Merge pull request #70 from nomad-coe/mdanalysis-cleanup

Implement clean up function for mdanalysis
nomad-coe · Oct 17, 2023 · 33ae2ef · 33ae2ef
2 parents a3a33dd + 689317e
commit 33ae2ef
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diff --git a/atomisticparsers/gromacs/parser.py b/atomisticparsers/gromacs/parser.py
@@ -1066,3 +1066,5 @@ def parse(self, filepath, archive, logger):
         self.parse_input()
 
         self.parse_workflow()
+
+        self.traj_parser.clean()
diff --git a/atomisticparsers/utils/mdanalysis.py b/atomisticparsers/utils/mdanalysis.py
@@ -18,6 +18,7 @@
 #
 
 import numpy as np
+import os
 try:
     import MDAnalysis
     import MDAnalysis.analysis.rdf as MDA_RDF
@@ -529,3 +530,8 @@ def get_nojump_positions(self, selection):
             nojump_positions.append(selection.positions - delta)
 
         return np.array(nojump_positions)
+
+    def clean(self):
+        for name in os.listdir(self.maindir):
+            if name.startswith('.') and (name.endswith('.lock') or name.endswith('.npz')):
+                os.remove(os.path.join(self.maindir, name))
diff --git a/tests/data/gromacs/argon/.traj.trr_offsets.npz b/tests/data/gromacs/argon/.traj.trr_offsets.npz
diff --git a/tests/data/gromacs/fe_test/.reference_d.trr_offsets.npz b/tests/data/gromacs/fe_test/.reference_d.trr_offsets.npz
diff --git a/tests/data/gromacs/water/.traj.trr_offsets.npz b/tests/data/gromacs/water/.traj.trr_offsets.npz
Original file line number	Diff line number	Diff line change
Expand Up		@@ -1066,3 +1066,5 @@ def parse(self, filepath, archive, logger):
		self.parse_input()

		self.parse_workflow()

		self.traj_parser.clean()