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Develop (#91)
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* fix: optomize dataloading for ambient profile

* fix: optomize dataloading for ambient profile

* docs: update installation

* feat: add functionality for batch ambient removal

* feat: add functionality for batch ambient removal

* fix: fix a bug and refactor dataloading

* fix: fix a bug

* fix: fix a bug

* fix: fix a bug

* fix: fix a bug

* refactor: refactor scar dataloader

* refactor: refactor codes for better GPU usage

* refactor: refactor codes for better GPU usage

* refactor: Refactor functions for compatibility with scipy 1.14

* refactor: load entire data to GPU

* refactor(scar): refactor dataloading to improve efficiency

* refactor(scar): refactor dataloading to improve efficiency

* refactor(scar): refactor dataloading to improve efficiency

* refactor(scar): refactor dataloading to improve efficiency

* feature(scar): introduce caching functionality

* doc(docs): update python version for readthedocs

* doc(docs): update sphinx-gallery version for readthedocs

* refactor(scar): delete unneccessary codes

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): not output native frequencies by default

* refactor(scar): refactor dataloader

* refactor(scar): remove redundant codes

* refactor(scar): optimize dataloading

* refactor(vae): refactor stochastic rounding for performance

* chore: rewrite device log information

* docs(scar): correct docs for scar

* docs(tutorials): update tutorial notebooks

* docs(scar): refactor docs

* docs(scar): add docs for cache_capacity parameter

* refactor(main): refactor command line tool

* refator(scar): refactor scar to automate calculation of ambient profile in the case of no ambient profile provided

* fix(main): fix a bug

* fix(main): fix a bug

* fix(test): lower down sample size for test

* docs(scar): update version in doc

* docs(tutorial): update notebooks

* docs(tutorial): add a tutorial for batch denoising

* refactor(docs): reset semantic_release to main branch

* docs(tutorial): update hyperlink

* Develop (#82)

* fix: optomize dataloading for ambient profile

* fix: optomize dataloading for ambient profile

* docs: update installation

* feat: add functionality for batch ambient removal

* feat: add functionality for batch ambient removal

* fix: fix a bug and refactor dataloading

* fix: fix a bug

* fix: fix a bug

* fix: fix a bug

* fix: fix a bug

* refactor: refactor scar dataloader

* refactor: refactor codes for better GPU usage

* refactor: refactor codes for better GPU usage

* refactor: Refactor functions for compatibility with scipy 1.14

* refactor: load entire data to GPU

* refactor(scar): refactor dataloading to improve efficiency

* refactor(scar): refactor dataloading to improve efficiency

* refactor(scar): refactor dataloading to improve efficiency

* refactor(scar): refactor dataloading to improve efficiency

* feature(scar): introduce caching functionality

* doc(docs): update python version for readthedocs

* doc(docs): update sphinx-gallery version for readthedocs

* refactor(scar): delete unneccessary codes

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): not output native frequencies by default

* refactor(scar): refactor dataloader

* refactor(scar): remove redundant codes

* refactor(scar): optimize dataloading

* refactor(vae): refactor stochastic rounding for performance

* chore: rewrite device log information

* docs(scar): correct docs for scar

* docs(tutorials): update tutorial notebooks

* docs(scar): refactor docs

* docs(scar): add docs for cache_capacity parameter

* refactor(main): refactor command line tool

* refator(scar): refactor scar to automate calculation of ambient profile in the case of no ambient profile provided

* fix(main): fix a bug

* fix(main): fix a bug

* fix(test): lower down sample size for test

* docs(scar): update version in doc

* docs(tutorial): update notebooks

* docs(tutorial): add a tutorial for batch denoising

* refactor(docs): reset semantic_release to main branch

* docs(tutorial): update hyperlink

---------

Co-authored-by: EC2 Default User <[email protected]>

* fix(workflow): update semantic release

* fix(workflow): update semantic release

* fix(workflow): update semantic release

* update semantic release (#84)

* fix: optomize dataloading for ambient profile

* fix: optomize dataloading for ambient profile

* docs: update installation

* feat: add functionality for batch ambient removal

* feat: add functionality for batch ambient removal

* fix: fix a bug and refactor dataloading

* fix: fix a bug

* fix: fix a bug

* fix: fix a bug

* fix: fix a bug

* refactor: refactor scar dataloader

* refactor: refactor codes for better GPU usage

* refactor: refactor codes for better GPU usage

* refactor: Refactor functions for compatibility with scipy 1.14

* refactor: load entire data to GPU

* refactor(scar): refactor dataloading to improve efficiency

* refactor(scar): refactor dataloading to improve efficiency

* refactor(scar): refactor dataloading to improve efficiency

* refactor(scar): refactor dataloading to improve efficiency

* feature(scar): introduce caching functionality

* doc(docs): update python version for readthedocs

* doc(docs): update sphinx-gallery version for readthedocs

* refactor(scar): delete unneccessary codes

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): refactor scar to allow efficient usage of GPU

* refactor(scar): not output native frequencies by default

* refactor(scar): refactor dataloader

* refactor(scar): remove redundant codes

* refactor(scar): optimize dataloading

* refactor(vae): refactor stochastic rounding for performance

* chore: rewrite device log information

* docs(scar): correct docs for scar

* docs(tutorials): update tutorial notebooks

* docs(scar): refactor docs

* docs(scar): add docs for cache_capacity parameter

* refactor(main): refactor command line tool

* refator(scar): refactor scar to automate calculation of ambient profile in the case of no ambient profile provided

* fix(main): fix a bug

* fix(main): fix a bug

* fix(test): lower down sample size for test

* docs(scar): update version in doc

* docs(tutorial): update notebooks

* docs(tutorial): add a tutorial for batch denoising

* refactor(docs): reset semantic_release to main branch

* docs(tutorial): update hyperlink

* fix(workflow): update semantic release

* fix(workflow): update semantic release

* fix(workflow): update semantic release

---------

Co-authored-by: EC2 Default User <[email protected]>

* fix(workflow): update semantic release

* chore: change semantic release branch

* chore: change semantic release branch

* chore: change semantic release branch

* chore: change semantic release branch

---------

Co-authored-by: EC2 Default User <[email protected]>
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@CaibinSh
CaibinSh and EC2 Default User authored Aug 14, 2024
1 parent 79805f5 commit cc09dd3
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6 changes: 3 additions & 3 deletions .github/workflows/semantic-release.yaml
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Expand Up @@ -18,10 +18,10 @@ jobs:
steps:
- uses: actions/checkout@v3
with:
ref: main
fetch-depth: 0

- name: Python Semantic Release
uses: relekang/python-semantic-release@master
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
repository_username: __token__
repository_password: ${{ secrets.PYPI_TOKEN }}
github_token: ${{ secrets.GITHUB_TOKEN }}
2 changes: 1 addition & 1 deletion .readthedocs.yaml
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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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