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Merged
Arvindiyer merged 1 commit into from
Jul 14, 2026
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perf: lazy-load plotting functions, drop unused seaborn dependency #2

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15 changes: 15 additions & 0 deletions NEWS.md
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Expand Up @@ -102,3 +102,18 @@ Initial feature-complete Python port of the [SelectSim R package](https://github
* This round of work was developed with the assistance of Claude Code
(Anthropic), directed and verified by Arvind Iyer throughout; see
`git log` for detailed commit history.

# SelectSim (Python) 0.3.1

* **Performance**: `import selectsim` dropped from ~1.5s to ~0.6s. The
top-level package eagerly imported `selectsim.plotting`, which pulls in
`matplotlib` and `scipy` (used nowhere outside `plotting.py`), even for
callers who only ever call `selectX()` and never plot anything.
Plotting functions (`obs_exp_scatter`, `ridge_plot_ed`, `oncoprint`,
etc.) are now resolved lazily on first access (PEP 562 module
`__getattr__`) instead -- same `ss.<name>` usage, just deferred. On the
bundled LUAD benchmark this cut whole-process wall time by ~23% and
peak memory by ~21%.
* **Removed**: the `seaborn` dependency. It was listed in
`pyproject.toml` and mentioned in a couple of docstrings, but never
actually imported or used anywhere in the codebase.
2 changes: 1 addition & 1 deletion docs/source/conf.py
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Expand Up @@ -13,7 +13,7 @@
project = 'SelectSim'
copyright = '2026, Arvind Iyer, Marco Mina, Miljan Petrovic, Giovanni Ciriello'
author = 'Arvind Iyer, Marco Mina, Miljan Petrovic, Giovanni Ciriello'
release = '0.3.0'
release = '0.3.1'

# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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114 changes: 56 additions & 58 deletions docs/source/tutorials/introduction.ipynb
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"outputs": [
Expand All @@ -843,27 +843,25 @@
"output_type": "stream",
"text": [
"python: 3.12.13 | packaged by conda-forge | (main, Mar 5 2026, 16:50:00) [GCC 14.3.0]\n",
"selectsim: 0.2.0\n",
"selectsim: 0.3.0\n",
"numpy: 2.1.3\n",
"pandas: 2.2.3\n",
"scipy: 1.14.1\n",
"matplotlib: 3.11.0\n",
"seaborn: 0.13.2\n"
"matplotlib: 3.11.0\n"
]
}
],
"source": [
"import sys\n",
"import numpy, pandas, scipy, matplotlib, seaborn\n",
"import numpy, pandas, scipy, matplotlib\n",
"import selectsim\n",
"\n",
"print(\"python:\", sys.version)\n",
"print(\"selectsim:\", selectsim.__version__)\n",
"print(\"numpy:\", numpy.__version__)\n",
"print(\"pandas:\", pandas.__version__)\n",
"print(\"scipy:\", scipy.__version__)\n",
"print(\"matplotlib:\", matplotlib.__version__)\n",
"print(\"seaborn:\", seaborn.__version__)"
"print(\"matplotlib:\", matplotlib.__version__)"
]
}
],
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3 changes: 1 addition & 2 deletions pyproject.toml
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@@ -1,6 +1,6 @@
[project]
name = "selectsim"
version = "0.3.0"
version = "0.3.1"
description = "A python package that implements the SelectSim algorithm"
authors = [
{ name = "Arvind Iyer", email = "ayalurarvind@gmail.com" },
Expand All @@ -22,7 +22,6 @@ dependencies = [
"tqdm>=4.66.0,<5",
"pyarrow>=18.0.0,<19",
"matplotlib>=3.9.0,<4",
"seaborn>=0.13.0,<0.14",
]

[project.urls]
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43 changes: 32 additions & 11 deletions selectsim/__init__.py
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Expand Up @@ -49,24 +49,14 @@
stat_maf_gene,
maf_to_gam
)
from selectsim.plotting import (
theme_publication,
obs_exp_scatter,
significance_heatmap,
overlap_pair_extract,
ridge_plot_ed,
ridge_plot_ed_compare,
oncoprint_pair,
oncoprint
)
from selectsim.io import (
read_parquet,
write_parquet,
create_zarr_null_store,
open_zarr_store
)

__version__ = "0.3.0"
__version__ = "0.3.1"

__all__ = [
# Main function
Expand Down Expand Up @@ -133,3 +123,34 @@
"create_zarr_null_store",
"open_zarr_store",
]

# Plotting functions are resolved lazily (PEP 562), rather than imported
# eagerly above like everything else: selectsim.plotting pulls in
# matplotlib and scipy (measured ~1s import overhead combined, mostly
# matplotlib.pyplot) -- overhead every `import selectsim` would otherwise
# pay even for pure-computation use (e.g. just calling selectX()) that
# never touches a plotting function. scipy is in fact used nowhere
# outside plotting.py either. Deferring the import to first access of one
# of these names (only) keeps `selectsim.<plotting name>` working exactly
# as before, without forcing the cost on callers who never ask for it.
_LAZY_PLOTTING_ATTRS = frozenset({
"theme_publication",
"obs_exp_scatter",
"significance_heatmap",
"overlap_pair_extract",
"ridge_plot_ed",
"ridge_plot_ed_compare",
"oncoprint_pair",
"oncoprint",
})


def __getattr__(name):
if name in _LAZY_PLOTTING_ATTRS:
from selectsim import plotting
return getattr(plotting, name)
raise AttributeError(f"module {__name__!r} has no attribute {name!r}")


def __dir__():
return sorted(set(globals()) | _LAZY_PLOTTING_ATTRS)
6 changes: 3 additions & 3 deletions selectsim/plotting.py
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Expand Up @@ -3,8 +3,8 @@

Python port of ``R/selectX_plot.R``. The R implementation is built on
``ggplot2``/``ggpubr``/``ggridges``; this module reproduces the same visual
intent using ``matplotlib`` + ``seaborn`` (the library choice made for the
Python port), since no display is assumed to be available.
intent using ``matplotlib`` (the library choice made for the Python port),
since no display is assumed to be available.

Functions
---------
Expand Down Expand Up @@ -503,7 +503,7 @@ def ridge_plot_ed(
Implementation note: this is the standard "joyplot"/ridgeline technique
-- per-row Gaussian KDEs evaluated on a shared x-grid and stacked with a
constant y-offset -- rather than ``ggridges::geom_density_ridges``,
since matplotlib/seaborn has no ridge-plot geom built in.
since matplotlib has no ridge-plot geom built in.

Parameters
----------
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