Revert "PipelineMake.__call__"

This reverts commit 1b2c48d.

src/cutadapt/cli.py

@@ -61,17 +61,7 @@
 import itertools
 import multiprocessing
 from pathlib import Path
-from typing import (
-    Tuple,
-    Optional,
-    Sequence,
-    List,
-    Any,
-    Iterator,
-    Union,
-    Dict,
-    Iterable,
-)
+from typing import Tuple, Optional, Sequence, List, Any, Iterator, Union, Dict, Iterable
 from argparse import ArgumentParser, SUPPRESS, HelpFormatter
 
 import dnaio
@@ -809,7 +799,7 @@ def __init__(self, args, paired, adapters, adapters2):
         self.adapters = adapters
         self.adapters2 = adapters2
 
-    def __call__(self) -> Pipeline:
+    def make(self) -> Pipeline:
         """
         Set up a processing pipeline from parsed command-line arguments.
 
@@ -1120,9 +1110,7 @@ def main(cmdlineargs, default_outfile=sys.stdout.buffer) -> Statistics:
         adapters, adapters2 = adapters_from_args(args)
         log_adapters(adapters, adapters2 if paired else None)
 
-        make_pipeline = PipelineMaker(args, paired, adapters, adapters2)
-        # Create the pipeline once without running it to get errors early
-        make_pipeline()
+        pipeline = PipelineMaker(args, paired, adapters, adapters2).make()
         adapter_names: List[Optional[str]] = [a.name for a in adapters]
         adapter_names2: List[Optional[str]] = [a.name for a in adapters2]
         outfiles = open_output_files(
@@ -1131,12 +1119,12 @@ def main(cmdlineargs, default_outfile=sys.stdout.buffer) -> Statistics:
         inpaths = InputPaths(*input_paths, interleaved=is_interleaved_input)
         logger.info(
             "Processing %s reads on %d core%s ...",
-            {False: "single-end", True: "paired-end"}[paired],
+            {False: "single-end", True: "paired-end"}[pipeline.paired],
             cores,
             "s" if cores > 1 else "",
         )
         stats = run_pipeline(
-            make_pipeline, inpaths, outfiles, cores, progress, args.buffer_size
+            pipeline, inpaths, outfiles, cores, progress, args.buffer_size
         )
 
     except KeyboardInterrupt:

src/cutadapt/runners.py

@@ -7,17 +7,7 @@
 from abc import ABC, abstractmethod
 from contextlib import ExitStack
 from multiprocessing.connection import Connection
-from typing import (
-    Any,
-    List,
-    Optional,
-    Tuple,
-    Sequence,
-    Iterator,
-    TYPE_CHECKING,
-    Union,
-    Callable,
-)
+from typing import Any, List, Optional, Tuple, Sequence, Iterator, TYPE_CHECKING, Union
 
 import dnaio
 
@@ -434,7 +424,7 @@ def close(self) -> None:
 
 
 def run_pipeline(
-    pipeline_maker: Callable[[], Pipeline],
+    pipeline: Pipeline,
     inpaths: InputPaths,
     outfiles: OutputFiles,
     cores: int,
@@ -465,17 +455,15 @@ def run_pipeline(
     runner: PipelineRunner
     if cores > 1:
         runner = ParallelPipelineRunner(
-            pipeline_maker(),
+            pipeline,
             inpaths,
             outfiles,
             progress,
             n_workers=cores,
             buffer_size=buffer_size,
         )
     else:
-        runner = SerialPipelineRunner(
-            pipeline_maker(), inpaths.open(), outfiles, progress
-        )
+        runner = SerialPipelineRunner(pipeline, inpaths.open(), outfiles, progress)
 
     with runner:
         statistics = runner.run()

tests/test_api.py

@@ -54,18 +54,14 @@ def test_pipeline_single(tmp_path):
         QualityTrimmer(cutoff_front=0, cutoff_back=15),
         AdapterCutter([adapter]),
     ]
-
-    def make_pipeline():
-        pipeline = SingleEndPipeline(modifiers)
-        pipeline.minimum_length = (10,)
-        pipeline.discard_untrimmed = True
-        return pipeline
-
+    pipeline = SingleEndPipeline(modifiers)
+    pipeline.minimum_length = (10,)
+    pipeline.discard_untrimmed = True
     inpaths = InputPaths(datapath("small.fastq"))
     info_file = file_opener.xopen_or_none(tmp_path / "info.txt", "wb")
     out = file_opener.xopen(tmp_path / "out.fastq", "wb")
     outfiles = OutputFiles(info=info_file, out=out)
-    stats = run_pipeline(make_pipeline, inpaths, outfiles, cores=1)
+    stats = run_pipeline(pipeline, inpaths, outfiles, cores=1)
     assert stats is not None
     json.dumps(stats.as_json())
     outfiles.close()
@@ -96,11 +92,10 @@ def test_pipeline_paired(tmp_path):
         (AdapterCutter([adapter]), None),
     ]
 
-    def make_pipeline():
-        pipeline = PairedEndPipeline(modifiers, "any")
-        pipeline.minimum_length = (10, None)
-        pipeline.discard_untrimmed = True
-        return pipeline
+    pipeline = PairedEndPipeline(modifiers, "any")
+
+    pipeline.minimum_length = (10, None)
+    pipeline.discard_untrimmed = True
 
     file_opener = FileOpener()
     inpaths = InputPaths(datapath("paired.1.fastq"), datapath("paired.2.fastq"))
@@ -113,7 +108,7 @@ def make_pipeline():
         out=out,
         out2=out2,
     )
-    stats = run_pipeline(make_pipeline, inpaths, outfiles, cores=1, progress=True)
+    stats = run_pipeline(pipeline, inpaths, outfiles, cores=1, progress=True)
     assert stats is not None
     _ = stats.as_json()
     outfiles.close()