maradoner 0.14.2__tar.gz → 0.14.3__tar.gz

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Files changed (26) hide show
  1. {maradoner-0.14.2 → maradoner-0.14.3}/PKG-INFO +5 -5
  2. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/__init__.py +3 -2
  3. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/grn.py +2 -0
  4. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/main.py +1 -1
  5. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner.egg-info/PKG-INFO +5 -5
  6. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner.egg-info/requires.txt +1 -0
  7. {maradoner-0.14.2 → maradoner-0.14.3}/setup.py +3 -4
  8. {maradoner-0.14.2 → maradoner-0.14.3}/README.md +0 -0
  9. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/create.py +0 -0
  10. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/dataset_filter.py +0 -0
  11. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/export.py +0 -0
  12. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/fit.py +0 -0
  13. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/mara/__init__.py +0 -0
  14. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/mara/export.py +0 -0
  15. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/mara/fit.py +0 -0
  16. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/mara/main.py +0 -0
  17. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/mara.py +0 -0
  18. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/meta_optimizer.py +0 -0
  19. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/select.py +0 -0
  20. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/synthetic_data.py +0 -0
  21. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner/utils.py +0 -0
  22. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner.egg-info/SOURCES.txt +0 -0
  23. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner.egg-info/dependency_links.txt +0 -0
  24. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner.egg-info/entry_points.txt +0 -0
  25. {maradoner-0.14.2 → maradoner-0.14.3}/maradoner.egg-info/top_level.txt +0 -0
  26. {maradoner-0.14.2 → maradoner-0.14.3}/setup.cfg +0 -0
{maradoner-0.14.2 → maradoner-0.14.3}/PKG-INFO RENAMED
@@ -1,17 +1,16 @@
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  Metadata-Version: 2.1
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  Name: maradoner
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- Version: 0.14.2
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+ Version: 0.14.3
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  Summary: Variance-adjusted estimation of motif activities.
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- Home-page: https://github.com/autosome-ru/nemara
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+ Home-page: https://github.com/autosome-ru/maradoner
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  Author: Georgy Meshcheryakov
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  Author-email: iam@georgy.top
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- Classifier: Programming Language :: Python :: 3.9
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- Classifier: Programming Language :: Python :: 3.10
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  Classifier: Programming Language :: Python :: 3.11
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  Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Programming Language :: Python :: 3.13
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  Classifier: Topic :: Scientific/Engineering
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  Classifier: Operating System :: OS Independent
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- Requires-Python: >=3.9
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+ Requires-Python: >=3.11
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  Description-Content-Type: text/markdown
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  Requires-Dist: pip>=24.0
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  Requires-Dist: typer>=0.13
@@ -27,6 +26,7 @@ Requires-Dist: dill>=0.3.9
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  Requires-Dist: rich>=12.6.0
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  Requires-Dist: tqdm>=4.0
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  Requires-Dist: scikit-learn>=1.6
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+ Requires-Dist: tables>=3.10
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  **MARADONER**
{maradoner-0.14.2 → maradoner-0.14.3}/maradoner/__init__.py RENAMED
@@ -1,5 +1,5 @@
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  # -*- coding: utf-8 -*-
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- __version__ = '0.14.2'
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+ __version__ = '0.14.3'
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  import importlib
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@@ -17,7 +17,8 @@ __min_reqs__ = [
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  'dill>=0.3.9',
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  'rich>=12.6.0',
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  'tqdm>=4.0',
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- 'scikit-learn>=1.6'
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+ 'scikit-learn>=1.6',
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+ 'tables>=3.10'
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  ]
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  def versiontuple(v):
{maradoner-0.14.2 → maradoner-0.14.3}/maradoner/grn.py RENAMED
@@ -60,6 +60,8 @@ def estimate_promoter_variance(project_name: str, prior_top=0.90):
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  B_hat = B ** 2 * fit.motif_variance.motif
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  B_hat = B_hat.sum(axis=1)
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  var = list()
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+ jax.config.update('jax_enable_x64', True)
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+ jax.config.update('jax_platform_name', 'cpu')
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  for inds, prior_mean, nu in tqdm(list(zip(group_inds, prior_means, fit.motif_variance.group))):
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  Yt = Y[:, inds].sum(axis=1)
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  s = len(inds)
{maradoner-0.14.2 → maradoner-0.14.3}/maradoner/main.py RENAMED
@@ -314,7 +314,7 @@ def _select_motifs(name: str = Argument(..., help='Project name'),
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  __grn_doc = 'Tests each promoter against each motif per each group. Some people call it GRN.'
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  @app.command('grn',
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- help=__select_motif_doc)
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+ help=__grn_doc)
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  def _grn(name: str = Argument(..., help='Project name'),
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  folder: Path = Argument(..., help='Output folder where results will be stored. In total, expect number_of_groups tables of size'
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  ' comparable to the expression file size.'),
{maradoner-0.14.2 → maradoner-0.14.3}/maradoner.egg-info/PKG-INFO RENAMED
@@ -1,17 +1,16 @@
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  Metadata-Version: 2.1
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  Name: maradoner
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- Version: 0.14.2
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+ Version: 0.14.3
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  Summary: Variance-adjusted estimation of motif activities.
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- Home-page: https://github.com/autosome-ru/nemara
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+ Home-page: https://github.com/autosome-ru/maradoner
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  Author: Georgy Meshcheryakov
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  Author-email: iam@georgy.top
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- Classifier: Programming Language :: Python :: 3.9
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- Classifier: Programming Language :: Python :: 3.10
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  Classifier: Programming Language :: Python :: 3.11
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  Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Programming Language :: Python :: 3.13
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  Classifier: Topic :: Scientific/Engineering
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  Classifier: Operating System :: OS Independent
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- Requires-Python: >=3.9
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+ Requires-Python: >=3.11
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  Description-Content-Type: text/markdown
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  Requires-Dist: pip>=24.0
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  Requires-Dist: typer>=0.13
@@ -27,6 +26,7 @@ Requires-Dist: dill>=0.3.9
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  Requires-Dist: rich>=12.6.0
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  Requires-Dist: tqdm>=4.0
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  Requires-Dist: scikit-learn>=1.6
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+ Requires-Dist: tables>=3.10
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  **MARADONER**
{maradoner-0.14.2 → maradoner-0.14.3}/maradoner.egg-info/requires.txt RENAMED
@@ -12,3 +12,4 @@ dill>=0.3.9
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  rich>=12.6.0
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  tqdm>=4.0
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  scikit-learn>=1.6
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+ tables>=3.10
{maradoner-0.14.2 → maradoner-0.14.3}/setup.py RENAMED
@@ -23,13 +23,12 @@ setup(
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  author='Georgy Meshcheryakov',
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  author_email='iam@georgy.top',
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  install_requires=__min_reqs__,
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- python_requires='>=3.9',
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- url="https://github.com/autosome-ru/nemara",
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+ python_requires='>=3.11',
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+ url="https://github.com/autosome-ru/maradoner",
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  classifiers=[
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- "Programming Language :: Python :: 3.9",
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- "Programming Language :: Python :: 3.10",
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  "Programming Language :: Python :: 3.11",
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  "Programming Language :: Python :: 3.12",
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+ "Programming Language :: Python :: 3.13",
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  "Topic :: Scientific/Engineering",
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  "Operating System :: OS Independent"]
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{maradoner-0.14.2 → maradoner-0.14.3}/README.md RENAMED
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{maradoner-0.14.2 → maradoner-0.14.3}/maradoner/fit.py RENAMED
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{maradoner-0.14.2 → maradoner-0.14.3}/maradoner/mara.py RENAMED
File without changes
{maradoner-0.14.2 → maradoner-0.14.3}/setup.cfg RENAMED
File without changes