Merge branch 'gabrieliacc-main'

.github/workflows/publish-release.yml

@@ -9,9 +9,9 @@ jobs:
   deploy-linux:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies
@@ -24,9 +24,9 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Build manylinux Python wheels
-      uses: RalfG/python-wheels-manylinux-build@v0.3.4-manylinux2010_x86_64
+      uses:  RalfG/python-wheels-manylinux-build@v0.5.0-manylinux2014_x86_64
       with:
-        python-versions: 'cp38-cp38 cp39-cp39'
+        python-versions: 'cp38-cp38 cp39-cp39 cp310-cp310'
         build-requirements: 'cython numpy'
     - name: Publish wheels to PyPI
       env:
@@ -38,18 +38,18 @@ jobs:
       continue-on-error: true
 
   deploy-macos:
-    runs-on: macos-latest
+    runs-on: macos-10.15
     env:
       TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
       TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       CC: /usr/local/bin/gcc-10
     strategy:
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: ['3.8', '3.9', '3.10']
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

.gitignore

@@ -2,7 +2,6 @@
 *.pickle
 *.pdb
 *.pse
-docs/
 
 # VScode
 .vscode

C/SERD.py

@@ -0,0 +1,123 @@
+# This file was automatically generated by SWIG (http://www.swig.org).
+# Version 4.0.2
+#
+# Do not make changes to this file unless you know what you are doing--modify
+# the SWIG interface file instead.
+
+from sys import version_info as _swig_python_version_info
+if _swig_python_version_info < (2, 7, 0):
+    raise RuntimeError("Python 2.7 or later required")
+
+# Import the low-level C/C++ module
+if __package__ or "." in __name__:
+    from . import _SERD
+else:
+    import _SERD
+
+try:
+    import builtins as __builtin__
+except ImportError:
+    import __builtin__
+
+def _swig_repr(self):
+    try:
+        strthis = "proxy of " + self.this.__repr__()
+    except __builtin__.Exception:
+        strthis = ""
+    return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
+
+
+def _swig_setattr_nondynamic_instance_variable(set):
+    def set_instance_attr(self, name, value):
+        if name == "thisown":
+            self.this.own(value)
+        elif name == "this":
+            set(self, name, value)
+        elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
+            set(self, name, value)
+        else:
+            raise AttributeError("You cannot add instance attributes to %s" % self)
+    return set_instance_attr
+
+
+def _swig_setattr_nondynamic_class_variable(set):
+    def set_class_attr(cls, name, value):
+        if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
+            set(cls, name, value)
+        else:
+            raise AttributeError("You cannot add class attributes to %s" % cls)
+    return set_class_attr
+
+
+def _swig_add_metaclass(metaclass):
+    """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
+    def wrapper(cls):
+        return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
+    return wrapper
+
+
+class _SwigNonDynamicMeta(type):
+    """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
+    __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
+
+
+
+def igrid(grid):
+    return _SERD.igrid(grid)
+
+def fill(grid, atoms, reference, sincos, step, probe, nthreads):
+    return _SERD.fill(grid, atoms, reference, sincos, step, probe, nthreads)
+
+def check_protein_neighbours(grid, i, j, k):
+    return _SERD.check_protein_neighbours(grid, i, j, k)
+
+def ses(grid, step, probe, nthreads):
+    return _SERD.ses(grid, step, probe, nthreads)
+
+def define_surface_points(grid, i, j, k):
+    return _SERD.define_surface_points(grid, i, j, k)
+
+def filter_surface(grid, nthreads):
+    return _SERD.filter_surface(grid, nthreads)
+
+def remove_noise_points(grid, i, j, k):
+    return _SERD.remove_noise_points(grid, i, j, k)
+
+def filter_noise_points(grid, nthreads):
+    return _SERD.filter_noise_points(grid, nthreads)
+
+def check_unclustered_neighbours(grid, i, j, k):
+    return _SERD.check_unclustered_neighbours(grid, i, j, k)
+
+def flood_and_fill(grid, i, j, k, tag):
+    return _SERD.flood_and_fill(grid, i, j, k, tag)
+
+def filter_enclosed_regions(grid, step, nthreads):
+    return _SERD.filter_enclosed_regions(grid, step, nthreads)
+
+def _surface(grid, nx, ny, nz, atoms, reference, sincos, step, probe, is_ses, nthreads, verbose):
+    return _SERD._surface(grid, nx, ny, nz, atoms, reference, sincos, step, probe, is_ses, nthreads, verbose)
+class res(object):
+    thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
+    __repr__ = _swig_repr
+    pos = property(_SERD.res_pos_get, _SERD.res_pos_set)
+    next = property(_SERD.res_next_get, _SERD.res_next_set)
+
+    def __init__(self):
+        _SERD.res_swiginit(self, _SERD.new_res())
+    __swig_destroy__ = _SERD.delete_res
+
+# Register res in _SERD:
+_SERD.res_swigregister(res)
+
+
+def create(pos):
+    return _SERD.create(pos)
+
+def insert(head, res_new):
+    return _SERD.insert(head, res_new)
+
+def _interface(grid, pdb, atoms, reference, sincos, step, probe, nthreads, verbose):
+    return _SERD._interface(grid, pdb, atoms, reference, sincos, step, probe, nthreads, verbose)
+
+