pg-sui 1.0.2.1__tar.gz → 1.6.8__tar.gz

pg_sui-1.6.8/.dockerignore

@@ -0,0 +1,16 @@
+.git
+__pycache__/
+.venv/
+dist/
+build/
+*.egg-info/
+pgsui/electron/app/dist/
+.venv/
+.vscode/
+.pytest_cache/
+.codex/
+*.pyc
+*.pyo
+*.pyd
+*.egg-info/
+

pg_sui-1.6.8/.gitattributes

@@ -0,0 +1 @@
+*.ipynb linguist-generated

pg_sui-1.6.8/.github/workflows/release.yaml

@@ -0,0 +1,45 @@
+name: publish
+
+on:
+  push:
+    tags: ["v*"] # e.g. v1.6.4
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # REQUIRED for setuptools-scm to see tags
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build deps
+        run: |
+          python -m pip install -U pip
+          pip install build twine
+
+      - name: Build
+        run: |
+          rm -rf dist/
+          python -m build
+
+      - name: Publish to TestPyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        run: |
+          twine upload --non-interactive --skip-existing --repository testpypi dist/*
+
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: |
+          twine upload --non-interactive --skip-existing dist/*

pg_sui-1.6.8/.gitignore

@@ -0,0 +1,142 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+*.egg-info/
+*.egg
+dist/
+*.whl
+build/lib/
+html/
+*.doctree
+doctrees/
+*_build/
+
+# Jupyter Notebook
+.ipynb_checkpoints/
+
+# Pyre type checker
+.pyre/
+
+# mypy
+.mypy_cache/
+dmypy.json
+dmypy.log
+
+# PyTorch
+*.pt
+*.pth
+
+# Pytest
+.cache/
+
+# PyCharm
+.idea/
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+pgsui/docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints/
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+dmypy.json
+dmypy.log
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# Custom
+pgsui_output/
+snpio_output/
+autoencoder_*_output/
+*.zip
+*.html
+DEPRECATED*.py
+.DS_Store
+BOX_concat_goodOnly_N214.nex
+box_scf.cf.tree
+partitioned_all.contree
+partitioned_all.iqtree
+docs/build/_build/doctrees/environment.pickle
+docs/build/_build/doctrees/pgsui.data_processing.doctree
+**/doctrees/
+.buildinfo
+./training_data/
+.training_data.nosync/
+training_data_2
+pgsui_*_output/
+summarize/
+old_tests/
+pgsui_output/
+*14K.vcf_output/
+.venv/
+**/node_modules/
+.codex/
+training_data_2*
+pgsui/electron/app/dist/
+_version.py

pg_sui-1.6.8/.readthedocs.yaml

@@ -0,0 +1,26 @@
+# .readthedocs.yaml
+# ReadTheDocs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html
+
+# Specify the version of the ReadTheDocs configuration file
+version: 2
+
+# Python version to use
+# Set the version of Python and other tools you might need
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.11"
+
+# Sphinx documentation options
+sphinx:
+  configuration: docs/build/conf.py
+  builder: html
+  fail_on_warning: false
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

pg_sui-1.6.8/.vscode/launch.json

@@ -0,0 +1,29 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: pg_sui.py",
+            "type": "python",
+            "python": "${command:python.interpreterPath}",
+            "request": "launch",
+            "program": "${workspaceFolder}/pgsui/pg_sui.py",
+            "justMyCode": true,
+            "console": "integratedTerminal",
+            "args": [
+                "-p",
+                "pgsui/example_data/phylip_files/test_n100.phy",
+                "-m",
+                "pgsui/example_data/popmaps/test.popmap",
+                "-t",
+                "pgsui/example_data/trees/test.tre",
+                "-i",
+                "pgsui/example_data/trees/test.iqtree",
+                "--site_rate",
+                "pgsui/example_data/trees/test_n100.rate"
+            ]
+        }
+    ]
+}

pg_sui-1.6.8/.vscode/settings.json

@@ -0,0 +1,16 @@
+{
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.black-formatter"
+    },
+    "python.formatting.provider": "none",
+    "editor.formatOnPaste": true,
+    "editor.formatOnSave": true,
+    "git.ignoreLimitWarning": true,
+    "python-envs.defaultEnvManager": "ms-python.python:venv",
+    "python-envs.defaultPackageManager": "ms-python.python:pip",
+    "python-envs.pythonProjects": [],
+    "yaml.schemas": {
+        "https://raw.githubusercontent.com/weaveworks/eksctl/main/pkg/apis/eksctl.io/v1alpha5/assets/schema.json": "*.eksctl.yaml",
+        "https://raw.githubusercontent.com/conda-forge/conda-smithy/main/conda_smithy/data/conda-forge.json": "file:///Users/btm002/Documents/Work/SHU/Research/Ongoing/Repositories/PG-SUI/conda/recipe/meta.yaml"
+    }
+}

pg_sui-1.6.8/Dockerfile

@@ -0,0 +1,38 @@
+# syntax=docker/dockerfile:1.7
+FROM python:3.12-slim
+
+# ---- Env ----
+ENV TZ=Etc/UTC \
+    LC_ALL=C.UTF-8 \
+    LANG=C.UTF-8 \
+    PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1 \
+    PIP_DISABLE_PIP_VERSION_CHECK=1
+
+# ---- OS deps for Nextflow shells and basic tooling ----
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        python3-pip python3-venv python-is-python3 bash coreutils findutils grep sed gawk curl \
+        ca-certificates tini \
+        && rm -rf /var/lib/apt/lists/*
+
+# ---- Non-root user and writable workspace ----
+RUN useradd -r -u 10001 -m appuser
+WORKDIR /workspace
+RUN chown -R appuser:appuser /workspace
+VOLUME ["/workspace"]
+
+# ---- Pin versions via build args ----
+ARG PGSUI_VERSION=1.6.4
+
+# ---- Security ----
+USER appuser
+
+SHELL ["/bin/bash", "-c"]
+
+RUN python -m venv /home/appuser/venv \
+    && source /home/appuser/venv/bin/activate \
+    && python -m pip install --upgrade pip setuptools wheel \
+    && python -m pip install pg-sui \
+    && pg-sui --version
+
+CMD []

pg_sui-1.6.8/MANIFEST.in

@@ -0,0 +1,25 @@
+include pgsui/example_data/structure_files/test.pops.2row.allsites.str
+include pgsui/example_data/phylip_files/test.phy
+include pgsui/example_data/popmaps/phylogen_nomx.popmap
+include pgsui/example_data/vcf_files/phylogen_subset14K.vcf.gz
+include pgsui/example_data/vcf_files/phylogen_subset14K.vcf.gz.tbi
+include README.md LICENSE
+exclude pgsui/electron/app/dist/*
+exclude pgsui/electron/app/node_modules/*
+exclude pgsui/figures/*
+exclude pgsui/training_data/*
+exclude pgsui/example_data/phylip_files/test_*.phy
+exclude pgsui/example_data/popmaps/test.popmap*
+exclude pgsui/example_data/vcf_files/*.vcf_sorted.vcf*
+exclude pgsui/example_data/trees/*
+exclude pgsui/example_data/structure_files/*.1row.*.str
+exclude pgsui/example_data/structure_files/*.2row.10sites.str
+exclude pgsui/example_data/structure_files/*.2row.100sites.str
+exclude pgsui/example_data/structure_files/*.2row.30sites.str
+exclude pgsui/example_data/structure_files/test.nopops*.str
+exclude pgsui/example_data/vcf_files/test.vcf
+exclude pgsui/example_data/vcf_files/test.vcf.gz*
+
+global-exclude *.pyc __pycache__ .DS_Store
+prune pgsui/electron/app/node_modules
+prune pgsui/electron/app/dist

{pg-sui-1.0.2.1/pg_sui.egg-info → pg_sui-1.6.8}/PKG-INFO

@@ -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: intel
 Requires-Dist: scikit-learn-intelex; extra == "intel"
 Provides-Extra: docs
-Requires-Dist: sphinx<7; 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-1.0.2.1 → pg_sui-1.6.8}/README.md

@@ -68,51 +68,20 @@ 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