feat: add pipen.run() as a function to run a pipeline

README.md

@@ -29,7 +29,7 @@ pip install -U pipen
 `example.py`
 
 ```python
-from pipen import Proc, Pipen
+from pipen import Proc, Pipen, run
 
 class P1(Proc):
     """Sort input file"""
@@ -45,11 +45,12 @@ class P2(Proc):
     output = "outfile:file:result.txt"
     script = "paste <(seq 1 3) {{in.infile}} > {{out.outfile}}"
 
-class MyPipeline(Pipen):
-    starts = P1
+# class MyPipeline(Pipen):
+#     starts = P1
 
 if __name__ == "__main__":
-    MyPipeline().run()
+    # MyPipeline().run()
+    run("MyPipeline", starts=P1)
 ```
 
 ```shell
@@ -64,12 +65,12 @@ if __name__ == "__main__":
 06-09 23:15:29 I core                  _  ____/__/ /  _  ____/_  /___  _  /|  /
 06-09 23:15:29 I core                  /_/     /___/  /_/     /_____/  /_/ |_/
 06-09 23:15:29 I core
-06-09 23:15:29 I core                              version: 0.14.5
+06-09 23:15:29 I core                              version: 0.15.3
 06-09 23:15:29 I core
 06-09 23:15:29 I core    ╔═══════════════════════════════════════════════════╗
 06-09 23:15:29 I core    ║                            MYPIPELINE                            ║
 06-09 23:15:29 I core    ╚═══════════════════════════════════════════════════╝
-06-09 23:15:29 I core    plugins         : verbose v0.11.0
+06-09 23:15:29 I core    plugins         : verbose v0.12.0
 06-09 23:15:29 I core    # procs         : 2
 06-09 23:15:29 I core    profile         : default
 06-09 23:15:29 I core    outdir          : /home/pwwang/github/pipen/MyPipeline-output
@@ -126,7 +127,8 @@ if __name__ == "__main__":
 ## Examples
 
 See more examples at `examples/` and a more realcase example at:
-https://github.com/pwwang/pipen-report/tree/master/example
+
+<https://github.com/pwwang/pipen-report/tree/master/example>
 
 ## Plugin gallery
 
@@ -150,7 +152,6 @@ Plugins make `pipen` even better.
 - [`pipen-cli-require`][24]: A pipen cli plugin check the requirements of a pipeline
 - [`pipen-cli-run`][22]: A pipen cli plugin to run a process or a pipeline
 
-
 [1]: https://pwwang.github.io/pipen
 [2]: https://pwwang.github.io/pipen/CHANGELOG
 [3]: https://pwwang.github.io/pipen/examples

docs/running.md

@@ -54,7 +54,6 @@ class P2(Proc):
 Pipen().set_starts(P1, P2).set_data(<data for P1>, None)
 ```
 
-
 ## Running with a different profile
 
 `Pipen.run()` accepts an argument `profile`, which allows you to use different profile from configuration files to run the pipeline:
@@ -65,4 +64,50 @@ Pipen().run("sge")
 
 See [configurations][1] for more details.
 
+## Shortcut for running a pipeline
+
+```python
+import pipen
+
+class P1(pipen.Proc):
+    ...
+
+class P2(pipen.Proc):
+    ...
+
+class P3(pipen.Proc):
+    requires = [P1, P2]
+    ...
+
+pipen.run("MyPipeline", starts=[P1, P2], data=[<data for P1>, <data for P2>])
+```
+
+```python
+>>> help(pipen.run)
+
+run(
+    name: 'str',
+    starts: 'Type[Proc] | List[Type[Proc]]',
+    data: 'Iterable' = None,
+    *,
+    desc: 'str' = None,
+    outdir: 'str | PathLike' = None,
+    profile: 'str' = 'default',
+    **kwargs,
+) -> 'bool'
+    Shortcut to run a pipeline
+
+    Args:
+        name: The name of the pipeline
+        starts: The start processes
+        data: The input data for the start processes
+        desc: The description of the pipeline
+        outdir: The output directory of the results
+        profile: The profile to use
+        **kwargs: Other options pass to Pipen to create the pipeline
+
+    Returns:
+        True if the pipeline ends successfully else False
+```
+
 [1]: ../configurations

pipen/__init__.py

@@ -1,5 +1,5 @@
 """A pipeline framework for python"""
-from .pipen import Pipen
+from .pipen import Pipen, run
 from .proc import Proc
 from .procgroup import ProcGroup
 

pipen/pipen.py

@@ -440,3 +440,37 @@ def build_proc_relationships(self) -> None:
                     )
 
         self.pbar = PipelinePBar(len(self.procs), self.name.upper())
+
+
+def run(
+    name: str,
+    starts: Type[Proc] | List[Type[Proc]],
+    data: Iterable = None,
+    *,
+    desc: str = None,
+    outdir: str | PathLike = None,
+    profile: str = "default",
+    **kwargs,
+) -> bool:
+    """Shortcut to run a pipeline
+
+    Args:
+        name: The name of the pipeline
+        starts: The start processes
+        data: The input data for the start processes
+        desc: The description of the pipeline
+        outdir: The output directory of the results
+        profile: The profile to use
+        **kwargs: Other options pass to Pipen to create the pipeline
+
+    Returns:
+        True if the pipeline ends successfully else False
+    """
+    pipeline = Pipen(
+        name=name,
+        desc=desc,
+        outdir=outdir,
+        **kwargs,
+    )
+    pipeline.set_starts(starts).set_data(data)
+    return pipeline.run(profile)

tests/test_pipen.py

@@ -1,8 +1,7 @@
 from re import template
 import pytest
-from pipen import Proc, Pipen
+from pipen import Proc, Pipen, run
 from pipen.exceptions import (
-    PipenException,
     ProcDependencyError,
     PipenSetDataError,
 )
@@ -207,3 +206,18 @@ class MyPipe4(Pipen):
 
     with pytest.raises(PipenOrProcNameError, match="already used by another"):
         MyPipe4().run()
+
+
+@pytest.mark.forked
+def test_run():
+    class RProc1(Proc):
+        input = "a"
+        output = "b:var:{{in.a}}"
+
+    class RProc2(Proc):
+        requires = RProc1
+        input = "b"
+        output = "c:file:{{in.b}}"
+        script = "touch {{out.c}}"
+
+    assert run("MyPipe", RProc1)