-
Notifications
You must be signed in to change notification settings - Fork 113
/
conf.py
77 lines (63 loc) · 2.08 KB
/
conf.py
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
from datetime import datetime
from importlib.metadata import metadata
from sphinx.application import Sphinx
from myst_nb.core.render import NbElementRenderer, MimeData
from docutils import nodes
meta = metadata("scanpy-tutorials")
project = meta["Name"]
author = meta["Author"]
copyright = f"{datetime.now():%Y}, {author}"
release = version = meta["Version"]
extensions = [
"myst_nb",
]
myst_enable_extensions = [
"colon_fence",
]
templates_path = ["_templates"]
source_suffix = ".rst"
master_doc = "index"
language = "en"
exclude_patterns = [
"_build",
"Thumbs.db",
".DS_Store",
"**.ipynb_checkpoints",
"scanpy_workshop/*",
]
pygments_style = "sphinx"
# -- Options for HTML output ----------------------------------------------
html_theme = "scanpydoc"
html_theme_options = dict(
repository_url="https://github.com/theislab/scanpy-tutorials",
repository_branch="master",
use_repository_button=True,
)
html_static_path = ["_static"]
html_logo = "_static/img/Scanpy_Logo_BrightFG.svg"
# -- Notebook settings ----------------------------------------------------
nb_execution_mode = "off"
nb_output_stderr = "remove"
myst_heading_anchors = 3
render_image_orig = NbElementRenderer.render_image
def render_image(self: NbElementRenderer, data: MimeData) -> list[nodes.Element]:
"""Makes images display size default to their jupyter setting.
Workaround for: https://github.com/executablebooks/MyST-NB/issues/522
"""
node_list = render_image_orig(self, data)
try:
[image] = node_list
if not isinstance(image, nodes.image):
raise ValueError(f"Expected nodes.image, got {type(image)}")
for key in ("width", "height"):
if key in image:
continue
if (v := data.output_metadata.get(data.mime_type, {}).get(key)) is None:
continue
image[key] = str(v)
except Exception:
return node_list
return [image]
def setup(app: Sphinx) -> None:
if NbElementRenderer.render_image is render_image_orig:
NbElementRenderer.render_image = render_image