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New release #26

Merged
merged 44 commits into from
Apr 27, 2022
Merged

New release #26

merged 44 commits into from
Apr 27, 2022

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CaibinSh
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  • Additions of readthedocs
  • Code refactoring
  1. Renaming module names, e.g. changing "scAR" -> "scar"
  2. Renaming parameter names, e.g.

changing "scRNAseq_tech" -> "feature_type"
changing "model" -> "count_model"
changing "scRNAseq_tech" -> "feature_type"

  • Black and Pylint re-formatting the code

fgypas and others added 30 commits March 2, 2022 12:04
@fgypas
Add github action to publish package to PyPi
959ec7f
@CaibinSh
Merge pull request #6 from CaibinSh/feature-pypi-github-action
a22c86f 
Add github action to publish package to PyPi
@fgypas @mr-nvs
Feature GitHub action conda build (#1)
23ee354 
* Add conda github action that builds the package with conda. It is triggered on pull request.

* Add pyro-ppl and pip as conda dependency. Trigger setup automatically via conda yaml. Split steps in conda build github action.

* Less strict in the setup.py dependencies for torch. Small change in the installation instructions in the documentation.

* Feature - Add basic unit tests to cover activation_functions.py (#3)

* adding first unit tests

* Format conda-build YAML file

* Update action name

* Fix path to __version__

* Test commit - Trigger workflow

* Revert dummy change

Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com>
@CaibinSh
Feature clean helper functions (#4)
501de71 
* delete _helper_functions.py

* delete _hyperparams_optimization.py

* delete plot_every_epoch function

* delete import _helper_functions

* delete gpyopt dependency
edit only README
71a3d5b
@fgypas
Add pylint github action
38fc141
@fgypas
Merge pull request #7 from Novartis/pylint-github-action
c1331e0 
Add pylint github action
@fgypas
Remove pypi github action (#9)
8bea098
@CaibinSh
support CPU, modify README (#10)
97292da 
* support CPU, modify README

* shorten the import, add model to __init__
@fgypas
More lenient scar installation specifications (#8)
a6ee6dd 
* Split scAR.yml to scAR-gpu.yaml and scAR-cpu.yaml.
* More lenient installation specifications.
* Bump version to 0.2.0
fix a typo, reorganise __init__.py
2880cfa
fix bugs
fbd5a94
@CaibinSh
Merge branch 'main' into develop
fe5d4ca
@CaibinSh
add synthetic data for integration test (#13)
1805102 
* add synthetic data for integration test

* change paths

* change paths
@fgypas
Remove torchaudio. Bump version to 0.2.2 (#14)
e41e343 
* Remove torchaudio
* Bump version to 0.2.2
@fgypas
Merge branch 'main' into develop
3bef86e
@CaibinSh
Update readme (#16)
6018a26 
* update README
@fgypas
Black github action (#17)
7a61e7f 
Addition of black github action that runs on every push and every pull request. It shows in the stdout all the changes that need to be made (--diff), but returns exit code 0, even if errors are observed.
@fgypas
Addition of integration test (#18)
ef7bfb4 
* Add integration test as unit test
update version
f6283c3
@CaibinSh
Merge branch 'main' into develop
c26be41
loweercase module name
e3b2fa9
lowercase module name
054744e
@CaibinSh
Update black.yaml
21c4689 
lowercase module name
@CaibinSh
Update python-conda-build.yaml
f982eef 
lowercase module name
lowercase module name
7931b98
Merge branch 'lowcase_package_name' of https://github.com/Novartis/scAR…
fccbc11 
… into lowcase_package_name
@CaibinSh
Update scar-gpu.yml
a77b6bd
@CaibinSh
Update scar-cpu.yml
ba51efe
@CaibinSh
Update __init__.py
0766f9f 
lowercase module name
CaibinSh and others added 13 commits April 25, 2022 08:44
@CaibinSh
refactor versioning (#21)
1502294 
* refactor versioning

* refactor versioning
update .gitignore
441a59d
solve conflict
1e54316
fix a bug
b1534fc
fix bugs
26dc46d
@CaibinSh
Documentation with readthedocs (#22)
c4832ba 
* Update .readthedocs.yaml

* Update .readthedocs.yaml

* Update .readthedocs.yaml

* Update requirements.txt

* Update requirements.txt

* Create README.md

* Create conf.py

* Update requirements.txt

* Update .readthedocs.yaml

* Update .readthedocs.yaml

* Update requirements.txt

* Update conf.py

* Update .readthedocs.yaml

* add documentations

* fix a bug

* update documentations

* update documentations

* update documentations

* update documentations

* update documentations

* update documentations

* update documentations

* update

* update

* fix a bug

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update document

* update README.md

* upadte documentations

* update documentations

* update documentations

* Update .readthedocs.yaml

* Update README.md

* update documentations

* add comments

* add comments

* update comment functionality

* update documentation
@CaibinSh
add documentations via readthedocs (#23)
88ba2e5 
* fix a bug

* update documentation -- denoising mRNAs

* update documentations -- CITEseq tutorials

* update documentations -- identity barcodes & sgRNA assignment
@CaibinSh
Update README.md
5a6680d 
add Git Action Badge
@CaibinSh
Update README.md
dc127db
@CaibinSh
Update README.md
47fbb2a 
Update Git Action Badge to default branch and default events
@CaibinSh
Black_formatting (#24)
d6e8b73 
* black_formatting

* Pylint checking

* optimize activation function and add docstring

* fix a bug

* fix a bug for activation functions

* update import torch in activation functions

* refactor _scar.py

* refactor _loss_functions.py

* refactor _vae.py

* refactor __main__.py

* refactor _data_generater.py

* refactor__version__.py

* Pylint formatting

* Update scar-cpu.yml

* Update scar-cpu.yml

* Update scar-cpu.yml

* Update scar-cpu.yml

restrict setuptools<=59.5.0

* Update scar-cpu.yml
@CaibinSh
further code refactoring (#25)
4385b22 
* black_formatting

* Pylint checking

* optimize activation function and add docstring

* fix a bug

* fix a bug for activation functions

* update import torch in activation functions

* refactor _scar.py

* refactor _loss_functions.py

* refactor _vae.py

* refactor __main__.py

* refactor _data_generater.py

* refactor__version__.py

* Pylint formatting

* Update scar-cpu.yml

* Update scar-cpu.yml

* Update scar-cpu.yml

* Update scar-cpu.yml

restrict setuptools<=59.5.0

* Update scar-cpu.yml

* refactor _scar.py and _vae.py

* code refactoring

* fix a bug

* fix a bug

* fix a bug

* fix a bug

* increase pylint score from 0.5 to 6

* bump version to 0.2.4

* update tutorials

* optimize command line
Merge branch 'main' into develop
e020108 
Conflicts:
	.github/workflows/black.yaml
	README.md
	scar/main/__init__.py
fgypas
fgypas reviewed Apr 27, 2022
View reviewed changes
scar/main/__version__.py Outdated
# -*- coding: utf-8 -*-
"""version here"""

__version__ = "0.2.4"
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I would make that a 0.3.0 release...

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Great! Will do so!

@CaibinSh CaibinSh requested a review from fgypas April 27, 2022 15:47
fgypas
fgypas approved these changes Apr 27, 2022
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Looks good to me. Just two comments. I would make that a 0.3.0 release. Also I see that the datasets that you add are relatively big. Do you plan to add more, or that's it?

@CaibinSh
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Looks good to me. Just two comments. I would make that a 0.3.0 release. Also I see that the datasets that you add are relatively big. Do you plan to add more, or that's it?

Good suggestion. I have marked it as 0.3.0 release.
There should be no more at the moment. I open an issue to discuss this folder, please go check out there.

@CaibinSh CaibinSh merged commit 7376aab into main Apr 27, 2022
This was linked to issues Apr 27, 2022
New release #27
Closed
ask for permission of Webhooks #28
Closed
@CaibinSh CaibinSh self-assigned this Apr 27, 2022
@CaibinSh CaibinSh added the enhancement New feature or request label Apr 27, 2022
CaibinSh added a commit that referenced this pull request Apr 27, 2022
@CaibinSh @fgypas @mr-nvs
harmonize development and main branches (#29)
2720895 
* New release (#26)

* Add github action to publish package to PyPi

* Feature GitHub action conda build (#1)

* Add conda github action that builds the package with conda. It is triggered on pull request.

* Add pyro-ppl and pip as conda dependency. Trigger setup automatically via conda yaml. Split steps in conda build github action.

* Less strict in the setup.py dependencies for torch. Small change in the installation instructions in the documentation.

* Feature - Add basic unit tests to cover activation_functions.py (#3)

* adding first unit tests

* Format conda-build YAML file

* Update action name

* Fix path to __version__

* Test commit - Trigger workflow

* Revert dummy change

Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com>

* Feature clean helper functions (#4)

* delete _helper_functions.py

* delete _hyperparams_optimization.py

* delete plot_every_epoch function

* delete import _helper_functions

* delete gpyopt dependency

* edit only README

* Add pylint github action

* Remove pypi github action (#9)

* support CPU, modify README (#10)

* support CPU, modify README

* shorten the import, add model to __init__

* More lenient scar installation specifications (#8)

* Split scAR.yml to scAR-gpu.yaml and scAR-cpu.yaml.
* More lenient installation specifications.
* Bump version to 0.2.0

* fix a typo, reorganise __init__.py

* fix bugs

* add synthetic data for integration test (#13)

* add synthetic data for integration test

* change paths

* change paths

* Remove torchaudio. Bump version to 0.2.2 (#14)

* Remove torchaudio
* Bump version to 0.2.2

* Update readme (#16)

* update README

* Black github action (#17)

Addition of black github action that runs on every push and every pull request. It shows in the stdout all the changes that need to be made (--diff), but returns exit code 0, even if errors are observed.

* Addition of integration test (#18)

* Add integration test as unit test

* update version

* loweercase module name

* lowercase module name

* Update black.yaml

lowercase module name

* Update python-conda-build.yaml

lowercase module name

* lowercase module name

* Update scar-gpu.yml

* Update scar-cpu.yml

* Update __init__.py

lowercase module name

* refactor versioning (#21)

* refactor versioning

* refactor versioning

* update .gitignore

* fix a bug

* fix bugs

* Documentation with readthedocs (#22)

* Update .readthedocs.yaml

* Update .readthedocs.yaml

* Update .readthedocs.yaml

* Update requirements.txt

* Update requirements.txt

* Create README.md

* Create conf.py

* Update requirements.txt

* Update .readthedocs.yaml

* Update .readthedocs.yaml

* Update requirements.txt

* Update conf.py

* Update .readthedocs.yaml

* add documentations

* fix a bug

* update documentations

* update documentations

* update documentations

* update documentations

* update documentations

* update documentations

* update documentations

* update

* update

* fix a bug

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update document

* update README.md

* upadte documentations

* update documentations

* update documentations

* Update .readthedocs.yaml

* Update README.md

* update documentations

* add comments

* add comments

* update comment functionality

* update documentation

* add documentations via readthedocs (#23)

* fix a bug

* update documentation -- denoising mRNAs

* update documentations -- CITEseq tutorials

* update documentations -- identity barcodes & sgRNA assignment

* Update README.md

add Git Action Badge

* Update README.md

* Update README.md

Update Git Action Badge to default branch and default events

* Black_formatting (#24)

* black_formatting

* Pylint checking

* optimize activation function and add docstring

* fix a bug

* fix a bug for activation functions

* update import torch in activation functions

* refactor _scar.py

* refactor _loss_functions.py

* refactor _vae.py

* refactor __main__.py

* refactor _data_generater.py

* refactor__version__.py

* Pylint formatting

* Update scar-cpu.yml

* Update scar-cpu.yml

* Update scar-cpu.yml

* Update scar-cpu.yml

restrict setuptools<=59.5.0

* Update scar-cpu.yml

* further code refactoring (#25)

* black_formatting

* Pylint checking

* optimize activation function and add docstring

* fix a bug

* fix a bug for activation functions

* update import torch in activation functions

* refactor _scar.py

* refactor _loss_functions.py

* refactor _vae.py

* refactor __main__.py

* refactor _data_generater.py

* refactor__version__.py

* Pylint formatting

* Update scar-cpu.yml

* Update scar-cpu.yml

* Update scar-cpu.yml

* Update scar-cpu.yml

restrict setuptools<=59.5.0

* Update scar-cpu.yml

* refactor _scar.py and _vae.py

* code refactoring

* fix a bug

* fix a bug

* fix a bug

* fix a bug

* increase pylint score from 0.5 to 6

* bump version to 0.2.4

* update tutorials

* optimize command line

* bump version to 0.3.0

Co-authored-by: Gypas, Foivos <foivos.gypas@novartis.com>
Co-authored-by: Foivos Gypas <fgypas@users.noreply.github.com>
Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com>

* delete scAR/test

Co-authored-by: Gypas, Foivos <foivos.gypas@novartis.com>
Co-authored-by: Foivos Gypas <fgypas@users.noreply.github.com>
Co-authored-by: Mathias Rechenmann <58425548+mr-nvs@users.noreply.github.com>
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@fgypas fgypas fgypas approved these changes

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@CaibinSh CaibinSh

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ask for permission of Webhooks New release
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@CaibinSh @fgypas