Add black flake8 and pylint, update setup.py

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 88
+extend-ignore = E203

.pylintrc

@@ -0,0 +1,3 @@
+[pylint]
+disable=bad-continuation,
+        invalid-name,

requirements-dev.txt

@@ -1,5 +1,3 @@
+ipython>=7.10.0
 mkdocs>=1.0.4
-pybids>=0.8.0
-pytest>=4.3.0
-pytest-cov>=2.6.1
-tox>=3.7.0
+tox>=3.14.0

requirements-test.txt

@@ -0,0 +1,6 @@
+pybids>=0.9.5
+pytest>=5.3.1
+pytest-black>=0.3.7
+pytest-cov>=2.8.1
+pytest-flake8>=1.0.4
+pytest-pylint>=0.14.1

setup.py

@@ -1,50 +1,86 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+# type: ignore
 
+"""Setup file for the dcm2bids package"""
 
 import glob
 import os
 from setuptools import setup
 
 
-#Get __version__ from dcm2bids.version
-exec(open(os.path.join("dcm2bids", "version.py")).read())
+def load_version():
+    """Execute dcm2bids.version in a global dictionary"""
+    global_dict = {}
+    with open(os.path.join("dcm2bids", "version.py")) as _:
+        exec(_.read(), global_dict)
+    return global_dict
 
 
-description = """Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure"""
-
-
-try:
-    with open('README.md', encoding='utf-8') as f:
-        long_description = f.read()
-except:
-    #python2 compatibility
-    from io import open
-    with open('README.md', encoding='utf-8') as f:
-        long_description = f.read()
+def install_requires():
+    """Get list of required modules"""
+    required = []
+    for module, meta in _VERSION["REQUIRED_MODULE_METADATA"]:
+        required.append(f"{module}>={meta['min_version']}")
+    return required
 
 
+_VERSION = load_version()
 DISTNAME = "dcm2bids"
-DESCRIPTION = description
-VERSION = __version__
+VERSION = _VERSION["__version__"]
 AUTHOR = "Christophe Bedetti"
 AUTHOR_EMAIL = "christophe.bedetti@umontreal.ca"
-URL = "https://github.com/cbedetti/Dcm2Bids"
-DOWNLOAD_URL = URL + "/archive/" + VERSION + ".tar.gz"
+DESCRIPTION = (
+    "Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure"
+)
+with open("README.md", encoding="utf-8") as _:
+    LONG_DESCRIPTION = _.read()
+LICENSE = "GPLv3+"
+PROJECT_URLS = {
+    "Documentation": "https://cbedetti.github.io/Dcm2Bids",
+    "Source Code": "https://github.com/cbedetti/Dcm2Bids",
+}
+CLASSIFIERS = [
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Science/Research",
+    # 'Operating System :: MacOS',
+    # 'Operating System :: Microsoft :: Windows',
+    # 'Operating System :: POSIX',
+    # 'Operating System :: Unix',
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.5",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
 
 
 if __name__ == "__main__":
     setup(
-            name=DISTNAME,
-            version=VERSION,
-            description=description,
-            long_description=long_description,
-            long_description_content_type='text/markdown',
-            author=AUTHOR,
-            author_email=AUTHOR_EMAIL,
-            url=URL,
-            download_url=DOWNLOAD_URL,
-            packages=['dcm2bids'],
-            scripts=glob.glob('scripts/dcm2bids*'),
-            install_requires=['future'],
-            )
+        name=DISTNAME,
+        version=VERSION,
+        packages=[DISTNAME],
+        scripts=glob.glob("scripts/dcm2bids*"),
+        entry_points={
+            "console_scripts": [
+                "dcm2bids = dcm2bids.dcm2bids:main",
+                "dcm2bids_helper = dcm2bids.helper:main",
+                "dcm2bids_scaffold = dcm2bids.scaffold:main",
+            ],
+            # "configurations": [],
+        },
+        python_requires=">=3.5",
+        install_requires=install_requires(),
+        package_data={"": ["README.md", "LICENSE.txt"]},
+        author=AUTHOR,
+        author_email=AUTHOR_EMAIL,
+        description=DESCRIPTION,
+        long_description=LONG_DESCRIPTION,
+        long_description_content_type="text/markdown",
+        # keywords="",
+        license=LICENSE,
+        project_urls=PROJECT_URLS,
+        classifiers=CLASSIFIERS,
+    )

tox.ini

@@ -4,13 +4,23 @@
 # and then run "tox" from this directory.
 
 [tox]
-envlist = py27, py35, py36, py37
+envlist = clean, py35, py36, py37, report
 
 [testenv]
-deps =
-    pybids
-    pytest-cov
-    pytest
-    backports.tempfile
+deps = -rrequirements-test.txt
+commands = pytest --cov --cov-append --black --flake8 --pylint
+depends =
+    {py35, py36, py37}: clean
+    report: py35, py36, py37
+
+[testenv:report]
+deps = coverage
+skip_install = true
 commands =
-    pytest --cov=dcm2bids --cov-report html
+    coverage html
+    coverage report
+
+[testenv:clean]
+deps = coverage
+skip_install = true
+commands = coverage erase