Update Python package setup (#3111)

* Cleanup setup.py and make Python 3 compatible

* Remove write_version_py()

* Add setup.cfg

* Add metadata to setup.cfg and code cleanup

setup.cfg

@@ -0,0 +1,44 @@
+[metadata]
+author = bcbio community
+author_email = [email protected]
+classifiers =
+    Environment :: Console
+    Intended Audience :: Education
+    Intended Audience :: Healthcare Industry
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: MIT License
+    Natural Language :: English
+    Operating System :: POSIX :: Linux
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Topic :: Scientific/Engineering :: Bio-Informatics
+description = Best-practice pipelines for fully automated high throughput sequencing analysis
+keywords = ChIP-seq, DNA, genomics, pipeline, RNA, RNA-seq, sequencing, SNP, variant calling
+license = MIT
+license_file = LICENSE.txt
+long_description = file: README.rst
+long_description_content_type = text/x-rst
+name = bcbio-nextgen
+project_urls =
+    Documentation = https://bcbio-nextgen.readthedocs.io/
+    Source = https://github.com/bcbio/bcbio-nextgen
+    Tracker = https://github.com/bcbio/bcbio-nextgen/issues
+url = https://github.com/bcbio/bcbio-nextgen
+
+[options]
+include_package_data = True
+packages = find:
+python_requires = >=3.6
+scripts =
+    scripts/bcbio_nextgen.py
+    scripts/bcbio_setup_genome.py
+    scripts/bcbio_prepare_samples.py
+    scripts/bcbio_fastq_umi_prep.py
+    scripts/cwltool2wdl.py
+zip_safe = False
+
+[options.packages.find]
+include = bcbio, bcbio.*

setup.py

@@ -1,41 +1,28 @@
 #!/usr/bin/env python
-"""Setup file and install script for NextGen sequencing analysis scripts.
-"""
+
+"""Setup file and install script for NextGen sequencing analysis scripts"""
+
 import os
-from setuptools import setup, find_packages
+import subprocess
+
+import setuptools
 
-version = "1.2.0"
+VERSION = '1.2.0'
 
-def write_version_py():
-    version_py = os.path.join(os.path.dirname(__file__), 'bcbio', 'pipeline',
-                              'version.py')
-    try:
-        import subprocess
-        p = subprocess.Popen(["git", "rev-parse", "--short", "HEAD"],
-                             stdout=subprocess.PIPE)
-        githash = p.stdout.read().strip()
-    except:
-        githash = ""
-    with open(version_py, "w") as out_handle:
-        out_handle.write("\n".join(['__version__ = "%s"' % version,
-                                    '__git_revision__ = "%s"' % githash]))
+# add bcbio version number and git commit hash of the current revision to version.py
+try:
+    git_run = subprocess.run(['git', 'rev-parse', '--short', 'HEAD'], stdout=subprocess.PIPE)
+    git_run.check_returncode()
+except subprocess.SubprocessError:
+    commit_hash = ''
+else:
+    commit_hash = git_run.stdout.strip().decode()
 
-install_requires = [] # install dependencies via conda
-zip_safe = False
-scripts = ['scripts/bcbio_nextgen.py', 'scripts/bcbio_setup_genome.py', 'scripts/bcbio_prepare_samples.py',
-           'scripts/bcbio_fastq_umi_prep.py', 'scripts/cwltool2wdl.py']
+here = os.path.dirname(os.path.abspath(__file__))
+with open(os.path.join(here, 'bcbio', 'pipeline', 'version.py'), 'w') as version_file:
+    version_file.writelines([f'__version__ = "{VERSION}"\n',
+                             f'__git_revision__ = "{commit_hash}"\n'])
 
-write_version_py()
-setup(name="bcbio-nextgen",
-      version=version,
-      author="bcbio community",
-      author_email="[email protected]",
-      description="Best-practice pipelines for fully automated high throughput sequencing analysis",
-      long_description=(open('README.rst').read()),
-      license="MIT",
-      url="https://github.com/bcbio/bcbio-nextgen",
-      packages=find_packages(exclude=["tests"]),
-      zip_safe=zip_safe,
-      scripts=scripts,
-      install_requires=install_requires,
-      include_package_data=True)
+# dependencies are installed via Conda from
+# https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml
+setuptools.setup(version=VERSION)