diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 1f5c839..2668bf9 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -18,13 +18,15 @@ jobs:
fetch-depth: 2
- name: Set up Python
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
- name: Install dependencies
- run: pip install ".[test]"
+ run: |
+ python -m pip install --upgrade pip
+ pip install -e ".[test]"
- name: Run tests
- run: pytest --cov --cov-branch --cov-report=xml
+ run: pytest --cov=lineagetree --cov-report=xml
- name: Upload results to Codecov
uses: codecov/codecov-action@v5
diff --git a/pyproject.toml b/pyproject.toml
index 72595ee..13da13f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ dependencies = [
"matplotlib",
"edist",
"svgwrite",
- "micromastodonreader",
+ "Micro-Mastodon-Reader",
]
[project.optional-dependencies]
@@ -123,6 +123,12 @@ root = ["./src", ]
[tool.ty.rules]
unresolved-import = "ignore"
-[tool.pytest.ini_options]
-addopts = "--cov"
+[tool.coverage.run]
+source = ["lineagetree"]
+[tool.coverage.report]
+omit = [
+ "*/test/*",
+ "*/.vscode/*",
+ "*/site-packages/*"
+]
\ No newline at end of file
diff --git a/src/lineagetree/_assembly.py b/src/lineagetree/_assembly.py
index 48af28c..0c65489 100644
--- a/src/lineagetree/_assembly.py
+++ b/src/lineagetree/_assembly.py
@@ -14,10 +14,12 @@
remove_nodes,
)
from ._basics._navigation import (
+ change_labels,
find_leaves,
get_all_chains_of_subtree,
get_ancestor_at_t,
get_ancestor_with_attribute,
+ get_available_labels,
get_chain_of_node,
get_labelled_ancestor,
get_predecessors,
@@ -104,6 +106,8 @@
LineageTree.calculate_dtw = calculate_dtw
# Navigation functions
+LineageTree.get_available_labels = get_available_labels
+LineageTree.change_labels = change_labels
LineageTree.find_leaves = find_leaves
LineageTree.get_all_chains_of_subtree = get_all_chains_of_subtree
LineageTree.get_ancestor_at_t = get_ancestor_at_t
diff --git a/src/lineagetree/_basics/_navigation.py b/src/lineagetree/_basics/_navigation.py
index f76f6ed..d83ff93 100644
--- a/src/lineagetree/_basics/_navigation.py
+++ b/src/lineagetree/_basics/_navigation.py
@@ -2,6 +2,7 @@
from collections.abc import Iterable
from typing import TYPE_CHECKING
+import warnings
if TYPE_CHECKING:
from ..lineage_tree import LineageTree
@@ -394,3 +395,101 @@ def get_subtree(lT: LineageTree, node_list: set[int]) -> LineageTree:
],
**{name: lT.__dict__[name] for name in lT._custom_property_list},
)
+
+
+def get_available_labels(lT: LineageTree) -> list[str]:
+ """Returns the list all the available label dictionaries
+
+ Returns
+ -------
+ list of string
+ list of the names of all the available properties
+ to label the nodes
+ """
+ available_labels = []
+ for prop_name, prop in lT.__dict__.items():
+ if (
+ 0 < len(prop_name)
+ and prop_name[0] != "_"
+ and isinstance(prop, dict)
+ and 0 < len(prop)
+ and all(isinstance(k, int) for k in prop.keys())
+ and all(isinstance(v, str) for v in prop.values())
+ ):
+ available_labels.append(prop_name)
+ return available_labels
+
+
+def change_labels(
+ lT: LineageTree,
+ new_labels_name: str | None = None,
+ new_labels_dict: dict[int, str] | None = None,
+ only_first_node_in_chain: bool = False,
+) -> None:
+ """Change the dictionary that serves at labels with
+ the `LineageTree` attribute `new_labels_name`.
+ It has to be a dictionary mapping node id to string.
+
+ If `new_labels_dict` is provided, it will be used to
+ label the cells.
+ If `new_labels_name` is not specified, the labels are reset.
+
+ One can decide to only label the first node of the chain
+ instead of all the nodes of the chain.
+ That can help readability in the napari plugin reLAX.
+
+ Parameters
+ ----------
+ lT : LineageTree
+ new_labels_name : string, optional
+ The name of the dictionary to use
+ (the list of potential dictionaries can be found
+ with `lT.available_labels`)
+ If `new_labels_name` is not provided,
+ the labels are reset to `"Unlabeleld"`
+ new_labels_dict : dictionary mapping integers to strings, optional
+ The new names as a dictionary mapping each named node id to its string label
+ If not provided and lT has a fitting attribute named `new_labels_name`,
+ it will therefore be used
+ only_first_node_in_chain : bool, default=True
+ If `True` only labels the first node of the chains
+ """
+ store_new_labels = True
+ if new_labels_name is not None:
+ lT.labels_name = new_labels_name
+ if new_labels_dict is None:
+ if new_labels_name in lT.__dict__:
+ new_labels_dict = lT.__dict__[new_labels_name]
+ store_new_labels = False
+ else:
+ raise AttributeError(
+ f"{new_labels_name} is not in the properties of {lT.name}"
+ )
+ if any(not isinstance(v, str) for v in new_labels_dict.values()):
+ raise TypeError(
+ "All values of new_labels dictionary should be `str`"
+ )
+
+ labelled_cells = lT.nodes.intersection(new_labels_dict)
+ if only_first_node_in_chain:
+ labelled_cells = labelled_cells.intersection(
+ {chain[0] for chain in lT.all_chains}
+ )
+
+ if len(labelled_cells) < 1:
+ warnings.warn(
+ "The labeling dictionary does not have any node labels.\n"
+ 'Defaulting to the "Unlabeled" labeling'
+ )
+ else:
+ lT._labels = {n: new_labels_dict[n] for n in labelled_cells}
+ if store_new_labels:
+ lT.__dict__[new_labels_name] = lT._labels
+ else:
+ lT.labels_name = ""
+ lT._labels = {
+ root: "Unlabeled"
+ for root in lT.roots
+ for leaf in lT.find_leaves(root)
+ if abs(lT._time[leaf] - lT._time[root]) >= abs(lT.t_e - lT.t_b) / 4
+ }
diff --git a/src/lineagetree/_basics/_properties.py b/src/lineagetree/_basics/_properties.py
index a235b63..36a967c 100644
--- a/src/lineagetree/_basics/_properties.py
+++ b/src/lineagetree/_basics/_properties.py
@@ -149,10 +149,13 @@ def labels(lT: LineageTree) -> dict[int, str]:
"""Dictionary that maps a node to its label"""
if not hasattr(lT, "_labels"):
if hasattr(lT, "node_name"):
+ lT.labels_name = "node_name"
lT._labels = {
- i: lT.node_name.get(i, "Unlabeled") for i in lT.roots
+ chain[0]: lT.node_name.get(chain[0], "Unlabeled")
+ for chain in lT.all_chains
}
else:
+ lT.labels_name = ""
lT._labels = {
root: "Unlabeled"
for root in lT.roots
diff --git a/src/lineagetree/_io/_loaders.py b/src/lineagetree/_io/_loaders.py
index beacc98..3cb7509 100644
--- a/src/lineagetree/_io/_loaders.py
+++ b/src/lineagetree/_io/_loaders.py
@@ -763,7 +763,7 @@ def read_from_tgmm_xml(
def read_from_mastodon(
- path: str, tag_set: int | None = None, name: None | str = None
+ path: str, tag_set: str | None = None, name: str | None = None
) -> LineageTree:
"""Read a maston lineage tree.
@@ -771,8 +771,9 @@ def read_from_mastodon(
----------
path : str
path to the mastodon file
- tag_set : int, optional
- The tag set that will be used to label.
+ tag_set : str, optional
+ If specified, `tag_set` will be used for labeling the cells
+ Otherwise a random tag set will be used
name : str, optional
The name attribute of the LineageTree file. If given a non-empty string, the value of the attribute
will be the name attribute, otherwise the name will be the stem of the file path.
@@ -793,20 +794,12 @@ def read_from_mastodon(
for succ, pred in zip(links[:, 1], links[:, 0]):
predecessor[int(succ)] = int(pred)
- label = {}
- all_tags = mr.read_tags(spots, links)
- properties = {}
- for tags in all_tags:
- properties[tags["name"]] = {
- tag["id"]: tag["label"] for tag in tags["tags"]
- }
+ _, properties, _ = mr.read_tags()
- if isinstance(tag_set, int):
- tags = all_tags[tag_set]
- for tag in tags["tags"]:
- label[tag["id"]] = tag["label"]
- elif isinstance(tag_set, str) and tag_set in properties:
- label = properties[tag_set]
+ if isinstance(tag_set, str) and tag_set in properties:
+ labels = properties[tag_set]
+ elif 0 < len(properties):
+ labels_name, labels = next(iter(properties.items()))
if not name:
if isinstance(path, Path):
@@ -816,11 +809,13 @@ def read_from_mastodon(
if name == "":
warn(f"Name set to default {tmp_name}", stacklevel=2)
name = tmp_name
+
return LineageTree(
predecessor=predecessor,
time=time,
pos=pos,
- label=label,
+ labels=labels,
+ labels_name=labels_name,
name=name,
**properties,
)
@@ -833,7 +828,7 @@ def read_from_mastodon_csv(
Parameters
----------
- paths : list[str]
+ paths : list of strings
list of paths to the csv files
name : None or str, optional
The name attribute of the LineageTree file. If given a non-empty string, the value of the attribute
diff --git a/src/lineagetree/test/data/demo.lT b/test/data/demo.lT
similarity index 100%
rename from src/lineagetree/test/data/demo.lT
rename to test/data/demo.lT
diff --git a/src/lineagetree/test/data/test-mamut.lT b/test/data/test-mamut.lT
similarity index 100%
rename from src/lineagetree/test/data/test-mamut.lT
rename to test/data/test-mamut.lT
diff --git a/src/lineagetree/test/data/test-mamut.xml b/test/data/test-mamut.xml
similarity index 99%
rename from src/lineagetree/test/data/test-mamut.xml
rename to test/data/test-mamut.xml
index 9fcf4c5..b83766e 100644
--- a/src/lineagetree/test/data/test-mamut.xml
+++ b/test/data/test-mamut.xml
@@ -1,5649 +1,5649 @@
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+ 0
+ 350.0
+ 600.0
+ -10027009
+ 0
+
+
+ 1
+ 15.0
+ 50.0
+ -65536
+ 1
+
+
+
+
+ 0
+ 0.0
+ 65535.0
+ 0.0
+ 65535.0
+ 350.0
+ 600.0
+
+
+ 1
+ 0.0
+ 65535.0
+ 0.0
+ 65535.0
+ 15.0
+ 50.0
+
+
+
+
+
+
diff --git a/src/lineagetree/test/data/test.mastodon b/test/data/test.mastodon
similarity index 100%
rename from src/lineagetree/test/data/test.mastodon
rename to test/data/test.mastodon
diff --git a/src/lineagetree/test/test_lineageTree.py b/test/test_lineageTree.py
similarity index 94%
rename from src/lineagetree/test/test_lineageTree.py
rename to test/test_lineageTree.py
index a4ba9a5..fad30b6 100644
--- a/src/lineagetree/test/test_lineageTree.py
+++ b/test/test_lineageTree.py
@@ -11,9 +11,9 @@
tree_approximation,
)
-lT1 = read_from_mamut_xml("src/lineagetree/test/data/test-mamut.xml")
-lT2 = read_from_mastodon("src/lineagetree/test/data/test.mastodon")
-lt = LineageTree.load("src/lineagetree/test/data/demo.lT")
+lT1 = read_from_mamut_xml("test/data/test-mamut.xml")
+lT2 = read_from_mastodon("test/data/test.mastodon")
+lt = LineageTree.load("test/data/demo.lT")
def test_read_MaMuT_xml():
@@ -121,7 +121,7 @@ def test_time_resolution():
def test_loading():
- lT = LineageTree.load("src/lineagetree/test/data/test-mamut.lT")
+ lT = LineageTree.load("test/data/test-mamut.lT")
assert lT.time_resolution == 0
lT.time_resolution = 1.51
assert lT.time_resolution == 1.5
@@ -632,3 +632,34 @@ def test_get_ancestor_with():
assert lt.get_labelled_ancestor(
list(lt.nodes)[0]
) == lt.get_ancestor_with_attribute(list(lt.nodes)[0], "labels")
+
+
+def test_mastodon_labeling():
+ assert lT2.labels[25] == "p"
+ assert lT2.labels[40] == "p(2)"
+ assert lT2.labels_name == "E"
+
+
+def test_available_labels():
+ assert lT2.get_available_labels() == ["E", "Ep", "Er", "El", "Extoderms"]
+
+
+def test_change_labels():
+ lT2.change_labels("Ep")
+ assert lT2.labels[19] == "alla"
+ assert lT2.labels[9] == "right1"
+
+ lT2.change_labels("test", {19: "a", 9: "b"})
+ assert lT2.labels[19] == "a"
+ assert lT2.labels[9] == "b"
+
+ lT2.change_labels("Ep", only_first_node_in_chain=True)
+ assert lT2.labels == {
+ 0: "right1",
+ 1: "right1",
+ 40: "right1",
+ 16: "left",
+ 19: "alla",
+ 24: "left",
+ 25: "left",
+ }
diff --git a/src/lineagetree/test/test_uted.py b/test/test_uted.py
similarity index 100%
rename from src/lineagetree/test/test_uted.py
rename to test/test_uted.py