Fix: Assign positions for unordered nodes (#30)

.github/workflows/run-tox.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: ["3.9", "3.10"]
 
     steps:
     - uses: actions/checkout@v2

netsalt/algorithm.py

@@ -2,7 +2,7 @@
 import logging
 
 import numpy as np
-from skimage.feature import peak_local_max
+from skimage.feature import peak_local_max  # pylint: disable=no-name-in-module
 
 from .quantum_graph import mode_quality
 

netsalt/quantum_graph.py

@@ -381,8 +381,8 @@ def _set_node_positions(graph, positions=None):
         positions = nx.spring_layout(graph)
         L.warning("No node positions given, plots will have random positions from spring_layout")
 
-    for u in graph.nodes():
-        graph.nodes[u]["position"] = positions[u]
+    for i, u in enumerate(graph.nodes()):
+        graph.nodes[u]["position"] = positions[i]
 
 
 def _set_edge_lengths(graph, lengths=None):

netsalt/tasks/analysis.py

@@ -11,7 +11,6 @@
 import seaborn as sns
 import yaml
 from matplotlib.backends.backend_pdf import PdfPages
-from matplotlib.cm import get_cmap
 from matplotlib.colors import ListedColormap
 
 from netsalt.io import load_graph, load_modes, load_qualities
@@ -67,7 +66,7 @@ def run(self):
         print("mean edge length", np.mean(lengths))
         print("total edge length", sum(lengths))
 
-        cmap = get_cmap("Pastel1_r")
+        cmap = plt.get_cmap("Pastel1_r")
         newcolors = cmap(np.take(np.linspace(0, 1, 9), [0, 4, 2, 3, 1, 8, 6, 7, 5]))
         newcmp = ListedColormap(newcolors)
         plot_quantum_graph(

netsalt/tasks/pump.py

@@ -55,7 +55,7 @@ def run(self):
                 disp=self.disp,
             )
 
-        if self.optimisation_mode == "linear_programming":
+        elif self.optimisation_mode == "linear_programming":
             optimal_pump, pump_overlapps, costs, final_cost = optimize_pump_linear_programming(
                 modes_df,
                 qg,
@@ -65,6 +65,8 @@ def run(self):
                 eps_n=self.eps_n,
                 cost_diff_min=self.cost_diff_min,
             )
+        else:
+            raise ValueError(f"unknown optimisation mode {self.optimisation_mode}")
 
         results = {
             "optimal_pump": optimal_pump,

tests/test_functional.py

@@ -1,4 +1,5 @@
 """Fuctional test of the workflow."""
+
 import shutil
 import os
 from pathlib import Path
@@ -38,15 +39,15 @@ def create_graph():
     netsalt.save_graph(graph, "graph.pkl")
 
     # create the index of refraction profile
-    custom_index = len(graph.edges) * [3.0 ** 2]
+    custom_index = len(graph.edges) * [3.0**2]
     custom_loss = len(graph.edges) * [0.0]
-    custom_index[0] = 1.0 ** 2
-    custom_index[-1] = 1.0 ** 2
+    custom_index[0] = 1.0**2
+    custom_index[-1] = 1.0**2
 
     count_inedges = len(graph.edges) - 2.0
     if count_inedges % 4 == 0:
         for i in range(round(count_inedges / 4)):
-            custom_index[i + 1] = 1.5 ** 2
+            custom_index[i + 1] = 1.5**2
 
     yaml.dump({"constant": custom_index, "loss": custom_loss}, open("index.yaml", "w"))
 
@@ -86,4 +87,6 @@ def test_ComputeLasingModes(working_directory):
 
     # Check the numerical results
     result_dir, expected_dir = working_directory
-    assert_equal_trees(expected_dir, result_dir)
+    assert_equal_trees(
+        expected_dir, result_dir, specific_args={"out": {"patterns": [r".*\.h5$"], "atol": 1e-5}}
+    )

tox.ini

@@ -50,6 +50,6 @@ max-line-length=100
 
 [gh-actions]
 python =
-  3.8: py38, lint
-  3.9: py39
+  3.9: py39, lint
+  3.10: py310