Fix inconsistent results produced on different platforms

Fix a bug that resulted in different results being returned when running
stripepy call on different platform (and potentially even when using
different versions of numpy and pandas).

The bug was caused by not forcing numpy and pandas to use stable
sorting algorithms.
This resulted in slightly different results produced on macOS
and Linux (Windows and Linux produced consistent results).

src/stripepy/cli/view.py

@@ -38,7 +38,7 @@ def _read_stripes(f: ResultFile, chrom: str) -> pd.DataFrame:
         df1 = pd.concat([geo_lt, bio_lt], axis="columns")
         df2 = pd.concat([geo_ut, bio_ut], axis="columns")
 
-        return pd.concat([df1, df2]).set_index("seed").sort_index()
+        return pd.concat([df1, df2]).set_index("seed").sort_index(kind="stable")
     except Exception as e:
         raise RuntimeError(f'failed to read stripes for chromosome "{chrom}": {e}')
 

src/stripepy/plot.py

@@ -521,10 +521,10 @@ def fetch(v: npt.NDArray[int], left_bound: int, right_bound: int) -> Tuple[npt.N
 
     min_persistence = result.min_persistence
     lt_idx, lt_seeds = fetch(
-        np.sort(TDA(pd_lt, min_persistence=min_persistence)[2]), start // resolution, end // resolution
+        np.sort(TDA(pd_lt, min_persistence=min_persistence)[2], stable=True), start // resolution, end // resolution
     )
     ut_idx, ut_seeds = fetch(
-        np.sort(TDA(pd_ut, min_persistence=min_persistence)[2]), start // resolution, end // resolution
+        np.sort(TDA(pd_ut, min_persistence=min_persistence)[2], stable=True), start // resolution, end // resolution
     )
 
     return {

src/stripepy/utils/TDA.py

@@ -27,7 +27,7 @@ def TDA(marginal_pd, min_persistence=0):
     )
 
     # Sorting maximum points (and, as a consequence, the corresponding minimum points) w.r.t. persistence:
-    argsorting = np.argsort(list(zip(*filtered_max_points_and_persistence))[1]).tolist()
+    argsorting = np.argsort(list(zip(*filtered_max_points_and_persistence))[1], stable=True).tolist()
 
     if len(filtered_min_points_and_persistence) == 0:
         filtered_min_points = []

src/stripepy/utils/common.py

@@ -31,7 +31,7 @@ def sort_based_on_arg0(*vectors: Sequence) -> Tuple[NDArray]:
     if len(vectors[0]) == 0:
         return tuple((np.array(v) for v in vectors))  # noqa
 
-    permutation = np.argsort(vectors[0])
+    permutation = np.argsort(vectors[0], stable=True)
 
     return tuple((np.array(v)[permutation] for v in vectors))  # noqa
 

src/stripepy/utils/persistence1d.py

@@ -41,7 +41,7 @@ def run_persistence(data, level_sets="lower"):
 
     # Number of data to break ties (leftmost index comes first):
     num_elements = len(data)
-    sorted_idx = np.argsort(data, kind="stable")[::-1] if level_sets == "upper" else np.argsort(data, kind="stable")
+    sorted_idx = np.argsort(data, stable=True)[::-1] if level_sets == "upper" else np.argsort(data, stable=True)
 
     # Get a union find data structure:
     uf = UnionFind(num_elements)