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Doc submodule #2901

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merged 49 commits into from
Mar 26, 2024
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3a9030d
Start going to tutorial submodule
ivirshup Mar 11, 2024
6add1fb
bump submodule
ivirshup Mar 12, 2024
f92e31e
Got plotting tutorial layout to a decent point
ivirshup Mar 13, 2024
eccf860
clear out git submodule
ivirshup Mar 13, 2024
9ae54b5
Using stubs to reference notebooks
ivirshup Mar 13, 2024
127da98
Use symlinks instead
ivirshup Mar 13, 2024
c5889bd
Add knn-transformers
ivirshup Mar 13, 2024
e4cf70d
Remove docutils.conf as it's no longer needed
ivirshup Mar 13, 2024
5f659e5
Update basic tutorial
ivirshup Mar 13, 2024
6382bcb
Update reference to ecosystem
ivirshup Mar 13, 2024
bb5bbac
Add bib
ivirshup Mar 13, 2024
a612698
Start a how-to section
ivirshup Mar 14, 2024
59ddfae
Update old tutorial link
ivirshup Mar 18, 2024
393e850
experimental tutorial module
ivirshup Mar 18, 2024
784a6b6
update spatial tutorials links
ivirshup Mar 18, 2024
0697a11
Update basic tutorials layout
ivirshup Mar 18, 2024
94439a3
Add trajectories
ivirshup Mar 18, 2024
37be5ec
Fix some links
ivirshup Mar 18, 2024
c7b6b14
fix some more links
ivirshup Mar 18, 2024
baeed7b
unfuck cite directive
ivirshup Mar 18, 2024
27b9761
update submodule
ivirshup Mar 18, 2024
dddcb37
Fix sphinx handling of ftp link
ivirshup Mar 18, 2024
c1d042a
Add submodule to readthedocs
ivirshup Mar 18, 2024
7d8aa97
add rapids-singlecell to news
ivirshup Mar 19, 2024
2e2aa41
Merge branch 'main' into doc-submodule
ivirshup Mar 19, 2024
da64e39
Update advanced plotting tutorial
ivirshup Mar 19, 2024
60457ee
apply pre-commit fixes on notebooks
ivirshup Mar 19, 2024
e603029
Fix link
ivirshup Mar 19, 2024
961e220
Cut down on tutorials
ivirshup Mar 19, 2024
962d3d9
Release notes (+ a release note fix)
ivirshup Mar 19, 2024
9d707f1
Merge branch 'main' into doc-submodule
ivirshup Mar 20, 2024
75d7a74
Merge branch 'main' into doc-submodule
ivirshup Mar 22, 2024
79e3519
Fix rapids-singlecell link
ivirshup Mar 22, 2024
e8a4694
Updae tutorials page
ivirshup Mar 22, 2024
c9f6d11
Merge branch 'main' into doc-submodule
ivirshup Mar 22, 2024
37c0f49
add setuptools dep for doc builds
ivirshup Mar 25, 2024
4caaf20
Use intersphinx for a link
ivirshup Mar 25, 2024
edc8d79
update notebooks
ivirshup Mar 25, 2024
041d7a7
add back blank line
ivirshup Mar 25, 2024
30bdd44
update submodule
ivirshup Mar 25, 2024
24b5564
Add dask notebook
ivirshup Mar 25, 2024
4c50e7a
Update notebook submodule
ivirshup Mar 25, 2024
6da7f17
Merge branch 'main' into doc-submodule
ivirshup Mar 25, 2024
5a062f8
Update notebook submodule
ivirshup Mar 25, 2024
d812981
update submodule
ivirshup Mar 25, 2024
47db99a
Prep release notes
ivirshup Mar 25, 2024
49773b4
update submodule
ivirshup Mar 25, 2024
d98c8c0
add release note for doc style overhaul
ivirshup Mar 25, 2024
b22084d
bump date
ivirshup Mar 26, 2024
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2 changes: 1 addition & 1 deletion pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,7 @@ doc = [
"ipython>=7.20", # for nbsphinx code highlighting
"matplotlib!=3.6.1",
"sphinxcontrib-bibtex",
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"setuptools",
# TODO: remove necessity for being able to import doc-linked classes
"dask",
"scanpy[paga]",
Expand Down Expand Up @@ -176,7 +177,6 @@ filterwarnings = [
"error:The specified parameters:FutureWarning",
# When calling `.show()` in tests, this is raised
"ignore:FigureCanvasAgg is non-interactive:UserWarning",

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# We explicitly handle the below errors in tests
"error:`anndata.read` is deprecated:FutureWarning",
"error:Observation names are not unique:UserWarning",
Expand Down