Merge branch 'mdeval_dev'

# Conflicts:
#	.gitignore
#	doc/conf.py
#	examples/plot_chi4.py
#	examples/plot_isf.py
#	examples/plot_spatialisf.py
#	examples/plot_temperature.py
#	src/mdevaluate/cli.py
#	src/mdevaluate/correlation.py
#	src/mdevaluate/distribution.py
#	src/mdevaluate/functions.py
#	test/test_atoms.py

test/test_atoms.py

@@ -2,6 +2,7 @@ from mdevaluate import atoms
 
 
 def test_compare_regex():
-    assert not atoms.compare_regex(["OW"], "O")[0]
-    assert not atoms.compare_regex(["WO"], "O")[0]
-    assert atoms.compare_regex(["O"], "O")[0]
+    assert atoms.compare_regex(['OW', ], 'O')[0]
+    assert not atoms.compare_regex(['OW', ], 'O$')[0]
+    assert not atoms.compare_regex(['WO', ], 'O')[0]
+    assert atoms.compare_regex(['O', ], 'O')[0]

test/test_free_energy_landscape.py

@@ -0,0 +1,54 @@
+import os
+
+import pytest
+import numpy as np
+
+import mdevaluate
+import mdevaluate.extra.free_energy_landscape as fel
+
+
+@pytest.fixture
+def trajectory(request):
+    return mdevaluate.open(os.path.join(os.path.dirname(__file__), "data/pore"))
+
+
+def test_get_fel(trajectory):
+    test_array = np.array(
+        [
+            174.46253634,
+            174.60905476,
+            178.57658092,
+            182.43001192,
+            180.57916378,
+            176.49886217,
+            178.96018547,
+            181.13561782,
+            178.31026314,
+            176.08903996,
+            180.71215345,
+            181.59703135,
+            180.34329368,
+            187.02474488,
+            197.99167477,
+            214.05788031,
+            245.58571282,
+            287.52457507,
+            331.53492965,
+        ]
+    )
+
+    OW = trajectory.subset(atom_name="OW")
+
+    box = np.diag(trajectory[0].box)
+    box_voxels = (box // [0.05, 0.05, 0.05] + [1, 1, 1]) * [0.05, 0.05, 0.05]
+    occupation_matrix = fel.occupation_matrix(OW, skip=0, segments=1000)
+    maxima_matrix = fel.find_maxima(occupation_matrix, box=box_voxels, edge_length=0.05)
+    maxima_matrix = fel.add_distances(maxima_matrix, "cylindrical", box / 2)
+    r_bins = np.arange(0, 2, 0.02)
+    distance_bins = np.arange(0.05, 2.05, 0.1)
+    energy_df = fel.distance_resolved_energies(
+        maxima_matrix, distance_bins, r_bins, box, 225
+    )
+    result = fel.find_energy_maxima(energy_df, r_min=0.05, r_max=0.15)
+
+    assert (np.round(np.array(result["energy"])) == np.round(test_array)).all()

test/test_utils.py

@@ -31,16 +31,3 @@ def test_filon_fourier_transformation(logdata):
         xdata, xdata, frequencies=freqs, derivative="linear", imag=False
     )
     assert np.isclose(filon_imag.real, filon_real).all()
-
-
-def test_histogram():
-    data = np.random.rand(100)
-    bins = np.linspace(0, 1)
-    np_hist = np.histogram(data, bins=bins)[0]
-    ut_hist = utils.histogram(data, bins=bins)[0]
-    assert (np_hist == ut_hist).all()
-
-    bins = np.linspace(0.3, 1.5)
-    np_hist = np.histogram(data, bins=bins)[0]
-    ut_hist = utils.histogram(data, bins=bins)[0]
-    assert (np_hist == ut_hist).all()