Omit runtime from report to make it reproducible

Closes #819

CHANGES.rst

@@ -16,6 +16,9 @@ development version
   Option ``-Z`` (equivalent to ``--compression-level=1``) is now deprecated.
 * The previously hidden option ``--compression-level`` is now shown in the
   ``--help`` output.
+* :issue:`819`: To enable reproducible output, the report no longer includes
+  the runtime (``Finished in XY.Z s``). Runtime is still shown as part of the
+  progress "bar".
 * :issue:`812`: Fixed an issue where multithreaded reading of unaligned BAM
   files would cause an error.
 * :issue:`820`: On Bioconda, Cutadapt is now also available for ARM64 Macs (M1/M2).

src/cutadapt/report.py

@@ -32,7 +32,6 @@
 )
 from .statistics import ReadLengthStatistics
 from .steps import HasStatistics, HasFilterStatistics
-from .utils import MICRO
 
 FILTERS = {
     "too_short": "that were too short",
@@ -609,20 +608,12 @@ def full_report(stats: Statistics, time: float, gc_content: float) -> str:  # no
     """Print report to standard output."""
     if stats.n == 0:
         return "No reads processed!"
-    if time == 0:
-        time = 1e-6
     sio = StringIO()
 
     def print_s(*args, **kwargs):
         kwargs["file"] = sio
         print(*args, **kwargs)
 
-    print_s(
-        "Finished in {:.3F} s ({:.3F} {}s/read; {:.2F} M reads/minute).".format(
-            time, 1e6 * time / stats.n, MICRO, stats.n / time * 60 / 1e6
-        )
-    )
-
     report = "\n=== Summary ===\n\n"
     if stats.paired:
         report += f"Total read pairs processed:      {stats.n:13,d}\n"

tests/test_command.py

@@ -170,3 +170,23 @@ def test_non_utf8_locale():
         [sys.executable, "-m", "cutadapt", "-o", os.devnull, datapath("small.fastq")],
         env={"LC_CTYPE": "C"},
     )
+
+
+def test_reproducible_report(tmp_path):
+    # Run Cutadapt twice and ensure the log is identical
+    report_paths = [os.fspath(tmp_path / f"report{i}.txt") for i in (1, 2)]
+    for report_path in report_paths:
+        with open(report_path, "w") as report_file:
+            py = subprocess.Popen(
+                [
+                    sys.executable,
+                    "-m",
+                    "cutadapt",
+                    "-o",
+                    os.devnull,
+                    datapath("small.fastq"),
+                ],
+                stdout=report_file,
+            )
+            _ = py.communicate()
+    assert_files_equal(*report_paths)