cutseq 0.0.71__tar.gz → 0.0.72__tar.gz

{cutseq-0.0.71 → cutseq-0.0.72}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: cutseq
-Version: 0.0.71
+Version: 0.0.72
 Summary: Automatically cut adapter / barcode / UMI from NGS data
 Project-URL: Repository, https://github.com/y9c/cutseq
 Author-email: Ye Chang <yech1990@gmail.com>

{cutseq-0.0.71 → cutseq-0.0.72}/cutseq/grammar.py

@@ -980,73 +980,51 @@ def _r2_five_emitter(kind):
     return _EMITTERS[kind][0]
 
 
-def _se_id_name(read, info):
-    """``{id}``: strip any trailing comment (identical to cutadapt Renamer)."""
-    read.name = read.name.split(maxsplit=1)[0]
-    return read
+class _FastSingleEndRenamer:
+    """Fast, picklable single-end renamer for the default cutseq templates.
 
-
-def _make_fast_renamer(paired, has_captures, name_format):
-    """Build a lean renamer that computes only the variables its template needs.
-
-    cutadapt's generic ``Renamer``/``PairedEndRenamer`` builds a full variable
-    dict (comment, header, adapter_name, match_sequence, ...) plus a
-    ``SimpleNamespace`` per read on every call even when the template uses just
+    cutadapt's generic ``Renamer`` builds a full variable dict (comment,
+    header, adapter_name, match_sequence, ...) plus a ``SimpleNamespace`` per
+    read on every call even when the template uses just
     ``id``/``cut_prefix``/``cut_suffix``. The default cutseq templates only use
-    those, so we special-case them and fall back to the native renamer for any
-    custom ``--name-format`` template. Output is byte-identical to the native
-    renamer for the same template.
+    those, so we compute them directly. This is a module-level class (not a
+    closure) so it pickles for cutadapt's multiprocessing runner.
     """
-    if name_format is not None:
-        return None
-    if not has_captures:
-        tpl = "{id}"
-        if paired:
-
-            def _rename(read1, read2, info1, info2):
-                read1.name = read1.name.split(maxsplit=1)[0]
-                read2.name = read2.name.split(maxsplit=1)[0]
-                return read1, read2
-
-            _rename._template = tpl
-            return _rename
-        _se_id_name._template = tpl
-        return _se_id_name
-    if paired:
-        tpl = "{id}_{r1.cut_prefix}{r2.cut_prefix}"
-
-        def _rename(read1, read2, info1, info2):
-            id1 = read1.name.split(maxsplit=1)[0]
-            id2 = read2.name.split(maxsplit=1)[0]
-            p1 = info1.cut_prefix if info1.cut_prefix else ""
-            p2 = info2.cut_prefix if info2.cut_prefix else ""
-            read1.name = f"{id1}_{p1}{p2}"
-            read2.name = f"{id2}_{p1}{p2}"
-            return read1, read2
 
-        _rename._template = tpl
-        return _rename
-    tpl = "{id}_{cut_prefix}{cut_suffix}"
+    def __init__(self, has_captures):
+        self.has_captures = bool(has_captures)
+        self._template = "{id}_{cut_prefix}{cut_suffix}" if has_captures else "{id}"
 
-    def _rename(read, info):
-        p = info.cut_prefix if info.cut_prefix else ""
-        s = info.cut_suffix if info.cut_suffix else ""
-        read.name = f"{read.name.split(maxsplit=1)[0]}_{p}{s}"
+    def __call__(self, read, info):
+        read.name = read.name.split(maxsplit=1)[0]
+        if self.has_captures:
+            p = info.cut_prefix if info.cut_prefix else ""
+            s = info.cut_suffix if info.cut_suffix else ""
+            read.name = f"{read.name}_{p}{s}"
         return read
 
-    _rename._template = tpl
-    return _rename
-
 
 class _FastPairedEndRenamer(_mods.PairedEndModifier):
-    """Wraps a fast paired rename callable so it plugs into the pipeline."""
+    """Fast, picklable paired-end renamer for the default cutseq templates."""
 
-    def __init__(self, fn):
-        self._fn = fn
-        self._template = fn._template
+    def __init__(self, has_captures):
+        self.has_captures = bool(has_captures)
+        self._template = (
+            "{id}_{r1.cut_prefix}{r2.cut_prefix}" if has_captures else "{id}"
+        )
 
     def __call__(self, read1, read2, info1, info2):
-        return self._fn(read1, read2, info1, info2)
+        id1 = read1.name.split(maxsplit=1)[0]
+        id2 = read2.name.split(maxsplit=1)[0]
+        if not self.has_captures:
+            read1.name = id1
+            read2.name = id2
+        else:
+            p1 = info1.cut_prefix if info1.cut_prefix else ""
+            p2 = info2.cut_prefix if info2.cut_prefix else ""
+            read1.name = f"{id1}_{p1}{p2}"
+            read2.name = f"{id2}_{p1}{p2}"
+        return read1, read2
 
 
 # --- labeled-capture template engine ----------------------------------------
@@ -1447,18 +1425,9 @@ def make_renamer(paired, has_captures=False, name_format=None, left=None, right=
         return _LabeledRenamer(fields, name_format)
 
     _RENAME_NEEDS_CAPTURES = False
-    if not has_captures:
-        tpl = "{id}"
-    elif paired:
-        tpl = "{id}_{r1.cut_prefix}{r2.cut_prefix}"
-    else:
-        tpl = "{id}_{cut_prefix}{cut_suffix}"
-    fast = _make_fast_renamer(paired, has_captures, name_format)
-    if fast is not None:
-        if paired:
-            return _FastPairedEndRenamer(fast)
-        return fast
-    return _mods.PairedEndRenamer(tpl) if paired else _mods.Renamer(tpl)
+    if paired:
+        return _FastPairedEndRenamer(has_captures)
+    return _FastSingleEndRenamer(has_captures)
 
 
 class CompiledScheme:

{cutseq-0.0.71 → cutseq-0.0.72}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cutseq"
-version = "0.0.71"
+version = "0.0.72"
 description = "Automatically cut adapter / barcode / UMI from NGS data"
 authors = [{ name = "Ye Chang", email = "yech1990@gmail.com" }]
 requires-python = "~=3.9"

{cutseq-0.0.71 → cutseq-0.0.72}/scripts/update_adapter_docs.py

@@ -462,7 +462,6 @@ def _write_exports(name, construct, constructs_dir):
 
 
 def main():
-    adapters_toml = project_root / "cutseq" / "adapters.toml"
     out_md = project_root / "docs" / "adapters.md"
     schemes = _load_schemes()
     if not schemes:

{cutseq-0.0.71 → cutseq-0.0.72}/test/test_rename_engine.py

@@ -222,6 +222,31 @@ def test_threaded_rename_deterministic():
         assert a and a == b
 
 
+def test_default_renamer_picklable():
+    """The default fast renamers (no --rename) must pickle so cutadapt's
+    ``ParallelPipelineRunner`` (multiprocessing) can ship the pipeline to
+    workers. They are module-level classes, not local closures, because
+    closures raise on spawn-based platforms (macOS/Windows) where
+    ``-t N`` broke. ``--rename '{id}'`` hid the bug by swapping in the
+    native picklable renamer.
+    """
+    import pickle
+
+    for paired in (False, True):
+        for has_captures in (False, True):
+            pickle.dumps(grammar.make_renamer(paired, has_captures, None))
+
+    s = CutadaptConfig()
+    cs = _build_scheme(
+        "AAGCAGTGGTATCAACGCAGAGTGAATGGG...GGG:"
+        "N12AGTCGTACGCCGATGCGAAACATCGGCCAC"
+        "N8CGAATGCTCTGGCCTCTCAAGCACGTGGAT"
+        "N8AGATGCGAGAAGCCAACGCTTG",
+        s,
+    )
+    pickle.dumps(_scheme_modifiers(cs, paired=True, settings=s))
+
+
 # --- spatial (DBiT) interleaved 3' structure ---------------------------------
 #
 # m6A-ARTR-DBiT / Glori style, Read 1 (single-end):
@@ -375,9 +400,8 @@ def test_polytail_direction_auto_detected():
     from the current position (never a global rightmost search, which would
     over-trim real insert). The read-through mirror is a back adapter. ``N``s
     in the run count as the base."""
-    from cutseq.grammar import (RightmostFrontAdapter,
-                                BackAdapter, _poly_seq, _mark_poly_front,
-                                _poly_head_trim_index, tokenize)
+    from cutseq.grammar import (_mark_poly_front, _poly_seq, BackAdapter,
+                                tokenize)
     from cutseq.grammar import _PolyRunTrim, _Token
     from cutadapt.modifiers import AdapterCutter
     from cutadapt.info import ModificationInfo

{cutseq-0.0.71 → cutseq-0.0.72}/uv.lock

@@ -163,7 +163,7 @@ wheels = [
 
 [[package]]
 name = "cutseq"
-version = "0.0.71"
+version = "0.0.72"
 source = { editable = "." }
 dependencies = [
     { name = "cutadapt" },