Merge pull request #27 from 23andMe/unrotate-newick

Unrotate Newick representation

Author: dpoznik

.gitignore

@@ -12,7 +12,6 @@ __pycache__/
 .minio.sys
 .mypy_cache
 .pytest_cache
-.tox
 
 # Distribution & packaging
 #----------------------------------
@@ -24,7 +23,6 @@ wheels/
 .eggs/
 *.egg
 *.egg-info/
-_version.py
 
 # Editors & IDEs
 #----------------------------------

CHANGELOG.md

@@ -3,6 +3,32 @@
 Format based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 
 
+## [Unreleased]
+
+No unreleased changes
+
+[Unreleased]: https://github.com/23andMe/yhaplo/compare/2.1.6..HEAD
+
+
+## [2.1.6] - 2024-02-07
+
+### Added
+- Python 3.12 support
+- `__str__` and `__repr__` methods
+- SNP-based haplogroup in MRCA output
+
+### Changed
+- Newick representation is now unrotated by default
+
+### Removed
+- `setuptools_scm`-generated version file
+
+### Fixed
+- When generating Newick representation, recalculate maximum depth to support pruned trees
+
+[2.1.6]: https://github.com/23andMe/yhaplo/compare/2.1.4..2.1.6
+
+
 ## [2.1.4] - 2024-01-29
 
 ### Added

README.md

@@ -1,7 +1,7 @@
 # Yhaplo | Identifying Y-Chromosome Haplogroups
 
 [![python](
-https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11-blue.svg)](
+https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue.svg)](
 https://docs.python.org)
 [![style](
 https://img.shields.io/badge/style-black-blue.svg)](

pyproject.toml

@@ -1,8 +1,5 @@
 [build-system]
-requires = [
-    "setuptools>=61.0",
-    "setuptools_scm[toml]>=6.2",
-]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -52,7 +49,6 @@ Repository = "https://github.com/23andMe/yhaplo.git"
 Changelog = "https://github.com/23andMe/yhaplo/blob/master/CHANGELOG.md"
 
 [tool.setuptools_scm]
-write_to = "yhaplo/_version.py"
 
 [tool.isort]
 profile = "black"
@@ -80,18 +76,3 @@ norecursedirs = [
     ".*",
     "build",
 ]
-
-[tool.tox]
-legacy_tox_ini = """
-[tox]
-envlist = py39, py310, py311
-
-[testenv]
-commands =
-    pytest
-sitepackages = false
-deps =
-    pytest
-extras =
-    vcf
-"""

scripts/validate_yhaplo.sh

@@ -40,7 +40,7 @@ yhaplo --example_text \
     --breadth_first \
     --depth_first \
     --depth_first_table \
-    --mrca Q J \
+    --mrca Q-M3 R-V88 \
     --snp_query L1335,S730,S530,foo
 echo -e "\n"
 

yhaplo/config.py

@@ -10,7 +10,7 @@
 import numpy as np
 from numpy.typing import NDArray
 
-from yhaplo._version import __version__
+from yhaplo import __version__
 from yhaplo.api.command_line_args import get_command_line_arg_defaults
 from yhaplo.utils.loaders import DataFile
 
@@ -216,6 +216,11 @@ def __init__(
         if self.suppress_output:
             self.override_output_generating_args()
 
+    def __repr__(self) -> str:
+        """Return string representation."""
+
+        return f"<{__name__}.{self.__class__.__name__}: command_line_args={self.args}>"
+
     def set_params_general(
         self,
         out_dir: Optional[str],

yhaplo/node.py

@@ -100,9 +100,17 @@ def __init__(
 
     # String representations
     # ----------------------------------------------------------------------
-    def __str__(self) -> str:
+    def __repr__(self) -> str:
         """Return string representation."""
 
+        return (
+            f"<{__name__}.{self.__class__.__name__}: "
+            f'label="{self.label}", hg_snp="{self.hg_snp}">'
+        )
+
+    def __str__(self) -> str:
+        """Return printable string representation."""
+
         return self.str_simple
 
     @property
@@ -516,14 +524,32 @@ def write_newick(
         use_hg_snp_label: bool = False,
         align_tips: bool = False,
         platform: Optional[str] = None,
+        rotate: bool = False,
     ) -> None:
-        """Write Newick string for the subtree rooted at this node."""
+        """Write Newick representation of the subtree rooted at this node.
+
+        Parameters
+        ----------
+        newick_fp : str
+            File path to which to write Newick representation.
+        use_hg_snp_label : bool, optional
+            Use SNP-based haplogroup labels rather than YCC haplogroup labels.
+        align_tips : bool, optional
+            When True, set branch lengths to align the tips of the tree.
+        platform : str | None, optional
+            23andMe platform to use for computing branch lengths.
+        rotate : bool, optional
+            Rotate nodes. By default, branches will be ordered top to bottom.
+            Rotating nodes orders branches bottom to top, which is left to right
+            when an image is rotated 90 degrees to the right.
 
+        """
         if not type(self).config.suppress_output:
             newick = self.build_newick(
                 use_hg_snp_label=use_hg_snp_label,
                 align_tips=align_tips,
                 platform=platform,
+                rotate=rotate,
             )
             with open(newick_fp, "w") as out_file:
                 out_file.write(newick + "\n")
@@ -550,6 +576,7 @@ def build_newick(
         use_hg_snp_label: bool = False,
         align_tips: bool = False,
         platform: Optional[str] = None,
+        rotate: bool = False,
     ) -> str:
         """Build Newick string for the subtree rooted at this node.
 
@@ -561,24 +588,25 @@ def build_newick(
             When True, set branch lengths to align the tips of the tree.
         platform : str | None, optional
             23andMe platform to use for computing branch lengths.
+        rotate : bool, optional
+            Rotate nodes. By default, branches will be ordered top to bottom.
+            Rotating nodes orders branches bottom to top, which is left to right
+            when an image is rotated 90 degrees to the right.
 
         Returns
         -------
         newick : str
             Newick representation of the tree.
 
         """
-        subtree_max_depth = (
-            self.tree.max_depth
-            if self.is_root
-            else np.max([node.depth for node in self.iter_depth_first()])
-        )
+        subtree_max_depth = np.max([node.depth for node in self.iter_depth_first()])
         newick = (
             self.build_newick_recursive(
                 use_hg_snp_label=use_hg_snp_label,
                 align_tips=align_tips,
                 subtree_max_depth=subtree_max_depth,
                 platform=platform,
+                rotate=rotate,
             )
             + ";"
         )
@@ -591,6 +619,7 @@ def build_newick_recursive(
         align_tips: bool = False,
         subtree_max_depth: Optional[int] = None,
         platform: Optional[str] = None,
+        rotate: bool = False,
     ) -> str:
         """Build Newick string recursively for the subtree rooted at this node.
 
@@ -605,6 +634,10 @@ def build_newick_recursive(
             Default to maximum depth of full tree.
         platform : str | None, optional
             23andMe platform to use for computing branch lengths.
+        rotate : bool, optional
+            Rotate nodes. By default, branches will be ordered top to bottom.
+            Rotating nodes orders branches bottom to top, which is left to right
+            when an image is rotated 90 degrees to the right.
 
         Returns
         -------
@@ -613,23 +646,27 @@ def build_newick_recursive(
 
         """
         subtree_max_depth = subtree_max_depth or type(self).tree.max_depth
-
-        if not self.is_leaf:
-            child_string_list = []
-            for child in self.child_list[::-1]:
-                child_string = child.build_newick_recursive(
-                    use_hg_snp_label=use_hg_snp_label,
-                    align_tips=align_tips,
-                    subtree_max_depth=subtree_max_depth,
-                    platform=platform,
+        child_list = self.child_list if not rotate else self.child_list[::-1]
+        children_string = (
+            (
+                "("
+                + ",".join(
+                    [
+                        child.build_newick_recursive(
+                            use_hg_snp_label=use_hg_snp_label,
+                            align_tips=align_tips,
+                            subtree_max_depth=subtree_max_depth,
+                            platform=platform,
+                            rotate=rotate,
+                        )
+                        for child in child_list
+                    ]
                 )
-                child_string_list.append(child_string)
-
-            children = ",".join(child_string_list)
-            children_string = f"({children})"
-        else:
-            children_string = ""
-
+                + ")"
+            )
+            if not self.is_leaf
+            else ""
+        )
         branch_label = self.hg_snp if use_hg_snp_label else self.label
         branch_length = self.get_branch_length(
             align_tips=align_tips,

yhaplo/path.py

@@ -88,17 +88,24 @@ def copy_all_attributes_other_than_node(self, other: Path) -> None:
         self.num_anc_since_push_through = other.num_anc_since_push_through
         self.num_der_since_push_through = other.num_der_since_push_through
 
-    def __str__(self) -> str:
+    def __repr__(self) -> str:
         """Return string representation."""
 
-        str_ = (
+        return (
+            f"<{__name__}.{self.__class__.__name__}: "
+            f"num_ancestral={self.num_ancestral}, num_derived={self.num_derived}, "
+            f'node_string="{self.node_string}", snp_string="{self.snp_string}">'
+        )
+
+    def __str__(self) -> str:
+        """Return printable string representation."""
+
+        return (
             f"{self.num_ancestral} {self.num_derived}\n"
             f"{self.node_string}\n"
             f"{self.snp_string}"
         )
 
-        return str_
-
     # Properties
     # ----------------------------------------------------------------------
     @property

yhaplo/sample.py

@@ -119,14 +119,22 @@ def __init__(self, iid: IID_TYPE):
 
         type(self).sample_list.append(self)
 
-    def __str__(self) -> str:
+    def __repr__(self) -> str:
         """Return string representation."""
 
-        sample_string = (
+        return (
+            f"<{__name__}.{self.__class__.__name__}: "
+            f'iid={str(self.iid)}, hg_snp_obs="{self.hg_snp_obs}", '
+            f'hg_snp="{self.hg_snp}", haplogroup="{self.haplogroup}">'
+        )
+
+    def __str__(self) -> str:
+        """Return printable string representation."""
+
+        return (
             f"{str(self.iid):8s} {self.hg_snp_obs:15s} "
             f"{self.hg_snp:15s} {self.haplogroup:25s}"
         )
-        return sample_string
 
     # Haplogroup calling
     # ----------------------------------------------------------------------

yhaplo/snp.py

@@ -108,14 +108,22 @@ def set_label(self, label: str) -> None:
         ) = parse_snp_label(label, Config.snp_label_letters_rank_dict)
         self.label_cleaned = clean_snp_label(label)
 
+    def __repr__(self) -> str:
+        """Return string representation."""
+
+        return (
+            f"<{__name__}.{self.__class__.__name__}: "
+            f'label="{self.label}", node.label="{self.node.label}", position={self.position}, '
+            f'mutation="{self.ancestral}->{self.derived}">'
+        )
+
     def __str__(self) -> str:
-        """Return medium-length string representation."""
+        """Return printable string representation."""
 
-        str_ = (
+        return (
             f"{self.label:15s} {self.node.label:25s} {self.position:8d} "
             f"{self.ancestral}->{self.derived}"
         )
-        return str_
 
     @property
     def str_with_all_names(self) -> str:
@@ -383,6 +391,14 @@ def __init__(
         self.haplogroup = haplogroup
         self.tree = tree
 
+    def __repr__(self) -> str:
+        """Return string representation."""
+
+        return (
+            f"<{__name__}.{self.__class__.__name__}: "
+            f'name="{self.name}", haplogroup="{self.haplogroup}">'
+        )
+
     def add_to_node(self) -> bool:
         """Add this dropped marker to the corresponding node, if it exists."""