Merge pull request #1 from delocalizer/20210913_crl_packaging

* modernize packaging & create stub for tests

Author: delocalizer

.gitignore

@@ -0,0 +1,4 @@
+.tox
+*.egg-info
+**/__pycache__
+**/*.pyc

MANIFEST.in

@@ -1,2 +1 @@
-#include README.rst
-#include docs/*.txt
+include VERSION

README.md

@@ -1,36 +1,42 @@
 # Somatic base substitution caller for LRS
 
-Python tool that calls somatic base substitutions from matched tumour normal whole genome pileups.
+Python tool that calls somatic base substitutions from matched tumour-normal whole genome pileups.
 
-## Getting Started
-
-Pip install
+#### Required
 
-### Prerequisites
+Python 3.6+
 
-samtools/1.10
-htslib/1.10.2
-tabix/0.2.6
+## Install
 
-Pileups from samtools
-bgzip pileup_name
-tabix -b 2 -e 2 pileup_name.gz
+Install into a virtualenv is recommended, _e.g._:
 
-#### Required
+    python3 -m venv SBSC
+    source SBSC/bin/activate
+    tempdir=$(mktemp -d)
+    git clone https://github.com/shimbalama/SBSC $tempdir
+    cd $tempdir
+    pip3 install -r requirements.txt .
 
-Python 3
-
-#### Optional
+### Prerequisites
 
-NA
+Tabix-indexed pileups from samtools
 
-### Installing
+    bgzip pileup_name
+    tabix -b 2 -e 2 pileup_name.gz
 
-pip install SBSC
+When the tool runs `.tbi` index files are presumed to exist adjacent to input pileup files.
 
 ## Running the program
 
-SBSC.py -h
+    # help
+    SBSCall.py --help
+
+    # basic example
+    SBSCall.py \
+        -r /path/to/reference \
+        -o /path/to/output \
+        -c /path/to/cancer_pileup.gz \
+        -n /path/to/normal_pileup.gz 
 
 ## Authors
 
@@ -42,4 +48,4 @@ This project is licensed under the MIT License. See LICENSE
 
 ## Acknowledgments
 
-QMIR medical genomics team
+QIMR Berghofer medical genomics team

SBSC/output/__init__.py

@@ -0,0 +1 @@
+0.0.12

VERSION

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+[build-system]
+requires = [
+    "pip",
+    "setuptools>=42",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"

pyproject.toml

@@ -0,0 +1,4 @@
+biopython==1.79
+pandas==1.3.3
+pysam==0.16.0.1
+scipy==1.7.1

requirements.txt

@@ -0,0 +1,20 @@
+[metadata]
+name = SBSC
+version = file: VERSION 
+description = A simple somatic SNV and MNV caller
+long_description = file: README.md, LICENSE
+author = Liam McIntyre
+author_email = shimbalama@gmail.com
+license = MIT License
+classifiers:
+    Programming Language :: Python :: 3.6
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+
+[options]
+include_package_data = True
+packages = find:
+python_requires = >=3.6
+scripts =
+    bin/SBSCall.py
+zip_safe = False

setup.cfg

@@ -0,0 +1,16 @@
+from unittest import TestCase
+import shlex
+import subprocess
+
+
+class TestMain(TestCase):                                                       
+    """                                                                         
+    Integration tests                                                           
+    """                                                                         
+    def test_help(self):                                                      
+        """
+        Test that the script can be called by the documented name
+        """
+        result = subprocess.run(shlex.split('python3 bin/SBSCall.py --help'),
+                                capture_output=True, text=True)
+        self.assertTrue(result.stdout.startswith('usage: SBSCall.py'))

setup.py

@@ -0,0 +1,7 @@
+[tox]
+envlist = py39
+isolated_build = True
+
+[testenv]
+commands = python3 -m unittest discover tests
+deps = -rrequirements.txt