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).
1 maintainer
Metadata
1 maintainer
Release files for pydynwrap-bio 0.1.0
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