pydynwrap-bio 0.1.0

Pure-Python port of dynwrap — single-cell trajectory data wrapper (Saelens et al. Nat Biotechnol 2019).

py-dynwrap

A Python port of dynverse/dynwrap (Saelens et al. Nat Biotechnol 2019) — the trajectory data wrapper used by the dynbenchmark / dyneval comparison framework.

• Pure NumPy/SciPy/NetworkX/pandas — no R, no rpy2, no docker
• byte-equivalent geodesic distances vs R (max|Δ| = 0.0 on canonical fixture)
• v0.1 scope: data structures + topology utilities + geodesic distances — the minimum needed for pydyneval::calculate_metrics

Install

pip install pydynwrap-bio

Quick-start

import pydynwrap as dw
import pandas as pd, numpy as np

# Build a 3-branch bifurcation trajectory
ds = dw.wrap_data(cell_ids=[f"c{i}" for i in range(30)])
ds = dw.add_branch_trajectory(
    ds,
    pseudotime=np.tile(np.linspace(0,1,10), 3),
    branch=np.repeat(["A","B","C"], 10),
)

# Geodesic distance matrix (every cell vs every cell)
gd = dw.calculate_geodesic_distances(ds, directed=False)

Function map

Python	R dynwrap::	Status
wrap_data	wrap_data	✅
add_trajectory	add_trajectory	✅
add_linear_trajectory	add_linear_trajectory	✅
add_branch_trajectory	add_branch_trajectory	✅
add_cluster_graph	add_cluster_graph	✅
add_pseudotime / add_grouping / add_dimred / add_expression	same	✅
add_cell_waypoints	add_cell_waypoints	✅
convert_progressions_to_milestone_percentages	same	✅
convert_milestone_percentages_to_progressions	same	✅
calculate_geodesic_distances	same	✅ (byte-equivalent)
classify_milestone_network	same	✅
simplify_trajectory	same	⏳ v0.2 (stub)
is_wrapper_with_trajectory etc. predicates	same	✅
Method runners (infer_trajectory, ti_* containers)	—	⛔ v0.3+ (need babelwhale/docker)
align_to_* cross-trajectory comparison	—	⏳ v0.2

Coverage: 14/91 R exports — the core data-wrapping API. Method-running (the dynbenchmark TI runners) is the remaining 60+ exports, deferred per Phase 0.5 scoping.

Citation

Saelens, W. et al. A comparison of single-cell trajectory inference methods. Nat Biotechnol 37, 547–554 (2019).

License

MIT (matches upstream dynwrap MIT).