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Make GPL dependencies optional #636

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72645b3
Make python-levenshtein an optional dependency
grst Aug 1, 2025
5764ea6
Merge branch 'main' into no-gpl
grst Aug 1, 2025
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50 changes: 20 additions & 30 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,8 @@ name = "scirpy"
description = "Python library for single-cell adaptive immune receptor repertoire (AIRR) analysis"
readme = "README.md"
license = { file = "LICENSE" }
maintainers = [
{ name = "Gregor Sturm", email = "mail@gregor-sturm.de" },
]
authors = [
{ name = "Gregor Sturm" },
{ name = "Tamas Szabo" },
]
maintainers = [ { name = "Gregor Sturm", email = "mail@gregor-sturm.de" } ]
authors = [ { name = "Gregor Sturm" }, { name = "Tamas Szabo" } ]
requires-python = ">=3.10"
classifiers = [
"Programming Language :: Python :: 3 :: Only",
Expand All @@ -28,8 +23,6 @@ dependencies = [
"airr>=1.4.1",
"anndata>=0.9",
"awkward>=2.1",
# 0.10.0 and 0.10.1 have the bug described in https://github.com/igraph/python-igraph/issues/570
"igraph!=0.10,!=0.10.1",
"joblib>=1.3.1",
"logomaker!=0.8.5",
"mudata>=0.2.3",
Expand All @@ -39,26 +32,17 @@ dependencies = [
"pandas>=1.5,!=2.1.2",
"pooch>=1.7",
"pycairo>=1.20; sys_platform=='win32'",
"python-levenshtein",
"scanpy>=1.9.3",
"scikit-learn",
"scipy",
"squarify",
"tqdm>=4.63", # https://github.com/tqdm/tqdm/issues/1082
]

optional-dependencies.cupy = [
"cupy-cuda12x",
]
optional-dependencies.dandelion = [
"sc-dandelion>=0.3.5",
]
optional-dependencies.dev = [
"pre-commit",
]
optional-dependencies.diversity = [
"scikit-bio>=0.5.7",
]
optional-dependencies.cupy = [ "cupy-cuda12x" ]
optional-dependencies.dandelion = [ "sc-dandelion>=0.3.5" ]
optional-dependencies.dev = [ "pre-commit" ]
optional-dependencies.diversity = [ "scikit-bio>=0.5.7" ]
optional-dependencies.doc = [
"docutils>=0.8,!=0.18.*,!=0.19.*",
# for tutorial
Expand All @@ -85,13 +69,16 @@ optional-dependencies.doc = [
# the documentation. Probably related to importing some types from anndata.
"zarr<3",
]
optional-dependencies.igraph = [
# 0.10.0 and 0.10.1 have the bug described in https://github.com/igraph/python-igraph/issues/570
"igraph!=0.10,!=0.10.1",
]
optional-dependencies.levenshtein = [ "python-levenshtein" ]
optional-dependencies.parasail = [
# parasail 1.2.1 fails to be installd on MacOS
"parasail!=1.2.1",
]
optional-dependencies.rpack = [
"rectangle-packer",
]
optional-dependencies.rpack = [ "rectangle-packer" ]
optional-dependencies.test = [
"black",
"coverage",
Expand Down Expand Up @@ -177,10 +164,15 @@ lint.ignore = [
# allow I, O, l as variable names -> I is the identity matrix
"E741",
]
lint.per-file-ignores."*.ipynb" = [ "E402" ] # Module level import not at top of cell
lint.per-file-ignores."*.ipynb" = [
"E402",
] # Module level import not at top of cell
lint.per-file-ignores."*/__init__.py" = [ "F401" ]
lint.per-file-ignores."docs/*" = [ "I" ]
lint.per-file-ignores."src/scirpy/datasets/_processing_scripts/*" = [ "B018", "E402" ]
lint.per-file-ignores."src/scirpy/datasets/_processing_scripts/*" = [
"B018",
"E402",
]
lint.per-file-ignores."tests/*" = [ "D" ]
lint.pydocstyle.convention = "numpy"

Expand All @@ -198,9 +190,7 @@ norecursedirs = [ '.*', 'build', 'dist', '*.egg', 'data', '__pycache__' ]

[tool.coverage.run]
source = [ "scirpy" ]
omit = [
"**/test_*.py",
]
omit = [ "**/test_*.py" ]

[tool.cruft]
skip = [
Expand Down
13 changes: 11 additions & 2 deletions src/scirpy/ir_dist/metrics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@
import numpy as np
import scipy.sparse
import scipy.spatial
from Levenshtein import distance as levenshtein_dist
from scanpy import logging
from scipy.sparse import coo_matrix, csr_matrix

Expand Down Expand Up @@ -306,7 +305,8 @@ class LevenshteinDistanceCalculator(ParallelDistanceCalculator):
events.

This class relies on `Python-levenshtein <https://github.com/ztane/python-Levenshtein>`_
to calculate the distances.
to calculate the distances. `Python-levenshtein` is an optional dependency that is not installed with
scirpy by default. You can install it with `pip install python-levenshtein`.

Choosing a cutoff:
Each modification stands for a deletion, addition or modification event.
Expand All @@ -322,9 +322,18 @@ class LevenshteinDistanceCalculator(ParallelDistanceCalculator):
"""

def __init__(self, cutoff: int = 2, **kwargs):
# Already fail during init if optional dependency not available. Otherwise will throw obscure error message
# from a worker thread
try:
from Levenshtein import distance # noqa
except ImportError:
raise ImportError("Please install optional dependency: pip install python-levenshtein.") from None

super().__init__(cutoff, **kwargs)

def _compute_block(self, seqs1, seqs2, origin):
from Levenshtein import distance as levenshtein_dist

origin_row, origin_col = origin
if seqs2 is not None:
# compute the full matrix
Expand Down
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