Merge pull request #214 from AlphaGenes/devel

Devel work from @XingerTang @AprilYUZhang and @RosCraddock and me!

Author: gregorgorjanc

.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

.gitattributes

@@ -0,0 +1 @@
+*.1 linguist-documentation

.github/workflows/publish.yml

@@ -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 AlphaPeel
+              run: pip install dist/alphapeel-1.3.0-py3-none-any.whl
+
+            - name: Install pytest
+              run: |
+                pip install pytest
+                pip install pytest-benchmark
+            
+            - name: Run pytest
+              run: |
+                pytest

.gitignore

@@ -11,3 +11,15 @@ build/
 docs/build/
 example/outputs
 AlphaPeel_env
+tests/functional_tests/**/outputs/
+tests/functional_tests/**/outputs/**
+tests/accuracy_tests/outputs/
+tests/accuracy_tests/outputs/**
+.pytest_cache
+tests/accuracy_tests/accu_report.txt
+.Rproj.user
+**/.RData
+**/.Rhistory
+**/*.Rproj
+**/segfile.txt
+tests/accuracy_tests/sim_for_alphapeel_accu_test/seg_file.txt

.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

@@ -11,6 +11,9 @@ build:
 sphinx:
   configuration: docs/source/conf.py
 
+python:
+  install:
+    - requirements: docs/source/requirements.txt
+
 formats:
-  - pdf
   - epub

Changelog.md

@@ -0,0 +1,71 @@
+
+# Changelog
+
+
+## [1.2.0] - 2025-03-21
+**New features**
+* allow metafounders, defined as “MF_”, in the pedigree file input ({pr}`175`, {user}`RosCraddock`, {user}`XingerTang`)
+
+* added ``alt_allele_prob_file`` to allow user-inputted alternative allele frequencies for each metafounder and loci. For now, these are restricted to be between 0.01 and 0.99 ({pr}`175`, {user}`RosCraddock`, {user}`XingerTang`)
+
+* added ``main_metafounder`` to allow user to assign the default metafounder to use where a metafounder has not been assigned to a founder in the pedigree ({pr}`175`, {user}`RosCraddock`, {user}`XingerTang`)
+
+* added ``update_alt_allele_prob`` to allow the base alternative allele frequencies to be updated after each peeling cycle based on the mean of the founders within the assigned metafounder ({pr}`182`, {user}`RosCraddock`)
+
+**Bug fixes**
+* Fixed bug due to setuptools package being updated for all wheel file naming to follow binary distribution specification (i.e all lower case) and updated documentation ({pr}`182`, {user}`RosCraddock`)
+
+**Maintenance**
+* User-warnings and documentation updates for metafounder implementation and estimation of alternative allele frequency ({pr} `152`, {pr}`175`, {pr}`182`, {user}`RosCraddock`, {user}`XingerTang`)
+
+* Functional and accuracy tests for metafounder implementation ({pr}`156`, {pr}`182`, {user}`XingerTang`, {user}`RosCraddock`)
+
+* Updated reference to tinyhouse ({pr}`177`, {user}`XingerTang`)
+
+
+## [1.1.6] - 2024-10-22
+**New features**
+* Addition of map file input for non-hybrid mode ({pr}`154`, {user}`XingerTang`)
+
+**Bug fixes**
+* resolved bug to produce output file with ``-hap`` and ``-geno`` ({pr}`157`, {user}`AprilYUZhang`)
+
+**Maintenance**
+* set default hap and geno threshold as 1/3 when calling genotypes ({pr}`157`, {user}`AprilYUZhang`)
+
+## [1.1.5] - 2023-12-01
+**New features**
+* Addition of output options: ``geno``, and ``hap_threshold`` ({pr}`119`, {user}``AprilYuZhang`)
+
+**Maintenance**
+* Updates in option and file names. These include:
+
+  * ``no_dosages`` to ``no_dosage``
+  * ``calling_threshold`` to ``geno_threshold``
+  * ``call_phase`` to ``hap``
+  * ``haps`` to ``phased_geno_prob``
+  * ``pedigree`` to ``ped_file``
+  * ``genotypes`` to ``geno_file``
+  * and more, for all changes please visit: https://github.com/AlphaGenes/AlphaPeel/issues/113#issue-1935197000 ({pr}`105`, {pr}`115`, {pr}`122`, {user}`XingerTang`, {user}`AprilYuZhang`)
+
+* Updates the documentation and help functions ({pr}`88`, {pr}`119`, {user}`XingerTang`, {user}`AprilYuZhang`).
+
+* Updates to accuracy and functional tests for new argument names ({pr}`126`, {pr}`130`, {pr}`131`, {user}`XingerTang`).
+
+## [1.1.4] - 2023-08-25
+**New features**
+* Implementation of functional and accuracy testing with pytest ({pr}`53`, {user}`XingerTang`)
+
+* Implementation of pre-committ protocol through Black and Flake8 ({pr}`40`, {user}`XingerTang`)
+
+* Implementation of cross-platform tests workflow through github actions ({pr}`59`, {user}`XingerTang`)
+
+* Added instructions for how to contribute to AlphaPeel ({pr}`27`, {pr}`31`, {user}`XingerTang`)
+
+**Bug Fixes**
+* Fixed bug on the loading of submodule ({pr}`22`, {user}`XingerTang`)
+
+**Maintenance**
+* Update theme for the HTML documentation ({pr}`38`, {user}`XingerTang`)
+
+* Modified the URL for installation ({pr}`11`, {user}`XingerTang`)

README.md

@@ -1,5 +1,9 @@
 # AlphaPeel
 
+<a href="https://alphapeel.readthedocs.io/en/latest/index.html">
+  <img src="https://app.readthedocs.org/projects/alphapeel/badge/"/>
+</a>
+
 AlphaPeel is a software package for calling, phasing, and imputing genotype and sequence data in pedigree populations. This program implements single-locus peeling, multi-locus peeling, and hybrid peeling. A complete description of these methods is given in the suggested citation:
 
 Whalen, A, Ros-Freixedes, R, Wilson, DL, Gorjanc, G, Hickey, JM. (2018). Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees. Genetics Selection Evolution; doi: <a href="https://doi.org/10.1186/s12711-018-0438-2">https://doi.org/10.1186/s12711-018-0438-2</a>
@@ -20,38 +24,4 @@ AlphaPeel is fully and freely available for all use under the MIT License.
 
 ## Installation
 
-AlphaPeel is available on [PyPI](https://pypi.org/project/AlphaPeel): 
-
-    pip install AlphaPeel
-
-## Distribution
-
-Wheel distribution and source distribution are both available on [PyPI](https://pypi.org/project/AlphaPeel/#files).
-
-## Build wheels
-
- If you want to build the wheels yourself, we require an installation of Python 3 and you need to fork and clone the repository to your local directory first (see [user guide](https://alphapeel.readthedocs.io/en/latest/contribute.html#fork-the-repository))
-
- Run the following to build the wheel distribution and the source distribution of the package.
-
-First, create the virtual environment:
-
-    python3 -m venv AlphaPeel_env
-
-Next, activate the environment:
-
-    source AlphaPeel_env/bin/activate
-
-Install build:
-
-    python3 -m pip install --upgrade build
-
-Build the distribution:
-
-    python3 -m build
-
-Now, the distributions of AlphaPeel should be available in ``dist/``.
-
-Finally, deactivate the environment:
-
-    deactivate
+See https://alphapeel.readthedocs.io/en/latest/get_started.html#install-software