Remove torchaudio. Bump version to 0.2.2 #14
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fgypas
commented
Apr 4, 2022
fgypas
commented
- Remove torchaudio.
- Bump version to 0.2.2
CaibinSh
approved these changes
Apr 4, 2022
CaibinSh
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Apr 19, 2022
* 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 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>
CaibinSh
added a commit
that referenced
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Apr 27, 2022
* 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>
CaibinSh
added a commit
that referenced
this pull request
Apr 27, 2022
* 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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