pg-sui 0.2.3__py3-none-any.whl → 1.6.14.dev9__py3-none-any.whl

{pg_sui-0.2.3.dist-info → pg_sui-1.6.14.dev9.dist-info}/METADATA

@@ -1,58 +1,73 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pg-sui
-Version: 0.2.3
-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: 1.6.14.dev9
+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: python,impute,imputation,imputer,machine learning,neural network,api,IterativeImputer,vae,ubp,nlpca,autoencoder,deep learning,population genomics
-Platform: UNKNOWN
+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: 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,<4
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
-Requires-Dist: importlib-resources (>=1.1.0)
-Requires-Dist: jupyterlab
-Requires-Dist: keras
+License-File: LICENSE
 Requires-Dist: matplotlib
-Requires-Dist: numpy (==1.24.3)
-Requires-Dist: pandas
-Requires-Dist: pyvolve
-Requires-Dist: scikeras
-Requires-Dist: scikit-learn (>=1.0)
+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: sklearn-genetic-opt[all] (>=0.6.0)
-Requires-Dist: snpio
-Requires-Dist: tensorflow
-Requires-Dist: toytree
+Requires-Dist: torch
 Requires-Dist: tqdm
-Requires-Dist: typing-extensions (<4.6.0)
-Requires-Dist: urllib3 (<2.0.0,>=1.26.7)
-Requires-Dist: xgboost
-Provides-Extra: docs
-Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
-Requires-Dist: sphinx (<7) ; extra == 'docs'
-Requires-Dist: sphinx-autodoc-typehints ; extra == 'docs'
+Requires-Dist: toytree
+Requires-Dist: optuna
+Requires-Dist: rich
+Requires-Dist: rich[jupyter]
+Requires-Dist: snpio
 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"
+Provides-Extra: optional
+Requires-Dist: PyObjC; extra == "optional"
+Provides-Extra: gui
+Requires-Dist: fastapi>=0.110; extra == "gui"
+Requires-Dist: uvicorn[standard]>=0.23; 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%">
@@ -64,13 +79,13 @@ Population Genomic Supervised and Unsupervised Imputation.
 
 ## About PG-SUI
 
-PG-SUI is a Python 3 API that uses machine learning to impute missing values from population genomic SNP data. There are several supervised and unsupervised machine learning algorithms available to impute missing data, as well as some non-machine learning imputers that are useful. 
+PG-SUI is a Python 3 API that uses machine learning to impute missing values from population genomic SNP data. There are several supervised and unsupervised machine learning algorithms available to impute missing data, as well as some non-machine learning imputers that are useful.
 
 Below is some general information and a basic tutorial. For more detailed information, see our [API Documentation](https://pg-sui.readthedocs.io/en/latest/).
 
 ### Supervised Imputation Methods
 
-Supervised methods utilze the scikit-learn's IterativeImputer, which is based on the MICE (Multivariate Imputation by Chained Equations) algorithm ([1](#1)), and iterates over each SNP site (i.e., feature) while uses the N nearest neighbor features to inform the imputation. The number of nearest features can be adjusted by users. IterativeImputer currently works with any of the following scikit-learn classifiers: 
+Supervised methods utilze the scikit-learn's IterativeImputer, which is based on the MICE (Multivariate Imputation by Chained Equations) algorithm ([1](#1)), and iterates over each SNP site (i.e., feature) while uses the N nearest neighbor features to inform the imputation. The number of nearest features can be adjusted by users. IterativeImputer currently works with any of the following scikit-learn classifiers:
 
 + K-Nearest Neighbors
 + Random Forest
@@ -120,55 +135,37 @@ If you have an Intel CPU and want to use the sklearn-genetic-intelex package to
 pip install pg-sui[intel]
 ```
 
+### Optional GUI (Electron)
+
+PG-SUI ships an Electron GUI wrapper around the Python CLI.
+
+1. Install the Python-side extras (FastAPI/uvicorn helper) if you want to serve from Python:  
+   `pip install pg-sui[gui]`
+2. Install Node.js (https://nodejs.org) and fetch the app dependencies once:  
+   `pgsui-gui-setup`
+3. Launch the GUI:  
+   `pgsui-gui`
+
+The GUI shells out to the same CLI underneath, so presets/overrides and YAML configs behave identically.
+
 ## Manual Installation
 
 ### 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
 
@@ -229,7 +226,7 @@ You can read your input files as a GenotypeData object from the [SNPio](https://
 ```
 
 # Import snpio. Automatically installed with pgsui when using pip.
-from snpio import GenotypeData 
+from snpio import GenotypeData
 
 # Read in PHYLIP, VCF, or STRUCTURE-formatted alignments.
 data = GenotypeData(
@@ -295,13 +292,40 @@ mf = ImputeMF(*args) # Matrix factorization
 
 ### Unsupervised Neural Networks
 
-```
+``` python
 vae = ImputeVAE(data) # Variational autoencoder
 nlpca = ImputeNLPCA(data) # Nonlinear PCA
 ubp = ImputeUBP(data) # Unsupervised backpropagation
 sae = ImputeStandardAutoEncoder(data) # standard autoencoder
 ```
 
+## Command-Line Interface
+
+Run the PG-SUI CLI with ``pg-sui`` (installed alongside the library). The CLI follows the same precedence model as the Python API:
+
+``code defaults  <  preset (--preset)  <  YAML (--config)  <  explicit CLI flags  <  --set key=value``.
+
+Recent releases add explicit switches for the simulated-missingness workflow shared by the neural and supervised models:
+
+- ``--sim-strategy`` selects one of ``random``, ``random_weighted``, ``random_weighted_inv``, ``nonrandom``, ``nonrandom_weighted``.
+- ``--sim-prop`` sets the proportion of observed calls to temporarily mask when building the evaluation set.
+- ``--simulate-missing`` disables simulated masking entirely (store-false flag); omit it to inherit preset/YAML defaults or re-enable via ``--set sim.simulate_missing=True``.
+
+Example:
+
+```
+pg-sui \
+  --vcf data.vcf.gz \
+  --popmap pops.popmap \
+  --models ImputeUBP ImputeVAE \
+  --preset balanced \
+  --sim-strategy random_weighted_inv \
+  --sim-prop 0.25 \
+  --set io.prefix=vae_vs_ubp
+```
+
+CLI overrides cascade into every selected model, so a single invocation can evaluate multiple imputers with a consistent simulation strategy and output prefix.
+
 ## To-Dos
 
 - simulations
@@ -318,5 +342,3 @@ sae = ImputeStandardAutoEncoder(data) # standard autoencoder
 <a name="4">4. </a>Scholz, M., Kaplan, F., Guy, C. L., Kopka, J., & Selbig, J. (2005). Non-linear PCA: a missing data approach. Bioinformatics, 21(20), 3887-3895.
 
 <a name="5">5. </a>Gashler, M. S., Smith, M. R., Morris, R., & Martinez, T. (2016). Missing value imputation with unsupervised backpropagation. Computational Intelligence, 32(2), 196-215.
-
-

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+pg_sui-1.6.14.dev9.dist-info/METADATA,sha256=F_9XvBZpZqKvrMnmD9TnwRuOkjXPEtnsUyGnRQu9orE,14443
+pg_sui-1.6.14.dev9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+pg_sui-1.6.14.dev9.dist-info/entry_points.txt,sha256=xidyl6yqQv7oj3XSzZC6Vv9l7aNgbHi_pjv-dJjGJds,129
+pg_sui-1.6.14.dev9.dist-info/top_level.txt,sha256=87-oDpfY6sDY_uN-OM2lcnrgPesifhzwqFOajp9ukz0,6
+pg_sui-1.6.14.dev9.dist-info/RECORD,,

{pg_sui-0.2.3.dist-info → pg_sui-1.6.14.dev9.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pg_sui-1.6.14.dev9.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-1.6.14.dev9.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 = '1.6.14.dev9'
+__version_tuple__ = version_tuple = (1, 6, 14, 'dev9')
+
+__commit_id__ = commit_id = None