# Generic Python CLI Wrapper
Wrap any CLI tool to Python like syntax.
## Quick start
```python
from pycliwrapper import CliWrapper
apt_cache = CliWrapper("apt-cache", parser=lambda stdout: stdout.splitlines())
# Equivalent to run: "apt-cache search bash" and parsing
# the output as a list
res = ~apt_cache.search.bash
print(res)
```
## Parsing output as JSON
```python
# Build a wrapper on top of main command
tw = CliWrapper("tw -o json", parser=json.loads)
# Build the command that you want to execute
# using Python syntax. A dot means a subcommand and
# flags are pass as normal python variables.
print("PIPELINES")
cmd = tw.pipelines.list(filter="hello")
# You can see the actual command that will be run
# >> tw -o json pipelines list --filter="hello"
print(f"Executing: {cmd}")
# Execute it using the ~ operator and automatically
# parse the output with the given parser
print(~cmd)
# Build and execute the command in one line
# >> tw -o json compute-envs list
print(~tw.compute_envs.list)
# Mixing positional and flag arguments
# >> tw -o json launch nf-core-nanoseq --workspace="community/showcase"
print(~tw.launch("nf-core-nanoseq", workspace="community/showcase"))
# More complex example
# >> tw -o json runs view -i 2gHGbjH9fRDuaW task -t=1 --execution-time
print(~tw.runs.view(i="2gHGbjH9fRDuaW").task(t=1, execution_time=True))
```
## Non standard CLI support
```python
# Build a wrapper on top of main command
nextflow = CliWrapper("nextflow")
# Hello world
# >> nextflow run "nextflow-io/hello"
print(~nextflow.run("nextflow-io/hello"))
# Mixing Nextflow options and pipeline options
# >> nextflow run "nf-core/rnaseq" -profile "docker,test" -r "3.10.1" --outdir="./results"
# TIP: the _ at the beginning means that you want to use a "-" instead of a "--" even if the key has more than one character
# TIP: the _ at the end means that you want to use a " " instead of a "=" even if the key has more than one character
print(~nextflow.run("nf-core/rnaseq", _profile_="docker,test", _r_="3.10.1", outdir="./results"))
```
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"description": "# Generic Python CLI Wrapper\n\nWrap any CLI tool to Python like syntax.\n\n## Quick start\n\n```python\nfrom pycliwrapper import CliWrapper\napt_cache = CliWrapper(\"apt-cache\", parser=lambda stdout: stdout.splitlines())\n\n# Equivalent to run: \"apt-cache search bash\" and parsing\n# the output as a list\nres = ~apt_cache.search.bash\nprint(res)\n```\n\n## Parsing output as JSON\n\n```python\n# Build a wrapper on top of main command\ntw = CliWrapper(\"tw -o json\", parser=json.loads)\n\n# Build the command that you want to execute\n# using Python syntax. A dot means a subcommand and\n# flags are pass as normal python variables.\nprint(\"PIPELINES\")\ncmd = tw.pipelines.list(filter=\"hello\")\n\n# You can see the actual command that will be run\n# >> tw -o json pipelines list --filter=\"hello\"\nprint(f\"Executing: {cmd}\")\n\n# Execute it using the ~ operator and automatically\n# parse the output with the given parser\nprint(~cmd)\n\n# Build and execute the command in one line\n# >> tw -o json compute-envs list\nprint(~tw.compute_envs.list)\n\n# Mixing positional and flag arguments\n# >> tw -o json launch nf-core-nanoseq --workspace=\"community/showcase\"\nprint(~tw.launch(\"nf-core-nanoseq\", workspace=\"community/showcase\"))\n\n# More complex example\n# >> tw -o json runs view -i 2gHGbjH9fRDuaW task -t=1 --execution-time\nprint(~tw.runs.view(i=\"2gHGbjH9fRDuaW\").task(t=1, execution_time=True))\n```\n\n## Non standard CLI support\n\n```python\n# Build a wrapper on top of main command\nnextflow = CliWrapper(\"nextflow\")\n\n# Hello world\n# >> nextflow run \"nextflow-io/hello\"\nprint(~nextflow.run(\"nextflow-io/hello\"))\n\n# Mixing Nextflow options and pipeline options\n# >> nextflow run \"nf-core/rnaseq\" -profile \"docker,test\" -r \"3.10.1\" --outdir=\"./results\"\n# TIP: the _ at the beginning means that you want to use a \"-\" instead of a \"--\" even if the key has more than one character\n# TIP: the _ at the end means that you want to use a \" \" instead of a \"=\" even if the key has more than one character\nprint(~nextflow.run(\"nf-core/rnaseq\", _profile_=\"docker,test\", _r_=\"3.10.1\", outdir=\"./results\"))\n```\n\n",
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