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renamed nmvae to bavaria
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‎CONTRIBUTING.rst‎

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Bug reports
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===========
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When `reporting a bug <https://github.com/wkopp/nmvae/issues>`_ please include:
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When `reporting a bug <https://github.com/wkopp/bavaria/issues>`_ please include:
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* Your operating system name and version.
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* Any details about your local setup that might be helpful in troubleshooting.
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Documentation improvements
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==========================
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nmvae could always use more documentation, whether as part of the
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official nmvae docs, in docstrings, or even on the web in blog posts,
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bavaria could always use more documentation, whether as part of the
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official bavaria docs, in docstrings, or even on the web in blog posts,
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articles, and such.
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Feature requests and feedback
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=============================
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The best way to send feedback is to file an issue at https://github.com/wkopp/nmvae/issues.
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The best way to send feedback is to file an issue at https://github.com/wkopp/bavaria/issues.
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If you are proposing a feature:
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Development
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===========
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To set up `nmvae` for local development:
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To set up `bavaria` for local development:
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1. Fork `nmvae <https://github.com/wkopp/nmvae>`_
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1. Fork `bavaria <https://github.com/wkopp/bavaria>`_
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(look for the "Fork" button).
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2. Clone your fork locally::
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git clone git@github.com:YOURGITHUBNAME/nmvae.git
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git clone git@github.com:YOURGITHUBNAME/bavaria.git
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3. Create a branch for local development::
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4. Add yourself to ``AUTHORS.rst``.
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.. [1] If you don't have all the necessary python versions available locally you can rely on Travis - it will
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`run the tests <https://travis-ci.org/wkopp/nmvae/pull_requests>`_ for each change you add in the pull request.
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`run the tests <https://travis-ci.org/wkopp/bavaria/pull_requests>`_ for each change you add in the pull request.
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It will be slower though ...
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‎README.rst‎

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::
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pip install https://github.com/BIMSBbioinfo/nmvae/archive/v0.0.1.zip
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pip install https://github.com/BIMSBbioinfo/bavaria/archive/v0.0.1.zip
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Documentation
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::
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nmvae -data <matrix.mtx>
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bavaria -data <matrix.mtx>
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-regions <regions.bed>
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-barcodes <barcodes.tsv>
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-output <outputdir>

‎docs/conf.py‎

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]
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source_suffix = '.rst'
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master_doc = 'index'
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project = 'nmvae'
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project = 'bavaria'
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year = '2020'
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author = 'Wolfgang Kopp'
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copyright = '{0}, {1}'.format(year, author)
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pygments_style = 'trac'
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templates_path = ['.']
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extlinks = {
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'issue': ('https://github.com/wkopp/nmvae/issues/%s', '#'),
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'pr': ('https://github.com/wkopp/nmvae/pull/%s', 'PR #'),
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'issue': ('https://github.com/wkopp/bavaria/issues/%s', '#'),
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'pr': ('https://github.com/wkopp/bavaria/pull/%s', 'PR #'),
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}
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# on_rtd is whether we are on readthedocs.org
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on_rtd = os.environ.get('READTHEDOCS', None) == 'True'

‎docs/installation.rst‎

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At the command line::
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pip install nmvae
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pip install bavaria

‎docs/usage.rst‎

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Usage
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=====
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To use nmvae in a project::
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To use bavaria in a project::
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import nmvae
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import bavaria

‎setup.cfg‎

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[tool:isort]
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force_single_line = True
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line_length = 120
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known_first_party = nmvae
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known_first_party = bavaria
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default_section = THIRDPARTY
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forced_separate = test_nmvae
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forced_separate = test_bavaria
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skip = .tox,.eggs,ci/templates,build,dist

‎setup.py‎

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setup(
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name='nmvae',
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name='bavaria',
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version='0.0.1',
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license='LGPL-3.0-or-later',
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description='Negative multinomial variational auto-encoder',
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),
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author='Wolfgang Kopp',
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author_email='wolfgang.kopp@mdc-berlin.de',
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url='https://github.com/wkopp/nmvae',
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url='https://github.com/wkopp/bavaria',
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packages=find_packages('src'),
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package_dir={'': 'src'},
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py_modules=[splitext(basename(path))[0] for path in glob('src/*.py')],
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'Private :: Do Not Upload',
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],
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project_urls={
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'Documentation': 'https://nmvae.readthedocs.io/',
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'Changelog': 'https://nmvae.readthedocs.io/en/latest/changelog.html',
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'Issue Tracker': 'https://github.com/wkopp/nmvae/issues',
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'Documentation': 'https://bavaria.readthedocs.io/',
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'Changelog': 'https://bavaria.readthedocs.io/en/latest/changelog.html',
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'Issue Tracker': 'https://github.com/wkopp/bavaria/issues',
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},
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keywords=[
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# eg: 'keyword1', 'keyword2', 'keyword3',
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},
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entry_points={
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'console_scripts': [
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'nmvae = nmvae.cli:main',
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'bavaria = bavaria.cli:main',
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]
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},
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)

‎src/bavaria/__init__.py‎

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__version__ = '0.0.1'
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#from bavaria.utils import VAE

src/nmvae/__main__.py renamed to src/bavaria/__main__.py

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"""
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Entrypoint module, in case you use `python -mnmvae`.
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Entrypoint module, in case you use `python -mbavaria`.
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Why does this file exist, and why __main__? For more info, read:
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- https://docs.python.org/2/using/cmdline.html#cmdoption-m
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- https://docs.python.org/3/using/cmdline.html#cmdoption-m
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"""
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from nmvae.cli import main
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from bavaria.cli import main
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if __name__ == "__main__":
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main()

src/nmvae/cli.py renamed to src/bavaria/cli.py

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You might be tempted to import things from __main__ later, but that will cause
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problems: the code will get executed twice:
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- When you run `python -mnmvae` python will execute
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- When you run `python -mbavaria` python will execute
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``__main__.py`` as a script. That means there won't be any
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``nmvae.__main__`` in ``sys.modules``.
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``bavaria.__main__`` in ``sys.modules``.
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- When you import __main__ it will get executed again (as a module) because
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there's no ``nmvae.__main__`` in ``sys.modules``.
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there's no ``bavaria.__main__`` in ``sys.modules``.
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Also see (1) from http://click.pocoo.org/5/setuptools/#setuptools-integration
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"""
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import pandas as pd
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import tensorflow as tf
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import keras
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from nmvae import __version__
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from nmvae.ensembles import EnsembleVAE
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from nmvae.ensembles import BatchEnsembleVAE
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from nmvae.data import load_data
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from nmvae.data import load_batch_labels
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from nmvae.data import one_hot_encode_batches
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from nmvae.utils import resnet_vae_params
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from nmvae.utils import resnet_vae_batch_params
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from nmvae.utils import get_variable_regions
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from bavaria import __version__
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from bavaria.ensembles import EnsembleVAE
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from bavaria.ensembles import BatchEnsembleVAE
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from bavaria.data import load_data
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from bavaria.data import load_batch_labels
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from bavaria.data import one_hot_encode_batches
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from bavaria.utils import resnet_vae_params
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from bavaria.utils import resnet_vae_batch_params
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from bavaria.utils import get_variable_regions
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import scanpy as sc
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import logging
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def main(args=None):
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parser = argparse.ArgumentParser('nmvae',
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parser = argparse.ArgumentParser('bavaria',
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description=f'Negative multinomial variational auto-encoders - v{__version__}')
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parser.add_argument('-data', dest='data', type=str,
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adata = metamodel.encode(adata)
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sc.pp.neighbors(adata, n_neighbors=15, use_rep="nmvae-ensemble")
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sc.pp.neighbors(adata, n_neighbors=15, use_rep="bavaria-ensemble")
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sc.tl.louvain(adata, resolution=args.resolution)
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sc.tl.umap(adata)
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