Update Chemfiles tests for 0.10.3 (MDAnalysis#3808)

* Update chemfiles tests for 0.10.3

* Update package/CHANGELOG

Co-authored-by: Irfan Alibay <[email protected]>

Co-authored-by: Irfan Alibay <[email protected]>

package/CHANGELOG

@@ -13,11 +13,12 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/?? IAlibay
+??/??/?? IAlibay, Luthaf
 
  * 2.4.0
 
 Fixes
+  * Upgrade to chemfiles 0.10.3 (Issue #3798)
 
 Enhancements
 
@@ -122,7 +123,7 @@ Enhancements
   * Added equations for `center_of_mass` and `center_of_geometry`to
     documentation (PR #3671)
   * Added `center_of_charge` attribute (PR #3671)
-  * Added `frames` argument to AnalysisBase.run to allow analysis to run on 
+  * Added `frames` argument to AnalysisBase.run to allow analysis to run on
     arbitrary list of frames (Issue #1985)
   * LinearDensity now works with updating AtomGroups (Issue #2508, PR #3617)
   * Link PMDA in documentation (PR #3652)

testsuite/MDAnalysisTests/coordinates/test_chemfiles.py

@@ -21,7 +21,9 @@
 #
 import numpy as np
 from numpy.testing import assert_allclose
+import scipy
 import pytest
+from packaging.version import Version
 
 import MDAnalysis as mda
 from MDAnalysis.coordinates.chemfiles import ChemfilesReader, ChemfilesWriter
@@ -40,9 +42,9 @@
 chemfiles = pytest.importorskip("chemfiles")
 
 
-@pytest.mark.parametrize('version', ['0.9.3', '0.11.0', '1.1.0'])
+@pytest.mark.parametrize("version", ["0.9.3", "0.11.0", "1.1.0"])
 def test_version_check(version, monkeypatch):
-    monkeypatch.setattr('chemfiles.__version__', version)
+    monkeypatch.setattr("chemfiles.__version__", version)
     assert not check_chemfiles_version()
 
     with pytest.raises(RuntimeError, match="Please install Chemfiles > 0.10"):
@@ -104,25 +106,30 @@ def ref():
 
     def test_copy(self, ref):
         # Issue #3664 - test not done in test_copying due to dependencies
-        original = ChemfilesReader(ref.trajectory, convert_units=False, dt=2,
-                                   time_offset=10, foo="bar")
+        original = ChemfilesReader(
+            ref.trajectory,
+            convert_units=False,
+            dt=2,
+            time_offset=10,
+            foo="bar",
+        )
         copy = original.copy()
 
-        assert original.format not in ('MEMORY', 'CHAIN')
+        assert original.format not in ("MEMORY", "CHAIN")
         assert original.convert_units is False
         assert copy.convert_units is False
-        assert original._ts_kwargs['time_offset'] == 10
-        assert copy._ts_kwargs['time_offset'] == 10
-        assert original._ts_kwargs['dt'] == 2
-        assert copy._ts_kwargs['dt'] == 2
+        assert original._ts_kwargs["time_offset"] == 10
+        assert copy._ts_kwargs["time_offset"] == 10
+        assert original._ts_kwargs["dt"] == 2
+        assert copy._ts_kwargs["dt"] == 2
 
-        assert original.ts.data['time_offset'] == 10
-        assert copy.ts.data['time_offset'] == 10
+        assert original.ts.data["time_offset"] == 10
+        assert copy.ts.data["time_offset"] == 10
 
-        assert original.ts.data['dt'] == 2
-        assert copy.ts.data['dt'] == 2
+        assert original.ts.data["dt"] == 2
+        assert copy.ts.data["dt"] == 2
 
-        assert copy._kwargs['foo'] == 'bar'
+        assert copy._kwargs["foo"] == "bar"
 
         # check coordinates
         assert original.ts.frame == copy.ts.frame
@@ -168,7 +175,7 @@ def test_read_chemfiles_format(self):
         # check that chemfiles format is passed to copies Issue #3664
         new_reader = u.trajectory.copy()
         assert new_reader._format == "LAMMPS Data"
-        assert new_reader._kwargs['chemfiles_format'] == "LAMMPS Data"
+        assert new_reader._kwargs["chemfiles_format"] == "LAMMPS Data"
 
     def test_changing_system_size(self, tmpdir):
         outfile = "chemfiles-changing-size.xyz"
@@ -236,10 +243,8 @@ def test_write_atom_group(self, tmpdir):
             check = mda.Universe(outfile)
             assert check.trajectory.ts.n_atoms == group.n_atoms
 
-    @pytest.mark.xfail  # Issue #3798 - float writing not consisten
     def test_write_velocities(self, tmpdir):
         u = mda.Universe.empty(4, trajectory=True)
-        u.add_TopologyAttr("type", values=["H", "H", "H", "H"])
 
         ts = u.trajectory.ts
         ts.dimensions = [20, 30, 41, 90, 90, 90]
@@ -256,16 +261,14 @@ def test_write_velocities(self, tmpdir):
             [40, 40, 40],
         ]
 
-        outfile = "chemfiles-write-velocities.lmp"
+        outfile = "chemfiles-write-velocities.nc"
         with tmpdir.as_cwd():
-            with ChemfilesWriter(
-                outfile, topology=u, chemfiles_format="LAMMPS Data"
-            ) as writer:
+            with ChemfilesWriter(outfile, topology=u) as writer:
                 writer.write(u)
 
-            with open(outfile) as file:
-                content = file.read()
-                assert content == EXPECTED_LAMMPS_DATA
+            with scipy.io.netcdf_file(outfile) as file:
+                assert np.all(file.variables["coordinates"][0] == ts.positions)
+                assert np.all(file.variables["velocities"][0] == ts.velocities)
 
 
 VARYING_XYZ = """2
@@ -279,41 +282,3 @@ def test_write_velocities(self, tmpdir):
 A 0 0 0
 A 0 0 0
 """
-
-
-EXPECTED_LAMMPS_DATA = """LAMMPS data file -- atom_style full -- generated by chemfiles
-4 atoms
-0 bonds
-0 angles
-0 dihedrals
-0 impropers
-1 atom types
-0 bond types
-0 angle types
-0 dihedral types
-0 improper types
-0 20.0 xlo xhi
-0 30.0 ylo yhi
-0 41.0 zlo zhi
-
-# Pair Coeffs
-# 1 H
-
-Masses
-
-1 0.0 # H
-
-Atoms # full
-
-1 1 1 0.0 1.0 1.0 1.0 # H
-2 2 1 0.0 2.0 2.0 2.0 # H
-3 3 1 0.0 3.0 3.0 3.0 # H
-4 4 1 0.0 4.0 4.0 4.0 # H
-
-Velocities
-
-1 10.0 10.0 10.0
-2 20.0 20.0 20.0
-3 30.0 30.0 30.0
-4 40.0 40.0 40.0
-"""