[pull] main from AlphaGenes:main

.flake8

@@ -0,0 +1,8 @@
+[flake8]
+# Black by its default setting the maximum length to 88
+max-line-length = 88
+extend-ignore = 
+    # also the Black's default, whitespace before ':'
+    E203,
+    # this is for the line length, all the lines too long are comments now
+    E501

.github/workflows/publish.yml

@@ -11,7 +11,7 @@ jobs:
         environment: release
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
             - name: Set up Python
               uses: actions/setup-python@v4
               with:
@@ -31,14 +31,14 @@ jobs:
             - name: Build SDist and wheel
               run: python3 -m build
 
-            - uses: actions/upload-artifact@v3
+            - uses: actions/upload-artifact@v4
               with:
                 path: dist/*
 
             - name: Check metadata
               run: pipx run twine check dist/*
 
-            - uses: actions/download-artifact@v3
+            - uses: actions/download-artifact@v4
               with:
                 name: artifact
                 path: dist

.github/workflows/tests.yml

@@ -0,0 +1,48 @@
+name: Evaluate code syntax and correctness
+on: [push, pull_request]
+
+jobs:
+    pre-commit_and_pytest:
+        name: Run pre-commit and pytest
+        strategy:
+          matrix:
+            os: [ubuntu-latest, Windows-latest, macos-latest]
+        runs-on: ${{ matrix.os }}
+        permissions:
+            contents: read
+
+        steps:
+            - uses: actions/checkout@v3
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                python-version: "3.11.x"
+
+            - uses: pre-commit/action@v3.0.0
+              name: Run pre-commit
+
+            - name: Install pypa/build
+              run: >-
+                python3 -m
+                pip install
+                --upgrade 
+                build
+
+            - name: Initialize submodules
+              run: |
+                  git submodule update --init
+
+            - name: Build SDist and wheel
+              run: python3 -m build
+
+            - name: Install AlphaImpute2
+              run: pip install dist/alphaimpute2-0.0.2-py3-none-any.whl
+
+            - name: Install pytest
+              run: |
+                pip install pytest
+                pip install pytest-benchmark
+
+            - name: Run pytest
+              run: |
+                pytest

.gitignore

@@ -6,3 +6,7 @@ __pycache__/
 *.py[cod]
 *.DS_Store
 *.egg-info/
+build/
+example/outputs
+.env
+tests/functional_tests/outputs

.pre-commit-config.yaml

@@ -0,0 +1,9 @@
+repos:
+-   repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+    -   id: flake8

.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+  jobs:
+    post_create_environment:
+      - pip install sphinx-rtd-theme
+
+sphinx:
+  configuration: docs/source/conf.py
+
+formats:
+  - pdf
+  - epub

README.md

@@ -3,6 +3,17 @@ AlphaImpute2
 
 AlphaImpute2 is a phasing and imputation algorithm for massive livestock populations. The method uses a approximate version of multi-locus iterative peeling for pedigree based imputation, and a novel imputation algorithm that uses the Positional Burrows Wheeler Transform for population imputation. AlphaImpute2 has been successfully used to perform imputation in populations of hundreds of thousands of individuals. AlphaImpute2 was developed by Andrew Whalen, and is currently being supported by Andrew Whalen and Steve Thorn.
 
+User guide
+============
+
+See [https://alphapeel.readthedocs.io/en/latest](https://alphaimpute2.readthedocs.io/en/latest/)
+
+Installation
+============
+
+AlphaImpute2 is available on [PyPI](https://pypi.org/project/AlphaImpute2/): 
+
+    pip install AlphaImpute2
 
 Availability
 ============

conftest.py

@@ -0,0 +1,12 @@
+import os
+import shutil
+
+
+def pytest_configure(config):
+    """
+    Prepare path and report file for functional tests
+    """
+    func_output_path = os.path.join("tests", "functional_tests", "outputs")
+    if os.path.exists(func_output_path):
+        shutil.rmtree(func_output_path)
+    os.mkdir(func_output_path)

docs/source/conf.py

@@ -1,8 +1,10 @@
+# -*- coding: utf-8 -*-
+#
 # Configuration file for the Sphinx documentation builder.
 #
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
 
 # -- Path setup --------------------------------------------------------------
 
@@ -17,56 +19,168 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'AlphaImpute2'
-copyright = '2020, Andrew Whalen'
-author = 'Andrew Whalen'
+project = "AlphaImpute2"
+copyright = "2020, Andrew Whalen"
+author = "Andrew Whalen"
+
+# The short X.Y version
+version = ""
+# The full version, including alpha/beta/rc tags
+release = ""
 
 
 # -- General configuration ---------------------------------------------------
 
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = ".rst"
+
+# The master toctree document.
+master_doc = "index"
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "python"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = None
+
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = []
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "AlphaImpute2doc"
+
+
+# -- Options for LaTeX output ------------------------------------------------
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
-    'extraclassoptions': 'openany,oneside'
-
+    "extraclassoptions": "openany,oneside"
 }
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (
+        master_doc,
+        "AlphaImpute2.tex",
+        "AlphaImpute2 Documentation",
+        "Andrew Whalen",
+        "manual",
+    ),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, "alphaimpute2", "AlphaImpute2 Documentation", [author], 1)]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        "AlphaPeel",
+        "AlphaPeel Documentation",
+        author,
+        "AlphaPeel",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ["search.html"]
+
+
+# -- Extension configuration -------------------------------------------------