Create python-package-conda.yml

.github/workflows/python-package-conda.yml

@@ -0,0 +1,34 @@
+name: Python Package using Conda
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file environment.yml --name base
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        pytest

environment.yml

@@ -0,0 +1,12 @@
+name: pytim
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python=3.9
+  - numpy
+  - scipy
+  - MDAnalysis>=2.0.0
+  - cython

pytim/surface.py

@@ -2,7 +2,7 @@
 # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 
 from __future__ import print_function
-from abc import ABCMeta, abstractproperty
+from abc import ABCMeta, abstractmethod
 import numpy as np
 from scipy.spatial import Delaunay, cKDTree
 from scipy.interpolate import LinearNDInterpolator
@@ -42,34 +42,38 @@ def __init__(self, interface, options=None):
         except (TypeError, KeyError):
             self._layer = 0
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def interpolation(self, inp):
         """ returns interpolated position on the surface """
         return utilities.extract_positions(inp)
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def distance(self, inp, *args, **kargs):
         """ returns distance from the surface """
         positions = utilities.extract_positions(inp)
         distance_array = positions[::, 2]
         return distance_array
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def triangulation(self):
         """ return a scipy.spatial.qhull.Delaunay triangulation
             of the surface
         """
-        return triangulation
+        return NotImplemented
 
-    @abstractproperty
+    @property
     def regular_grid(self):
         """ returns the points defining the regular grid in 2 dimensions, and
             the elevation values evaluated at the grid points
             (like the input of scipy.interpolate.RegularGridInterpolator )
         """
         return (x, y), elevations
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def dump(self):
         """ save the surface to file """
         return True