Fix: Remove weird characters and fix no louvain (#91)

README.md

@@ -190,21 +190,21 @@ If you are interested in trying our other packages, see the below list:
 
 ## References
 
-[1] J.-C. Delvenne, S. N. Yaliraki, and M. Barahona, ‘Stability of graph communities across time scales’, *Proceedings of the National Academy of Sciences*, vol. 107, no. 29, pp. 12755–12760, Jul. 2010, doi: 10.1073/pnas.0903215107.
+[1] J.-C. Delvenne, S. N. Yaliraki, and M. Barahona, 'Stability of graph communities across time scales', *Proceedings of the National Academy of Sciences*, vol. 107, no. 29, pp. 12755–12760, Jul. 2010, doi: 10.1073/pnas.0903215107.
 
-[2] R. Lambiotte, J.-C. Delvenne, and M. Barahona, ‘Random Walks, Markov Processes and the Multiscale Modular Organization of Complex Networks’, *IEEE Trans. Netw. Sci. Eng.*, vol. 1, no. 2, pp. 76–90, Jul. 2014, doi: 10.1109/TNSE.2015.2391998.
+[2] R. Lambiotte, J.-C. Delvenne, and M. Barahona, 'Random Walks, Markov Processes and the Multiscale Modular Organization of Complex Networks', *IEEE Trans. Netw. Sci. Eng.*, vol. 1, no. 2, pp. 76–90, Jul. 2014, doi: 10.1109/TNSE.2015.2391998.
 
-[3] M. T. Schaub, J.-C. Delvenne, R. Lambiotte, and M. Barahona, ‘Multiscale dynamical embeddings of complex networks’, *Phys. Rev. E*, vol. 99, no. 6, Jun. 2019, doi: 10.1103/PhysRevE.99.062308.
+[3] M. T. Schaub, J.-C. Delvenne, R. Lambiotte, and M. Barahona, 'Multiscale dynamical embeddings of complex networks', *Phys. Rev. E*, vol. 99, no. 6, Jun. 2019, doi: 10.1103/PhysRevE.99.062308.
 
-[4] V. D. Blondel, J.-L. Guillaume, R. Lambiotte, and E. Lefebvre, ‘Fast unfolding of communities in large networks’, *J. Stat. Mech.*, vol. 2008, no. 10, Oct. 2008, doi: 10.1088/1742-5468/2008/10/p10008.
+[4] V. D. Blondel, J.-L. Guillaume, R. Lambiotte, and E. Lefebvre, 'Fast unfolding of communities in large networks', *J. Stat. Mech.*, vol. 2008, no. 10, Oct. 2008, doi: 10.1088/1742-5468/2008/10/p10008.
 
-[5] V. A. Traag, L. Waltman, and N. J. van Eck, ‘From Louvain to Leiden: guaranteeing well-connected communities’, *Sci Rep*, vol. 9, no. 1, p. 5233, Mar. 2019, doi: 10.1038/s41598-019-41695-z.
+[5] V. A. Traag, L. Waltman, and N. J. van Eck, 'From Louvain to Leiden: guaranteeing well-connected communities', *Sci Rep*, vol. 9, no. 1, p. 5233, Mar. 2019, doi: 10.1038/s41598-019-41695-z.
 
-[6] D. J. Schindler, J. Clarke, and M. Barahona, ‘Multiscale Mobility Patterns and the Restriction of Human Movement’, *Royal Society Open Science*, vol. 10, no. 10, p. 230405, Oct. 2023, doi: 10.1098/rsos.230405.
+[6] D. J. Schindler, J. Clarke, and M. Barahona, 'Multiscale Mobility Patterns and the Restriction of Human Movement', *Royal Society Open Science*, vol. 10, no. 10, p. 230405, Oct. 2023, doi: 10.1098/rsos.230405.
 
-[7] A. Arnaudon, D. J. Schindler, R. L. Peach, A. Gosztolai, M. Hodges, M. T. Schaub, and M. Barahona, ‘PyGenStability: Multiscale community detection with generalized Markov Stability‘, *arXiv pre-print*, Mar. 2023, doi: 10.48550/arXiv.2303.05385.
+[7] A. Arnaudon, D. J. Schindler, R. L. Peach, A. Gosztolai, M. Hodges, M. T. Schaub, and M. Barahona, 'PyGenStability: Multiscale community detection with generalized Markov Stability', *arXiv pre-print*, Mar. 2023, doi: 10.48550/arXiv.2303.05385.
 
-[8] S. Gómez, P. Jensen, and A. Arenas, ‘Analysis of community structure in networks of correlated data‘. *Physical Review E*, vol. 80, no. 1, p. 016114, Jul. 2009, doi: 10.1103/PhysRevE.80.016114.
+[8] S. Gomez, P. Jensen, and A. Arenas, 'Analysis of community structure in networks of correlated data'. *Physical Review E*, vol. 80, no. 1, p. 016114, Jul. 2009, doi: 10.1103/PhysRevE.80.016114.
 
 ## Licence
 

extra/lemon/soplex.h

@@ -40,7 +40,7 @@ namespace lemon {
   ///
   /// This class implements an interface for the SoPlex LP solver.
   /// The SoPlex library is an object oriented lp solver library
-  /// developed at the Konrad-Zuse-Zentrum für Informationstechnik
+  /// developed at the Konrad-Zuse-Zentrum fur Informationstechnik
   /// Berlin (ZIB). You can find detailed information about it at the
   /// <tt>http://soplex.zib.de</tt> address.
   class SoplexLp : public LpSolver {

src/pygenstability/constructors.py

@@ -254,7 +254,7 @@ class constructor_signed_modularity(Constructor):
     positive and negative degree vectors.
 
     References:
-        .. [1] Gómez, S., Jensen, P., & Arenas, A. (2009). Analysis of community structure in
+        .. [1] Gomez, S., Jensen, P., & Arenas, A. (2009). Analysis of community structure in
                 networks of correlated data. Physical Review E, 80(1), 016114.
     """
 
@@ -309,7 +309,7 @@ def prepare(self, **kwargs):
         degrees_abs = np.array(abs(self.graph).sum(1)).flatten()
         laplacian = sp.diags(degrees_abs) - self.graph
 
-        if self.exp_comp_mode == "spectral":
+        if self.exp_comp_mode == "spectral":  # pragma: no cover
             self.spectral_decomp = _compute_spectral_decomp(laplacian)
         if self.exp_comp_mode == "expm":
             self.partial_quality_matrix = laplacian

src/pygenstability/optimal_scales.py

@@ -59,8 +59,8 @@ def identify_optimal_scales(results, kernel_size=3, window_size=3, max_nvi=1, ba
         result dictionary with two new keys: 'selected_partitions' and 'block_detection_curve'
 
     References:
-        .. [1] D. J. Schindler, J. Clarke, and M. Barahona, ‘Multiscale Mobility Patterns and
-               the Restriction of Human Movement’, *arXiv:2201.06323*, 2023
+        .. [1] D. J. Schindler, J. Clarke, and M. Barahona, 'Multiscale Mobility Patterns and
+               the Restriction of Human Movement', *arXiv:2201.06323*, 2023
     """
     # get NVI(t) and NVI(t,t')
     nvi_t = np.asarray(results["NVI"])

src/pygenstability/pygenstability.py

@@ -33,7 +33,13 @@
 from sklearn.metrics.cluster import entropy
 from tqdm import tqdm
 
-from pygenstability import generalized_louvain
+try:
+    from pygenstability import generalized_louvain
+
+    _NO_LOUVAIN = False
+except ImportError:  # pragma: no cover
+    _NO_LOUVAIN = True
+
 from pygenstability.constructors import load_constructor
 from pygenstability.io import save_results
 from pygenstability.optimal_scales import identify_optimal_scales
@@ -108,10 +114,10 @@ def _get_constructor_data(constructor, scales, pool, tqdm_disable=False):
 
 
 def _check_method(method):  # pragma: no cover
-    if _NO_LEIDEN and not hasattr(generalized_louvain, "evaluate_quality"):
+    if _NO_LEIDEN and _NO_LOUVAIN:
         raise Exception("Without Louvain or Leiden solver, we cannot run PyGenStability")
 
-    if method == "louvain" and not hasattr(generalized_louvain, "evaluate_quality"):
+    if method == "louvain" and _NO_LOUVAIN:
         print("Louvain is not available, we fallback to leiden.")
         return "leiden"
 

tests/test_constructors.py

@@ -78,7 +78,11 @@ def test_linearized_directed(graph_directed):
 
 def test_spectral_exp(graph):
     """Test spectral exp computation."""
-    _skip = ["directed", "linearized_directed"]
+    _skip = [
+        "directed",
+        "linearized_directed",
+        "signed_combinatorial",  # unstable computations on github
+    ]
     for constr in CONSTRUCTORS:
         if constr not in _skip:
             data = _list_data(

tox.ini

@@ -17,6 +17,8 @@ extras = all
 commands = pytest -s \
     --basetemp={envtmpdir} \
     --cov={[base]name} \
+    --no-cov-on-fail \
+    --cov-report term-missing \
     --cov-fail-under=100
 
 allowlist_externals = make