Skip to content

📝 Fix documentation #45

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
enryH merged 5 commits into from
Feb 27, 2026
Merged

📝 Fix documentation #45

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
9bead28
:art: remove outputs
enryH Feb 25, 2026
fbe1247
:art: allow again to pass step or n_fits via entry point function
enryH Feb 25, 2026
faf7596
:bug: parameter renamed from spline_s to spline
enryH Feb 25, 2026
9bea397
:art: format
enryH Feb 25, 2026
29db0ac
Merge branch 'main' into fix_sphinx_docs
enryH Feb 27, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
488 changes: 15 additions & 473 deletions docs/tutorial/analysis.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

6 changes: 3 additions & 3 deletions docs/tutorial/plotting.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@
" N,\n",
" model_family=\"all\", # Include mechanistic, phenomenological, and non-parametric\n",
" phase_boundary_method=\"tangent\", # tangent or threshold\n",
" spline_s=0.2,\n",
" spline=0.2,\n",
" window_points=7,\n",
")\n",
"\n",
Expand Down Expand Up @@ -245,7 +245,7 @@
" N,\n",
" model_family=\"all\", # Include mechanistic, phenomenological, and non-parametric\n",
" phase_boundary_method=\"tangent\", # tangent or threshold\n",
" spline_s=0.2,\n",
" spline=0.2,\n",
" window_points=7,\n",
")\n",
"\n",
Expand Down Expand Up @@ -325,7 +325,7 @@
"source": [
"# Phase boundary comparison on spline fit\n",
"fit_spline = gc.non_parametric.fit_non_parametric(\n",
" t, N, method=\"spline\", spline_s=0.2, window_points=7\n",
" t, N, method=\"spline\", spline=0.2, window_points=7\n",
")\n",
"\n",
"phase_boundary_rows = []\n",
Expand Down
8 changes: 7 additions & 1 deletion src/growthcurves/non_parametric.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,16 @@
All methods operate in linear OD space (not log-transformed).
"""

from logging import getLogger

import numpy as np
from scipy.interpolate import make_smoothing_spline
from scipy.stats import theilslopes

from .inference import bad_fit_stats

logger = getLogger(__name__)

# Default settings for the auto-spline (sigma-based smoothing + OD weights).
_SPLINE_SMOOTH_MULT = 5.0
_SPLINE_GCV_WEIGHT_FLOOR_Q = 0.15
Expand All @@ -27,7 +31,7 @@
# -----------------------------------------------------------------------------


def fit_sliding_window(t, N, window_points=15, step=None, n_fits=None):
def fit_sliding_window(t, N, window_points=15, step=None, n_fits=None, **kwargs):
"""
Calculate maximum specific growth rate using the sliding window method.

Expand All @@ -54,6 +58,8 @@ def fit_sliding_window(t, N, window_points=15, step=None, n_fits=None):
Returns None if calculation fails.

"""
if kwargs:
logger.warning("fit_sliding_window received unused kwargs: %s", kwargs)
if len(t) < window_points or np.ptp(t) <= 0:
return None

Expand Down