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Develop #83

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Develop #83

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8b77310
fix: optomize dataloading for ambient profile
CaibinSh May 26, 2024
3896417
fix: optomize dataloading for ambient profile
CaibinSh May 26, 2024
3a0058d
docs: update installation
CaibinSh May 26, 2024
5bc0d84
feat: add functionality for batch ambient removal
CaibinSh May 26, 2024
353059f
feat: add functionality for batch ambient removal
CaibinSh May 26, 2024
5066899
fix: fix a bug and refactor dataloading
CaibinSh May 26, 2024
e5ebaf8
fix: fix a bug
CaibinSh May 26, 2024
d6c1663
fix: fix a bug
CaibinSh May 26, 2024
24e1f95
fix: fix a bug
CaibinSh May 26, 2024
db17c87
fix: fix a bug
CaibinSh May 26, 2024
7bb5d9a
refactor: refactor scar dataloader
CaibinSh May 28, 2024
535326f
refactor: refactor codes for better GPU usage
CaibinSh May 28, 2024
73f737c
refactor: refactor codes for better GPU usage
CaibinSh May 28, 2024
7ada773
refactor: Refactor functions for compatibility with scipy 1.14
CaibinSh Jul 24, 2024
cab3872
refactor: load entire data to GPU
CaibinSh Jul 25, 2024
c4901cd
refactor(scar): refactor dataloading to improve efficiency
CaibinSh Jul 27, 2024
cbf222b
refactor(scar): refactor dataloading to improve efficiency
CaibinSh Jul 27, 2024
99665da
refactor(scar): refactor dataloading to improve efficiency
CaibinSh Jul 27, 2024
707a0e0
refactor(scar): refactor dataloading to improve efficiency
CaibinSh Jul 27, 2024
3f07c35
feature(scar): introduce caching functionality
CaibinSh Jul 27, 2024
7d85da3
doc(docs): update python version for readthedocs
CaibinSh Jul 28, 2024
7d436e4
doc(docs): update sphinx-gallery version for readthedocs
CaibinSh Jul 28, 2024
6b101f1
refactor(scar): delete unneccessary codes
CaibinSh Jul 28, 2024
c846d9b
refactor(scar): refactor scar to allow efficient usage of GPU
CaibinSh Jul 29, 2024
4c808ab
refactor(scar): refactor scar to allow efficient usage of GPU
CaibinSh Jul 29, 2024
5eb2ebb
refactor(scar): refactor scar to allow efficient usage of GPU
CaibinSh Jul 29, 2024
6529b97
refactor(scar): refactor scar to allow efficient usage of GPU
CaibinSh Jul 29, 2024
4ba263a
refactor(scar): not output native frequencies by default
CaibinSh Aug 7, 2024
4930798
refactor(scar): refactor dataloader
CaibinSh Aug 8, 2024
51a85e7
refactor(scar): remove redundant codes
CaibinSh Aug 8, 2024
41dd2a2
refactor(scar): optimize dataloading
CaibinSh Aug 8, 2024
0af1c99
refactor(vae): refactor stochastic rounding for performance
CaibinSh Aug 8, 2024
08f9e22
chore: rewrite device log information
CaibinSh Aug 9, 2024
d44f3a3
docs(scar): correct docs for scar
CaibinSh Aug 10, 2024
06f3d7e
docs(tutorials): update tutorial notebooks
Aug 10, 2024
78f8f76
docs(scar): refactor docs
CaibinSh Aug 10, 2024
43038ca
Merge branch 'develop' of https://github.com/Novartis/scar into develop
CaibinSh Aug 10, 2024
2262e34
docs(scar): add docs for cache_capacity parameter
CaibinSh Aug 11, 2024
d3d4d1b
refactor(main): refactor command line tool
CaibinSh Aug 11, 2024
9ef0272
refator(scar): refactor scar to automate calculation of ambient profi…
CaibinSh Aug 11, 2024
bedfa6e
fix(main): fix a bug
CaibinSh Aug 11, 2024
1615684
fix(main): fix a bug
CaibinSh Aug 11, 2024
7363753
Merge branch 'main' into develop
CaibinSh Aug 12, 2024
4c86c1b
fix(test): lower down sample size for test
CaibinSh Aug 12, 2024
6b00c74
docs(scar): update version in doc
CaibinSh Aug 12, 2024
d581d7c
docs(tutorial): update notebooks
CaibinSh Aug 14, 2024
631e4bb
docs(tutorial): add a tutorial for batch denoising
CaibinSh Aug 14, 2024
53b839b
refactor(docs): reset semantic_release to main branch
CaibinSh Aug 14, 2024
8a7b448
docs(tutorial): update hyperlink
CaibinSh Aug 14, 2024
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2 changes: 1 addition & 1 deletion .readthedocs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ version: 2
build:
os: "ubuntu-20.04"
tools:
python: "3.10"
python: "3.11"

sphinx:
configuration: docs/conf.py
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2 changes: 1 addition & 1 deletion docs/requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
jinja2<3.1.0
myst_parser
nbsphinx
sphinx-gallery
sphinx-gallery<0.17.0
sphinx-argparse
sphinx-disqus
autodocsumm
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1 change: 1 addition & 0 deletions docs/tutorials/index.rst
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Expand Up @@ -13,6 +13,7 @@ Run scar with Python API
scAR_tutorial_denoising_CITEseq
scAR_tutorial_denoising_scRNAseq
scAR_tutorial_denoising_scATACseq
scAR_tutorial_batch_denoising_scRNAseq

Run scar with the command line tool
---------------------------------
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