Make it compatible with scikit-image version >= 0.19.0

README.md

@@ -11,12 +11,19 @@ pip install fortecubeview
 ```
 
 ## Dependencies
-forte4cubeview requires [pythreejs](https://github.com/jupyter-widgets/pythreejs).
+forte4cubeview requires [pythreejs](https://github.com/jupyter-widgets/pythreejs) and [scikit-image](https://github.com/scikit-image/scikit-image).
 
 To install pythreejs via pip:
 ```
 pip install pythreejs
 ```
+
+To install pythreejs via conda:
+```
+conda install -c conda-forge pythreejs
+conda install nodejs -c conda-forge --repodata-fn=repodata.json
+```
+
 And then install the extension for jupyter notebooks
 ```
 jupyter nbextension install --py --symlink --sys-prefix pythreejs

examples/psi4/example.ipynb

@@ -4,13 +4,26 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# fortecubeview\n",
+    "# How to use `fortecubeview`\n",
     "\n",
-    "fortecubeview is a simple cube file viewer. It is designed to work with `psi4` and `forte`. However, it should work with any cube file.\n",
+    "---\n",
+    "\n",
+    "`fortecubeview` is a simple cube file viewer. It is designed to work with `psi4` and `forte`. However it is compatible with any other code that can generate standard cube files.\n",
     "\n",
-    "The cube file in this directory were generated with the following psi4 input file:\n",
+    "This directory contains the following cube files:\n",
     "\n",
+    "```bash\n",
+    "Da.cube\n",
+    "Db.cube\n",
+    "Ds.cube\n",
+    "Dt.cube\n",
+    "Psi_a_5_1-B1.cube\n",
+    "Psi_a_6_4-A1.cube\n",
     "```\n",
+    "\n",
+    "These were generated with the following psi4 input file:\n",
+    "\n",
+    "```python\n",
     "import psi4\n",
     "\n",
     "h2o = psi4.geometry(\"\"\"\n",
@@ -136,18 +149,11 @@
    "source": [
     "fortecubeview.vib('output.nh3.molden_normal_modes')"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -161,7 +167,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.9.9"
   }
  },
  "nbformat": 4,

fortecubeview/py3js_renderer.py

@@ -1093,7 +1093,13 @@ def __compute_isosurface(self, data, level, color, extent=None):
         -------
         a tuple of vertices and faces
         """
-        values = skimage.measure.marching_cubes_lewiner(data, level * 0.995)
+        # call the appropriate version of skimage's marching cubes
+        from packaging.version import parse as parse_version
+        if parse_version(skimage.__version__) >= parse_version('0.19.0'):
+            values = skimage.measure.marching_cubes(data, level)
+        else:
+            values = skimage.measure.marching_cubes_lewiner(data, level)
+
         sk_verts, sk_faces, normals, values = values
         x, y, z = sk_verts.T
 

requirements.txt

@@ -1 +1,2 @@
 pythreejs
+scikit-image

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="fortecubeview",
-    version="0.2.2",
+    version="0.2.3",
     author="Francesco Evangelista",
     author_email="",
     description="A geometry, cube file, and vibrational modes viewer for Psi4 and Forte",