Streamlined setup.py,

put most options into setup.cfg

setup.cfg

@@ -23,7 +23,83 @@
 #    See the License for the specific language governing permissions and
 #    limitations under the License.
 
-# TODO: Check if everything is taylored to pyramid!
+
+# CONFIGURATION FOR SETUP.PY:
+
+[metadata]
+name = pyramid
+version = 0.1.0.dev0
+author = Jan Caron
+author-email = j.caron@fz-juelich.de
+description = PYthon based Reconstruction Algorithm for MagnetIc Distributions
+long-description = file: README.md
+url = https://jugit.fz-juelich.de/j.caron/pyramid
+license = GPLv3
+classifiers =
+    Development Status :: 3 - alpha
+    Intended Audience :: Developers
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+    Programming Language :: Python :: 3.7
+    Topic :: Scientific/Engineering
+    Operating System :: OS Independen
+
+[options]
+zip_safe = False
+include_package_data = True
+packages = find:
+python_requires = >=3.7
+# TODO: Check (Comment out everything and test what's really needed)!
+setup_requires =
+    setuptools
+    numpy>=1.6
+    pytest
+    pytest-runner
+# TODO: Check!
+tests_require =
+    coverage
+    pytest
+    pytest-cov
+    pytest-flake8
+    pytest-runner
+# TODO: Check!
+install_requires =
+    numpy>=1.6
+    tqdm
+    scipy
+    matplotlib
+    Pillow
+    h5py
+    hyperspy
+    cmocean
+ #   jutil  # TODO: How to handle this??? Ask Jörn!
+
+[options.extras_require]
+# TODO: necessary? Does it work with pip/conda?
+3Dplot =
+    qt==4.8
+    mayavi==4.5
+# TODO: Pillow and such?
+io =
+    hyperspy
+fftw =
+    pyfftw
+# TODO: Notebooks and stuff
+# demos =
+# TODO: Add? How?
+# snippets =
+# TODO: make this optional? Or silent fallback to matplotlib? stylesheet?
+colors =
+    cmocean
+# TODO: Don't use too many!
+# TODO: What about jupyter notebooks?
+# TODO: Check all submodules if anything should be optional or is missing?
+# TODO: in general, make CI test THESE requirements (maybe in addition to the environment.yml)
+# TODO: more for mayavi (plotting in general) and hyperspy, etc (see below)...
+# TODO: what about demos? see Hyperspy?
+
+
+# CONFIGURATION FOR TESTING:
 
 [aliases]
 test=pytest
@@ -34,12 +110,16 @@ source = pyramid
 omit =
     tests/*
 
-[tool:pytest]
-addopts = --cov --flake8
+[tool:pytest]  # TODO: Check if everything is taylored to pyramid!
+#addopts = --cov --flake8
 flake8-max-line-length = 100
 flake8-ignore =
-    ALL  # TODO: PEP8 deactivated by this line (remove at a later point)!
-    E402 E124 E125
-    pyramid/__init__.py F401
-    doc/conf.py ALL
-    scripts/*.py ALL
+    #ALL  # TODO: PEP8 deactivated by this line (remove at a later point)!
+    E402  # module import not at top of file
+    E124  # closing bracket does not match visual indentation
+    E125  # continuation line with same indent as next logical line
+    E226  # missing whitespace around arithmetic operator
+    W503  # line break before binary operator
+    E741  # do not use variables named ‘l’, ‘O’, or ‘I’
+    pyramid/__init__.py F401  # module imported but unused
+    #doc/conf.py ALL

setup.py

@@ -3,172 +3,52 @@
 """Setup for testing, building, distributing and installing the 'Pyramid'-package"""
 
 import os
-import re
 import subprocess
-import sys
 import itertools
-#from distutils.command.build import build
+from setuptools import setup
+from setuptools.config import read_configuration
 
-#import numpy
-from setuptools import setup, find_packages
 
-
-DISTNAME = 'pyramid'
-DESCRIPTION = 'PYthon based Reconstruction Algorithm for MagnetIc Distributions'
-MAINTAINER = 'Jan Caron'
-MAINTAINER_EMAIL = 'j.caron@fz-juelich.de'
-URL = ''
-VERSION = '0.1.0.dev0'  # TODO: Better way?
-PYTHON_VERSION = (2, 7)  # TODO: get rid of!!!
-DEPENDENCIES = {'numpy': (1, 10)}  # TODO: get rid of!!!
-LONG_DESCRIPTION = 'long description (TODO!)'  # TODO: Long description! put in (Readme?) file!
-
-
-# TODO: get rid of superfluous functions!
-def get_package_version(package):
-    """Return the package version of the specified package.
-
-    Parameters
-    ----------
-    package: basestring
-        Name of the package whic should be checked.
-
-    Returns
-    -------
-    version: tuple (N=3)
-        Version number as a tuple.
-
-    """
-    version = []
-    for version_attr in ('version', 'VERSION', '__version__'):
-        if (hasattr(package, version_attr) and
-                isinstance(getattr(package, version_attr), str)):
-            version_info = getattr(package, version_attr, '')
-            for part in re.split('\D+', version_info):
-                try:
-                    version.append(int(part))
-                except ValueError:
-                    pass
-    return tuple(version)
-
-
-def check_requirements():
-    """Checks the requirements of the Pyramid package."""
-    if sys.version_info < PYTHON_VERSION:
-        raise SystemExit('You need Python version %d.%d or later.'
-                         % PYTHON_VERSION)
-    for package_name, min_version in DEPENDENCIES.items():
-        dep_error = False
-        try:
-            package = __import__(package_name)
-        except ImportError:
-            dep_error = True
-        else:
-            package_version = get_package_version(package)
-            if min_version > package_version:
-                dep_error = True
-        if dep_error:
-            raise ImportError('You need `%s` version %d.%d or later.'
-                              % ((package_name,) + min_version))
-
-
-def hg_version():  # TODO: Replace with GIT! Also check build output on GitLab! See numpy setup.py!
-    """Get the Mercurial reference identifier.
-
-    Returns
-    -------
-    hg_ref: basestring
-        The Mercurial reference identifier.
-
-    """
+def git_version():
+    '''Get current git revision.'''
     try:
-        hg_rev = subprocess.check_output(['hg', 'id', '--id']).strip()
-    except:
-        hg_rev = "???"
-    return hg_rev
+        git_rev = subprocess.check_output(['git', 'rev-parse', 'HEAD']).strip().decode()
+    except Exception:
+        git_rev = "???"
+    return git_rev
 
 
-def write_version_py(filename='pyramid/version.py'):
-    """Write the version.py file.
-
-    Parameters
-    ----------
-    filename: basestring, optional
-        Write the version and hg_revision into the specified python file.
-        Defaults to 'pyramid/version.py'.
-
-    """
+def write_version_py(version, git_version, filename='pyramid/version.py'):
+    '''Write version.py file.'''
     version_string = '# -*- coding: utf-8 -*-\n' + \
-                     '""""This file is generated automatically by the Pyramid `setup.py`"""\n' + \
-                     'version = "{}"\n'.format(VERSION) + \
-                     'hg_revision = "{}"\n'.format(hg_version())
+                     '""""This file was automatically generated by `setup.py`"""\n' + \
+                     f'version = "{version}"\n' + \
+                     f'git_revision = "{git_version}"\n'
     with open(os.path.join(os.path.dirname(__file__), filename), 'w') as vfile:
         vfile.write(version_string)
 
 
-def get_files(rootdir):
-    """Returns a list of .py-files inside rootdir.
-
-    Parameters
-    ----------
-    rootdir: basestring
-        Root directory in which to search for ``.py``-files.
-
-    Returns
-    -------
-    filepaths: list
-        List of filepaths which were found.
+# Read setup.cfg (setup() would auto-read it, but we want to read the version and modify it here):
+conf_dict = read_configuration('setup.cfg')
+metadata_dict = conf_dict['metadata']
+options_dict = conf_dict['options']
 
-    """
-    filepaths = []
-    for root, dirs, files in os.walk(rootdir):
-        for filename in files:
-            if filename.endswith('.py'):
-                filepaths.append(os.path.join(root, filename))
-    return filepaths
+# Read version and write to version.py:
+version = metadata_dict['version']
+write_version_py(version, git_version())
 
+# Add 'full' convenience option to extras_require for full install: python setup.py install .[full]
+full_list = list(itertools.chain(*list(options_dict['extras_require'].values())))
+options_dict['extras_require']['full'] = full_list
 
-# TODO: Outsource stuff to setup.cfg? See https://github.com/pypa/setuptools/pull/862
+# Run setup:
+setup(**metadata_dict, **options_dict)  # TODO: Is this overwritten by setup.cfg again?
 
-# TODO: Use requirements.txt? extras_require for optional stuff (hyperspy, plotting)?
-# TODO: After split of Pyramid, comment out and see what really is used (is e.g. scipy?)!
-install_requires = ['numpy>=1.6', 'tqdm', 'scipy', 'matplotlib', 'Pillow', 'h5py',
-                    'hyperspy', 'jutil', 'cmocean']
 
-# TODO: extend extras_require for plotting and IO:
-# TODO: extra: 'pyfftw', 'mayavi' (not easy to install... find a way!)
-# TODO: See https://stackoverflow.com/a/28842733 for extras_require...
-# TODO: ...replace [dev] with [IO] (hyperspy) and [plotting] (separate plotting library)!
-extras_require = {
-    # TODO: Test all if really needed! don't use nose, if possible (pure pytest)!
-    'tests': ['pytest', 'pytest-runner', 'pytest-cov', 'pytest-flake8', 'coverage'],
-    '3Dplot': ['qt==4.8', 'mayavi==4.5']  # TODO: not current!
-    # TODO: in general, make CI test THESE requirements (maybe in addition to the environment.yml)
-    # TODO: more for mayavi (plotting in general) and hyperspy, etc (see below)...
-}
+# TODO: Currently does not work, find out why!
 
-extras_require["all"] = list(itertools.chain(*list(extras_require.values())))
-# TODO: What about the demo?
+# TODO: HOW TO GET JUTIL???
 
-print('\n-------------------------------------------------------------------------------')
-# print('checking requirements')  # TODO: Get rid of!
-# check_requirements()
-print('write version.py')
-write_version_py()
-setup(name=DISTNAME,
-      description=DESCRIPTION,
-      long_description=LONG_DESCRIPTION,
-      maintainer=MAINTAINER,
-      maintainer_email=MAINTAINER_EMAIL,
-      url=URL,
-      download_url=URL,
-      version=VERSION,
-      packages=find_packages(exclude=['tests', 'doc']),  # TODO: necessary?
-      #include_dirs=[numpy.get_include()],  # TODO: Maybe used for sphinx?!
-      #setup_requires=['numpy>=1.6', 'pytest', 'pytest-runner'],
-      #tests_require=['pytest', 'pytest-cov', 'pytest-flake8'],
-      install_requires=install_requires,
-      extras_require=extras_require,
-      #cmdclass={'build': build}  # TODO: necessary?
-    )
-print('-------------------------------------------------------------------------------\n')
+# TODO: Also create conda recipe!
+# TODO: Handle extras via metapackage (depends on pyramid-base that holds the core code and extras?)
+# TODO: https://docs.conda.io/projects/conda-build/en/latest/user-guide/tutorials/build-pkgs.html