Merge branch 'release/v4.0.0'

.github/workflows/func_tests.yml

@@ -26,6 +26,7 @@ jobs:
           pip install pylint
           pip install anybadge
           pip install coverage
+          sudo apt-get install bcftools samtools tabix
           python -m pip install .
       - name: Running ssshtest
         run: |

.readthedocs.yaml

@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/api/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt

README.md

@@ -1,50 +1,45 @@
-```
-████████╗██████╗ ██╗   ██╗██╗   ██╗ █████╗ ██████╗ ██╗
-╚══██╔══╝██╔══██╗██║   ██║██║   ██║██╔══██╗██╔══██╗██║
-   ██║   ██████╔╝██║   ██║██║   ██║███████║██████╔╝██║
-   ██║   ██╔══██╗██║   ██║╚██╗ ██╔╝██╔══██║██╔══██╗██║
-   ██║   ██║  ██║╚██████╔╝ ╚████╔╝ ██║  ██║██║  ██║██║
-   ╚═╝   ╚═╝  ╚═╝ ╚═════╝   ╚═══╝  ╚═╝  ╚═╝╚═╝  ╚═╝╚═╝
-```
 [![PyPI version](https://badge.fury.io/py/Truvari.svg)](https://badge.fury.io/py/Truvari)
 [![pylint](imgs/pylint.svg)](https://github.com/acenglish/truvari/actions/workflows/pylint.yml)
 [![FuncTests](https://github.com/acenglish/truvari/actions/workflows/func_tests.yml/badge.svg?branch=develop&event=push)](https://github.com/acenglish/truvari/actions/workflows/func_tests.yml)
 [![coverage](imgs/coverage.svg)](https://github.com/acenglish/truvari/actions/workflows/func_tests.yml)
 [![develop](https://img.shields.io/github/commits-since/acenglish/truvari/v3.5.0)](https://github.com/ACEnglish/truvari/compare/v3.5.0...develop)
 [![Downloads](https://pepy.tech/badge/truvari)](https://pepy.tech/project/truvari)
 
+![Logo](https://raw.githubusercontent.com/ACEnglish/truvari/develop/imgs/BoxScale1_DarkBG.png)  
 Toolkit for benchmarking, merging, and annotating Structrual Variants
 
-[WIKI page](https://github.com/acenglish/truvari/wiki) has detailed documentation.  
-See [Updates](https://github.com/acenglish/truvari/wiki/Updates) on new versions.  
-Read our [Paper](https://doi.org/10.1101/2022.02.21.481353) for more details.
+📚 [WIKI page](https://github.com/acenglish/truvari/wiki) has detailed documentation.  
+📈 See [Updates](https://github.com/acenglish/truvari/wiki/Updates) on new versions.  
+📝 Read our [Paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02840-6) to learn more.
 
-## Installation
+## 💻 Installation
 Truvari uses Python 3.6+ and can be installed with pip:
 ```
   python3 -m pip install Truvari 
 ```
 For details and more installation options, see [Installation](https://github.com/acenglish/truvari/wiki/Installation) on the wiki.
 
-## Quick Start
+## ⏩ Quick Start
 
 Each sub-command contains help documentation. Start with `truvari -h` to see available commands.
 
 The current most common Truvari use case is for structural variation benchmarking:
 ```
   truvari bench -b base.vcf.gz -c comp.vcf.gz -o output_dir/
 ```
-## Truvari Commands
+## 🧬 Truvari Commands
 
  - [bench](https://github.com/acenglish/truvari/wiki/bench) - Performance metrics from comparison of two VCFs
  - [collapse](https://github.com/acenglish/truvari/wiki/collapse) - Collapse possibly redundant VCF entries
  - [anno](https://github.com/acenglish/truvari/wiki/anno) - Add SV annotations to a VCF
- - [vcf2df](https://github.com/acenglish/truvari/wiki/vcf2df) - Turn a VCF into a pandas DataFrame
  - [consistency](https://github.com/acenglish/truvari/wiki/consistency) - Consistency report between multiple VCFs
- - [divide](https://github.com/ACEnglish/truvari/wiki/divide) - Divide a VCF into independent parts
+ - [vcf2df](https://github.com/acenglish/truvari/wiki/vcf2df) - Turn a VCF into a pandas DataFrame
  - [segment](https://github.com/acenglish/truvari/wiki/segment) - Normalization of SVs into disjointed genomic regions
+ - [stratify](https://github.com/acenglish/truvari/wiki/stratify) - Count variants per-region in vcf
+ - [divide](https://github.com/ACEnglish/truvari/wiki/divide) - Divide a VCF into independent shards
  - [phab](https://github.com/ACEnglish/truvari/wiki/phab) - Harmonize variant representations using MSA
+ - [refine](https://github.com/ACEnglish/truvari/wiki/refine) - Automated bench result refinement with phab
 
-## More Information
+## 🔎 More Information
 
-Find more details and discussions about Truvari on the [WIKI page](https://github.com/acenglish/truvari/wiki).
+All documentation about Truvari is on the [WIKI](https://github.com/acenglish/truvari/wiki). Additional information about using Truvari can be found in [Discussions](https://github.com/ACEnglish/truvari/discussions)

Singularity.def

@@ -6,20 +6,32 @@ Stage: spython-base
 . /opt/truvari-source
 %post
 
-apt-get -qq update && apt-get install -yq \
-python3-pip \
-python3-dev \
-curl \
-&& \
-rm -rf /var/lib/apt/lists/*
+
+apt-get -qq update \
+  && DEBIAN_FRONTEND=noninteractive apt-get install -yq \
+  bcftools \
+  curl \
+  python3-dev \
+  python3-pip \
+  samtools \
+  tabix \
+  vcftools \
+  wget \
+  && \
+  rm -rf /var/lib/apt/lists/*
 
 cd /opt/truvari-source
 
+wget https://mafft.cbrc.jp/alignment/software/mafft_7.505-1_amd64.deb \
+    && dpkg -i mafft_7.505-1_amd64.deb && rm mafft_7.505-1_amd64.deb
+
 python3 -m pip install --upgrade pip && \
-python3 -m pip install setproctitle pylint anybadge coverage && \
-python3 -m pip install --upgrade setuptools && \
-python3 -m pip install ./
+    python3 -m pip install setproctitle pylint anybadge coverage && \
+    python3 -m pip install --upgrade setuptools && \
+    python3 -m pip install ./
+
 
+mkdir /data
 cd /data
 
 %runscript

docs/api/conf.py

@@ -9,12 +9,15 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../'))
 
 
 # -- Project information -----------------------------------------------------
 
 project = 'Truvari'
-copyright = '2021, Adam English'
+copyright = '2023, Adam English'
 author = 'Adam English'
 
 

docs/api/index.rst

@@ -8,10 +8,10 @@ Welcome to Truvari's documentation!
 
 This documentation is aimed at developers looking to reuse truvari's code.
 
-For those looking to use truavari as a tool for analysis, full documentation 
-is available via the github page
+For those looking to use truvari for analysis, full documentation 
+is available via the github wiki
 
-https://github.com/ACEnglish/truvari
+https://github.com/ACEnglish/truvari/wiki
 
 .. toctree::
    :maxdepth: 2

docs/api/local_build.sh

@@ -1,7 +1,6 @@
-#sphinx-apidoc -f -F ../../truvari/ -o /data/docs/api/ --ext-autodoc -M 
-# requires pip install  sphinx & sphinx_rtd_theme 
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-# will overwrite your python
+python3 -m pip install sphinx sphinx_rtd_theme
+# will overwrite your current environment's truvari
 cd ../../
 python3 setup.py install
 cd -