pg-sui 1.0.2.1__py3-none-any.whl → 1.6.8__py3-none-any.whl

{pg_sui-1.0.2.1.dist-info → pg_sui-1.6.8.dist-info}/METADATA

@@ -1,58 +1,70 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pg-sui
-Version: 1.0.2.1
-Summary: Python machine and deep learning package to impute missing SNPs
-Home-page: https://github.com/btmartin721/PG-SUI
-Author: Bradley T. Martin and Tyler K. Chafin
-Author-email: evobio721@gmail.com
-Maintainer: Bradley T. Martin
-Maintainer-email: evobio721@gmail.com
+Version: 1.6.8
+Summary: Python machine and deep learning API to impute missing genotypes
+Author-email: "Drs. Bradley T. Martin and Tyler K. Chafin" <evobio721@gmail.com>
+Maintainer-email: "Dr. Bradley T. Martin" <evobio721@gmail.com>
 License: GNU General Public License v3 (GPLv3)
 Project-URL: Homepage, https://github.com/btmartin721/PG-SUI
 Project-URL: Documentation, https://pg-sui.readthedocs.io/en/latest/
 Project-URL: Source, https://github.com/btmartin721/PG-SUI.git
-Project-URL: Bug Tracker, https://github.com/btmartin721/PG-SUI/issues
-Keywords: impute,imputation,imputer,machine learning,neural network,deep learning,python,api,vae,autoencoder,ubp,nlpca,population genomics,unsupervised,supervised,IterativeImputer
+Project-URL: BugTracker, https://github.com/btmartin721/PG-SUI/issues
+Keywords: impute,imputation,AI,deep learning,machine learning,neural network,vae,autoencoder,ubp,nlpca,population genetics,unsupervised,supervised,bioinformatics,snp,genomics,genotype,missing data,data analysis,data science,statistics,data visualization,python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Unix
+Classifier: Operating System :: POSIX
 Classifier: Natural Language :: English
-Requires-Python: >=3.8
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: matplotlib
+Requires-Dist: numpy>=2.1
+Requires-Dist: pandas>=2.2.2
+Requires-Dist: scikit-learn>=1.4
+Requires-Dist: scipy
 Requires-Dist: seaborn
-Requires-Dist: jupyterlab
-Requires-Dist: scikit-learn >=1.0
+Requires-Dist: torch
 Requires-Dist: tqdm
-Requires-Dist: pandas <2.1.0
-Requires-Dist: numpy ==1.24.3
-Requires-Dist: scipy
-Requires-Dist: xgboost
-Requires-Dist: tensorflow
-Requires-Dist: keras
 Requires-Dist: toytree
-Requires-Dist: sklearn-genetic-opt[all] >=0.6.0
-Requires-Dist: importlib-resources >=1.1.0
-Requires-Dist: pyvolve
-Requires-Dist: scikeras
+Requires-Dist: optuna
 Requires-Dist: snpio
-Requires-Dist: urllib3 <2.0.0,>=1.26.7
-Requires-Dist: typing-extensions <4.6.0
-Provides-Extra: docs
-Requires-Dist: sphinx <7 ; extra == 'docs'
-Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
-Requires-Dist: sphinx-autodoc-typehints ; extra == 'docs'
 Provides-Extra: intel
-Requires-Dist: scikit-learn-intelex ; extra == 'intel'
+Requires-Dist: scikit-learn-intelex; extra == "intel"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: sphinx_autodoc_typehints; extra == "docs"
+Requires-Dist: sphinxcontrib-napoleon; extra == "docs"
+Requires-Dist: sphinxcontrib-programoutput; extra == "docs"
+Provides-Extra: dev
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: wheel; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: sphinx-rtd-theme; extra == "dev"
+Requires-Dist: sphinx-autodoc-typehints; extra == "dev"
+Requires-Dist: sphinxcontrib-napoleon; extra == "dev"
+Requires-Dist: sphinxcontrib-programoutput; extra == "dev"
+Requires-Dist: requests; extra == "dev"
+Requires-Dist: PyObjC; extra == "dev"
+Provides-Extra: optional
+Requires-Dist: PyObjC; extra == "optional"
+Provides-Extra: gui
+Dynamic: license-file
 
 
 <img src="https://github.com/btmartin721/PG-SUI/blob/master/img/pgsui-logo-faded.png" alt="PG-SUI Logo" width="50%" height="50%">
@@ -124,51 +136,20 @@ pip install pg-sui[intel]
 
 ### Dependencies
 
-+ python >= 3.8
++ python >= 3.11
 + pandas
-+ numpy==1.24.3
++ numpy
 + scipy
 + matplotlib
 + seaborn
 + plotly
 + kaleido
-+ jupyterlab
 + tqdm
 + toytree
-+ pyvolve
 + scikit-learn
-+ tensorflow >= 2.7
-+ keras >= 2.7
 + xgboost
-+ scikeras >= 0.6.0
 + snpio
-
-
-### Manual Install
-
-If you want to install everything manually, the requirements can be installed with conda and pip. sklearn-genetic-opt and scikeras are only avaiable via pip, and scikeras requires tensorflow >= 2.7 and scikit-learn >= 1.0.
-
-```
-conda create -n pg-sui python
-conda activate pg-sui
-
-conda install matplotlib seaborn jupyterlab scikit-learn tqdm pandas numpy scipy xgboost lightgbm kaleido
-
-# Only works if using Intel CPUs; speeds up processing
-conda install scikit-learn-intelex
-
-conda install -c conda-forge toytree kaleido
-
-conda install -c bioconda pyvolve
-
-conda install -c plotly plotly
-
-pip install sklearn-genetic-opt[all]
-
-pip install scikeras snpio
-
-pip install tensorflow-cpu
-```
++ optuna
 
 #### Installation troubleshooting
 

pg_sui-1.6.8.dist-info/RECORD

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{pg_sui-1.0.2.1.dist-info → pg_sui-1.6.8.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pg_sui-1.6.8.dist-info/entry_points.txt

@@ -0,0 +1,4 @@
+[console_scripts]
+pg-sui = pgsui.cli:main
+pgsui-gui = pgsui.electron.launch:main
+pgsui-gui-setup = pgsui.electron.bootstrap:main

pg_sui-1.6.8.dist-info/top_level.txt

@@ -0,0 +1 @@
+pgsui

pgsui/__init__.py

@@ -1,63 +1,44 @@
 ## PG-SUI package by Bradley T. Martin and Tyler K. Chafin
 ## E-mail: evobio721@gmail.com
-## Version 0.1, completed 13-Dec-2021
-
-# Suppresses tensorflow GPU warnings.
-import os
-import warnings
-
-os.environ["TF_CPP_MIN_LOG_LEVEL"] = "2"
-
-from pgsui.utils.misc import get_processor_name
-
-
-# Requires scikit-learn-intellex package
-if get_processor_name().strip().startswith("Intel"):
-    try:
-        from sklearnex import patch_sklearn
-
-        patch_sklearn()
-        intelex = True
-    except (ImportError, TypeError):
-        warnings.warn(
-            "Intel CPU detected but scikit-learn-intelex is not installed. We recommend installing it to speed up computation if your hardware supports it."
-        )
-        intelex = False
-else:
-    intelex = False
-
-os.environ["intelex"] = str(intelex)
-
-from pgsui.impute.estimators import (
-    ImputeKNN,
-    ImputeNLPCA,
-    ImputeRandomForest,
-    ImputeStandardAutoEncoder,
-    ImputeUBP,
-    ImputeVAE,
-    ImputeXGBoost,
+from ._version import version as __version__
+
+from pgsui.data_processing.containers import (
+    AutoencoderConfig,
+    HGBConfig,
+    MostFrequentConfig,
+    NLPCAConfig,
+    RefAlleleConfig,
+    RFConfig,
+    UBPConfig,
+    VAEConfig,
 )
-
-from pgsui.impute.simple_imputers import (
-    ImputePhylo,
-    ImputeMF,
-    ImputeAlleleFreq,
-    ImputeRefAllele,
+from pgsui.impute.deterministic.imputers.mode import ImputeMostFrequent
+from pgsui.impute.deterministic.imputers.ref_allele import ImputeRefAllele
+from pgsui.impute.supervised.imputers.hist_gradient_boosting import (
+    ImputeHistGradientBoosting,
 )
-
-from pgsui.data_processing.transformers import SimGenotypeDataTransformer
+from pgsui.impute.supervised.imputers.random_forest import ImputeRandomForest
+from pgsui.impute.unsupervised.imputers.autoencoder import ImputeAutoencoder
+from pgsui.impute.unsupervised.imputers.nlpca import ImputeNLPCA
+from pgsui.impute.unsupervised.imputers.ubp import ImputeUBP
+from pgsui.impute.unsupervised.imputers.vae import ImputeVAE
 
 __all__ = [
-    "ImputeUBP",
+    "ImputeAutoencoder",  # Unsupervised imputer classes
     "ImputeVAE",
-    "ImputeXGBoost",
-    "ImputeStandardAutoEncoder",
-    "ImputeRandomForest",
     "ImputeNLPCA",
-    "ImputeKNN",
-    "SimGenotypeDataTransformer",
-    "ImputePhylo",
-    "ImputeMF",
-    "ImputeAlleleFreq",
-    "ImputeRefAllele",
+    "ImputeUBP",
+    "ImputeRandomForest",  # Supervised imputer classes
+    "ImputeHistGradientBoosting",
+    "ImputeRefAllele",  # Deterministic imputer classes
+    "ImputeMostFrequent",
+    "AutoencoderConfig",  # Unsupervised imputer configs
+    "VAEConfig",
+    "NLPCAConfig",
+    "UBPConfig",
+    "MostFrequentConfig",  # Deterministic imputer configs
+    "RefAlleleConfig",
+    "RFConfig",  # Supervised imputer configs
+    "HGBConfig",
+    "__version__",
 ]

pgsui/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '1.6.8'
+__version_tuple__ = version_tuple = (1, 6, 8)
+
+__commit_id__ = commit_id = None