phenocoder/pyproject.toml at main · devsystemslab/phenocoder · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
[project]
name = "phenocoder"
version = "0.1.0"
description = "A machine-learning framework that combines conditional variational autoencoders with spatial graph analysis to learn unsupervised phenotypic embeddings of complex tissue architectures from microscopy images."
requires-python = ">=3.10, <3.13"
dependencies = [
    # Linux: full CUDA stack
    "tensorflow[and-cuda]>=2.19.0; sys_platform == 'linux'",
    # macOS (and any non-Linux): plain TF, no CUDA. Capped at <2.20 because
    # tensorflow-metal 1.2.0 (latest) only supports TF up to 2.19/2.20 — newer
    # TF breaks the Metal plugin load on macOS.
    "tensorflow>=2.19.0,<2.20; sys_platform != 'linux'",
    # Mac GPU acceleration via Metal
    "tensorflow-metal>=1.2.0; sys_platform == 'darwin'",
    "keras",
    "setuptools<81",
    "spatialdata>=0.5.0",
    "matplotlib>=3.10.6",
    "squidpy>=1.8.2",
    "bbknn>=1.6.0",
    "spatialdata-plot>=0.2.12",
    "igraph>=1.0.0",
    "leidenalg>=0.11.0",
]

[project.optional-dependencies]
dev = [
    "ipdb>=0.13.13",
    "ipython>=8.37.0",
    "pytest>=8.4.2",
    "ruff>=0.13.2",
]
docs = [
    "sphinx>=8.0",
    "furo>=2024.8",
    "myst-parser>=4.0",
]

[tool.pytest.ini_options]
# Suppress only known-irreducible warnings from third-party library internals
# that our calls trigger. Message-specific ignores keep our own future
# FutureWarnings/UserWarnings visible.
filterwarnings = [
    # docrep docstring decoration, fires at squidpy import time
    "ignore:.*is not a valid key.*:SyntaxWarning",
    # scanpy legacy_api_wrap dtype coercion
    "ignore:X converted to numpy array with dtype float64:UserWarning",
    # anndata index coercion
    "ignore:Transforming to str index.*:UserWarning",
    # spatialdata table/region handling
    "ignore:Converting .*region.* to categorical dtype.*:UserWarning",
    "ignore:The table is annotating .*which is not present.*:UserWarning",
    # squidpy spatial_autocorr Moran permutation on degenerate test graphs
    "ignore:divide by zero encountered in matmul:RuntimeWarning",
    "ignore:overflow encountered in matmul:RuntimeWarning",
    "ignore:invalid value encountered in matmul:RuntimeWarning",
    # squidpy interaction-matrix normalization on zero-sum rows (small test graph)
    "ignore:invalid value encountered in divide:RuntimeWarning",
    # keras/tensorflow tensor -> numpy conversion internals
    "ignore:__array__ implementation doesn't accept a copy keyword:DeprecationWarning",
    # spatialdata -> ome_zarr deprecated downsampler
    "ignore:Call to deprecated class Scaler.*:DeprecationWarning",
]

[tool.ruff]
line-length = 120
[tool.basedpyright]
typeCheckingMode = "basic"
reportUnknownVariableType = false
reportUnknownParameterType = false
reportMissingTypeStubs = false
reportUnknownMemberType = false
reportArgumentType = false
reportOptionalMemberAccess = false
reportAttributeAccessIssue = false
reportIndexIssue = false
reportOptionalSubscript = false
reportCallIssue = false
reportAssignmentType = false
reportReturnType = false
reportOptionalIterable = false
reportOperatorIssue = false