Transforms haddock3 into a python package

README.md

@@ -1,4 +1,3 @@
-
 # WARNING: The `main` branch is not production-ready
 
 The `main` branch is a prototype of newly refined architecture and it
@@ -27,12 +26,14 @@ cd haddock3
 virtualenv-3.8 venv
 source venv/bin/activate
 pip install -r requirements.txt
+python setup.py develop --no-deps
 ```
 
 #### with `conda`
 ```bash
 conda env create -f requirements.yml
 conda activate haddock3
+python setup.py develop --no-deps
 ```
 
 ### 1.3 Copy CNS binary to the expected path:
@@ -63,11 +64,26 @@ Save and exit. Source the file:
 source bin/activate_haddock
 ```
 
+You need to `source bin/activate_haddock` at each new terminal window
+you wish to use `haddock3`.
+
+### 1.5 Keep up to date
+
+In the `github` folder of `haddock3` run:
+
+```bash
+git pull
+```
+
+This will pull the latest changes to your local folder and because you
+installed `haddock3` with the option `develop` those changes become
+available immediately.
+
 ## 2. Examples
 
 ### 2.1. Basic scoring of an ensemble of 5 structures:
 
 ```bash
 cd examples/recipes/scoring/
-haddock3.py scoring.toml
+haddock3 scoring.toml
 ```

setup.py

@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+# -*- encoding: utf-8 -*-
+"""Setup dot py."""
+from glob import glob
+from os.path import basename, dirname, join, splitext
+
+from setuptools import find_packages, setup
+
+
+def read(*names, **kwargs):
+    """Read description files."""
+    path = join(dirname(__file__), *names)
+    with open(path, encoding=kwargs.get('encoding', 'utf8')) as fh:
+        return fh.read()
+
+
+# activate once added, do not remove
+#long_description = '{}\n{}'.format(
+#    read('README.rst'),
+#    read(join('docs', 'CHANGELOG.rst')),
+#    )
+
+
+setup(
+    name='haddock3',
+    version='0.0.3-alpha',
+    description='Haddock 3.',
+    long_description='',#long_description,
+    long_description_content_type='text/x-rst',
+    license='Apache License 2.0',
+    author='HADDOCK',
+    author_email='A.M.J.J.Bonvin@uu.nl',
+    url='https://github.com/haddocking/haddock3',
+    packages=find_packages('src'),
+    package_dir={'': 'src'},
+    #py_modules=[splitext(basename(i))[0] for i in glob("src/*.py")],
+    include_package_data=True,
+    zip_safe=False,
+    classifiers=[
+        # complete classifier list:
+        # http://pypi.python.org/pypi?%3Aaction=list_classifiers
+        'Development Status :: 3 - Alpha',
+        #'Development Status :: 4 - Beta',
+        'License :: OSI Approved :: Apache Software License',
+        'Natural Language :: English',
+        'Operating System :: POSIX',
+        'Operating System :: MacOS',
+        'Operating System :: Microsoft',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        ],
+    project_urls={
+        'webpage': 'https://github.com/haddocking/haddock3',
+        'Documentation': 'https://github.com/haddocking/haddock3#readme',
+        'Changelog': '',
+        'Issue Tracker': 'https://github.com/haddocking/haddock3/issues',
+        'Discussion Forum': 'https://github.com/haddocking/haddock3/issues',
+        },
+    keywords=[
+        'Structural Biology',
+        'Biochemistry',
+        'Docking',
+        'Protein docking',
+        'Proteins',
+        ],
+    python_requires='>=3.8, <4',
+    install_requires=[
+        # not added on purpose
+        ],
+    extras_require={
+        },
+    setup_requires=[
+        ],
+    entry_points={
+        'console_scripts': [
+            'haddock3 = haddock.clis.cli:main',
+            ]
+        },
+    # cmdclass={'build_ext': optional_build_ext},
+    # ext_modules=[
+    #    Extension(
+    #        splitext(relpath(path, 'src').replace(os.sep, '.'))[0],
+    #        sources=[path],
+    #        include_dirs=[dirname(path)]
+    #    )
+    #    for root, _, _ in os.walk('src')
+    #    for path in glob(join(root, '*.c'))
+    # ],
+    )