cogent3 · GavinHuttley · Jun 12, 2025 · Jun 12, 2025 · Jun 12, 2025 · Jun 12, 2025
diff --git a/src/cogent3/app/data_store.py b/src/cogent3/app/data_store.py
@@ -13,12 +13,13 @@
 from functools import singledispatch
 from io import TextIOWrapper
 from pathlib import Path
-from typing import TYPE_CHECKING, Union
+from typing import TYPE_CHECKING
 
 from scitrack import get_text_hexdigest
 
 from cogent3.core import alignment as old_alignment
 from cogent3.core import new_alignment
+from cogent3.core import tree as c3tree
 from cogent3.core.table import Table
 from cogent3.util.deserialise import deserialise_object
 from cogent3.util.io import get_format_suffixes, open_
@@ -37,7 +38,7 @@
 # used for log files, not-completed results
 _special_suffixes = re.compile(r"\.(log|json)$")
 
-StrOrBytes = Union[str, bytes]
+StrOrBytes = str | bytes
 NoneType = type(None)
 
 
@@ -748,42 +749,52 @@ def get_data_source(data: object) -> str | None:
 
 
 @get_data_source.register
-def _(data: old_alignment.SequenceCollection):
+def _(data: old_alignment.SequenceCollection) -> str | None:
     return get_data_source(data.info)
 
 
 @get_data_source.register
-def _(data: old_alignment.ArrayAlignment):
+def _(data: old_alignment.ArrayAlignment) -> str | None:
     return get_data_source(data.info)
 
 
 @get_data_source.register
-def _(data: old_alignment.Alignment):
+def _(data: old_alignment.Alignment) -> str | None:
     return get_data_source(data.info)
 
 
 @get_data_source.register
-def _(data: new_alignment.Alignment):
-    return get_data_source(data.source)
+def _(data: new_alignment.Alignment) -> str | None:
+    return data.source
 
 
 @get_data_source.register
-def _(data: new_alignment.SequenceCollection):
-    return get_data_source(data.source)
+def _(data: new_alignment.SequenceCollection) -> str | None:
+    return data.source
 
 
 @get_data_source.register
-def _(data: str):
+def _(data: c3tree.TreeNode) -> str | None:
+    return data.source
+
+
+@get_data_source.register
+def _(data: c3tree.PhyloNode) -> str | None:
+    return data.source
+
+
+@get_data_source.register
+def _(data: str) -> str | None:
     return get_data_source(Path(data))
 
 
 @get_data_source.register
-def _(data: Path):
-    return str(data.name)
+def _(data: Path) -> str | None:
+    return data.name
 
 
 @get_data_source.register
-def _(data: dict):
+def _(data: dict) -> str | None:
     try:
         source = data.get("info", {})["source"]
     except KeyError:
@@ -792,7 +803,7 @@ def _(data: dict):
 
 
 @get_data_source.register
-def _(data: DataMemberABC):
+def _(data: DataMemberABC) -> str | None:
     return str(data.unique_id)
 
 

diff --git a/src/cogent3/app/dist.py b/src/cogent3/app/dist.py
@@ -16,6 +16,7 @@
 from cogent3.util.misc import get_true_spans
 
 from .composable import NotCompleted, define_app
+from .data_store import get_data_source
 from .typing import (
     AlignedSeqsType,
     PairwiseDistanceType,
@@ -48,7 +49,6 @@ class fast_slow_dist:
 
     Uses fast (but less numerically robust) approach where possible, slow (robust)
     approach when not.
-
     """
 
     def __init__(
@@ -170,7 +170,7 @@ def main(
         else:
             empty = dict.fromkeys(itertools.product(aln.names, aln.names), 0)
             dists = DistanceMatrix(empty)
-        dists.source = aln.info.source
+        dists.source = get_data_source(aln)
         if self._sm:
             for a in dists.template.names[0]:
                 for b in dists.template.names[1]:
@@ -237,7 +237,7 @@ def jaccard_dist(seq_coll: UnalignedSeqsType, k: int = 10) -> PairwiseDistanceTy
             f"could not compute distances between {names}",
             source=seq_coll,
         )
-    return DistanceMatrix(dists)
+    return DistanceMatrix(dists, source=get_data_source(seq_coll))
 
 
 @define_app

diff --git a/src/cogent3/app/tree.py b/src/cogent3/app/tree.py
@@ -8,6 +8,7 @@
 from cogent3.util.misc import is_url
 
 from .composable import define_app
+from .data_store import get_data_source
 from .typing import PairwiseDistanceType, SerialisableType, TreeType
 
 NoneType = type(None)
@@ -51,6 +52,7 @@ def __init__(
         self._min_length = min_length
 
     def main(self, tree: TreeType) -> SerialisableType | TreeType:
+        source = tree.source
         scalar = self._scalar
         min_length = self._min_length
         tree = tree.deepcopy()
@@ -61,14 +63,17 @@ def main(self, tree: TreeType) -> SerialisableType | TreeType:
             length = length / scalar if length else min_length
             edge.length = abs(length)  # force to be positive
 
+        tree.source = source
         return tree
 
 
 @define_app
 class uniformize_tree:
     """Standardises the orientation of unrooted trees."""
 
-    def __init__(self, root_at="midpoint", ordered_names=None) -> None:
+    def __init__(
+        self, root_at: str = "midpoint", ordered_names: list[str] | None = None
+    ) -> None:
         """
         Parameters
         ----------
@@ -82,14 +87,18 @@ def __init__(self, root_at="midpoint", ordered_names=None) -> None:
         self._ordered_names = ordered_names
 
     def main(self, tree: TreeType) -> SerialisableType | TreeType:
+        source = tree.source
         if self._root_at == "midpoint":
             new = tree.root_at_midpoint()
         else:
             new = tree.rooted_with_tip(self._root_at)
 
         if self._ordered_names is None:
             self._ordered_names = tree.get_tip_names()
-        return new.sorted(self._ordered_names)
+
+        result = new.sorted(self._ordered_names)
+        result.source = source
+        return result
 
 
 @define_app
@@ -126,7 +135,7 @@ def main(self, dists: PairwiseDistanceType) -> SerialisableType | TreeType:
             (result,) = gnj(dists.to_dict(), keep=1, show_progress=False)
             _, tree = result
 
-        tree.params["source"] = dists.source
+        tree.source = get_data_source(dists)
         return tree
 
 

diff --git a/src/cogent3/core/new_alignment.py b/src/cogent3/core/new_alignment.py
@@ -2637,7 +2637,8 @@ def prep_for_seqs_data(
     for name, seq in data.items():
         name = seq_namer(seq=seq, name=name)  # noqa: PLW2901
         seq_data = coerce_to_raw_seq_data(seq, moltype, name=name)
-        offsets[seq_data.parent_name or name] = seq_data.offset
+        if seq_data.offset:
+            offsets[seq_data.parent_name or name] = seq_data.offset
         seqs[seq_data.parent_name or seq_data.name] = seq_data.seq
         if seq_data.is_reversed:
             rvd.add(name)

diff --git a/src/cogent3/core/tree.py b/src/cogent3/core/tree.py
@@ -79,27 +79,28 @@ class TreeNode:
     Parameters:
         name: label for the node, assumed to be unique.
         children: list of the node's children.
+        parent: parent to this node
         params: dict containing arbitrary parameters for the node.
         name_loaded: ?
     """
 
-    _exclude_from_copy = dict.fromkeys(["_parent", "children"])
+    _exclude_from_copy = frozenset(["_parent", "children"])
 
     def __init__(
         self,
-        name=None,
-        children=None,
-        parent=None,
-        params=None,
-        name_loaded=True,
+        name: str | None = None,
+        children: list[TreeNode] | None = None,
+        parent: TreeNode | None = None,
+        params: dict[str, object] | None = None,
+        name_loaded: bool = True,
         **kwargs,
     ) -> None:
         """Returns new TreeNode object."""
         self.name = name
         self.name_loaded = name_loaded
         self.params = params or {}
         self.children = []
-        if children is not None:
+        if children:
             self.extend(children)
         self._parent = parent
         if parent is not None and self not in parent.children:
@@ -142,6 +143,18 @@ def __gt__(self, other):
 
         return self_name > other_name
 
+    @property
+    def source(self) -> str | None:
+        return self.params.get("source")
+
+    @source.setter
+    def source(self, value: str | None) -> None:
+        """Sets the source of the node."""
+        if value:
+            self.params["source"] = value
+        else:
+            self.params.pop("source", None)
+
     def compare_name(self, other):
         """Compares TreeNode by name"""
         return True if self is other else self.name == other.name
@@ -2320,6 +2333,7 @@ def make_tree(
     tip_names: list[str] | None = None,
     format: str | None = None,
     underscore_unmunge: bool = False,
+    source: str | None = None,
 ) -> PhyloNode | TreeNode:
     """Initialises a tree.
 
@@ -2335,6 +2349,8 @@ def make_tree(
     underscore_unmunge : bool
         replace underscores with spaces in all names read, i.e. "sp_name"
         becomes "sp name"
+    source
+        path to file tree came from, string value assigned to tree.source
 
     Notes
     -----
@@ -2346,10 +2362,13 @@ def make_tree(
     PhyloNode
     """
     assert treestring or tip_names, "must provide either treestring or tip_names"
+    source = str(source) if source else None
     if tip_names:
         tree_builder = TreeBuilder().create_edge
         tips = [tree_builder([], str(tip_name), {}) for tip_name in tip_names]
-        return tree_builder(tips, "root", {})
+        result = tree_builder(tips, "root", {})
+        result.source = source
+        return result
 
     if format is None and treestring.startswith("<"):
         format = "xml"
@@ -2363,6 +2382,7 @@ def make_tree(
     if not tree.name_loaded:
         tree.name = "root"
 
+    tree.source = source
     return tree
 
 
@@ -2390,16 +2410,25 @@ def load_tree(
     of the Newick format. Only the cogent3 json and xml tree formats are
     supported.
 
+    filename is assigned to root node tree.source attribute.
+
     Returns
     -------
     PhyloNode
     """
     file_format, _ = get_format_suffixes(filename)
     format = format or file_format
     if format == "json":
-        return load_from_json(filename, (TreeNode, PhyloNode))
+        tree = load_from_json(filename, (TreeNode, PhyloNode))
+        tree.source = str(filename)
+        return tree
 
     with open_(filename) as tfile:
         treestring = tfile.read()
 
-    return make_tree(treestring, format=format, underscore_unmunge=underscore_unmunge)
+    return make_tree(
+        treestring,
+        format=format,
+        underscore_unmunge=underscore_unmunge,
+        source=filename,
+    )
diff --git a/tests/test_app/test_align.py b/tests/test_app/test_align.py
@@ -33,6 +33,8 @@
 from cogent3.core.location import gap_coords_to_map
 
 DNA = get_moltype("dna")
+
+
 _NEW_TYPE = "COGENT3_NEW_TYPE" in os.environ
 
 if _NEW_TYPE:

diff --git a/tests/test_app/test_evo.py b/tests/test_app/test_evo.py
@@ -9,6 +9,7 @@
 
 from cogent3 import (
     get_app,
+    get_dataset,
     load_aligned_seqs,
     make_aligned_seqs,
     make_tree,
@@ -1002,3 +1003,13 @@ def test_model_bounds_kappa():
     rules = result.lf.get_param_rules()
     kappa_bounds = {(r["lower"], r["upper"]) for r in rules if r["par_name"] == "kappa"}
     assert kappa_bounds == {(lower_kappa, upper_kappa)}
+
+
+def test_source_propagated():
+    aln = get_dataset("brca1")
+    three = get_app("take_n_seqs", 4)
+    dcalc = get_app("fast_slow_dist", fast_calc="pdist", moltype="dna")
+    qtree = get_app("quick_tree")
+    app = three + dcalc + qtree
+    result = app(aln)
+    assert result.source == pathlib.Path(aln.source).name
diff --git a/tests/test_app/test_io.py b/tests/test_app/test_io.py
@@ -31,6 +31,8 @@
 
 DNA = get_moltype("dna")
 
+NEW_TYPE = "COGENT3_NEW_TYPE" in os.environ
+
 
 @pytest.fixture
 def tmp_dir(tmp_path_factory):
@@ -588,12 +590,15 @@ def uniqid(source):
     assert m.unique_id == expect
 
 
+src_attr = "source" if NEW_TYPE else "info"
+
+
 @pytest.mark.parametrize(
     ("writer", "data", "attr", "dstore"),
     [
-        ("write_seqs", seqs(), "info", dir_dstore),
-        ("write_db", seqs(), "info", db_dstore),
-        ("write_json", seqs(), "info", dir_dstore),
+        ("write_seqs", seqs(), src_attr, dir_dstore),
+        ("write_db", seqs(), src_attr, db_dstore),
+        ("write_json", seqs(), src_attr, dir_dstore),
         ("write_tabular", table(), "source", dir_dstore),
     ],
 )