Update template

.gitlab-ci.yml

@@ -14,6 +14,7 @@ cache:
   paths:
     - .cache/pip
     - venv/
+    - .cache/apt
 
 stages:
   - build
@@ -28,6 +29,10 @@ before_script:
 dist:
   stage: build
   script:
+    - mkdir -p .cache/apt
+    - apt-get update -yqq
+    - apt-get install -y gfortran libopenblas-dev liblapack-dev
+    - apt-get -o dir::cache::archives=".cache/apt" install -y -qq gfortran liblapack-dev libgmp-dev
     - python setup.py bdist_wheel
     # an alternative approach is to install and run:
     - pip install dist/*

.pre-commit-config.yaml

+default_language_version:
+    python: python3
 repos:
 -   repo: https://github.com/ambv/black
-    rev: stable
+    rev: 21.6b0
     hooks:
     - id: black
-      language_version: python3.6
 -   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.3
+    rev: 3.9.2
     hooks:
     - id: flake8
 -   repo: https://github.com/pre-commit/pre-commit-hooks 
-    rev: v3.1.0
+    rev: v4.0.1
     hooks:
     - id: check-json
     - id: pretty-format-json
@@ -21,6 +22,6 @@ repos:
     - id: detect-private-key
     - id: end-of-file-fixer
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.7.0
+    rev: v1.10.0
     hooks:
     - id: blacken-docs

.readthedocs.yml

@@ -19,7 +19,6 @@ sphinx:
 python:
   version: 3.7
   install:
-    - requirements: docs/requirements.txt
     - method: pip
       path: .
       extra_requirements:

LICENSE.rst

 MIT License
 
-Copyright (c) 2020, Daniel Böckenhoff
+Copyright (c) 2021, Daniel Böckenhoff
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-

Makefile

@@ -13,6 +13,7 @@ part ?= patch
 
 test: FORCE
 	flake8 rna tests
+	pylint rna tests
 	py.test
 
 coverage:
@@ -47,7 +48,7 @@ untag:
 
 requirements: setup.cfg
 	# We have all the information in the setup.cfg file. For some reasons (e.g. bug in setuptools or limitations to use setup.cfg in readthedocs) we still need a requirements file
-	python -c "import configparser; import os; config = configparser.ConfigParser(); config.read('setup.cfg'); deps = config['metadata']['install_requires'].split('\n'); deps = [x for x in deps if x]; head = '# Autogenerated by Makefile from setup.cfg install_requies section. Remove this line if you want to fix this file.'; path = 'requirements.txt'; f = open(path, 'r') if os.path.exists(path) else None; line = f.readline() if f else ''; quit('User defined requirements already existing.') if f and not line.startswith(head[:20]) else None; f = open('requirements.txt', 'w'); f.write('\n'.join([head] + deps))"
+	python -c "import configparser; import os; config = configparser.ConfigParser(); config.read('setup.cfg'); deps = config['options']['install_requires'].split('\n'); deps = [x for x in deps if x]; head = '# Autogenerated by Makefile from setup.cfg install_requies section. Remove this line if you want to fix this file.'; path = 'requirements.txt'; f = open(path, 'r') if os.path.exists(path) else None; line = f.readline() if f else ''; quit('User defined requirements already existing.') if f and not line.startswith(head[:20]) else None; f = open('requirements.txt', 'w'); f.write('\n'.join([head] + deps))"
 
 doc: Makefile $(SOURCES) $(DOCUMENTATION) docs/conf.py docs/apidoc-template/*
 	# link apidoc to source and build html documentation with sphinx

docs/apidoc-template/toc.rst_t

@@ -8,4 +8,3 @@ API Documentation
 {% for docname in docnames %}
    {{ docname }}
 {%- endfor %}
-

docs/cookiecutter_input.json

@@ -16,3 +16,4 @@
     "remote_username": "dboe",
     "summary": "Basic and essential code building blocks of all pythons"
 }
+

docs/installation.rst

@@ -23,6 +23,7 @@ you through the process.
 .. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
 
 
+
 From sources
 ------------
 

docs/usage.rst

@@ -4,4 +4,4 @@ Usage
 
 To use rna in a project::
 
-    >>> import rna
\ No newline at end of file
+    >>> import rna

rna/__main__.py

@@ -8,49 +8,64 @@ import rna
 
 
 class SomeAction(argparse.Action):
+    """Some actions."""
+
     def __init__(self, option_strings, dest, nargs=None, **kwargs):
         if nargs is not None:
             raise ValueError("nargs not allowed")
         super().__init__(option_strings, dest, **kwargs)
 
     def __call__(self, parser, namespace, values, option_string=None):
-        print("Example action invoked by manage in namespace: %r with values %r"
-              " and option string %r" % (namespace, values, option_string))
+        print(
+            "Example action invoked by manage in namespace: %r with values %r"
+            " and option string %r" % (namespace, values, option_string)
+        )
         setattr(namespace, self.dest, values)
 
+    def showcase_dummy(self):
+        """
+        You can define a method to expose functionality of the class
+        """
+        print(self)
+
 
-def manage(args):
+def manage(args_):
+    """Example function."""
     print("Managing!")
-    print(args.x * args.y)
+    print(args_.x * args_.y)
 
 
-def parse_args(args):
+def parse_args(args_):
+    """Parse args."""
     # create the top-level parser
-    parser = argparse.ArgumentParser(prog='rna app')
-    parser.add_argument('--version', action='version',
-                        version='v' + rna.__version__,
-                        help="Show program's version number and exit")
-    parser = argparse.ArgumentParser(prog='rna app')
+    parser = argparse.ArgumentParser(prog="rna app")
+    parser.add_argument(
+        "--version",
+        action="version",
+        version="v" + rna.__version__,
+        help="Show program's version number and exit",
+    )
+    parser = argparse.ArgumentParser(prog="rna app")
 
     # subparsers
-    subparsers = parser.add_subparsers(help='sub-command help')
+    subparsers = parser.add_subparsers(help="sub-command help")
 
     # create the parser for the "test" command
-    example_sub_parser = subparsers.add_parser('manage', help='manage something')
-    example_sub_parser.add_argument('-x', type=int, default=1)
-    example_sub_parser.add_argument('-y', type=float, default=42.)
+    example_sub_parser = subparsers.add_parser("manage", help="manage something")
+    example_sub_parser.add_argument("-x", type=int, default=1)
+    example_sub_parser.add_argument("-y", type=float, default=42.0)
     example_sub_parser.set_defaults(func=manage)
 
     # If no arguments were used, print base-level help with possible commands.
-    if len(args) == 0:
+    if len(args_) == 0:
         parser.print_help(file=sys.stderr)
         sys.exit(1)
 
-    args = parser.parse_args(args)
+    args_ = parser.parse_args(args_)
     # let argparse do the job of calling the appropriate function after
     # argument parsing is complete
-    args.func(args)
+    return args_.func(args_)
 
 
-if __name__ == '__main__':
-    args = parse_args(sys.argv[1:])
+if __name__ == "__main__":
+    _ = parse_args(sys.argv[1:])

setup.cfg

@@ -8,9 +8,16 @@ message = release-v{new_version}
 search = __version__ = '{current_version}'
 replace = {new_version}
 
+[bumpversion:file:setup.py]
+search = version='{current_version}'
+replace = {new_version}
+
+[bumpversion:file:docs/cookiecutter_input.json]
+search = 'package_version': '{current_version}'
+replace = {new_version}
+
 [metadata]
 name = rna
-version = attr: rna.__version__
 url = https://gitlab.mpcdf.mpg.de/dboe/rna
 author = Daniel Böckenhoff
 author_email = dboe@ipp.mpg.de
@@ -30,18 +37,18 @@ description = Basic and essential code building blocks of all pythons
 long_description = file: README.rst, LICENSE.rst
 long_description_content_type = text/x-rst
 keywords = plotting, matplotlib, pyqtgraph, backend, logging, path, argparse
-install_requires = 
-    pathlib
 project_urls =
     Documentation = https://rna.readthedocs.io
     Source = https://gitlab.mpcdf.mpg.de/dboe/rna
-tests_require =
-    doctest
-    unittest
-python_requires = >=3.0
 
 [options]
+python_requires = >=3.0
 packages = find:
+install_requires = 
+    pathlib
+tests_require =
+    doctest
+    unittest
 
 [options.packages.find]
 exclude = 
@@ -64,6 +71,7 @@ docs =
     sphinx_rtd_theme>=0.4.3
 test =
     flake8
+    pylint
     pytest
     pytest-cov
     coverage
@@ -81,14 +89,16 @@ exclude_lines =
     pragma: no cover
     if False
 
-[coverage:run]
-omit = 
-    rna/plotting/*.py
-
 [flake8]
 max-line-length = 99
 doctests = True
 exclude = .git, .eggs, __pycache__, docs, dist, venv, .tox
+ignore = E203 W503 W504  # wrong flake defaults: see https://github.com/psf/black/issues/315, https://github.com/psf/black/issues/43
+per-file-ignores =
+    __init__.py: F401
+
+[pylint.]
+ignore = setup.py
 
 [build_sphinx]
 builder = html,man
@@ -106,6 +116,7 @@ skip_missing_interpreters = true
 envlist = 
 	py{35,36,37,38}
 recreate = true
+usedevelop = true
 
 [gh-actions]
 python = 
@@ -117,14 +128,13 @@ python =
 [testenv]
 description = run test suite under {basepython}
 deps = 
-	{[metadata]install_requires}
+	{[options]install_requires}
 	{[options.extras_require]test}
 extras = test
 commands = 
 	pytest \
 	--cov={[metadata]name} \
 	--ignore=docs \
-	--ignore=rna/plotting \
 	--junitxml=report/junit.xml
 
 [testenv:flake8]

tests/test_package.py

@@ -3,9 +3,10 @@
 """Tests for `rna` package."""
 
 import unittest
+import rna
 
 
-class Test_rna(unittest.TestCase):
+class TestPackage(unittest.TestCase):
     """Tests for `rna` package."""
 
     def setUp(self):
@@ -16,5 +17,5 @@ class Test_rna(unittest.TestCase):
 
     def test_version_type(self):
         """Assure that version type is str."""
-        import rna
+
         self.assertIsInstance(rna.__version__, str)