update project to zpdb-tools

.bumpversion.cfg

@@ -1,7 +1,9 @@
 [bumpversion]
 current_version = 2.5.1
 commit = True
-message = [SKIP] version bump {current_version} -> {new_version}
+message = version bump {current_version} -> {new_version}
 tag = True
 
-[bumpversion:file:setup.py]
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"

.github/workflows/yaml_linter.yml

@@ -5,7 +5,7 @@ jobs:
   lintAllTheThings:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: yaml-lint
         uses: ibiqlik/action-yamllint@v3
         with:

.gitignore

@@ -4,3 +4,4 @@ dist/
 *egg-info/
 *__pycache__
 *.pyc
+.coverage

pdbtools/pdb_delinsertion.py

@@ -39,7 +39,7 @@
 import sys
 import warnings
 
-from pdbtools import pdb_fixinsert
+from zpdbtools import pdb_fixinsert
 
 __author__ = "Joao Rodrigues"
 __email__ = "j.p.g.l.m.rodrigues@gmail.com"

pyproject.toml

@@ -0,0 +1,55 @@
+[project]
+name = "zpdb-tools"
+readme = "README.md"
+description='A swiss army knife for PDB files.'
+requires-python = ">=3.7"
+version = "2.5.1"
+dynamic = ["scripts"]
+keywords = [
+    "zymvol",
+    "bioinformatics",
+    "proteins",
+    "pdb",
+    "structural-biology",
+    ]
+classifiers = [
+    'Development Status :: 5 - Production/Stable',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.6',
+    'Programming Language :: Python :: 3.7',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
+    'Intended Audience :: Science/Research',
+    'Topic :: Scientific/Engineering',
+    'Topic :: Scientific/Engineering :: Chemistry',
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
+    'License :: OSI Approved :: Apache Software License',
+    ]
+authors = [
+    {name = "João Rodrigues", email = "j.p.g.l.m.rodrigues@gmail.com" },
+    {name = "João M.C. Teixeira", email = "joaomcteixeira@gmail.com" },
+    {name = "Haddocking", email = "a.m.j.j.bonvin@uu.nl" },
+    ]
+
+maintainers = [
+    {name = "João M.C. Teixeira", email = "jteixeira@zymvol.com" },
+    {name = "Zymvol Biomodeling"},
+    ]
+
+[project.urls]
+Repository = "https://github.com/zymvol/zpdb-tools"
+Issues = "https://github.com/zymvol/zpdb-tools/issues"
+
+[build-system]
+requires = [
+    "setuptools >= 75",
+    ]
+build-backend = "setuptools.build_meta"
+
+#[tool.setuptools.packages.find]
+#where = ["zpdbtools"]
+[tool.setuptools.package-dir]
+zpdbtools = "pdbtools"

setup.py

@@ -1,108 +1,15 @@
-"""A setuptools based setup module.
+from pathlib import Path
 
-See:
-https://packaging.python.org/en/latest/distributing.html
-https://github.com/pypa/sampleproject
-"""
+from setuptools import setup
 
-# Always prefer setuptools over distutils
-from setuptools import setup, find_packages
-from os import listdir, path
-# io.open is needed for projects that support Python 2.7
-# It ensures open() defaults to text mode with universal newlines,
-# and accepts an argument to specify the text encoding
-# Python 3 only projects can skip this import
-from io import open
-
-here = path.abspath(path.dirname(__file__))
-
-# Get the long description from the README file
-with open(path.join(here, 'README.md'), encoding='utf-8') as f:
-    long_description = f.read()
-
-# Collect names of bin/*py scripts
-# e.g. 'pdb_intersect=bin.pdb_intersect:main',
-binfiles = listdir(path.join(here, 'pdbtools'))
-bin_py = [f[:-3] + '=pdbtools.' + f[:-3] + ':main' for f in binfiles
-          if f.endswith('.py')]
+binfiles = Path(Path(__file__).parent, 'pdbtools').resolve().glob('*.py')
+bin_py = [
+    f.stem + '=zpdbtools.' + f.stem + ':main'
+    for f in binfiles
+    ]
 
 setup(
-    name='pdb-tools',  # Required
-    version='2.5.1',  # Required
-    description='A swiss army knife for PDB files.',  # Optional
-    long_description=long_description,  # Optional
-    long_description_content_type='text/markdown',  # Optional (see note above)
-    url='http://bonvinlab.org/pdb-tools',  # Optional
-    author='Joao Rodrigues',  # Optional
-    author_email='j.p.g.l.m.rodrigues@gmail.com',  # Optional
-    license='Apache Software License, version 2',
-    classifiers=[  # Optional
-        # How mature is this project? Common values are
-        #   3 - Alpha
-        #   4 - Beta
-        #   5 - Production/Stable
-        'Development Status :: 5 - Production/Stable',
-        #'Development Status :: 4 - Beta',
-
-        # Indicate who your project is intended for
-        'Intended Audience :: Science/Research',
-        'Topic :: Scientific/Engineering',
-        'Topic :: Scientific/Engineering :: Chemistry',
-        'Topic :: Scientific/Engineering :: Bio-Informatics',
-
-
-        # Pick your license as you wish
-        'License :: OSI Approved :: Apache Software License',
-
-        # Specify the Python versions you support here. In particular, ensure
-        # that you indicate whether you support Python 2, Python 3 or both.
-        'Programming Language :: Python :: 2',
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-    ],
-
-    keywords='bioinformatics protein structural-biology pdb',  # Optional
-
-    # You can just specify package directories manually here if your project is
-    # simple. Or you can use find_packages().
-    #
-    # Alternatively, if you just want to distribute a single Python file, use
-    # the `py_modules` argument instead as follows, which will expect a file
-    # called `my_module.py` to exist:
-    #
-    #   py_modules=["my_module"],
-    #
-    packages=find_packages(),  # Required
-
-    # To provide executable scripts, use entry points in preference to the
-    # "scripts" keyword. Entry points provide cross-platform support and allow
-    # `pip` to create the appropriate form of executable for the target
-    # platform.
-    #
-    # For example, the following would provide a command called `sample` which
-    # executes the function `main` from this package when invoked:
-    entry_points={  # Optional
+    entry_points={
         'console_scripts': bin_py,
-    },
-
-    # scripts=[path.join('bin', f) for f in listdir(path.join(here, 'bin'))],
-
-    # List additional URLs that are relevant to your project as a dict.
-    #
-    # This field corresponds to the "Project-URL" metadata fields:
-    # https://packaging.python.org/specifications/core-metadata/#project-url-multiple-use
-    #
-    # Examples listed include a pattern for specifying where the package tracks
-    # issues, where the source is hosted, where to say thanks to the package
-    # maintainers, and where to support the project financially. The key is
-    # what's used to render the link text on PyPI.
-    project_urls={  # Optional
-        'Bug Reports': 'https://github.com/haddocking/pdb-tools/issues',
-        'Source': 'https://github.com/haddocking/pdb-tools',
-    },
-
-    # Test Suite
-    test_suite='tests.test_all',
-)
+        },
+    )

tests/__init__.py

@@ -14,25 +14,66 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-"""
-Unit Tests for all pdb-tools scripts
-"""
-
+"""Unit Tests for all pdb-tools scripts."""
 import os
 import sys
 import unittest
+from io import StringIO
+from importlib import import_module
+
+
+class OutputCapture(object):
+    """Context manager to capture output usually redirected to stdout.
+
+    Use as:
+    >>> with OutputCapture() as output:
+    >>> ....run_stuff()
+    >>> print(output)  # list with lines
+    """
+
+    def __enter__(self):
+        self.stdout = []
+        self.stderr = []
+
+        self._stdout = sys.stdout
+        self._stderr = sys.stderr
+        sys.stdout = self._stringout = StringIO()
+        sys.stderr = self._stringerr = StringIO()
+        return self
+
+    def __exit__(self, *args):
+
+        self.stdout.extend(self._stringout.getvalue().splitlines())
+        self.stderr.extend(self._stringerr.getvalue().splitlines())
+        del self._stringout    # free up some memory
+        del self._stringerr    # free up some memory
+        sys.stdout = self._stdout
+        sys.stderr = self._stderr
+
+
+
+class TestPDBTools(unittest.TestCase):
 
-from .config import test_dir
+    @classmethod
+    def setUpClass(cls):
+        # Dynamically import the module
+        cls.module = import_module(cls.name)
 
+    def exec_module(self):
+        """
+        Execs module.
+        """
+        with OutputCapture() as output:
+            try:
+                self.module.main()
+            except SystemExit as e:
+                self.retcode = e.code
 
-def test_all():
-    mpath = os.path.abspath(os.path.join(test_dir, '..'))
-    sys.path.insert(0, mpath)  # so we load dev files before  any installation
+        self.stdout = output.stdout
+        self.stderr = output.stderr
 
-    loader = unittest.defaultTestLoader
+        return
 
-    tpath = os.path.join(mpath, 'tests')
-    suite = loader.discover(tpath)
 
-    return suite
+test_dir = os.path.dirname(os.path.abspath(__file__))
+data_dir = os.path.join(test_dir, 'data')

tests/test_pdb_b.py

@@ -23,35 +23,15 @@
 import sys
 import unittest
 
-from config import data_dir
-from utils import OutputCapture
+from . import TestPDBTools, data_dir
 
 
-class TestTool(unittest.TestCase):
+class TestTool(TestPDBTools):
     """
     Generic class for testing tools.
     """
 
-    def setUp(self):
-        # Dynamically import the module
-        name = 'pdbtools.pdb_b'
-        self.module = __import__(name, fromlist=[''])
-
-    def exec_module(self):
-        """
-        Execs module.
-        """
-
-        with OutputCapture() as output:
-            try:
-                self.module.main()
-            except SystemExit as e:
-                self.retcode = e.code
-
-        self.stdout = output.stdout
-        self.stderr = output.stderr
-
-        return
+    name = 'zpdbtools.pdb_b'
 
     def test_default(self):
         """$ pdb_b data/dummy.pdb"""
@@ -150,12 +130,3 @@ def test_not_an_option(self):
         self.assertEqual(len(self.stdout), 0)
         self.assertEqual(self.stderr[0],
                          "ERROR! First argument is not an option: '20'")
-
-
-if __name__ == '__main__':
-    from config import test_dir
-
-    mpath = os.path.abspath(os.path.join(test_dir, '..'))
-    sys.path.insert(0, mpath)  # so we load dev files before  any installation
-
-    unittest.main()

tests/test_pdb_chain.py

@@ -23,35 +23,15 @@
 import sys
 import unittest
 
-from config import data_dir
-from utils import OutputCapture
+from . import TestPDBTools, data_dir
 
 
-class TestTool(unittest.TestCase):
+class TestTool(TestPDBTools):
     """
     Generic class for testing tools.
     """
 
-    def setUp(self):
-        # Dynamically import the module
-        name = 'pdbtools.pdb_chain'
-        self.module = __import__(name, fromlist=[''])
-
-    def exec_module(self):
-        """
-        Execs module.
-        """
-
-        with OutputCapture() as output:
-            try:
-                self.module.main()
-            except SystemExit as e:
-                self.retcode = e.code
-
-        self.stdout = output.stdout
-        self.stderr = output.stderr
-
-        return
+    name = 'zpdbtools.pdb_chain'
 
     def test_default(self):
         """$ pdb_chain data/dummy.pdb"""
@@ -149,12 +129,3 @@ def test_not_an_option(self):
         self.assertEqual(len(self.stdout), 0)
         self.assertEqual(self.stderr[0],
                          "ERROR! First argument is not an option: 'A'")
-
-
-if __name__ == '__main__':
-    from config import test_dir
-
-    mpath = os.path.abspath(os.path.join(test_dir, '..'))
-    sys.path.insert(0, mpath)  # so we load dev files before  any installation
-
-    unittest.main()