe = fc-cache\n\n[python]\n_exe = /home/user/miniconda3/bin/python3\n```\n\nThen you don't need to care about the paths any more:\n```python\nfrom cmdy import fc_cache, python\nfc_cache(vf = '~/.fonts/', _prefix = '-')\n# fc-cache -vf ~/.fonts/\n\npython(version = True)\n# /home/user/miniconda3/bin/python3 --version\n```\n\n## Configuration\n`cmdy` will first load default arguments:\n```python\n{\n  '_okcode'  : 0,\n  '_exe'     : None,\n  '_sep'     : ' ',\n  '_prefix'  : 'auto',\n  '_dupkey'  : False,\n  '_bake'    : False,\n  '_iter'    : False,\n  '_pipe'    : False,\n  '_raw'     : False,\n  '_timeout' : 0,\n  '_encoding': 'utf-8',\n  '_bg'      : False,\n  '_fg'      : False,\n  '_out'     : None,\n  '_out_'    : None,\n  '_err'     : None,\n  '_err_'    : None\n}\n```\nAnd then try to load `$HOME/.cmdy.ini`, `./.cmdy.ini` and environment variables starting with `CMDY_`, so you can overwrite the configurations with temporary environment variables.\n\nFor example, I want to always use raw keyword option:\n`~/.cmdy.ini`  \n```ini\n[default]\n_raw: True\n```\n\n`ontotator.py`:  \n```python\nfrom cmdy import oncotator\noncotator(log_name = '/path/to/log', ...)\n# oncotator --log_name LOG_NAME ...\n# you don't have to specify _raw = True any more.\n```\n\n__Override the settings with environment variable:__\n```bash\nexport CMDY_oncotator__raw=False\npython oncotator.py\n# will run:\n# oncotator --log-name LOG_NAME ...\n#                ^\n```\n\n",
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