LineageTree 1.8.0__tar.gz → 2.0.3__tar.gz

lineagetree-2.0.3/PKG-INFO

@@ -0,0 +1,130 @@
+Metadata-Version: 2.4
+Name: LineageTree
+Version: 2.0.3
+Summary: Structure for Lineage Trees
+Author: Giannis Liaskas, Christopher Mazzerbo
+Author-email: Léo Guignard <leo.guignard@univ-amu.fr>
+Maintainer-email: Léo Guignard <leo.guignard@univ-amu.fr>
+License-Expression: MIT
+Project-URL: Bug Tracker, https://github.com/GuignardLab/LineageTree/issues
+Project-URL: Documentation, https://github.com/GuignardLab/LineageTree#README.md
+Project-URL: Source Code, https://github.com/GuignardLab/LineageTree
+Project-URL: User Support, https://github.com/GuignardLab/LineageTree/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scipy>=1.9
+Requires-Dist: numpy>=1.23
+Requires-Dist: mastodon-reader
+Requires-Dist: matplotlib
+Requires-Dist: edist
+Requires-Dist: svgwrite
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: bumpver; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: sphinx-rtd-theme; extra == "doc"
+Requires-Dist: myst-parser; extra == "doc"
+Requires-Dist: sphinx_book_theme; extra == "doc"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Dynamic: license-file
+
+# LineageTree
+
+This library allows to import and work with cell (but not limited to cells) lineage trees.
+With LineageTree you can read from:
+
+- TGMM algorithm outputs described in [Amat et al. 2014](https://www.nature.com/articles/nmeth.3036)
+- TrackMate files described in [Tinevez et al. 2017](https://doi.org/10.1016/j.ymeth.2016.09.016)
+- MaMuT files described in [Wolff et al. 2018](https://doi.org/10.7554/eLife.34410)
+- SVF algorithm outputs described in [McDole, Guignard et al. 2018](https://doi.org/10.1016/j.cell.2018.09.031)
+- ASTEC algorithm outputs described in [Guignard, Fiuza et al. 2020](https://doi.org/10.1126/science.aar5663)
+- Data from the [Digital development Database](http://digital-development.org/index.html) described in [Du et al. 2014](https://www.cell.com/fulltext/S0092-8674(13)01542-0) and [Du et al. 2015](https://www.sciencedirect.com/science/article/pii/S1534580715004876?via%3Dihub)
+- and few others
+
+## Basic usage
+
+Once installed the library can be called the following way (as an example):
+
+```python
+from LineageTree import lineageTree
+```
+
+and one can then load lineage trees the following way:
+
+For `.lT` files:
+
+```python
+lT = lineageTree.load('path/to/file.lT')
+```
+
+For ASTEC data:
+
+```python
+from LineageTree import read_from_ASTEC
+lT = read_from_ASTEC('path/to/ASTEC.pkl')
+```
+
+For MaMuT or TrackMate:
+
+```python
+from LineageTree import read_from_mamut_xml
+lT = read_from_mamut_xml('path/to/MaMuT.xml')
+```
+
+For TGMM:
+
+```python
+from LineageTree import read_from_tgmm_xml
+lT = read_from_tgmm_xml('path/to/single_time_file{t:04d}.xml', tb=0, te=500)
+```
+
+For Mastodon:
+
+```python
+from LineageTree import read_from_mastodon
+lT = read_from_mastodon('path/to/Mastodon.mastodon')
+```
+
+or, for Mastodon csv file:
+
+```python
+from LineageTree import read_from_mastodon_csv
+lT = read_from_mastodon_csv(['path/to/nodes.csv', 'path/to/links.csv'])
+```
+
+## Quick install
+
+To quickly install the library together with its dependencies one can run:
+
+```shell
+pip install LineageTree
+```
+
+or, for the latest version if you have cloned the directory:
+
+```shell
+pip install .
+```
+
+or for the latest version wihtout cloning the directory
+
+```shell
+pip install git+https://github.com/leoguignard/LineageTree
+```

{lineagetree-1.8.0 → lineagetree-2.0.3}/README.md

@@ -3,7 +3,7 @@
 This library allows to import and work with cell (but not limited to cells) lineage trees.
 With LineageTree you can read from:
 
-- TGMM algorithm outputs described in [Fernando et al. 2014](https://www.nature.com/articles/nmeth.3036)
+- TGMM algorithm outputs described in [Amat et al. 2014](https://www.nature.com/articles/nmeth.3036)
 - TrackMate files described in [Tinevez et al. 2017](https://doi.org/10.1016/j.ymeth.2016.09.016)
 - MaMuT files described in [Wolff et al. 2018](https://doi.org/10.7554/eLife.34410)
 - SVF algorithm outputs described in [McDole, Guignard et al. 2018](https://doi.org/10.1016/j.cell.2018.09.031)
@@ -24,66 +24,44 @@ and one can then load lineage trees the following way:
 For `.lT` files:
 
 ```python
-lT = lineageTree('path/to/file.lT')
+lT = lineageTree.load('path/to/file.lT')
 ```
 
 For ASTEC data:
 
 ```python
-lT = lineageTree('path/to/ASTEC.pkl', file_type='ASTEC')
+from LineageTree import read_from_ASTEC
+lT = read_from_ASTEC('path/to/ASTEC.pkl')
 ```
 
-or
+For MaMuT or TrackMate:
 
 ```python
-lT = lineageTree('path/to/ASTEC.xml', file_type='ASTEC')
-```
-
-For SVF:
-
-```python
-lT = lineageTree('path/to/SVF.bin')
-```
-
-For MaMuT:
-
-```python
-lT = lineageTree('path/to/MaMuT.xml', file_type='MaMuT')
-```
-
-For TrackMate:
-
-```python
-lT = lineageTree('path/to/MaMuT.xml', file_type='TrackMate')
+from LineageTree import read_from_mamut_xml
+lT = read_from_mamut_xml('path/to/MaMuT.xml')
 ```
 
 For TGMM:
 
 ```python
-lT = lineageTree('path/to/single_time_file{t:04d}.xml', tb=0, te=500, file_type='TGMM')
+from LineageTree import read_from_tgmm_xml
+lT = read_from_tgmm_xml('path/to/single_time_file{t:04d}.xml', tb=0, te=500)
 ```
 
 For Mastodon:
 
 ```python
-lT = lineageTree('path/to/Mastodon.mastodon', file_type='mastodon')
+from LineageTree import read_from_mastodon
+lT = read_from_mastodon('path/to/Mastodon.mastodon')
 ```
 
 or, for Mastodon csv file:
 
 ```python
-lT = lineageTree(['path/to/nodes.csv', 'path/to/links.csv'], file_type='mastodon')
+from LineageTree import read_from_mastodon_csv
+lT = read_from_mastodon_csv(['path/to/nodes.csv', 'path/to/links.csv'])
 ```
 
-## Dependencies
-
-Some dependecies are requiered:
-
-- general python dependecies:
-  - numpy, scipy
-- specific dependency:
-  - svgwrite if svg output is needed
-
 ## Quick install
 
 To quickly install the library together with its dependencies one can run:

lineagetree-2.0.3/pyproject.toml

@@ -0,0 +1,152 @@
+[build-system]
+requires = ["setuptools>=42.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[project]
+authors = [
+    { name = "Léo Guignard", email = "leo.guignard@univ-amu.fr"},
+    { name = "Giannis Liaskas"},
+    { name = "Christopher Mazzerbo"},
+]
+maintainers = [
+    {name = "Léo Guignard", email = "leo.guignard@univ-amu.fr"}
+]
+name = "LineageTree"
+description = "Structure for Lineage Trees"
+version = "2.0.3"
+license = "MIT"
+license-files = [ "LICENSE" ]
+readme = {file = "README.md", content-type = "text/markdown"}
+requires-python = ">= 3.10"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+
+dependencies = [
+    "scipy>=1.9",
+    "numpy>=1.23",
+    "mastodon-reader",
+    "matplotlib",
+    "edist",
+    "svgwrite",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytest-cov",
+    "tox",
+    "black",
+    "ruff",
+    "bumpver",
+]
+doc = [
+    "sphinx-rtd-theme",
+    "myst-parser",
+    "sphinx_book_theme",
+]
+test = [
+    "pytest",
+    "pytest-cov",
+]
+
+[project.urls]
+"Bug Tracker" = "https://github.com/GuignardLab/LineageTree/issues"
+Documentation = "https://github.com/GuignardLab/LineageTree#README.md"
+"Source Code" = "https://github.com/GuignardLab/LineageTree"
+"User Support" = "https://github.com/GuignardLab/LineageTree/issues"
+
+[tool.black]
+line-length = 79
+
+[tool.isort]
+profile = "black"
+line_length = 79
+
+[tool.bumpver]
+current_version = "2.0.3"
+version_pattern = "MAJOR.MINOR.PATCH[-TAG]"
+commit_message = "bump version {old_version} -> {new_version}"
+commit = true
+tag = true
+push = false
+
+[tool.bumpver.file_patterns]
+"pyproject.toml" = [
+    'current_version = "{version}"',
+    'version = "{version}"',
+]
+"src/LineageTree/__init__.py" = [
+    '__version__ = "{version}"',
+]
+
+[tool.ruff]
+line-length = 79
+lint.select = [
+    "E", "F", "W", #flake8
+    "UP", # pyupgrade
+    "I", # isort
+    "BLE", # flake8-blind-exception
+    "B", # flake8-bugbear
+    "A", # flake8-builtins
+    "C4", # flake8-comprehensions
+    "ISC", # flake8-implicit-str-concat
+    "G", # flake8-logging-format
+    "PIE", # flake8-pie
+    "SIM", # flake8-simplify
+    "I", # imports
+    "T201", # print statements
+    "ERA001", #commented out code
+]
+lint.ignore = [
+    "E501", # line too long. let black handle this
+    "SIM300", # yoda conditions
+]
+
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".mypy_cache",
+    ".pants.d",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+    "*vendored*",
+    "*_vendor*",
+]
+
+target-version = "py310"
+
+[tool.ty.src]
+root = "./src"
+
+[tool.ty.rules]
+unresolved-import = "ignore"
+
+[tool.pytest.ini_options]
+addopts = "--cov"
+
+[report]
+show_missing=true

lineagetree-2.0.3/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

lineagetree-2.0.3/src/LineageTree/__init__.py

@@ -0,0 +1,30 @@
+__version__ = "2.0.3"
+from .lineageTree import lineageTree
+from .lineageTreeManager import lineageTreeManager
+from .loaders import (
+    read_from_ASTEC,
+    read_from_binary,
+    read_from_csv,
+    read_from_mamut_xml,
+    read_from_mastodon,
+    read_from_mastodon_csv,
+    read_from_tgmm_xml,
+    read_from_txt_for_celegans,
+    read_from_txt_for_celegans_BAO,
+    read_from_txt_for_celegans_CAO,
+)
+
+__all__ = (
+    "lineageTree",
+    "lineageTreeManager",
+    "read_from_tgmm_xml",
+    "read_from_txt_for_celegans_BAO",
+    "read_from_ASTEC",
+    "read_from_binary",
+    "read_from_csv",
+    "read_from_mamut_xml",
+    "read_from_mastodon_csv",
+    "read_from_mastodon",
+    "read_from_txt_for_celegans",
+    "read_from_txt_for_celegans_CAO",
+)

lineagetree-2.0.3/src/LineageTree/legacy/export_csv.py

@@ -0,0 +1,70 @@
+import csv
+
+from lineageTree import lineageTree
+
+"""Writes a lineage tree into a series of csv files.
+
+ * spots.csv: id; label; timePoint; x; y; z; volume
+ * links.csv: source spot id; target spot id
+ * fates1.csv: tagValue
+ * fate_values1.csv: spot id; tagValue
+ * fates2.csv: tagValue
+ * fate_values2.csv: spot id; tagValue
+ * fates3.csv: tagValue
+ * fate_values3.csv: spot id; tagValue
+"""
+
+
+def export_to_csv():
+    tree = lineageTree("Astec-Pm10_properties.pkl", file_type="ASTEC")
+
+    spots = [["id", "label", "timePoint", "x", "y", "z", "volume"]]
+    for node_id in tree.nodes:
+        cell_name = tree["cell_name"].get(node_id, "unknown")
+        spots.append(
+            [
+                node_id,
+                cell_name,
+                tree.time.get(node_id),
+                tree.pos[node_id][0],
+                tree.pos[node_id][1],
+                tree.pos[node_id][2],
+                tree.volume[node_id],
+            ]
+        )
+    write("spots.csv", spots)
+
+    links = [["source", "target"]]
+    for edge in tree.edges:
+        links.append([edge[0], edge[1]])
+    write("links.csv", links)
+
+    write_fate(tree.fates, "fates1.csv", tree, "fate_values1.csv")
+    write_fate(tree["cell_fate_2"], "fates2.csv", tree, "fate_values2.csv")
+    write_fate(tree["cell_fate_3"], "fates3.csv", tree, "fate_values3.csv")
+
+
+def write_fate(fates, fate_name, tree, fate_value_name):
+    all_fates = []
+    for index in fates:
+        all_fates.append(fates[index])
+    unique_fates = set(all_fates)
+    fates_list = [["fate"]]
+    for fate in unique_fates:
+        fates_list.append([fate])
+    write(fate_name, fates_list)
+
+    fate_values = [["id", "value"]]
+    for node_id in tree.nodes:
+        fate_values.append([node_id, tree.fates.get(node_id)])
+    write(fate_value_name, fate_values)
+
+
+def write(file_path, data):
+    with open(file_path, mode="w", newline="") as file:
+        writer = csv.writer(file)
+        writer.writerows(data)
+
+
+if __name__ == "__main__":
+    export_to_csv()

lineagetree-2.0.3/src/LineageTree/legacy/to_lineajea.py

@@ -0,0 +1,30 @@
+import csv
+
+
+def write_csv_from_lT_to_lineaja(
+    lT, path_to, start: int = 0, finish: int = 300
+):
+    csv_dict = {}
+    for time in range(start, finish):
+        for node in lT.time_nodes[time]:
+            csv_dict[node] = {"pos": lT.pos[node], "t": time}
+    with open(path_to, "w", newline="\n") as file:
+        fieldnames = [
+            "time",
+            "positions_x",
+            "positions_y",
+            "positions_z",
+            "id",
+        ]
+        writer = csv.DictWriter(file, fieldnames=fieldnames)
+        writer.writeheader()
+        for node in csv_dict:
+            writer.writerow(
+                {
+                    "time": csv_dict[node]["t"],
+                    "positions_z": csv_dict[node]["pos"][0],
+                    "positions_y": csv_dict[node]["pos"][1],
+                    "positions_x": csv_dict[node]["pos"][2],
+                    "id": node,
+                }
+            )

lineagetree-2.0.3/src/LineageTree/legacy/to_motile.py

@@ -0,0 +1,36 @@
+import warnings
+
+from ..lineageTree import lineageTree
+
+try:
+    import motile
+except ImportError:
+    warnings.warn(
+        "No motile installed therefore you will not be able to produce links with motile.",
+        stacklevel=2,
+    )
+
+
+def to_motile(
+    lT: lineageTree, crop: int | None = None, max_dist=200, max_skip_frames=1
+):
+    try:
+        import networkx as nx
+    except ImportError:
+        raise Warning("Please install networkx")  # noqa: B904
+
+    fmt = nx.DiGraph()
+    if not crop:
+        crop = lT.t_e
+    for time in range(crop):
+        for time_node in lT.nodes_at_t(time):
+            fmt.add_node(
+                time_node,
+                t=lT.time[time_node],
+                pos=lT.pos[time_node],
+                score=1,
+            )
+
+    motile.add_cand_edges(fmt, max_dist, max_skip_frames=max_skip_frames)
+
+    return fmt