Merge pull request #23 from CarlosBergillos/develop

Use C++ and refactor CLI

docs/source/changelog.rst

@@ -1,6 +1,17 @@
 Changelog
 =========
 
+**1.2.2** 
+---------
+
+*10-04-2023*
+
+Highlights:
+
++ Fixed and refactored CLI application.
++ Switched to C++ for Cython files and now using native C++ queue class.
+
+
 **1.2.1** 
 ---------
 

setup.py

@@ -10,9 +10,6 @@ def main():
 
     # fmt: off
     extensions = [
-        Extension('ts2vg.utils.pairqueue',
-                  [f'ts2vg/utils/pairqueue.pyx']),
-
         Extension('ts2vg.graph._base',
                   [f'ts2vg/graph/_base.pyx'],
                   include_dirs=include_dirs,

tests/naive_implementations.py

@@ -6,7 +6,7 @@
 """
 
 
-def natural_visibility_graph(ts, xs):
+def natural_visibility_graph(ts, xs, penetrable_limit=0):
     n = len(ts)
     edges = []
 
@@ -18,19 +18,24 @@ def natural_visibility_graph(ts, xs):
             x_b = xs[i_b]
             y_b = ts[i_b]
 
+            penetrations = 0
+
             for i_c in range(i_a + 1, i_b):
                 x_c = xs[i_c]
                 y_c = ts[i_c]
 
                 if y_c >= y_b + (y_a - y_b) * (x_b - x_c) / (x_b - x_a):
-                    break
+                    penetrations += 1
+
+                    if penetrations > penetrable_limit:
+                        break
             else:
                 edges.append((i_a, i_b))
 
     return edges
 
 
-def horizontal_visibility_graph(ts, xs):
+def horizontal_visibility_graph(ts, xs, penetrable_limit=0):
     n = len(ts)
     edges = []
 
@@ -42,12 +47,17 @@ def horizontal_visibility_graph(ts, xs):
             x_b = xs[i_b]
             y_b = ts[i_b]
 
+            penetrations = 0
+
             for i_c in range(i_a + 1, i_b):
                 x_c = xs[i_c]
                 y_c = ts[i_c]
 
                 if y_c >= min(y_a, y_b):
-                    break
+                    penetrations += 1
+
+                    if penetrations > penetrable_limit:
+                        break
             else:
                 edges.append((i_a, i_b))
 

tests/test_horizontal_penetrable.py

@@ -4,16 +4,9 @@
 import pytest
 from pytest import approx
 
+from fixtures import *
 import ts2vg
-from fixtures import (
-    empty_ts,
-    flat_ts,
-    sample_ts,
-    sample_ts_2,
-    linear_ts_small,
-    linear_ts_large,
-    linear_ts_large_negative,
-)
+from naive_implementations import horizontal_visibility_graph as naive_hvg
 
 
 def test_negative_parametric(sample_ts):
@@ -117,6 +110,59 @@ def test_penetrable_3(sample_ts):
     assert sorted(sorted(e) for e in out_got) == sorted(sorted(e) for e in out_truth)
 
 
+
+def test_penetrable_1_white_noise(white_noise_ts):
+    ts = white_noise_ts
+    xs = list(range(len(ts)))
+
+    vg = ts2vg.HorizontalVG(penetrable_limit=1)
+
+    out_got = vg.build(ts, xs).edges
+
+    out_truth = naive_hvg(ts, xs, penetrable_limit=1)
+
+    assert sorted(sorted(e) for e in out_got) == sorted(sorted(e) for e in out_truth)
+
+
+def test_penetrable_3_white_noise(white_noise_ts):
+    ts = white_noise_ts
+    xs = list(range(len(ts)))
+
+    vg = ts2vg.HorizontalVG(penetrable_limit=3)
+
+    out_got = vg.build(ts, xs).edges
+
+    out_truth = naive_hvg(ts, xs, penetrable_limit=3)
+
+    assert sorted(sorted(e) for e in out_got) == sorted(sorted(e) for e in out_truth)
+
+
+def test_penetrable_1_brownian_motion(brownian_motion_ts):
+    ts = brownian_motion_ts
+    xs = list(range(len(ts)))
+
+    vg = ts2vg.HorizontalVG(penetrable_limit=1)
+
+    out_got = vg.build(ts, xs).edges
+
+    out_truth = naive_hvg(ts, xs, penetrable_limit=1)
+
+    assert sorted(sorted(e) for e in out_got) == sorted(sorted(e) for e in out_truth)
+
+
+def test_penetrable_3_brownian_motion(brownian_motion_ts):
+    ts = brownian_motion_ts
+    xs = list(range(len(ts)))
+
+    vg = ts2vg.HorizontalVG(penetrable_limit=3)
+
+    out_got = vg.build(ts, xs).edges
+
+    out_truth = naive_hvg(ts, xs, penetrable_limit=3)
+
+    assert sorted(sorted(e) for e in out_got) == sorted(sorted(e) for e in out_truth)
+
+
 def test_penetrable_1_ltr(sample_ts):
     vg = ts2vg.HorizontalVG(directed="left_to_right", penetrable_limit=1)
     out_got = vg.build(sample_ts).edges

tests/test_natural_penetrable.py

@@ -4,16 +4,9 @@
 import pytest
 from pytest import approx
 
+from fixtures import *
 import ts2vg
-from fixtures import (
-    empty_ts,
-    flat_ts,
-    sample_ts,
-    sample_ts_2,
-    linear_ts_small,
-    linear_ts_large,
-    linear_ts_large_negative,
-)
+from naive_implementations import natural_visibility_graph as naive_nvg
 
 
 def test_negative_parametric(sample_ts):
@@ -128,6 +121,58 @@ def test_penetrable_3(sample_ts):
     assert sorted(sorted(e) for e in out_got) == sorted(sorted(e) for e in out_truth)
 
 
+def test_penetrable_1_white_noise(white_noise_ts):
+    ts = white_noise_ts
+    xs = list(range(len(ts)))
+
+    vg = ts2vg.NaturalVG(penetrable_limit=1)
+
+    out_got = vg.build(ts, xs).edges
+
+    out_truth = naive_nvg(ts, xs, penetrable_limit=1)
+
+    assert sorted(sorted(e) for e in out_got) == sorted(sorted(e) for e in out_truth)
+
+
+def test_penetrable_3_white_noise(white_noise_ts):
+    ts = white_noise_ts
+    xs = list(range(len(ts)))
+
+    vg = ts2vg.NaturalVG(penetrable_limit=3)
+
+    out_got = vg.build(ts, xs).edges
+
+    out_truth = naive_nvg(ts, xs, penetrable_limit=3)
+
+    assert sorted(sorted(e) for e in out_got) == sorted(sorted(e) for e in out_truth)
+
+
+def test_penetrable_1_brownian_motion(brownian_motion_ts):
+    ts = brownian_motion_ts
+    xs = list(range(len(ts)))
+
+    vg = ts2vg.NaturalVG(penetrable_limit=1)
+
+    out_got = vg.build(ts, xs).edges
+
+    out_truth = naive_nvg(ts, xs, penetrable_limit=1)
+
+    assert sorted(sorted(e) for e in out_got) == sorted(sorted(e) for e in out_truth)
+
+
+def test_penetrable_3_brownian_motion(brownian_motion_ts):
+    ts = brownian_motion_ts
+    xs = list(range(len(ts)))
+
+    vg = ts2vg.NaturalVG(penetrable_limit=3)
+
+    out_got = vg.build(ts, xs).edges
+
+    out_truth = naive_nvg(ts, xs, penetrable_limit=3)
+
+    assert sorted(sorted(e) for e in out_got) == sorted(sorted(e) for e in out_truth)
+
+
 def test_penetrable_1_ltr(sample_ts):
     vg = ts2vg.NaturalVG(directed="left_to_right", penetrable_limit=1)
     out_got = vg.build(sample_ts).edges

ts2vg/_version.py

@@ -1 +1 @@
-__version__ = "1.2.1"
+__version__ = "1.2.2"