Move package directory to src/

This goes against the currently officially recommended package layout, but
there are quite a few reasons for doing it this way. In particular, having
the package directory *not* directly importable ensures that the tests
actually run against the packaged version of the code, not against what
happens to be in the working copy.

Blog articles:

* https://hynek.me/articles/testing-packaging/
* https://blog.ionelmc.ro/2014/05/25/python-packaging/#the-structure

Recommendation in the pytest documentation:

* https://docs.pytest.org/en/latest/goodpractices.html#tests-outside-application-code

MANIFEST.in

@@ -1,19 +1,13 @@
-# documentation
-include README.rst
 include CHANGES.rst
 include CITATION
 include LICENSE
 include doc/*.rst
 include doc/conf.py
 include doc/Makefile
-include cutadapt/*.pyx
-include cutadapt/_align.c
-include cutadapt/_qualtrim.c
-include cutadapt/_seqio.c
-include bin/_preamble.py
-include tests/test*.py
+include versioneer.py
+include src/cutadapt/*.c
+include src/cutadapt/*.pyx
 include tests/utils.py
+include tests/test_*.py
 graft tests/data
 graft tests/cut
-include versioneer.py
-include cutadapt/_version.py

setup.cfg

@@ -1,7 +1,7 @@
 [versioneer]
 VCS = git
 style = pep440
-versionfile_source = cutadapt/_version.py
+versionfile_source = src/cutadapt/_version.py
 versionfile_build = cutadapt/_version.py
 tag_prefix = v
 parentdir_prefix = cutadapt-

setup.py

@@ -4,7 +4,7 @@
 import sys
 import os.path
 
-from setuptools import setup, Extension
+from setuptools import setup, Extension, find_packages
 from distutils.version import LooseVersion
 from distutils.command.sdist import sdist as _sdist
 from distutils.command.build_ext import build_ext as _build_ext
@@ -54,9 +54,9 @@ def check_cython_version():
 
 
 extensions = [
-	Extension('cutadapt._align', sources=['cutadapt/_align.pyx']),
-	Extension('cutadapt._qualtrim', sources=['cutadapt/_qualtrim.pyx']),
-	Extension('cutadapt._seqio', sources=['cutadapt/_seqio.pyx']),
+	Extension('cutadapt._align', sources=['src/cutadapt/_align.pyx']),
+	Extension('cutadapt._qualtrim', sources=['src/cutadapt/_qualtrim.pyx']),
+	Extension('cutadapt._seqio', sources=['src/cutadapt/_seqio.pyx']),
 ]
 
 cmdclass = versioneer.get_cmdclass()
@@ -108,7 +108,8 @@ def run(self):
 	license = 'MIT',
 	cmdclass = cmdclass,
 	ext_modules = extensions,
-	packages = ['cutadapt', 'cutadapt.scripts'],
+	package_dir = {'': 'src'},
+	packages = find_packages('src'),
 	install_requires = ['xopen>=0.1.1'],
 	entry_points = {'console_scripts': ['cutadapt = cutadapt.scripts.cutadapt:main']},
 	classifiers = [

cutadapt/_version.py → src/cutadapt/_version.py

@@ -42,7 +42,7 @@ def get_config():
     cfg.style = "pep440"
     cfg.tag_prefix = "v"
     cfg.parentdir_prefix = "cutadapt-"
-    cfg.versionfile_source = "cutadapt/_version.py"
+    cfg.versionfile_source = "src/cutadapt/_version.py"
     cfg.verbose = False
     return cfg