🐛 make sure version is available in wheels distribution (#10)

* 🐛 change steup.json file location
* 🔧 manage 1 file for version inside module
* 🎨 clean up a bit
* 🎨 clean up setup.cfg
* 👕 remove unused statements in MANIFEST.in
* 🔧 remove unused imports in __init__.py
* 🔧 remove unused imports in __init__.py
* 🐛 pydocstyle was checking the wrong directory
* 🐛 use absolute paths in setup.py
* 🐛 use absolute paths in __init__.py
* 🔧 simplify tox.ini
* 👕 clean up tox.ini

.travis.yml

@@ -1,4 +1,3 @@
-
 language: python
 
 sudo: false

CONTRIBUTING.md

@@ -124,22 +124,7 @@ Additionally, a `.pydocstyle` defines *docstrings* conventions to be tested with
 
 ## Tox
 
-Use [tox][tox] run tests on a isolated python environment. The `tox.ini` file enables you to get [pytest][pytest], [pylint][pylint], [pydocstyle][pydocstyle] and a [coverage][coverage] html report. Tox also tests the installation procedure. To execute the default environments run:
-
-    tox
-
-You can run a set of specific test environments:
-
-    tox -e report,lint
-
-The `report` enviroment will create a html coverage report. Use `tox --recreate` when you need to rebuild the tox environments (e.g. you changed one of the `deps` lists in the `tox.ini` file). The available tox environments are:
-
-| Name   | function                                                                                          |
-| ------ | ------------------------------------------------------------------------------------------------- |
-| py27   | Test package using python 2 (Toil)                                                                |
-| lint   | Run [pylint][pylint] and [pydocstyle][pydocstyle] using the `.pylintrc` and `.pydocstylerc` files |
-| report | Run base tests and generate coverage statistics                                                   |
-| clean  | Clean a previously generated coverage report                                                      |
+Use [tox][tox] run tests on a isolated python environment. The `tox.ini` file enables you to get [pytest][pytest], [pylint][pylint] and [pydocstyle][pydocstyle]. Tox also tests the installation procedure.
 
 <!-- References -->
 

MANIFEST.in

@@ -1,22 +1,5 @@
-graft tests
-graft docker
-
-include CONTRIBUTING.md
-include LICENSE
-include README.md
-
-include .coveragerc
-include .pylintrc
-
-include pytest.ini
-include setup.json
-include tox.ini
-include Makefile
-
 global-exclude *.dylib
 global-exclude *.py[cod]
 global-exclude *.so
 global-exclude __pycache__
-
 recursive-include toil_container *
-recursive-include setup.json Makefile

setup.cfg

@@ -1,22 +1,8 @@
-[bumpversion]
-current_version = 0.1.0
-commit = True
-tag = True
-
-[bumpversion:file:setup.py]
-search = version='{current_version}'
-replace = version='{new_version}'
-
-[bumpversion:file:toil_container/__init__.py]
-search = __version__ = '{current_version}'
-replace = __version__ = '{new_version}'
-
 [bdist_wheel]
 universal = 1
 
-[flake8]
-exclude = docs
+[metadata]
+license_file = LICENSE
 
 [aliases]
 test = pytest
-# Define setup.py command aliases here

setup.json

@@ -13,7 +13,7 @@
         "Programming Language :: Python :: 2 :: Only",
         "Topic :: Utilities"
     ],
-    "description": "A base package to create Toil pipelines, using containerized jobs.",
+    "description": "A python package with a Toil Job Class capable of containerized system calls.",
     "install_requires": [
         "Click>=6.7",
         "docker==2.5.1",
@@ -42,6 +42,5 @@
     },
     "test_suite": "tests",
     "url": "https://github.com/leukgen/toil_container",
-    "version": "0.1.0",
     "zip_safe": false
 }

setup.py

@@ -1,41 +1,41 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 """toil_container setup.py."""
 
-from os.path import join
 from os.path import abspath
 from os.path import dirname
+from os.path import join
 import io
 import json
 
 from setuptools import find_packages
 from setuptools import setup
 
-ROOT = abspath(dirname(__file__))
-CONF = join(ROOT, "setup.json")
-
 
 def read(path, **kwargs):
     """Return content of a file."""
     return io.open(path, encoding=kwargs.get("encoding", "utf8")).read()
 
+# make sure we use absolute paths
+ROOT = abspath(dirname(__file__))
 
-# Please put setup keywords in the setup.json to keep this file clean.
-with open(CONF, "r") as f:
+# please put setup keywords in the setup.json to keep this file clean
+with open(join(ROOT, "setup.json"), "r") as f:
     SETUP = json.load(f)
 
 setup(
-    # Load description from README.
+    # load description from README
     long_description=read(join(ROOT, "README.md")),
 
-    # In combination with MANIFEST.in, package non-python files included
+    # in combination with MANIFEST.in, non-python files included
     # inside the toil_container will be copied to the
-    # site-packages installation directory.
+    # site-packages and wheels installation directory
     include_package_data=True,
 
-    # Return a list all Python packages found within the ROOT directory.
+    # return a list all Python packages found within the ROOT directory
     packages=find_packages(),
 
-    # Pass parameters loaded from setup.json including author and version.
+    # The version is only defined in one place
+    version=read(join(ROOT, "toil_container", "VERSION")).strip(),
+
+    # pass parameters loaded from setup.json including author and version
     **SETUP
 )

tests/test_version.py

@@ -5,4 +5,4 @@
 
 def test_version():
     """Sample test for the __version__ variable."""
-    assert __version__ == "0.1.0"
+    assert __version__

toil_container/VERSION

@@ -0,0 +1 @@
+0.1.1

toil_container/__init__.py

@@ -1,20 +1,23 @@
 """toil_container module."""
 
-from os.path import join
 from os.path import abspath
 from os.path import dirname
-import json
+from os.path import join
+
+from toil_container.jobs import (
+    ContainerCallJob
+)
 
-from toil_container.jobs import ContainerCallJob
 from toil_container.parsers import (
     ContainerArgumentParser,
     ContainerShortArgumentParser,
     ToilShortArgumentParser
 )
 
-with open(join("setup.json"), "r") as f:
-    SETUP = json.load(f)
+# make sure we use absolute paths
+ROOT = abspath(dirname(__file__))
 
-__version__ = SETUP.get("version")
+with open(join(ROOT, "VERSION"), "r") as f:
+    VERSION = f.read().strip()
 
-__author__ = SETUP.get("author")
+__version__ = VERSION

tox.ini

@@ -1,43 +1,17 @@
 [tox]
-envlist = py27, lint
+envlist = py27
 
 
 [travis]
-python =
-    2.7: py27
+python = 2.7: py27
 
 
 [testenv]
-usedevelop=false
-passenv=*
-deps=-r{toxinidir}/requirements.txt
-basepython={lint,py27,report,clean}: {env:TOXPYTHON27:python2.7}
-commands=
-    pip install -U pip
+usedevelop = True
+passenv = *
+deps = -r./requirements.txt
+basepython = {py27}: {env:TOXPYTHON27:python2.7}
+commands =
     py.test {env:TOX_PYTEST_ARGS:-s --cov=toil_container --cov-report=term-missing -vv tests}
-
-
-[testenv:lint]
-skip_install=True
-commands=
     pylint toil_container --rcfile={toxinidir}/.pylintrc
-    pydocstyle --config={toxinidir}/.pydocstylerc click_pileup
-
-
-[testenv:report]
-skip_install=True
-commands=
-    coverage erase
-    {[testenv]commands}
-    coverage combine --append
-    coverage report
-    coverage html
-
-
-[testenv:clean]
-skip_install=true
-commands=coverage erase
-
-
-
-
+    pydocstyle toil_container --config={toxinidir}/.pydocstylerc