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Dev - #47

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MayraRuizT merged 52 commits into
mainfrom
dev
Sep 9, 2026
Merged

Dev#47
MayraRuizT merged 52 commits into
mainfrom
dev

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@MayraRuizT

@MayraRuizT MayraRuizT commented Sep 9, 2026

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Update main branch for new version with review improvements

MayraRuizT and others added 30 commits February 24, 2026 15:26
@MayraRuizT
set development version 1.1.0-dev in dev branch pyproject.toml
f94af5b
@MayraRuizT
pypi version badge
da3cd44
Initial plan
63d68a0
@jsnagai
Fix pandas 3.0 and matplotlib compatibility issues
0149238 
Co-authored-by: jsnagai <8943000+jsnagai@users.noreply.github.com>
@jsnagai
Add .gitignore to exclude pycache and build artifacts
7ea2076 
Co-authored-by: jsnagai <8943000+jsnagai@users.noreply.github.com>
@jsnagai
Merge pull request #1 from jsnagai/copilot/update-compatibility-new-p…
1a2243f 
…andas

Fix pandas 3.0 Copy-on-Write and matplotlib deprecation compatibility
@MayraRuizT
update readthedocs config and dependencies for dev branch
d6d090b
@MayraRuizT
add readthedocs sphinx dependencies to generate docs for the dev branch
9b9ea7e
@MayraRuizT
docs: add nbsphinx for notebook support
00a0727
@jsnagai
Relax and align anndata/scanpy dependency constraints
d7aed1f 
Agent-Logs-Url: https://github.com/jsnagai/Nichesphere/sessions/5ab6365a-5e56-439a-85d6-365670f1469c

Co-authored-by: jsnagai <8943000+jsnagai@users.noreply.github.com>
@jsnagai
Update anndata to 0.12.11 and zarr to 3.1.6; bump Python minimum to 3.11
449fbdf 
Agent-Logs-Url: https://github.com/jsnagai/Nichesphere/sessions/1c8da52e-4e3e-4197-9151-72d8d34e9ef4

Co-authored-by: jsnagai <8943000+jsnagai@users.noreply.github.com>
@jsnagai
Tighten anndata upper bound to <0.13 for safer compatibility
438ad63 
Agent-Logs-Url: https://github.com/jsnagai/Nichesphere/sessions/1c8da52e-4e3e-4197-9151-72d8d34e9ef4

Co-authored-by: jsnagai <8943000+jsnagai@users.noreply.github.com>
@jsnagai
Pin Pillow to >=12.2.0 to fix FITS GZIP decompression bomb and PSD ou…
083c95c 
…t-of-bounds write CVEs

Agent-Logs-Url: https://github.com/jsnagai/Nichesphere/sessions/1c8da52e-4e3e-4197-9151-72d8d34e9ef4

Co-authored-by: jsnagai <8943000+jsnagai@users.noreply.github.com>
@jsnagai
Merge pull request #2 from jsnagai/copilot/fix-nichesphere-dependencies
c2b5cad 
Resolve anndata/scanpy version incompatibility by normalizing package constraints
@MayraRuizT
Fix poetry lock file conflict
673f7b6
@MayraRuizT
revision updates
31193a2
@MayraRuizT
signed network statistics
9b15555
@MayraRuizT
add functions for co-localization in spatial sc data
ec79db1
@MayraRuizT
add sankey_plot module
c142c6b
@MayraRuizT
add sankey module to init
168ca5b
@MayraRuizT
optimize getColocProbs with matrix operation
6644fca
@MayraRuizT
optimize coloc and comm modules changing for loops for other operations
e65b363
@MayraRuizT
reshapeColoc bug fix
c2ef41e
@MayraRuizT
debug comm optimized functions
8946b3b
@MayraRuizT
Update .gitignore with missing rules
83dca80
@MayraRuizT
Update tutorial files and docs
a0c253b
@MayraRuizT
add data load function
c8d75a6
@MayraRuizT
update tutorials
1e613ed
@MayraRuizT
Stop tracking tutorial result files
7799467
@MayraRuizT
Update tests and delete old files
f101030
MayraRuizT and others added 22 commits July 30, 2026 14:40
@MayraRuizT
fix: adjust python version matrix in CI workflow
64a291b
@MayraRuizT
fix: add plotly to dependencies in pyproject.toml
29d60a1
@MayraRuizT
add spotweights parameter to getColocProbs in case eg: cell number pe…
fb8d67f 
…r spot is given
@MayraRuizT
Fix cell type names bug in colocNW and optimize get_spatial_radius_BG…
28ab9e3 
…_OEratios_DF
@MayraRuizT
Update tutorials
42361e5
@MayraRuizT
Fix cell type color bug for catNW
9794082
@MayraRuizT
update main tutorial
42b4acb
@MayraRuizT
add signed stats node sizes options in network functions
5484bff
@MayraRuizT
add documentation to comm network new nodeSize options, fix small bug
ce08051
@MayraRuizT
add signed stats node sizes for interactive network vis
4fcc059
@MayraRuizT
small fix in assign_properties
be1e1cf
@MayraRuizT
another small fix in assign_properties
f2e6e9b
@MayraRuizT
another small fix in assign_properties...
2ad6154
@MayraRuizT
fix node sizes for signed stats in assign_properties
9e8ce24
@MayraRuizT
last touch to node sizes for signed stats in assign_properties
49c4927
@jmichellejm
New Layout Design
da1ac84
@jmichellejm
new layout requirements
50f2343
@jmichellejm
style: break line before parameters in getColocProbs (coloc_module)
571babc
@MayraRuizT
Merge pull request #45 from CostaLab/dev_doc
187c50e 
Dev doc: Update readthedocs layout
@jmichellejm
small fix in tutorials python code color
655cb8f
@MayraRuizT
Merge pull request #46 from CostaLab/dev_doc
dae6f72 
small fix in tutorials python code color
@MayraRuizT
add CODEX tutorial , correct PILOT acronym
e848219
@MayraRuizT
MayraRuizT merged commit 07fc572 into main Sep 9, 2026
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4 participants

@MayraRuizT @jsnagai @jmichellejm