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Abc meta classes #96

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Abc meta classes #96

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f363077
Added ABC as meta class for Pipeline
jlvdb Aug 3, 2023
88bace9
Added ABC as meta class for PipelineStage
jlvdb Aug 3, 2023
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4 changes: 2 additions & 2 deletions ceci/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import collections
import yaml
import shutil
from abc import abstractmethod
from abc import ABC, abstractmethod

from .stage import PipelineStage
from . import minirunner
Expand Down Expand Up @@ -286,7 +286,7 @@ def insert_outputs(self, stage, outdir):
return stage_outputs


class Pipeline:
class Pipeline(ABC):
"""
The Pipeline base class models the shared information and behaviour
that pipelines need, no matter which workflow manager runs them.
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4 changes: 2 additions & 2 deletions ceci/stage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
import pdb
import datetime

from abc import abstractmethod
from abc import ABC, abstractmethod
from . import errors
from .monitor import MemoryMonitor
from .config import StageParameter, StageConfig, cast_to_streamable
Expand All @@ -21,7 +21,7 @@
IN_PROGRESS_PREFIX = "inprogress_"


class PipelineStage:
class PipelineStage(ABC):
"""A PipelineStage implements a single calculation step within a wider pipeline.

Each different type of analysis stage is represented by a subclass of this
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